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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

A learning path for working adults
2009-02-09

 
From the left are: Ms Maquida du Preez (MDP Programme Manager), Ms Eliche Lorandi ( Marketing Executive), Mr Theo Potgieter (BEE and Transformation Manager), Ms Marie Griebenouw (Programme Manager) and Mr Danie Jacobs (Head: Centre fro Business Dynamics).
Photo: Mangaliso Radebe
 
 In the short space of five years, the Centre for Business Dynamics at the University of the Free State (UFS) has grown in stature to such an extent that it is currently offering leadership development programmes at 45 institutions all over the country.

Speaking at the fifth anniversary of the centre’s establishment, its director, Mr Danie Jacobs, said the centre was the first commercial unit in South Africa, attached to a business school, to establish a desk focusing on Black Economic Empowerment (BEE) and Transformation in association with Empowerdex.

The main purpose of this joint venture with Empowerdex is to deliver comprehensive BEE training through the development and presentation of various programmes.

The centre has also introduced the High-Performing Directors’ Programme in association with ABSA. A total of about 40 students have enrolled for this programme so far,and their numbers fluctuate every year.

It is also the first unit in the country to link up with Thinking Fusion, one of the three consultancies contracted by the UFS, to introduce two unique leadership programmes, namely a programme in Creating Leadership and Personal Capacity in Women and the Leadership in the Connection Economy programme.

“Our aim is to prepare women for full participation as managers and leaders in transforming organizations to become truly integrated and representative of the full diversity spectrum of South Africa,” Mr Jacobs said.

“We have built amazing relationships with various clients, both in the private and public sector, over the last five years,” said Mr Jacobs. “I believe the success of the Centre for Business Dynamics lies within our methodology of action learning, as well as creating a learning path for working adults.”

“Because of our country’s history not all people are on an equal footing when it comes to prior learning, so we level the playing field by breaking the training up into easily absorbable components. The centre can address the training needs of any company because of the multiple resources that we are fortunate enough to have at our fingertips,” he said.

The centre also offers a Postgraduate Diploma in Tax Strategy and Management, aimed at bringing all parties involved in the field of taxation up to date with the latest developments and changes.

In addition, the centre has introduced The Choice and The Choice at Work programme in association with the Arbinger Institute in the United States of America. There are also two management programmes, namely the Management Preparation Programme and the Management Development Programme.

Apart from these programmes, the centre also offers products and services such as short courses, workshops and consultations.

Media Release
Issued by: Mangaliso Radebe
Assistant Director: Media Liaison
Tel: 051 401 2828
Cell: 078 460 3320
E-mail: radebemt.stg@ufs.ac.za  
9 February 2009
 

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