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31 August 2021 | Story Leonie Bolleurs | Photo Supplied
UFS scientists involved in revolutionary protein structure prediction
Left: Dr Ana Ebrecht, a former postdoctoral student of the UFS, was part of the team that validated the data for the Science paper. Right: Prof Dirk Opperman was involved in a revolutionary finding in biology, which predicts the structure of a protein. His work in collaboration with other scientists has been published in Science.

Prof Dirk Opperman, Associate Professor in the Department of Microbiology and Biochemistry at the University of the Free State (UFS), in collaboration with Dr Ana Ebrecht (a former postdoc in the same department) and Prof Albie van Dijk from the Department of Biochemistry at the North-West University (NWU), was part of an international collaboration of researchers who participated in solving an intricate problem in science – accurate protein structure prediction.

The team of researchers recently contributed to an influential paper describing new methods in protein structure prediction using machine learning. The paper was published in the prestigious scientific journal, Science.

“These new prediction methods can be a game changer,” believes Prof Opperman.

“As some proteins simply do not crystalise, this could be the closest we get to a three-dimensional view of the protein. Accurate enough prediction of proteins, each with its own unique three-dimensional shape, can also be used in molecular replacement (MR) instead of laborious techniques such as incorporating heavy metals into the protein structure or replacing sulphur atoms with selenium,” he says.

Having insight into the three-dimensional structure of a protein has the potential to enable more advanced drug discovery, and subsequently, managing diseases.

Exploring several avenues …

According to Prof Opperman, protein structure prediction has been available for many years in the form of traditional homological modelling; however, there was a big possibility of erroneous prediction, especially if no closely related protein structures are known.

Besides limited complementary techniques such as nuclear magnetic resonance (NMR) and electron microscopy (Cryo-EM), he explains that the only way around this is to experimentally determine the structure of the protein through crystallisation and X-ray diffraction. “But it is a quite laborious and long technique,” he says.

Prof Opperman adds that with X-ray diffraction, one also has to deal with what is known in X-ray crystallography as the ‘phase problem’ – solving the protein structure even after you have crystallised the protein and obtained good X-ray diffraction data, as some information is lost.

He states that the phase problem can be overcome if another similar-looking protein has already been determined.

This indeed proved to be a major stumbling block in the determination of bovine glycine N-acyltransferase (GLYAT), a protein crystallised in Prof Opperman’s research group by Dr Ebrecht, currently a postdoc in Prof Van Dijk’s group at the NWU, as no close structural homologous proteins were available.

“The collaboration with Prof Opperman’s research group has allowed us to continue with this research that has been on hold for almost 16 years,” says Prof Van Dijk, who believes the UFS has the resources and facilities for structural research that not many universities in Africa can account for.

The research was conducted under the Synchrotron Techniques for African Research and Technology (START) initiative, funded by the Global Challenges Research Fund (GCRF). After a year and multiple data collections at a specialised facility, Diamond Light Source (synchrotron) in the United Kingdom, the team was still unable to solve the structure.

Dr Carmien Tolmie, a colleague from the UFS Department of Microbiology and Biochemistry, also organised a Collaborative Computational Project Number 4 (CCP4) workshop, attended by several well-known experts in the field. Still, the experts who usually participate in helping students and researchers in structural biology to solve the most complex cases, were stumped by this problem.

Working with artificial intelligence

“We ultimately decided to turn to a technique called sulphur single-wavelength anomalous dispersion (S-SAD), only available at specialised beam-lines at synchrotrons, to solve the phase problem, says Prof Opperman.

Meanwhile, Prof Randy Read from the University of Cambridge, who lectured at the workshop hosted by Dr Tolmie, was aware of the difficulties in solving the GLYAT structure. He also knew of the Baker Lab at the University of Washington, which is working on a new way to predict protein structures; they developed RoseTTAaFold to predict the folding of proteins by only using the amino acid sequence as starting point.

RoseTTAaFold, inspired by AlphaFold 2, the programme of DeepMind (a company that develops general-purpose artificial intelligence (AGI) technology), uses deep learning artificial intelligence (AI) to generate the ‘most-likely’ model. “This turned out to be a win-win situation, as they could accurately enough predict the protein structure for the UFS, and the UFS in turn could validate their predictions,” explains Prof Opperman.

A few days after the predictions from the Baker Lab, the S-SAD experiments at Diamond Light Source confirmed the solution to the problem when they came up with the same answer.

Stunning results in a short time

“Although Baker’s group based their development on the DeepMind programme, the way the software works is not completely the same,” says Dr Ebrecht. “In fact, AlphaFold 2 has a slightly better prediction accuracy. Both, however, came with stunningly good results in an incredibly short time (a few minutes to a few hours),” she says.

Both codes are now freely available, which will accelerate improvements in the field even more. Any researcher can now use that code to develop new software. In addition, RoseTTAFold is offered on a platform accessible to any researcher, even if they lack knowledge in coding and AI.

News Archive

During 2011: Appointments
2011-12-01

Dr Lis Lange: Senior Director: DIRAP

Description: 2011 Appointments_Lis Lange Tags: 2011 Appointments_Lis Lange

Dr Lis Lange, an Argentinean by birth, immigrated to South Africa twenty years ago – a few weeks after Nelson Mandela had walked through the gates of Victor Verster. For the past ten years, she has been involved in quality assurance for higher education institutions at the Council on Higher Education at national level.

She is assisting our university in the areas of quality assurance and academic planning, contributing to the development of deep intellectual debate and multi-disciplinary research.


Prof. Charles Dumas, Department of Drama and Theatre Arts

Description: 2011 Appointments_Charles Dumas Tags: 2011 Appointments_Charles Dumas

Prof. Charles Dumas, Extraordinary Professor in our Department of Drama and Theatre Arts, will be spending three months per year for the next three years at our university to help develop filmmaking, specifically focusing on the development of the Video Unit Planned for the Department.

Prof. Dumas started the year off with the production, Our Father’s Daughters, which was produced during the Mini-festival as well as at the Reitz Four reconciliation meeting. The production was also turned into a short film. Prof. Dumas gave film-acting classes to the third-year drama students. He directed multiple productions, such as the third-year module production Ipi Zombi, the Grahamstown Festival production, Seven Guitars and the Dance/drama production, Race, Reconciliation and the Reitz Four.


Prof. Daniel Plaatjies, UFS Business School

Description: 2011 Appointments_Daniel Plaatjies Tags: 2011 Appointments_Daniel Plaatjies

Prof. Daniel Plaatjies is the former Director and Head of the Graduate School of Public and Development Management at the University of the Witwatersrand. He was mainly responsible for the leading, directing and managing of strategic academic programmes, teaching, research, governance, service management and monitoring. Prof. Plaatjies, who was appointed as Visiting Professor at our Business School this year, will as part of his new duties at our Faculty of Economic and Management Sciences, be lecturing part-time and supervise our PhD students.


Prof. Johann Neethling, Department of Private Law

Description: 2011 Appointments_Johann Neethling Tags: 2011 Appointments_Johann Neethling

Prof. Johann Neethling’s career is now completing its full circle with his appointment as Senior Professor in our Department of Private Law. In 1965 he was a first-year at this university. With his nine law text books and nearly 200 articles, together with 40 years’ experience in academic training he is of inestimable value to this Department. His publications contribute to the establishment of our university as a research institute.


Prof. Hussein Solomon, Department of Political Science

 Description: 2011 Appointments_Hussein Solomon Tags: 2011 Appointments_Hussein Solomon

Prof. Hussein Solomon joined our university this year as Senior Professor in the Department of Political Science. Formerly he worked in peace NGOs, advised diplomats and acts as a serving officer in the South African Air Force.

His area of research expertise includes conflict and conflict resolution in Africa; South African Foreign Policy; international relations theory; religious fundamentalism and population movements within the developing world. He is also the author of a number of books, including one on global jihad and one on India's secret relationship with apartheid South Africa.

He is also member of the internationally renowned Our Humanity in the Balance (OHIB) organisation, where his role is to bring these disparate communities together and to focus energies on a common project.


Prof. André Keet, International Institute for Studies in Race, Reconciliation and Social Justice

Description: 2011 Appointments_Andre Keet Tags: 2011 Appointments_Andre Keet

Prof. André Keet, our Director of the International Institute for Studies in Race, Reconciliation and Social Justice, joined the University of Pretoria on a part-time basis in 2008, whilst being a Commissioner on the Commission for Gender Equality. Later he left the Commission and joined the University of Fort Hare. “I was happy to join academia and now also serve on the Stellenbosch University Council; therefore I am very aware of the challenges facing higher education,” he said.

His vision for the Institute is to support higher-education transformation, promote non-discrimination, reconciliation and human rights, build national, regional and international networks, and developing ‘new’ languages, knowledge and discourses for reconciliation and social justice, all to the benefit of our university and South Africa.”


Prof. Helene Strauss, Department of English

Description: 2011 Appointments_Helena Strauss Tags: 2011 Appointments_Helena Strauss

Prof. Helene Strauss completed her PhD at the University of Western Ontario, London, Canada, where she taught courses on Film Studies, Children’s Literature and South African Literature and Culture. “I was subsequently appointed as an Assistant Professor in the Department of English and Cultural Studies at McMaster University, Hamilton, Canada.” She joined our Department of English this year.

Prof. Strauss has an on-going preoccupation with questions concerning social justice, race, gender and ethical interpersonal interaction in South Africa and beyond.


Prof. EC Ejiogu, Centre for Africa Studies

Description: 2011 Appointments_EC Ejiogu Tags: 2011 Appointments_EC Ejiogu

After 22 years in the United States of America, Prof. EC Ejiogu decided to return to Africa – to his roots – to join our university’s Centre for Africa Studies at the beginning of 2011.

Before joining the Centre, he was Assistant Research Professor in the Centre for Innovation at the University of Maryland, College Park. As Senior Researcher at the Centre, he has already helped with the streamlining of the academic programme, restructuring it to enable students to gain skills necessary to deliver a research proposal towards a dissertation after their three years of study. He has also taken up PhD and Master’s supervision.

His latest publications include a book published in March 2011 with the title, Roots of Political Instability in Nigeria, and a book co-edited with Prof. Kwandiwe Kondlo, Director of the Centre for Africa Studies, Africa in focus: Governance in the 21st century, published in April 2011.


Pura Mgolombane, Vice-Dean: Student Affairs

Description: 2011 Appointments_Pura Tags: 2011 Appointments_Pura

Bringing with him a decade of experience in Student Affairs our new Assistant-Dean for Student Life and Leadership, Pura Mgolombane, has big plans for student development. He says his office wants to help Kovsies increase its throughput rate and produce socially well-adjusted and employable graduates in South Africa, the continent and anywhere in the world.

Before joining Kovsies, he was employed as Director: Student Life, Governance and Culture at Walter Sisulu University. Pura, who has a background in Human Resources, Business Management and Corporate Law, says his academic training has empowered him with skills to ensure that the Student Life and Leadership is properly led, governed and managed.


Prof. Hasina Ebrahim, School for Social Sciences and Language Education

Description: 2011 Appointments_Hasina Ebrahim Tags: 2011 Appointments_Hasina Ebrahim

This former academic from the University of Kwa-Zulu Natal was appointed as Associate Professor at our School for Social Sciences and Language Education in the Faculty of Education. Amongst others, she is the project coordinator for the Faculty’s Early Childhood and Foundation Phase Teacher Education Programme and the MEd and PhD supervisor in the programme.

Prof. Ebrahim is also the Deputy-President of the first South African Research Association for Early Childhood Education (birth to nine). “This is certainly a milestone to profile the university in terms of its thrust towards excellence in research,” she says. One of the main aims of the association is to shape the research agenda for a marginalised field in South Africa. 


Prof. Corli Witthuhn, Faculty of Natural and Agricultural Sciences

 Description: 2011 Appointments_Corli Witthuhn Tags: 2011 Appointments_Corli Witthuhn

Prof. Corli Witthuhn, a former Bloemfonteiner, attained her PhD in Microbiology at our university. Therafter, in 1999, she was appointed as a lecturer at Stellenbosch University and later as Vice-Dean.

Currently she is our Vice-Dean in the Faculty of Natural and Agricultural Sciences. She hopes to sustain her research here at our University.

Her life motto? “Opportunities are presented in the form of obstacles,” she says.
 


Prof. Melanie Walker

Description: 2011 Appointments_Melanie Walker Tags: 2011 Appointments_Melanie Walker

Prof. Melanie Walker is a prominent South African scholar who has been working as Professor of Higher Education Studies at the world-leading University of Nottingham in the UK, where she been Director of Postgraduate Students and a Director of Research in the Faculty of Social Sciences. She will join the University of the Free State in February 2012 as Senior University Professor in the Postgraduate School.

She is a graduate of the University of KwaZulu-Natal and the University of Cape Town, where she completed her PhD, after teaching in disadvantaged secondary schools for a number of years. Prior to working at Nottingham she worked at the Universities of Sheffield, West of England and Glasgow, as well as the Universities of Cape Town and the Western Cape. She is also a Fellow of the Human Development and Capability Association. She is currently Director of Research Training and a senior researcher in the EU-funded Marie Curie EDUWEL project, which includes senior researchers from eight European countries and 15 early-stage researchers.

With a long-standing commitment to social-justice research and equality practices, she is currently widely recognised internationally as leading in the application of the capability approach and human development to higher education policy and practice. Among others, she has led or participated in research projects funded by the NRF (South Africa), the Higher Education Academy (UK), HEFCE (UK), EU, and ESRC/DfID, which funded the Public-Good Professionals’ Capability Index research project. 
 

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