Data Collection to Structure Refinement and Beyond – Digital Conference
The first CCP4 Crystallographic School South Africa took place on the 22 February – 5 March 2021 hosted online due to the COVID-19 pandemic. More than 90 attendees – including 39 students and postdoctoral researchers represented by 14 different nationalities – participated in the workshop, which covered fundamental topics relating to theoretical concepts and practical approaches in protein structure solution by X-ray crystallography.
The event involved both newly emerging scientists as well as seasoned experts from across Africa, the UK, Europe, the USA, and Australia and was supported and co-hosted by the GCRF START grant, the UK’s national synchrotron – Diamond Light Source (Diamond), the Collaborative Computational Project Number 4 (CCP4), and the University of Cape Town (UCT). The workshop consisted of informal social events, formal lectures, question and answer sessions, one-on-one tutorials on data processing, case studies, and data collection where students collected data remotely from Diamond or provided their own data.
Describing the impact on the small but growing structural biology community in Africa, workshop co-organiser, Professor Trevor Sewell from UCT’s Aaron Klug Centre for Imaging and Analysis, said,
“The value of knowing a protein structure is widely appreciated by the scientific community but the knowledge and experience of how protein structures are determined is rare in Africa. The Covid-19 pandemic has shown us that we remain ignorant of this key area of science that has already led to successful vaccines and may lead to valuable drugs at our peril. The pandemic has also focused our minds on finding new ways of working and this has enabled us to hold this extraordinary workshop remotely. This has enabled African students to engage with the world’s best without the need to travel.”
“The success of the new medium was extraordinary and can potentially be extended to cover all fields. The workshop was the brainchild of Dr Carmien Tolmie from the University of the Free State here in South Africa, and it owes its success to her dedication and organizational abilities. We are grateful for the generous sponsorship from the National Research Foundation, IUPAP and the IUCr, which made this trendsetting virtual workshop possible,” Prof. Sewell added.
Three beamlines at Diamond Light Source, namely i03, i04 and i24, were dedicated to the remote data collection of students’ protein crystals, and each student was allocated to a beamline appropriate for their crystal system, as well as one-on-one assistance from beamline scientists. The workshop also had a coordinated effort involving beamline scientists from Diamond’s MX team. Diamond MX support scientists and co-hosts of the workshop – Felicity Bertram, Elliot Nelson and Marco Mazzorana – ensured the samples belonging to the workshop participants reached the correct beamline for the dedicated data collection day, in addition to organising access to the computing resources at Diamond Light Source for the data processing sessions.
Commenting on the importance of co-hosting the event from a South African perspective, Dr Carmien Tolmie said,
“It is an immense privilege to be part of the organization of this workshop and I am extremely grateful to the other members of the organization who worked extremely hard to make sure that this workshop was realized, despite the numerous setbacks we encountered because of the Covid-19 pandemic. Due to the high cost associated with traveling overseas to attend CCP4 workshops on other continents, this was a once-in-a-lifetime opportunity to learn from and engage with experts on crystallographic data processing for many of the participants attending this workshop. These are scarce skills, and this workshop will greatly aid in developing human capital in the country, as well as have a marked impact on advancing the projects of the participants who attended the workshop.”
For some of the students this was the first time attending a crystallographic workshop, including Taryn Adams, an MSc student recently starting a project in protein structure and function. Taryn heard about the workshop through her supervisor, Professor Yasien Sayed, head of the Protein Structure and Function Research Unit at the University of the Witwatersrand in South Africa. Taryn said,
“In science, success is often achieved with significant collaboration and group learning. I am looking forward to meeting scientists who are also new to the field and those with experience who could advise me as I embark on my project.”
Another participant, Dr Stanley Makumire, is a GCRF START funded Postdoctoral Research Fellow at the University of Cape Town. Stanley said,
“Being a novice in the field of structural biology attending the CCP4 workshop will equip me with the necessary skills for my research project which is to understand the mechanism of the amidase enzyme family. I am also really excited about the remote data collection and data processing tools available on CCP4.”
Commenting on the impact of the GCRF START grant on capacity building in the field of structural biology, Dr Gwyndaf Evans, START co-Investigator and Principal beamline scientist on Diamond’s VMXm beamline, said,
“We are seeing critical scientific discoveries and the emergence of a new generation of experts that have resulted directly from our training programmes in advanced methods and the use of synchrotron facilities and tools.”
“GCRF START has been pretty awesome, in the way it’s allowed us to help accelerate some truly cutting-edge South African science with the tools we get to develop and provide at Diamond.”
Professor Frank Von Delft, GCRF START Co-I at Diamond Light Source, UK
According to the World Health Organization (WHO), antimicrobial resistance is one of the top 10 global public health threats facing humanity. In South Africa, infections caused by Staphylococcus aureus and Mycobacterium tuberculosis are an all-too-common reality. While M. tuberculosis is the causative agent of tuberculosis (TB) which shows increasing prevalence of drug-resistance, S. aureus is one of the ESKAPE[1] pathogens [2] – a group of organisms that are leading causes for community- and hospital-acquired infections globally. ESKAPE pathogens are also notoriously difficult to treat and are resistant to many first line antibiotics. Considering the rise in antimicrobial-resistant organisms there is a desperate need to identify new antimicrobial compounds that work differently from those currently in clinical use.
With the GCRF START grant, the Strauss Laboratory has established new, cutting edge structural biology capabilities at Stellenbosch University in South Africa to collect data onsite and remotely from Diamond. This includes embarking on an exciting approach in drug discovery initiatives to identify new antimicrobial compounds, using the UK’s world class national synchrotron, Diamond Light Source (Diamond).
Research in the Strauss Laboratory is focused on understanding the biosynthetic pathway of the central metabolic cofactor coenzyme A (CoA)[3], as well as other enzymes that play a role in maintaining the redox balance in the human pathogen S. aureus. The Lab makes use of a number of chemical biology tools to develop novel agents for the selective inhibition of both drug-sensitive and drug-resistant strains of S. aureus by targeting enzymes involved in the biosynthesis and utilisation of CoA[4] and other enzymes associated with its resistance to oxidative stress.
“While we would be keen to develop a new antimicrobial compound that could one day be used in a clinical setting, our current primary goal is to see if we can use small molecules to modulate the survival of S. aureus in the host–pathogen interface,” says Professor Erick Strauss, Group Leader at Stellenbosch University’s Strauss Laboratory in South Africa. “Ideally, such compounds would work synergistically with the body’s natural defences to ward off infections, thereby reducing the likelihood of antimicrobial resistance arising.”
“Through Diamond’s X-ray structure-accelerated, synthesis-aligned fragment medicinal chemistry facility, under guidance from GCRF START Co-Investigator, Prof Frank von Delft, we have been able to fast-track the identification of novel compounds that we are currently pursuing further as promising leads of such modulators of the survival of S. aureus”, adds GCRF START-funded Postdoctoral Research Fellow, Dr Blake Balcomb. “This is the first time that researchers from Stellenbosch University have used this cutting-edge technology in drug discovery initiatives.”
Diamond’s XChem workflow is geared towards automation and high-throughput screening of hundreds of compound fragments with automated structure determination of the protein of interest with each individually bound fragment, which is what enables a process that could normally take months to be fast-tracked to take just a few days.
“To explain the process in simple terms, it is like the protein represents a sponge and one by one individual compounds would be soaked into the sponge and only those compounds that have a natural propensity or chemical attraction to bind to the sponge would remain bound,” says Balcomb. “If one had to do this manually one by one it would take several months to go through each of the compounds and investigate if the compound fragment is bound to the protein of interest and, importantly, what orientation it is bound. With XChem one can obtain data and final results within a week!”
Researchers in the Strauss Laboratory have completed two successful XChem experiments on two separate S. aureus enzymes. One enzyme is involved in the biosynthesis of CoA and a second enzyme is involved in detoxification of a host derived antimicrobial. Through XChem they have collected data on >800 crystals and obtained >150 novel crystal structures all containing different fragment compounds.
“To mitigate the usual slow progression of fragment hits to promising drug leads we are pursuing two hits in two separate approaches,” explains Prof. Strauss. “The first approach, also developed by the Frank Von Delft team, is similar to the XChem workflow and is optimized and streamlined for automation and high-throughput analysis. This technique makes use of an Opentrons pipetting robot[5], which is used to perform automated multi-step parallel syntheses in a checkerboard format, therefore allowing one to do combinatorial synthesis and to make many similar compounds at the same time. The added benefit is there is no need to purify the end-products, as these are soaked directly into crystals of the target enzyme to determine their inhibition potential. These experiments again would feed back into the XChem workflow.”
In a second approach, the team has initiated a new collaboration with Dr Nir London at the Weizmann Institute of Science to develop compounds that target proteins covalently (to form an irreversible attachment to proteins). This approach is also based on a high-throughput setup that screens several fragments that contain specific reactive groups. The results of the most reactive fragments are then again fed back into the XChem workflow, whereby one would be able to visualise the compound-protein complex. All of these findings help aid in the development of potent and specific compounds that could be assessed further in the drug discovery pipeline and in turn, the discovery of novel antimicrobials.
In addition to Diamond’s XChem facilities, the Strauss Laboratory also has regular access to Diamond’s MX instruments through a dedicated South African BAG . This BAG access is a highly effective means in which a consortium of other scientists can work together to share a full beamtime shift for data collection. Through the BAG access the Strauss Laboratory, has on average, sent three to four shipments of samples per year to Diamond, and has so far solved eight novel crystal structures.
Capacity building and peer training in structural biology
Alongside the cutting-edge science, the GCRF START grant has enabled the Strauss Laboratory to invest in training and capacity development in techniques like fragment screening. Dr Blake Balcomb, formally trained in structural biology, and Dr Anton Hamann originally trained as an organic chemist but now a GCRF START grant funded Postdoctoral Fellow skilled in protein X-ray crystallography, have participated in two separate CCP4 workshops as well as training on the use of XChem facilities. These skills they pass on in their research group, as well as cascade to other research groups at Stellenbosch that show interest in structural biology as a research tool.
The scientists have, in addition, transferred skills to several students and Postdoctoral students in the Strauss Laboratory, including Dr Koketso Mogwera, who is now a Post-doc at H3D at the University of Cape town (UCT), Tim Kotze (PhD), Warrick Sitzer (MSc), Karli Bothma (MSc) and Nicholas Herbert (BSc Hons), now an MSc. student at the AHRI.
The GCRF START grant has also enabled the Strauss Laboratory to call on expertise and initiate new collaborations with scientists in other African universities. For example, MSc student Warrick Sitzer is currently investigating the structure of one of the enzymes involved in CoA biosynthesis using CryoEM and is co-supervised by GCRF START Co-I, Dr Jeremy Woodward, from the University of Cape Town.
Warrick Sitzer reports below on the training and mentoring he received,
“As an MSc. student, learning about CryoEM has given me a deeper appreciation on how it is used in structural biology research as opposed to other major techniques in the field such as X-ray crystallography and NMR spectroscopy. I find that the scientific progress made in detector technology and software algorithms to unravel difficult or complex biomolecular structures at near atomic resolution without the need of crystallization to be very exciting. The ability to determine these biomolecular complexes in their native state opens up a door to a room full of possibilities that may contribute significantly to structure-based drug discovery.”
Describing the impact that GCRF START has had on his research, Anton said,
“The GCRF START grant has opened a new field for me in medicinal chemistry and has introduced me to protein crystallography. Through the GCRF START grant, I had the privilege to carry out crystallographic fragment screening experiments at Diamond’s XChem facility, which has accelerated my research in developing novel antibiotics for S. aureus. Thanks to START, I am now a better and more developed medicinal chemist.“
Commenting on the capacity building achievements supported by the GCRF START grant, Frank von Delft said,
“While a lot of Diamond’s facilities for macromolecular crystallography can be offered through remote access, our XChem facility must be attended in person; and it is only thanks to the GCRF START grant that those persons include South Africans. What’s been equally exciting is seeing those researchers being able to use those results to accelerate not only their science, but their careers.”
Read about the UN’s Sustainable Development Goals for Health and Wellbeing here
[1]Enterococcus faecium,Staphylococcus aureus,Klebsiella pneumoniae,Acinetobacter baumannii,Pseudomonas aeruginosa, and Enterobacter species
[2] Front Microbiol. 2019 Apr 1;10:539. doi: 10.3389/fmicb.2019.00539. eCollection 2019
[3] Strauss E. Coenzyme A Biosynthesis and Enzymology, in Comprehensive Natural Products II Chemistry and Biology Vol. 7 (Eds. Lew Mander & Hung-Wen Liu) 351-410 (Elsevier, 2010).
The Agenda for Sustainable Development calls for the world to “ensure healthy lives and promoting well-being for all at all ages” by 2030 (SDG3). Although there has been progress in many health areas, the UN reported in 2020 that the rate of improvement has slowed and may not be sufficient to meet SDG 3 targets, particularly with the Covid-19 pandemic disrupting progress around the world.[1] This also applies to related Sustainable Development Goals (SDGs), such as ensuring availability and sustainable management of water and sanitation for all (SDG 6). Currently billions of people throughout the world still lack access to safely managed water and sanitation services and basic handwashing facilities at home. The need for solutions, the UN reports, is vast and accelerating: “Countries need comprehensive health strategies and increased spending on health systems to meet urgent needs and protect health workers, while a global coordinated effort is needed to support countries in need”.[2]
Scientists are increasingly at the forefront of global and local efforts to tackle these challenges, not least in clinical drug design and discovery and vaccine development for countries where some of the need is the greatest. This includes the small but growing community of structural biologists in Africa, many of whom are just starting out on their careers.
Established in 2013, the Structural Biology Research Group at the University of Pretoria in South Africa focuses its research on molecules involved in mechanisms of infectious diseases – primarily from Mycobacterium tuberculosis (Mtb, causing tuberculosis or TB), enterotoxigenic Escherichia coli (travellers’ diarrhoea), and Listeria monocytogenes (listeriosis). The aim is to elucidate the molecular processes that allow these microorganisms to invade and/or persist within the human body or individual cells to improve our understanding of these diseases for clinical drug design and discovery.
Collaborating with the GCRF START grant – three case studies investigating infectious diseases
In 2016, the Group moved to newly renovated laboratories in the University of Pretoria’s Agricultural Science building designed for molecular biology, protein production and structural analyses, and in 2018 commenced collaborating with the GCRF START grant programme. The benefit of being part of this international grant and research network is explained by Group leader and GCRF START Co-I, Prof. Wolf-Dieter Schubert,
“The GCRF START grant has enabled the Group to access the UK’s national synchrotron, Diamond Light Source (Diamond) for experiments using state-of-the- art synchrotron techniques not available on the African continent,” Prof. Schubert says. “It has also exposed students to international networks and workshops/training to share knowledge and build capacity in the field of structural biology for solutions to infectious diseases rife on our continent and beyond.Our Group currently includes 6 PhD students and 4 MSc students from countries as far afield as Nigeria, Cameroon, Namibia and Zimbabwe, in addition to South Africa, and we welcome two Honours students during 2021”.
The case studies below highlight the research of three emerging scientists from across Africa who are studying for their PhD’s in the Structural Biology Research Group at the University of Pretoria. Each describes how their careers and their research benefit from the collaboration between the Group and the GCRF START grant.
Clifford Manyo Ntui: Using synchrotrons in the fight against infectious diseases
My name is Clifford Manyo Ntui and I am a PhD student in Biochemistry. I was born in Ewelle village, in South West Province of Cameroon. Growing up in the village where no clear explanation was given for the cause of countless illnesses and deaths was always a nightmare to me. To seek answers, I decided to pursue a career in the field of infectious diseases. My path towards this journey gained ground when I joined the Structural Biology Research Group at the University of the Western Cape under the supervision of Prof. Wolf-Dieter Schubert in 2012 for my Honour’s degree, with a focus on the molecular basis of infectious diseases. This was followed by an MSc working on Mtb in the same group but now at the University of Pretoria. My PhD studies on Escherichia coli (ETEC), have benefited greatly from the Group’s collaboration with the GCRF START grant.
The field of Biochemistry is one of great interest and importance in Africa as attested by the need for more medicinal drugs towards the fight against infectious diseases. My training and expertise in the field of structural biology of infectious diseases makes me one of only a handful of scientists working in this area on the entire continent. I have worked with more than one synchrotron light source, which has given me skills that are scarce on the African continent. Moreover, I have a strong background and interest in communicating structural biology skills to student learners and the public.
In 2014, four years before the GCRF START collaboration, I started on my MSc studies at the University of Pretoria working on the crystals structure determination of novel drug targets of Mycobacterium tuberculosis, the bacterium that elicits tuberculosis. I was quite successful in my endeavour, solving the structure of one potential new drug target, thiamine phosphate kinase. As part of my MSc training, I twice travelled to the European Synchrotron Radiation Facility (ESRF) in Grenoble, France, to undertake diffraction experiments using highly brilliant and monochrome X‐rays. South Africa is a member of the ESRF, providing access to world class, cutting‐edge equipment. The data collected on these trips allowed me to solve the crystal structure of the protein mentioned above. In addition, I was able to collect diffraction data for a number of colleagues, again leading to the successful determination of a range of crystal structures in the field of Infection Biology as well as Microbial Ecology and Genomics. This formed the foundation of my training in synchrotron techniques which I could use in my PhD research.
For my PhD, I am working on EtpA protein from enterotoxigenic Escherichia coli (ETEC), a bacterium that causes severe diarrhoea in many African countries. This disease leads to the death of hundreds of thousands of children under the age of five all over the developing world.[3] EtpA is an adhesin which has been found to associate with flagellin from flagella allowing for bacterial adherence and toxin delivery. Currently, there is no crystal structure of EtpA from ETEC. This research aims to structurally characterise EtpA alone, as well as in complex with flagellin from ETEC as a possible vaccine target against ETEC diarrhoeal disease.
This project has produced the first crystal structure of the secretion domain of EtpA protein from ETEC using X-ray diffraction on the beamline I04 at the Diamond Light Source synchrotron, the experiments conducted at Diamond remotely from our labs at the University of Pretoria. The project is the product of a successful research programme thanks to funding provided by the GCRF START grant which has ensured the smooth running of our molecular biology laboratory. START has also contributed to organising workshops which have been invaluable for enhancing my protein structural biology knowledge, such as the CCP4 workshop of which GCRF START is a sponsor.
Vukosi Edwin Munyai: Characterising the protein structures of Listerial adhesion protein (LAP)
My name is Vukosi Edwin Munyai. I was born and raised at Kurhuleni village, located in Limpopo Province, South Africa. Collaborating with the GCRF START grant, provides me with the opportunity to contribute to Global challenges in line with the UN’s Sustainable Development Goals for creating a better future for all. As one of the first students to enrol for a PhD in science in my village, I am so grateful to do research that impacts human lives.
The GCRF START grant has given us a platform for learning in structural biology aspects, conducting experiments, associating with other scientists, and access to the Diamond synchrotron. I have the opportunity to learn more professionally and to learn how to handle different tasks as an independent researcher. In the future, I would like to spend time in academia, teaching and influencing young people, using my own story and research to inspire them.
In 2011, I completed my BSc degree in Biochemistry and Microbiology at the University of Venda, South Africa. From 2012 to 2014, I was working at United National Breweries in South Africa as a laboratory assistant when I decided to go back to study. In 2015, I enrolled for an Honours degree in Microbiology and a year later, for a Master’s degree in Biotechnology at the University of Western Cape, which I completed in 2018. After completing my Master’s degree, I relocated to Pretoria in 2019, where I enrolled for PhD in Biochemistry and structural biology.
My main objective is to characterise the protein structures of Listerial adhesion protein (LAP) and also its complex structure with human HSP60 (‘heat shock protein’). It has been proposed recently[4] that L. monocytogenes uses alcohol and acetaldehyde dehydrogenase/LAP interaction with human intestinal HSP60 to enable its para-cellular translocation to the sites of its pathogenicity/cause of disease. Characterising the complex structure of LAP and HSP60 will help to explain how L. monocytogenes infects its host alongside the established modes of invasion through the Internalin surface proteins. Understanding the LAP/HSP60 interaction may help in developing clinical drugs to prevent listerial infections. Dehydrogenase enzymes for industrial applications are presently in short supply. The structure of LAP will thus enhance knowledge about its roles in both disease and industrial applications.
Maria Hamuyela: Studying the functions and the structure of the ETEC EatA passenger domain
My name is Maria Hamuyela and I study the secreted EatA protein of enterotoxigenic Escherichia coli (ETEC) bacteria. I am currently employed as a technologist for the University of Namibia in Windhoek. After more than a year of searching for opportunities, I came across Prof Wolf-Dieter Schubert and he accepted me to join the Structural Biology Research Group at the University of Pretoria to carry out my PhD studies whilst retaining my job as a technologist in Namibia.
The GCRF START programme has afforded me an opportunity to study towards my PhD studies allowing me access to world class equipment and techniques like X-ray diffraction at the UK’s Diamond synchrotron and provides me with access to the reagents that I need to do my research. I am also getting scientific training, not only in the laboratory but through workshops.
Maria Hamunyela is a technologist at the University of Namibia and a PhD student in the structural biology research group at the University of Pretoria, South Africa.
ETEC commonly causes watery diarrhoea in children younger than five years old – a cause of death due to diarrhoeal diseases in this age group, as well as malnutrition and stunting in children. Lack of access to clean water and sanitation means infectious diseases such as ETEC and Shigella spread through water and food. Studying ETEC has a potential to provide knowledge needed to develop vaccines and drugs against ETEC and other related diseases in line with the WHO/UNICEF Integrated Global Action Plan for the Prevention and Control of Pneumonia and Diarrhoea (GAPPD). The GAPPD has, as a key goal, the reduction of deaths from diarrhoea in children younger than five to less than 1 per 1000 live births by 2025 (WHO/UNICEF, 2013)[5]. Hopefully designing an inhibitor for EatA will be a fundamental step in achieving this goal.
The EatA passenger domain protein is required for the virulence of ETEC. It degrades Mucin 2, a major mucin secreted by the intestinal epithelium. Previous reports show that EatA passenger domain shows potential as a candidate vaccine for ETEC and other enteric pathogens such as Shigella flexneri. The EatA passenger domain has however not been extensively studied with regards to functional and structural properties. Therefore, the main aim of my project is to characterise both the structure and functional properties of the EatA passenger domain to design an inhibitor for EatA.
Impact of the GCRF START grant – Structural Biology students trained from seven African countries
Prof Wolf-Dieter Schubert from the University of Pretoria acknowledges the dramatic impact the GCRF START programme has had from its inception in 2018:
“Overall, GCRF START has helped support the research of six PhD students, five MSc students and six BSc Honours students in our research group. In addition to supporting individual research projects, the programme also allowed them to meet and interact with international experts, provided access to internationally competitive infrastructure such as the Diamond Light Source, and supported their participation in a number of workshops and conferences.
The impact is thus clearly multidimensional. Coupled to the fact that supported students came from seven African countries with a balanced gender distribution throughout, the long-term impact will be considerable. This will apply particularly if students are able to continue on their path towards independent research careers and possibly return to their home countries. The impact of the grant so far bodes well for structural biology and health related, and as well as industrial research throughout the African continent.”
[2] The Covid-19 pandemic is threatening health systems and in particular, ones with poor resources, insufficient health facilities, medical supplies and health-care workers to meet the surge in demand. For example, an estimated 10 million persons fell ill with Tuberculosis (TB) globally in 2018, and drug-resistant Tuberculosis is also a continuing threat with the goal to end TB by 2030 no longer a possibility (UN, 2020).
[4] Kim K-P, Jagadeesan B, Burkholder KM, Jaradat ZW, Wampler JL, Lathrop AA, Morgan MT, Bhunia AK. (2006) Adhesion characteristics of Listeria adhesion protein(LAP)-expressing Escherichia coli to Caco-2 cells and of recombinant LAP to eukaryotic receptorHsp60 as examined in a surface plasmon resonance sensor., FEMS Microbiol Lett 256, 324-332, doi:10.1111/j.1574-6968.2006.00140.x
As a biochemist/biophysicist working primarily with proteins, I am naturally drawn to the mechanisms of interactions of biological macromolecules. My name is Sylvia Fanucchi, and I am a senior Lecturer in the Protein Structure Function Research Unit (PSFRU) at the University of the Witwatersrand (Wits) in South Africa. I am interested in how things work at the molecular and atomic level, and how the structure of macromolecules leads to their function. This has inspired my research for the past six years which involves disentangling the neuromolecular networks involved in speech and language. With the GCRF START grant, the doors to collecting the detailed structural information we need through studying and obtaining crystal structures, have been opened for groups in Africa like ours. I have had multiple opportunities, thanks to the grant, to send crystals to the UK’s world class national synchrotron, Diamond Light Source (Diamond).
My research appeals so much to me because our ability to speak, to think, to read is fundamental to humankind. Indeed, my research question started with “what defines speech and language?” but has since expanded to include questions about cognition, reading, and a number of disorders associated with these such as Autism, Dyslexia, Epilepsy and Schizophrenia. Dyslexia, for example, occurs in at least one in 10 people world-wide, putting more than 700 million children and adults worldwide at risk of life-long illiteracy and social exclusion.[1].
Globally, it is estimated that one in 160 children has an Autism Spectrum Disorder (ASD), although estimates vary significantly across studies, and between developed[2] and developing countries[3]. In Southern Africa, very little is known about the prevalence ASD and it is understood that many cases go undiagnosed. Because these disorders can be debilitating and impact on the quality of life of those living with these disorders, and because there is currently no known cure, it is of utmost importance that the complex neuromolecular mechanisms that define these disorders be explored and far better understood. It is hoped that through our research more robust forms of therapeutics could be developed.
Piecing together neuromolecular complexes and networks
In my work, I investigate protein-protein and protein-nucleic acid interactions and try to piece together the neuromolecular complexes and networks that form in both space and time to better understand the mechanism of their interaction and how this is associated with language and cognition, as well as how changes in these may lead to certain disorders. I use an array of biochemical and biophysical techniques to achieve this study and the most prominent of these include, fluorescence anisotropy, isothermal titration calorimetry, hydrogen exchange mass spectrometry and single molecule kinetics. These techniques are used to study binding kinetics and thermodynamics as well as the dynamics and motions of molecules and their interactions with each other, such as the interaction between a protein and DNA, or the interaction between two proteins. The work we have done has mostly been conducted at the PSFRU but I also have collaborations with Dr Previn Naicker and Dr Stoyan Stoychev at the CSIR in Pretoria who assist with mass spectroscopy, and Dr Carlos Penedo[4] from the University of St Andrews in Scotland, UK, who assists with single molecule studies.
The promising biophysical studies conducted in this work will benefit greatly from detailed structural information, provided currently through access to Diamond with the GCRF START grant. Knowledge of the structures of macromolecular complexes allows us to fully understand our system at a level of detail that is otherwise unattainable. And this information, in addition to the dynamics/thermodynamics/kinetics data, will enable us to understand the complexity of these networks at atomic resolution. This will foster a deeper understanding of these mechanisms and enable detailed therapeutics to be designed that would help regulate these disorders, particularly if single strong contributing factors could be identified. Crystallography and solving the structures of the individual interacting partners, as well as of the complexes is therefore of fundamental importance in this project.
FOXP2 protein – the “the language gene”
The protein that sparked this investigation is a transcription factor (a protein that regulates the expression of genes) called FOXP2. FOXP2 was dubbed “the language gene” in the early 2000s when a mutation in this gene that severely impeded DNA binding was found to result in a form of verbal dyspraxia in a family of individuals in the UK. Because FOXP2 is a transcription factor, it is located in the nucleus of cells and its role is to bind to the promotor region of certain genes and facilitate/regulate their transcription to mRNA which ultimately results in the translation and thus expression of that particular protein. Therefore, the regulation of transcription (and hence translation) of any protein will have a direct effect on the functioning of that protein. Our focus is thus on transcriptional regulation because it is the process that initiates downstream effects and predicts which genes will be turned on or off and hence, crudely put, controls the way we function.
Over the past three years, this project therefore focused on the mechanism of DNA binding of FOXP2. Through this work we were able to meticulously describe what drives the interaction of the DNA-binding domain with cognate DNA. We identified electrostatic interactions that played a critical role, we studied binding sequences to gain insight into binding specificity and affinity, we outlined how a domain-swapped dimerisation event that is unique to this subfamily of FOX proteins was able to assist in the dynamics of the DNA binding event, and we described the thermodynamic and kinetic events that occur during binding. In essence, by describing how the transcription factor interacted with DNA, we were able to tell which sequences it preferred, which conditions were most favourable for transcription, and how the structure and fold of the protein was necessary for transcription to occur. Knowing this helps us understand what is necessary for certain genes to be turned on or turned off and how we could interfere with this process.
The focus of our work then moved from DNA binding to the complex network of neuromolecular protein-protein interactions and we began to piece together other interacting partners of FOXP2 and how these interactions affected transcriptional regulation. One specific interaction has yielded a very interesting link to Autism that we are currently exploring further. I have established a very fruitful collaboration with Dr Carlos Penedo from the University of St Andrews primarily through a Newton Fellowship from the Royal Society and the single molecule work done through this collaboration has helped to resolve intricate details about these interactions that I am very excited about[5].
Fast and remote access to diffraction and data collection with Diamond and the GCRF START grant
The opportunities to send crystals to Diamond with the assistance of the GCRF START grant have been revolutionary in enabling us to have fast and remote access to diffraction and data collection that would otherwise have been logistically far more difficult to achieve, and therefore far more sparsely accomplished. Unfortunately, up to now, crystallisation in this project has been a challenge and so far, we are yet to achieve the crystals we require. The fact that the proteins we are attempting to crystallise have not yet had their structures solved and published in the Global Protein Data Bank (PDB) attests to the challenge we knew we would face in obtaining good diffraction data. And while we have obtained some crystals successfully, none of the data we have obtained has been worthy of solving the structure. Nevertheless, the fact that we can obtain crystals is promising and I am determined to persevere with this work until we are successful.
My students are all working on aspects of this project. They work on protein-protein interactions, crystallisation and structural biology, biophysics, and biochemistry. I am currently supervising 5 PhD students and 4 MSc students from diverse backgrounds, 8 of whom are females. I also have 2 postdoctoral Fellows – one from Lesotho and one from Kenya – that have worked under me for the past two years. In 2020, I graduated 2 PhD students and 2 MSc students. The students are given the autonomy to operate equipment, design experiments and analyse their data. Where possible, and covid-19 pandemic permitting, I encourage them to participate in international workshops and to visit other labs to gain experience and exposure.
Riyaadh Mayet is one of the early career MSc Students in my team.
“The GCRF START grant has enabled the African continent to foster development in synchrotron techniques through collaboration with the UK.” she says. “My MSc project deals with the structural biology of DNA-binding by the TBR1 T-box transcription factor implicated in Autism. The grant has enabled me to send my samples to the Diamond Light Source for diffraction, and without it, it would be very difficult if not impossible to obtain such data. It has also taught me how to better collaborate with fellow researchers, as well as given me the opportunity to learn how to diffract crystals to obtain atomic resolution data. Lastly, I have indirectly benefitted through learning about protein crystallography from fellow researchers who have used the START grant.”
Despite the challenges we have encountered with solving structures in this project, I am very grateful for the support received through the GCRF START grant and the support structures put in place – in particular, in bringing together a strong network of South African crystallographers. Knowing that I have this group of colleagues available across the country that forms a support structure is very reassuring. I am confident that the assistance and opportunities offered to me by this grant over the years is going to result in the ultimate success of my crystal structure dreams for this project and I am both grateful and excited for what the future holds.
Commenting on Sylvia’s research project and the access to infrastructure such as the Diamond synchrotron, Head of School of Molecular and Cell Biology (MCB), Prof Marianne J. Cronje, says,
“I am wholly in support of these research endeavours. Dr Sylvia Fanucchi is an incredibly talented researcher and her position within the school’s Protein Structure Function Research Unit strengthens her efforts by providing access to high-end research infrastructure to support her research in the school.”
Senior Lecturer, Dr Sylvia Fanucchi, in the laboratory at the Protein Structure Function Research Unit, University of the Witwatersrand in South Africa. Photo credit: Sylvia Fanucchi. Diamond Light Source
Addressing disability is referenced in many of the UN’s Sustainable Development Goals (SDGs), namely health, education, economic growth and employment, inequality, accessibility of human settlements, and others. Read more about the SDGs here.
[2] In the USA~10% of school children struggle with dyslexia and ~1 of every 59 school children is diagnosed with ASD (Yuhang Lin et al Int. J. Environ. Res. Public Health 2020, 17, 7140). The number with ASD has increased over the years reflecting both an increase in awareness as well as a potential increase in environmental triggers although the disorder is currently believed to be predominantly genetically determined.
In a bid to design clinical drugs to improve health outcomes for people living with a particular strain of HIV and its mutants, scientists at the University of the Witwatersrand’s Protein Structure-Function Research Unit (PSFRU) in South Africa have embarked on a clinical drug discovery journey with promising results. The aim of the research, which receives funding from the GCRF START grant, is to develop a novel inhibitor specifically designed to target the South African HIV-1 subtype C protease (C-SA PR) and its mutants.
The purpose of developing an inhibitor is to stop C-SA PR’s activity by preventing the formation of mature copies of the human immunodeficiency virus (HIV). This would improve health outcomes in line with Sustainable Development goals across South Africa by increasing drug efficacy, reducing adverse side effects and drug resistance, as well as benefitting populations infected with the HIV subtype C in other sub-Saharan countries, India, China and Brazil[1].
There is no permanent cure for HIV/AIDS which has claimed the lives of an estimated 32.7 million people globally since the beginning of the HIV pandemic (UNAIDS, 2020[2]). A number of drugs have been developed and approved by the USA’s Food and Drug Association (FDA) to increase the quality and duration of life in HIV infected individuals in some parts of the world. However, these are not specific to the HIV-1 protease subtype C which is dominant in South Africa – a country with approximately 20% of the global HIV infection rate and 10.44% of the global AIDS-related deaths (UNAIDS, 2020)[3].
To date, the scientists at the PSFRU have screened ten drugs in the FDA approved and Zinc drug databases, with seven hits that show promise for optimisation as inhibitors. They have solved one protein structure through sophisticated computational modelling, and with high-resolution X-ray crystallography data collected on beamline i03 at the UK’s national synchrotron – Diamond Light Source (Diamond) – have solved the structure of the South African HIV-1 subtype C protease (C-SA PR), the results of which were deposited in the global Protein Data Bank (6I45.pdb) in 2018 (Fig.1).
Fig.1 Ribbon structural representations of the HIV-1 subtype C-SA PR (cyan) and a mutant protease (purple). The structure of the mutant protease was determined using diffraction data obtained at the UK’s national synchrotron, Diamond Light Source (Diamond). PDB ID: 6I45. Sherry, D., Pandian, R., Achilonu, I.A., Dirr, H.W., Sayed, Y. (2018), Crystal structure of I13V/I62V/V77I South African HIV-1 subtype C protease containing a D25A mutation. DOI: 10.2210/pdb6I45/pdb[4]; PyMOL Molecular Graphics System (Schrödinger LLC., Portland, USA[5]).
The research involves characterising the structure and function of the South African HIV-1 subtype C protease (C-SA PR) and its mutants using state-of-the-art computational and experimental methods made possible by the GCRF START grant. The scientists want to understand what role amino acid insertions and mutations the HIV-1 protease may have on clinical drug binding so they can design an effective inhibitor.
This research builds on a previous study[6], in which a blood sample was taken from a drug naive infant born to an HIV positive mother. To prevent the transmission of the virus to her baby, the mother had received reverse transcript inhibitor treatment (but not protease inhibitors) prior to the birth. However, when the baby was born it was found to be HIV positive and a mutation was present rendering current drug therapy ineffective.
“It is the results like this of other research on the South African HIV-1 C-SA PR, and the impact of the disease on individual lives and livelihoods, which drives our motivation. The fact that the baby had developed drug resistance mutations is very rare in mother-to-child transmission but no less concerning,” says Professor Yasien Sayed, who heads up the PSFRU and leads the research on the HIV-1 C-SA PR, “and there is evidence that some adults are also failing drug therapies.We therefore need to develop treatments which work more effectively against the HIV-1 C-SA PR and its mutants if we are going to improve clinical outcomes for the large population of HIV positive adults and children in South Africa, and further afield.”
Some of the first steps in the team’s drug discovery journey have been computational involving Molecular Dynamics Simulation[7] of the HIV wild type C-SA PR and its mutants. After this, drugs in various databases were screened[8]. As a result, the scientists found a promising drug from the FDA database that binds with the HIV wild type C-SA PR and its mutant with best docking scores and energies.
“We modelled the homology structures of the HIV wild type protease and its mutants using the template South African wild type HIV-1 Subtype C Protease (PDB ID: 3U71),” explains Dr Pandian who is a Post-Doctoral Research Fellow funded by the GCRF START grant specialising in the computational aspects of the research. “The structure was solved at 2.72Å using the software packages: Swiss model/modeler/I-Tasser, followed by experimental validation of the modelled structures with in-house computer software. We are excited by the preliminary results, which are better than the current FDA approved drugs, although the computational results now have to be proved through wet lab experiments, along with the best results from the screened from the Zinc database.”
To conduct these studies, the PSFRU has its own computational and wet lab facilities for Molecular Dynamics simulation, docking studies, protein expression and purification. Screening of crystals is carried out using an Oryx8Protein Crystallization Robot (Douglas Instruments, UK) and testing of crystals using a home-source X-ray diffractometer. However, synchrotron facilities are not available on the African continent, so access to the Diamond Light Source synchrotron (Beamlines i03, i04, and also i04-1 and i24) is achieved remotely from the PSFRU lab in South Africa in order to characterise the structure and function of proteins at high resolution.
“Having access through the GCRF START grant to experimental synchrotron techniques like X-Ray crystallography at Diamond to obtain crystals and to solve the structures at high resolutions has been revolutionary for us,” reports Dr Pandian. “It is ultimately the combination of computational and experimental techniques that makes it possible to see how well the drugs are binding to optimise them for the South African HIV-1 subtype C protease (C-SA PR)” [9].
“During the wet lab experiments,” Dr Pandian continues, “we can’t screen the whole drug library for the target protein and it’s very costly to purchase the drugs for screening. The theoretical part of the drug discovery method is therefore useful for generating three dimensional structures for any proteins when the crystal structures are not available in the PDB databases, and for sorting out the best ligand / inhibitors for the protein target before starting protein characterisation wet lab experiments.”
Scientific results are not the only progress being made by the PSFRU team in their research which is meeting the UN’s Sustainable Development Goals for health (SDG 3); great strides have also been made in the PSFRU in terms of education and capacity building in structural biology (SDG 4) with more than 30 postgraduate students involved in the collaboration with the GCRF START grant since 2019. This includes Dr Ramesh Pandian, and Ms Mpho Setshedi who is a MSc. candidate working on the wet lab studies of the HIV-1 C-SA PR and its mutants.
“The research is meaningful,” says Ms Setshedi, “I feel like we are doing a good job and doing something to solve a challenge that impacts South Africa. I hope it contributes something big – an effective HIV inhibitor. In terms of what I am learning, there are challenges in this field but once you get the hang of the techniques you just need to persevere. Getting funding is a struggle in my field generally and there aren’t a lot of women doing this work. There have also been challenges caused by the COVID-19 lockdown in 2020 – but I haven’t let anything discourage me.”
[7]The Molecular Dynamics (MD) simulations of validated structures were performed under physiological conditions for 100ns using GROMACS software packages. The MD simulated structures were analysed thoroughly and extracted the energy minimised structure for further analysis. Important parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radiation of gyration (Rg) and hydrogen bonding analysis were carried out.
[8]The energy minimised structures of HIV wild type and its mutants were used for the screening of drugs from different data bases such as the Zinc database and FDA approved drugs database.
[9]The results of the binding pocket analysis of the protease complex form obtained by the docking studies with best ligand directed the scientists to modify the side chain with the combination of different R group of the drug to improve the binding affinity.
The effects of human activity on climate change are evident in accelerated changes to global climatic conditions. As a result, there have been efforts to decrease human impact on the environment. This includes sustainable and environmentally friendly waste management systems, bioremediation of damaged ecosystems and biocatalysis as a replacement for conventional chemical synthesis in industries in line with the UN’s Sustainable Development Goals.
One way to address these challenges is through the use of enzyme biotechnology in which proteins (enzymes) are used as industrial catalysts. Nitrilases are widely used enzymes with potential in the production of high-value fine chemicals including medicines, bioremediation and waste management. A problem with using enzymes in environmental remediation is that naturally occurring enzymes are susceptible to degradation and inactivation under harsh conditions. They can, however, be engineered to make them more tolerant of these conditions. Nitrilases have intrinsically robust, spiral structures that suggest that substantial improvements in stability are possible.
My name is Lenye Dlamini and my PhD study in the Structural Biology Research group at the University of Cape Town (UCT) concerns the engineering of a cyanide-degrading nitrilase enzyme that can be used to remediate cyanide waste in the textile, electroplating and gold-mining industries. In particular, cyanide is used in huge quantities in these industries and spills or unsafe disposal results in environmental degradation and causes harm (and occasionally death) to humans and livestock.
My study will use predictive biophysical methods based on structural knowledge of cyanide degrading nitrilases to measurably improve their tolerance of non-optimal temperature ranges and enhance the operational stability of the enzyme so that they can be routinely used for safe and cheap disposal of cyanide waste. The project builds on the work of Dr Andani Mulelu[1],2 and several of Prof Michael Benedik’s students at Texas A&M University who used directed evolution, a technique in which random amino acid mutations are introduced throughout the protein, to increase protein stability and ultimately led to the first structure of an enzyme of this type. My goal is to use this structure to identify specific amino acid changes that will lead to increased stability.
I am working from Prof Trevor Sewell’s (GCRF START Co-I) laboratory at UCT and the Electron Microscope Unit at the Aaron Klug Centre for Imaging and Analysis. My work is a component of the work on nitrilases being done by a large team of local and international collaborators (my first experience of collaborating with scientists outside of South Africa) that includes in South Africa: Dr Jeremy Woodward (GCRF START Co-I), Dr Gerhard Venter and Prof Roger Hunter at UCT, Prof Dean Brady at the University of the Witwatersrand, Dr Nishal Pharbhoo at UNISA; in Germany: Prof Andreas Stolz and Mr Erik Eppinger at the University of Stuttgart, Prof Markus Piotrowski of the Ruhr University at Bochum, and Prof Achilleas Frangakis at Goethe-University, Frankfurt.
While the direct impact of my research project is environmental, it has broader implications in a variety of industries. There is growing demand for biological agents and processes that will replace conventional processes of managing waste and chemical synthesis. Enzymes, including the nitrilases, have taken centre-stage in this regard and present not just an environmentally benign alternative but one that produces better reaction products (they are highly specific in the enantiomers and regions on compounds that they bind to, leading to more specific reaction products).
It is critical that we understand and can adapt enzymes for these new uses. Nitrile-containing compounds are widespread in nature and are also utilised in industries including agriculture, mining, pharmaceuticals and the plastics and paper industry. Most nitrile-containing compounds are toxic, mutagenic, and carcinogenic. We are trying to design a way that will result in the use of harmful compounds as substrates for the catalysis of useful compounds in a sustainable and environmentally benign manner.
In my research on nitrilases, I am building on previous research skills I gained through my MSc. project which also benefitted from access to the UK’s national synchrotron, Diamond Light Source (Diamond). Through supporting research, workshops, mentoring and supervision, and other aspects of these labs, the GCRF START grant has also, by extension, supported the development of my research career. In addition, workshops presented by structural biologists from Diamond in South Africa, have enabled me to acquire skills that include molecular biology techniques, protein crystallography, electron microscopy and data collection at synchrotrons.
My Master’s research was in rational drug design against Mycobacterium tuberculosis using molecular and structural biology techniques. One of the main outcomes of my study was the crystal structure of thiamine monophosphate kinase from Mycobacterium tuberculosis, solved at a resolution of 2.19 Å, with data collected using the i04 beamline at Diamond with access through the GCRF START grant.
Commenting on the research outlined above, Prof Trevor Sewell, Lenye’s supervisor, said,
“The work of the last 30 years has provided a wealth of knowledge about the structures, occurrence and chemistry of members of the ubiquitous nitrilase superfamily of enzymes. This has led to their widespread use as industrial enzymes and a recognition that some superfamily members are potential drug targets. Even so, our understanding of their mechanism and our ability to introduce desirable properties through design is very limited. Lenye’s work seeks to surmount the barriers, leading to the ability to enhance at least one property of the cyanide degrading nitrilases, the thermostability, by design and then verify that the desired goal has been achieved experimentally using CryoEM and differential scanning calorimetry.”
Find out more about the UN’s Sustainable Development Goals here
About Lenye Dlamini
Lenye Dlamini was born and raised in Mbabane, the capital city of Swaziland, which is also where she received her primary and high school education. Lenye was inspired into science at high school through her biology and chemistry teacher who, Lenye says, saw the potential in her and motivated her to work extra hard. Prior to embarking on her PhD studies, Lenye’s tertiary education was at the University of Pretoria in the laboratory of GCRF START Co-I, Prof Wolf-Dieter Schubert. Lenye is currently a PhD candidate in Medical Biochemistry in the Structural Biology Research group, Department of Integrative Biomedical Sciences, Faculty of Health Sciences at the University of Cape Town, South Africa.
[1] Mulelu, A. 2017. Factors involved in the oligomerisation of the cyanide dihydratase from Bacillus pumilus C1. University of Cape Town. http://hdl.handle.net/11427/24446
2 Sewell, BT, Frangakis, A, Mulelu, A and Reitz, J. (2017). The structure of the cyanide dihydratase (CynD) from Bacillus pumilus. Acta Cryst.A73, C1296. DOI: 10.1107/S2053273317082791
“The atomic structure of proteins provides an intimate insight into these magnificent macromolecules. This knowledge is crucial to truly understand how they function; whether it is to answer a burning question or to manipulate them – either to enhance if their reactions are desirable, or to inhibit if they are harmful.”
Prof. Dirk Opperman, University of the Free State, South Africa
Our research studies the structures of bacterial and fungal oxidoreductases (enzymes) which are possible drug targets to combat infectious disease. The current focus is fungal drug targets for fungal infectious diseases which can be very serious, especially for immune-compromised patients, such as those who are HIV/AIDS positive, organ transplant receivers, patients undergoing chemotherapy, and many more. This research is performed at the University of the Free State’s (UFS’s) Department of Microbial, Biochemical and Food Biotechnology1 and is led by the two Principal Investigators (PIs) of the Biocatalysis group at UFS, Prof. Dirk Opperman, who is a GCRF START Co-Investigator (Co-I), and Prof. Martie Smit. In our laboratory, we have solved the structures of a number of bacterial and fungal enzymes by X-ray crystallography over the past few years, two of the most recent – solving the structures of fungal cytochrome P450 reductase (Dec 2019) and Baeyer-Villiger monooxygenase (Feb 2020) – were assisted by the GCRF START grant and published in the journals Scientific reports2 and Catalysts3respectively, as described later in this article.
The scale of the Fungal infection and drug resistance challenge
Currently, there are three classes of anti-fungal drugs that are used to combat infectious fungal disease, but there is an increasing number of drug resistant (and even multi-drug resistant) fungi against these drugs meaning that these pathogenic fungi have become or are becoming resistant to the current medication used to treat patients. If no drugs are effective against invasive opportunistic fungi, the prognosis for immune-compromised patients is very poor, and many people will die.
“It is therefore imperative that we search for and develop new antifungal compounds to address the growing challenge [of drug-resistance to opportunistic fungi], which impacts countries across Africa, as well as globally. This is especially urgent if the world is to meet the UN’s Sustainable Development Goals of Health and Wellbeing and Food Security by 2030.”
Dr Carmien Tolmie, University of the Free State, South Africa
Fungal infections are often underreported and because of this the extent of the situation is not fully known. In South Africa, this is of particular concern because of our high incidence of HIV/AIDS. For example, one group4 reported that 90 % of HIV/AIDS positive patients on prolonged treatment contract oropharyngeal candidiasis (also called Thrush), an infection caused by a yeast, which is a type of fungus called Candida (Dos Santos Abrantes, McArthur and Africa 2014). However, this is only one statistic, and the problem is much wider. In another example, Cryptococcal meningitis is a deadly brain infection caused by the soil-dwelling fungus Cryptococcus. Worldwide, nearly 220,000 new cases of cryptococcal meningitis occur each year, resulting in 181,000 deaths, most of which occur in sub-Saharan Africa (CDC, 2020).
Using the powerful beams of Diamond’s synchrotron light to determine protein structures
Our quest to find new drug targets involves examining the chemical processes that happen in the fungal cell in order to keep the cell alive. We choose an enzyme – a special type of protein involved in these processes – which will be a good target for anti-fungal medication. The experiments we do to produce our protein crystals include molecular biology, protein expression, purification and crystallisation. We clone the gene that encodes the enzyme and insert it into a suitable host to produce the protein, such as the bacterium Escherichia coli, by protein expression methods. Escherichia coli is easy to manipulate and inexpensive to culture in large volumes. We then isolate the enzyme by protein purification methods which exploit the physicochemical properties of the enzyme to separate the target from the host proteins, and crystallise it before we examine it by X-ray crystallography.
We use an in-house crystallisation robot at UFS to prepare the crystallisation trials and we regularly collect crystal diffraction data via remote access at the macromolecular beamlines of the UK’s national synchrotron – Diamond Light Source (Diamond). This is a great help as we can control the beamline equipment from our offices, so we don’t incur the expense of travelling to the UK to use synchrotron techniques essential for our research. While we have X-ray diffractometers at the University of the Free State, they are not nearly as powerful as the beamlines of the Diamond synchrotron. Diamond’s beamline hardware has been developed to such an advanced stage that data collection can proceed very rapidly, enabling us to collect data much faster (minutes) than at our home sources (days). This high throughput is essential when searching for and identify tiny molecules that might potentially bind to the protein and possibly act as inhibitors, as large libraries of fragments must be screened.
“The brilliant light generated by Diamond (10 billion times brighter than the sun!) enables us to determine the structure of the proteins to extremely high resolutions, as well as structures from small or weakly diffracting crystals that we cannot study with our own laboratory techniques.”
Dr Carmien Tolmie, University of the Free State, South Africa
We use the protein structure to search for small molecules that will bind to the enzyme and possibly stop it from working (act as inhibitors). In Biocatalysis, knowledge of the protein structure can identify ways in which one can change, or mutate, the enzyme to perform the specific reactions desired. If the protein is a drug target, the structure can be used in Structure-Based Drug Discovery to develop new medications. This process can also be used for other applications like developing new pesticides for agriculture. Therefore, the next step in the research process is to use fragment screening methods to identify lead compounds that can be further developed into inhibitors, thus helping develop a next generation drug. The fragment screening is done in collaboration with Prof. Frank von Delft and the XChem group on the I04-1 beamline at Diamond through the GCRF START grant and will be undertaken once Covid19 travel restrictions are lifted.
Solving the structures of fungal cytochrome P450 reductase and Baeyer-Villiger monooxygenase
Recently, we were able to solve and gain new insights into the structures and mechanisms of the fungal cytochrome P450 reductase (CPR) from Candida tropicalis and the Baeyer-Villiger monooxygenase BVMOAFL210 from Aspergillus flavus, research that was made possible by the GCRF START grant. The results were published in the journals Scientific reports and Catalystsrespectively, and the research on the CPR was done in collaboration with scientists from the University of Cape Town5, who are also part of the START project. The publications were co-authored by START PDRAs Ana Ebrecht (first author on CPR paper) and Rodolpho do Aido Machado (co-author on BVMOAFL210).
The CPR plays a pivotal role in primary and secondary metabolism of different species, from bacteria to animals and plants. In fungi, it supplies electrons to enzymes that are vital for the survival of the organism. The CPR mechanism is complex and involves conformational changes that need to be finely tuned to optimise the process. The structural characterisation of the CPR helps to understand how this process occurs and what are the differences with the human homolog, opening the possibility to use it as a drug target. The structure and mutation data of BVMOAFL210 allowed us to better understand the role of the amino acid at a specific position in the enzyme, in terms of regioselectivity (the position in the substrate where the oxygen atom is inserted) as well as the sulfoxidation (the number of oxygen atoms inserted in a sulfur-containing compound). This residue may be used in future studies for directed evolution experiments to evolve the enzyme to catalyse a desired reaction.
In order to achieve the results, we first needed to produce pure protein. The proteins were crystallised by the vapour-diffusion method with the Douglas Oryx Nano crystallization robot located in our crystallography lab in our department. In these experiments, a library of 384 crystallisation conditions were screened and a few conditions yielded crystals. These crystals were cryo-cooled and shipped at liquid nitrogen conditions in a specialised container to Diamond where we collected data on the macromolecular crystallography beamlines through remote access. We processed the data and solved the structure with programs from the CCP4 suite of macromolecular data processing software. The proteins were characterised further by investigating their kinetic properties with several spectrophotometric assays using a UV/Visible light spectrophotometer.
For BVMOAFL210, we created mutations at a specific position and determined how these mutations alter the biocatalytic profile of the enzyme using whole-cell biotransformation experiments, followed by Gas-Chromatography Mass Spectrometry (GC-MS) analyses. In terms of the fungal cytochrome P450 reductase (CPR), the next steps will be to use the CPR for fragment screening to gain further, more detailed insights. This method uses protein crystals of the target enzyme to identify small molecule fragments that bind to the enzyme. These fragments are then elaborated into larger molecules with higher potency, which will hopefully not only inhibit the specific enzyme, but also the growth of pathogenic fungi.
Benefitting from increased research capacity through the GCRF START grant
The grant has contributed greatly to the research capacity of the Biocatalysis and Structural Biology Research group, making it possible to appoint a START Postdoctoral Research Assistant (PDRA) who focused on structural biology research, the research itself partially funded by START. START also helped to develop the skills of the researchers in the group by funding workshops, as well as workshop attendance, and a research exchange of the START PDRA to the UK in 2019. In addition, START has introduced us to world-class scientists at Diamond and other institutions who we can consult if we need advice on our experiments.
“With this sharing of knowledge, capacity building and cutting-edge research enabled by the GCRF START grant, it is our fervent aim to make a lasting, positive impact in terms of sustainable health, well-being and food security solutions now, and well into the future.”
Dr Carmien Tolmie, University of the Free State, South Africa
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Acknowledgements
We would like to thank Prof. Trevor Sewell from the START Centre of Excellence at the University of Cape Town’s Aaron Klug Centre for Imaging and Analysis for the pivotal role he has played both in GCRF START and Structural Biology in South Africa. The START Centre of Excellence is a collaborative, shared resource where participants in the START programme can access everything they need to get started with their research, such as advice and the necessary equipment which may not be available in their own laboratories elsewhere. This also includes the technological support and expertise to access the UK’s national synchrotron – Diamond Light Source – through the GCRF START grant (such as support with sample preparation, shipping, and remote access experiments).
[1] Research in the Department falls broadly into three main areas: (i) production of safe and novel food products, (ii) biocatalytic production of chemicals or bioremediation of chemical pollution, and (iii) improvement of human and animal health. Our Biocatalysis Group focuses heavily on biocatalysis which involves the use of one or more enzymes, either as cell-free enzymes or enzymes in whole cells, to convert a substrate into a value-added product. This includes converting alkanes, alcohols, fatty acids or monoterpenes into value added building blocks of pharmaceuticals, bio-plastics, cosmetics, flavours and/or fragrances.
[2] Ebrecht AC, Van der Bergh N, Harrison STL, Smit MS, Sewell BT and DJ Opperman (2019). Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis. Scientific Reports 9:20088. doi: 10.1038/s41598-019-56516-6: https://www.nature.com/articles/s41598-019-56516-6
[3] Tolmie C,Do Aido Machado R, Ferroni FM, Smit MS and DJ Opperman (2020). Natural variation in the ‘control loop’ of BVMOAFL210 and its influence on regioselectivity and sulfoxidation. Catalysts 10(3): 339. doi: 10.3390/catal10030339: https://www.mdpi.com/2073-4344/10/3/339
[4] Dos Santos Abrantes PM, McArthur CP, Africa CWJ. Multi-drug resistant oral Candida species isolated from HIV-positive patients in South Africa and Cameroon. Diagn Microbiol Infect Dis 2014;79:222–7.
“Africa is a bank when it comes to diseases. The beauty of the GCRF START grant is that it offers us the opportunity to deal with these challenges in Africa, while enabling international collaboration and access to amazing synchrotron facilities with world class results.”
Dr Ikechukwu Anthony Achilonu, Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand, South Africa
Neglected Tropical Diseases (NTD’s) and Antimicrobial Resistance (AMR) are major challenges threatening the world’s sustainability and development efforts across the spectrum of the UN’s Sustainable Development Goals, causing millions of deaths each year1. My name is Dr Ikechukwu Achilonu and I work in the PSFRU at the University of the Witwatersrand, in South Africa, where I focus on rational design and discovery of new generation anthelminthic and anti-bacterial drug targets to tackle NTD’s and Nosocomial infections by ESKAPE2 pathogens.
To design inhibitors to serve as potential drugs against these pathogens, high-resolution 3D protein structures are needed to test the ability of certain drugs to interact with and inhibit the properties of the proteins being studied. This is made possible with the GCRF START grant which provides us with access to state-of-the-art synchrotron techniques, equipment and expertise at the UK’s world class national synchrotron, Diamond Light Source (Diamond), enabling the X-ray diffraction from protein crystals generated in our research. The GCRF START grant is currently our only conduit to the UK to enable us to conduct these ultra-high-quality experiments.
My recent research success is solving the Schistosomiasis joponicum Glutathione S-transferase (GST) enzyme has been recently published and is a tribute to the value of collaborating with Diamond and GCRF START. The solved structure is among the crystal structures with the highest resolution in the global protein database for this enzyme with two different ligands. Of the authors, Dr Ramesh Pandian is a GCRF START postdoctoral fellow (Host: Prof. Yasian Sayed), and Dr Sylvia Fanucchi, Prof. Yasien Sayed, Prof. Heine W. Dirr, and I – Dr Ikechukwu Achilonu – are collaborators on the GCRF START grant.
The resulting publication emphasises the need to exploit the unique structural diversity between Schistosoma GST and other human GSTs for a rational approach to design new generation anthelminthics. This research, outlined later in this article, will pave the way for the next exciting step in the structural validation of druggable targets for this debilitating and life-threatening Schistosomiasis (Bilharzia), a NTD which infects large numbers of people across several countries each year4.
The extent of the challenge: NTD’s and ESKAPE pathogens
AMR is described by the World Health Organization5 as “one of the biggest threats to global health, food security, and development today…compromising our ability to treat infectious diseases, as well as undermining many other advances in health and medicine.”
NTD’s are a diverse group of communicable diseases caused by a variety of pathogens prevalent in tropical and subtropical conditions, such as viruses, bacteria, protozoa and parasitic worms (helminths). More than a billion people in over 149 countries are impacted by NTD’s with huge costs to developing economies of billions of US dollars every year. My research on NTD’s focuses on Schistosoma and Wuchereria (Wuchereria is a human parasitic worm (Filariworm) that is the major cause of lymphatic filariasis) – both of which display AMR. Populations living in poverty, without adequate sanitation and in close contact with infectious vectors and domestic animals and livestock, are those worst affected by NTD’s6.
The six nosocomial ESKAPE pathogens that exhibit multidrug resistance and virulence are often acquired in health care settings like hospitals (Health Care Acquired Infection/HAI) and feature on the World Health Organization’s ‘Priority Pathogens list’7. The persistent use of antibiotics has provoked the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) bacteria, which can make even the most effective drugs ineffective. These bacteria have built-in abilities to find new ways to become resistant and can pass on genetic materials which enable other bacteria to become drug resistant. Like NTD’s, this situation is made worse by limited or non-existent infection prevention and control (IPC) programmes, combined with an inadequate water supply, poor sanitation, and a weak hygiene infrastructure in health facilities, which make the burden of HAI several fold higher in low- and middle-income countries than in high-income ones.
Over the past three years, I have been working on the Schistosoma GST enzyme, which is a protein that is involved in detoxification of foreign molecules in the Schistosome parasite that causes the disease Schistosomiasis/Bilharzia. This enzyme very critical to the survival of the parasite. If the enzyme is not functioning properly, the parasite cannot move from egg stage to lava stage. Therefore, if the enzyme could be effectively inhibited, one would have a drug against the parasite.
In my research, I used a molecule which is a natural product found in pomegranate juice called Ellagic Acid. One of my MSc. students, Ms Blessing Akumadu, carried out the study I had conceptualised, showing that this molecule can inhibit the activity of the Schistosoma GST by 66%. The concept was based on an earlier study that ellagic acid and its derivative inhibits Plasmodium GST (duly acknowledged in the forthcoming paper).To be more confident about making extrapolations from the structure of the Schistosoma japonicum GST enzyme, we needed to see that our wet lab results had meaning in 3D high resolution. Using the I038 and I04 beamlines at Diamond, we were able to solve the structure of the 26 kilodalton GST at 1.53 Å resolution and were amazed when we saw the results! We had achieved the highest resolution of any of the several variants of the Schistosoma japonicum GST in the global protein database!
What we observed is the Schistosoma 26 kilodalton GST enzyme (Sj26GST), which is a dimeric protein (it has two similar subunits joined together) with an interface where the subunits are joined. The unique thing about this protein is that the dimer interface can be exploited for drug interaction, unlike other GST’s in humans. The results have enabled us to see where the Ellagic Acid molecule (the potential drug) can bind to the protein. In this parasite we only have two classes of GSTs (in humans there are several) – the 26 kilodalton (kDa) GST and the 28 kDa GST. Having studied the 26 kDa GST, we are now currently working on the 28 kDa GST across the three species of the Schistosoma parasite that infect humans (mansoni, haematobium and japonicum) to see if the Ellagic Acid molecule can also inhibit the 28 kDa GST of the Schistosoma parasite.
The implications of these results mean we can go on and redesign this potential drug molecule because we can see the type of interaction this drug is making with the protein in the 3D images. The more the drug interacts, the stronger the binding. Therefore, we can start to redesign this drug for better binding so that the binding and the efficiency is improved beyond the 66% to maybe 75% or even to 99 % in order to completely shut down the activity of the enzyme at a very low amounts of the drug. Without the high-resolution 3D crystal structure solved using Diamond, we could not do this. We can now exploit this interaction by adding a bond here or a functional group there to improve the strength of the interaction and potency of the drug, and produce new high resolution structures until we have a drug that shuts down the enzyme and produces a new drug target to which the Schistosoma parasite is not resistant to.
The benefit of studying multiple NTD and ESKAPE pathogens simultaneously – the case of nicotinamide adenine transferase enzyme in klebsiella pneumonia and Enterococcus faecium.
In my experience, the techniques one applies to studying one protein can also be applied to the others, which is why I study a range of druggable proteins from several human NTD and ESKAPE pathogens simultaneously. For example, my students and I are examining the nicotinate-nucleotide adenylyltransferaseenzyme which is important in the redox metabolism in both klebsiella pneumonia and Enterococcus faecium. Klebsiella pneumonia is a Gram-negative bacterium resistant to multiple drugs and increasingly resistant to most available antibiotics (it has a thin cell wall surrounded by a protective cell membrane which makes it harder for antibodies to penetrate). In health care settings, patients who require devices like ventilators or intravenous catheters, and patients who are taking long courses of certain antibiotics are most at risk for Klebsiella infections.
The Gram-positive Enterococcus faecium is a human pathogen that causes nosocomial bacteremia, surgical wound infection, endocarditis, and urinary tract infections (it has thick cell walls but no outer membrane). Studying both simultaneously has led to us noticing that the Gram-negative function of the nicotinamide adenine transferase enzyme performs differently from the Gram-positive function of the same enzyme which is exciting because this enables us to infer structural and functional differences between this enzymes from different bacteria that are supposed to perform similar activities in these bacterial pathogens. This has serious implication in the design of a broad-spectrum antibiotics that will target this enzyme in different organisms.
The process of solving protein structures –systematic integration of multi-facted ‘new generation’ theoretical and empirical studies
The approaches we use in the research outlined above are multi-faceted and multi-disciplinary involving the integration of sophisticated ‘new generation’ theoretical and empirical studies and, as already indicated, a range of cutting-edge equipment. To design drugs against disease pathogens, the three-dimensional architecture of the druggable protein is needed. Druggable proteins are proteins that are key to the survival of the pathogen which enables it to replicate inside the human host, either intracellularly or extracellularly. In the case of bacteria, for example, they need to manufacture their own energy and without the enzyme (protein) that makes this possible, the bacteria would not survive. Therefore, if we know the protein’s DNA sequence, we should be able to predict that we can synthesis this protein and develop the druggable target.
To elucidate the crystal structure of these druggable proteins it is possible to use home X-ray sources. Ultimately, however, there is a major advantage of using a powerful synchrotron light source like Diamond over most home X-ray sources because the amount of inferences made from a protein crystal with resolutions in the range of 1.3 – 1.7 Å is unprecedented. Such crystals can be further studied using computational algorithms and can also serve as models for replacement when solving the crystal structure of a protein that is very similar in structure.
In order to generate the recombinant proteins that are druggable targets, we need large amounts of these proteins. For this we use E. coli bacteria like a factory to synthesize our target proteins and carry out a rigorous ‘quality assurance’ process to ensure the proteins we make are pure, stable and homogenous for successful crystallisation experiments. If the protein is an enzyme, it should be able to catalyze the same function it does naturally in an organism (in vivo), inside a test tube (in vitro), which means that whatever we send off to Diamond for X-ray diffraction experiments, we need to be sure that the biological function is intact. To do this, the proteins are assayed (measured) for catalytic activity in vitro (if they are enzymes) and are further characterised using several biophysical techniques to test their structure and the function to the point we are satisfied that the proteins are active, properly folded and can perform the function they are supposed to perform properly (biological activity is maintained).
We purify the proteins to homogeneity using an ensemble of protein chromatography techniques. For ‘quality assurance’, we check the secondary structure content (Far-UV circular dichroism), the tertiary structure (intrinsic and extrinsic fluorescence spectroscopy); and the quaternary structure (using size exclusion HPLC). Every physical interaction between two biomolecules generates heat or absorbs heat as part of the function of the protein to interact with another molecule (molecular recognition). Therefore, to estimate the thermodynamics of protein-ligand interaction (interaction ability), we use isothermal titration calorimetry.
Once we are satisfied that the proteins are of good quality and quantity, we begin protein crystallisation. I like to use the analogy that structural biologists are akin to photographers and using X-ray diffraction is like taking a snapshot of the protein which has been forced to assemble as repeating units in a crystalline form. There are several approaches we use. We can either conduct crystallisation manually, or we can do it robotically using our in-house Douglas Instrument Oryx 8 crystallography robot for high throughput protein crystallisation.
To solve the protein structure – sometimes in complex with potential drugs – X-ray light is invaluable. However, X-rays have very short wavelengths and if you keep bombarding a protein crystal with X-rays, it will heat it up and gradually fall apart because of X-ray damage. By changing the protein from solution to a crystal, and then embedding it in a liquid able to resist the intense bombardment of X-ray (cryo-protection) by freezing it at the temperature of liquid nitrogen (-196 degrees Celsius), the sample stays stable and the X-rays will last 100x longer in the X-ray beam! Our crystal samples are therefore sent to Diamond in special containers which keep the samples crystals frozen. GCRF START makes it very easy to ship our crystals to the UK without lots of red tape. We use DHL and we have an easy system which means it only takes a few days to get to Diamond ready for the experiments; the GCRF START grant helps this process at no cost to us.
We can use an X-ray diffractometer such as a small in-house diffractometer to solve the protein structure, or the ultimate technique for X-ray crystallography – a massive synchrotron like Diamond! Diamond’s I03 and I04 beamlines are used to fire X-rays onto our crystal samples. The X-ray will be scattered based on the structure of the protein/molecule (X-ray diffraction). Then, using mathematical modelling and other techniques, the 3D structure of the protein is resolved, either on its own or in a complex with a drug or other biomolecules such as DNA.
My theoretical (computational) studies involve several molecular modelling techniques to model the atomistic behaviour of our proteins of interest, especially how the dynamics of these proteins are altered upon drug binding. We also screen various in silico (virtual) libraries (including PubChem, ZINC and Drug Bank databases) for potential hits that we further extend to the theoretical studies, including high-throughput virtual screening, induced-fit ligand docking, molecular dynamic simulation and free binding energy calculations.
Sometimes, however, the process provides a few surprises, which was the case in our journey to solving the structure of the Schistosoma japonicum GST enzyme. We usually send our crystals to Diamond at the same time as the other groups in South Africa because we have the same slots for data collection. Two weeks before we were supposed to ship our crystals, we found that none were ready yet to ship. This wasn’t good. Therefore, to hurry things along, I asked one of my MSc students, Jessica Olfsen, who knows the crystallization robot very well to generate the crystals we needed within one week. This she did, but they were very ugly looking crystals! I did not think we would get any data out of these crystals but at least we had crystals to send. I so doubted their usefulness that when I collected the data, I didn’t even want to look at it, let alone solve the protein structure. In my disappointment I asked one of our new post-docs (Dr Pandian) who needed a task to look at it. The resulting 3D high resolution structure blew him away! When we both looked at it, we saw just how beautiful it was. I had written the paper already, but it had needed more experimental data for publishing so now I had it! The structure was solved at unprecedented resolution and the paper was accepted for publishing.
As a structural biologist, drug discovery and protein biochemistry are completely intertwined and multidisciplinary in the sense that I cannot do without a synthetic chemist (organic chemist). These are the people who will synthesize the drug. For example, once we add the extra functional groups, it will improve the binding capacity of the drug. The synthetic chemist will then go into the laboratory, resynthesize the drug before I will return to my lab and see if the inhibition improves. When an improvement in the inhibition is apparent, we go through the whole process again: recrystallize the protein with the proposed drug, and then use Diamond again to produce another high-resolution 3D structure of the re-modelled drug molecule and protein interaction.
“This whole drug discovery process can take some time, so it is vital that we have access to world class synchrotron facility like Diamond for the lifetime of this research we until we have the results needed to tackle the NTD’s and ESKAPE pathogens which impact countless lives.”
Dr Ikechukwu Anthony Achilonu, Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand, South Africa
Read more here about the UN’s Sustainable Development Goals.
More about Dr Achilonu
Dr Ikechukwu Anthony Achilonu is Senior Researcher and the Interim South African Research Chair (NRF/SARChI) in Protein Biochemistry and Structural Biology at the Protein Structure-Function Research Unit (PSFRU), School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand in South Africa.
[1] Transforming our world: the 2030 Agenda for Sustainable Development – A/RES/70/1. New York, USA: United Nations; 2015.
[2] ESKAPE is an acronym for the group of bacteria, encompassing both Gram-positive and Gram-negative species, made up of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species.
[3] Authors: Blessing O. Akumadu, Ramesh Pandian, Jessica Olfsen, Roland Worth, Monare Thulo, Tshireletso Mentor, Sylvia Fanucchi, Yasien Sayed, Heini W. Dirr, Ikechukwu Achilonu. Title: Molecular basis of inhibition of Schistosoma japonicum glutathione transferase by ellagic acid: insights into biophysical and structural studies. Publication: Molecular and Biochemical Parasitology (2020);Elsevier. https://doi.org/10.1016/j.molbiopara.2020.111319
A team of researchers from the University of Cape Town (UCT) and University of the Free State (UFS) has achieved a remarkable feat in the field of structural biology by determining the structure of an enzyme that could be a key component in producing valuable commodity chemicals in greener, sustainable processes.
Known as cytochrome P450 reductase (CPR), the enzyme has received much attention – not only for its ability to perform difficult chemistry, but also for its role as drug target.
“The task was enormous,” said team member Naadia van der Bergh, a PhD student in UCT’s Centre for Bioprocess Engineering Research (CeBER). “CPR is a massive enzyme. It contains 679 amino acids and there were two molecules in the asymmetric unit. Added to that, our initial structure was determined and solved on the basis of a low-resolution map. Interpreting this structure was a truly gruelling effort.”
The results of the research were published on 27 December 2019 in the journal Scientific Reports (9:20088) by the Nature Publishing Group.
International exposure
With support from the Global Challenges Research Fund’s (GCRF) Synchrotron Techniques for African Research and Technology (START) programme, the team was given the opportunity to conduct parts of their research at the Diamond Light Source synchrotron in Oxfordshire in the United Kingdom (UK)
Image: Ana Ebrecht (left) and Naadia van der Bergh are part of a team of researchers from UCT and UFS that achieved a remarkable feat in the field of structural biology.
In a ‘double first’, Dr Priscilla Masamba, has become the first University of Zululand student to use the UK’s National Synchrotron Light Source, Diamond,and solve the partial structure of a protein from Schistosoma mansoni. With access to the synchrotron made possible by GCRF START, Priscilla employed sophisticated robotic instruments and macromolecular X-ray crystallography techniques remotely from South Africa to solve the partial structure of the G4LZI3 universal stress protein – a protein regarded as a target for novel medicines for treating the disease Schistosomiasis. The experiments took place in February 2020, using the Diamond’s I04-1 beamline.
Schistosomiasis is an acute and chronic disease caused by parasitic worms (schistosomes) endemic in more than 78 countries with an estimated 4 million people infected in South Africa alone. The disease requires an intermediate host, the freshwater snail Bulinus africanus, and occurs most often in rural areas where people become infected during routine agricultural, domestic, occupational, and recreational activities which expose them to infested water.
Only one drug, Praziquantel, is available to treat Schistosomiasis leaving people vulnerable to schistosome resistance and this treatment is only partially effective in treating adults. The aim of Priscilla ’s research is therefore to generate insights for the design of alternative treatment regimen targeting specific stages during the developmental cycle of the schistosome.
Describing the experiments at Diamond as “close to a cool sci-fi movie,” Dr Masamba was able to control the sophisticated instruments on I04-1 beamline and collect data in real time from the University of Cape Town’s (UCT’s) Aaron Klug Centre for Imaging and Analysis – established as a GCRF START Centre of Excellence for structural biology research.
“Remote data collection at Diamond was so exciting!” Dr Masamba explains, “I could literally control and see a robot that was thousands of miles away on the other side of the world, mount a microscopic crystal (sample) within the firing line of a powerful X-ray beam, and determine the amount of energies released by light emitted from the sample caused by incident X-ray beams, and all of this while working from the laboratory in Cape Town. I didn’t need to get in a plane to achieve the one of the most imperative steps in the crystallography process! The whole experience provided me with rare exposure to the world of X-ray crystallography, impacting my view of science in a spectacular way.”
Proteins are thermodynamically and kinetically responsible for all biochemical processes that occur, and are therefore responsible for coordinating, regulating and dictating numerous metabolic functions. Exposure of the Schistosome parasite to extreme conditions during its developmental stage triggers the expression of heat shock proteins and universal stress proteins, of which the G4LZI3 USP has been identified as a potential druggable target for the development of alternative treatments (schistosomicides). Techniques like X-ray crystallography can provide insight, not only into the composition of these biomolecules, but also into their various interactions with other compounds and their roles in biological mechanisms, an imperative foundation for rational drug design and development.
Before the experiments took place, diffraction of the crystals was first checked at UCT using a diffractometer. Crystals from these conditions were then flash-frozen in liquid nitrogen and shipped to the Diamond synchrotron to be used as samples.
The solved structure of the S. mansoni G4LZI3 is a success story for the University of Zululand, a small resource-constrained university in the rural part of KwaZulu-Natal Province of South Africa. The University of Zululand lacked the resources required for Dr Masamba to achieve all her objectives for her PhD, which meant the collaboration through START in order to carry out the experiments needed was imperative both professionally and personally.
Priscilla is thankful for the guidance and mentoring from her PhD supervisor, Professor Abidemi Paul Kappo, who heads up the Biotechnology and Structural Biology (BSB) Research Group in the Department of Biochemistry and Microbiology at the University of Zululand, and from START Principal Investigator, Professor Trevor Sewell, of UCT’s Aaron Klug Centre for Imaging and Analysis, both of whom helped Priscilla overcome various challenges.
“I have been able to learn and cultivate scarce, critical and sought-after skills here in Africa in the fields of bioinformatics and drug discovery, molecular biology and especially, structural biology,” says Dr Masamba. “These include gene cloning, recombinant protein expression and purification, as well as characterisation of proteins. This has not been an easy task because I am from an underrepresented group in science as a black female and study at a historically-disadvantaged and resource-constrained institution.”
An important objective of the START programme is to increase the number of structural biologists in similar less developed universities in South Africa and across the continent. This can present complex challenges, not least because many students are ill-equipped for work in the field of structural biology.
“A key concept behind the creation of the START Centre of Excellence at UCT’s Aaron Klug Centre for Imaging and Analysis, for example, is to provide the necessary infrastructure to enable senior students and staff at South Africa’s historically disadvantaged universities to access both the human and material resources necessary to overcome the difficulties and determine protein structures,” Professor Sewell says. “We count the collaboration with Professor Paul Abidemi Kappo and Dr Masamba as a major success in this respect.”
This collaboration between Prof. Kappo and Prof. Sewell was enabled by GCRF START with Prof. Sewell providing the technological resource for the G4LZI3 structural biology project, as well as the linkage to Diamond.
“Above all, Professor Sewell’s enthusiasm to train and develop a “critical mass” of students in Structural Biology is second to none,” Prof. Kappo says. “This has been a joint effort and a model of national and international collaboration. In addition to the technological resources through UCT and linkage with Diamond in the UK, funding for this project was provided by the National Research Foundation (NRF) of South Africa through a doctoral bursary awarded Dr Masamba. It is expected that structure-guided drug discovery for schistosomiasis will be the concluding part the project.”
Born to Congolese parents in the DR Congo, Dr Masamba lived in the UK and Zimbabwe as a child, before moving to South Africa where she matriculated and studied for her first degree in Biological Sciences at Walter Sisulu University, Mthatha. Thereafter, Priscilla joined the Biotechnology and Structural Biology (BSB) Research Group in the Department of Biochemistry and Microbiology at the University of Zululand headed by Prof Abidemi Paul Kappo and registered under his tutelage for a BSc (Hons) degree, followed by an MSc and later a PhD in Biochemistry. Priscilla’s desire is to continue in the path of macromolecular X-ray crystallography of proteins through the NRF Postdoctoral Fellowship in Structural Biology at the University of Johannesburg.
Acknowledgements
Dr Priscilla Masamba extends a special thanks to Dr Brandon Weber (UCT), Dr Phillip Venter (UCT), Kaylene Baron (UCT), and Ndibonani Qokoyi (University of Zululand) who were involved in different ways in the production, purification and crystallisation of the G4LZI3 protein, as well as in data collection.
