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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

Qwaqwa Campus honours academic excellence
2014-05-21


Photo: Sonia Small (Kaleidoscope Studios)

  • Photo Gallery

      Our Qwaqwa Campus was this past weekend a hive of activity when graduates, their parents and well-wishers descended on the campus to honour outstanding academic excellence during the Winter Graduation ceremonies.

      On Friday graduates from the Faculty of Humanities, as well as the Faculty of Economic and Management Sciences, were addressed by Tommy Makhatho, Managing Director of the Qwaqwa-based Bibi Cash and Carry.

      Makhatho urged graduates to continue working hard way beyond their graduation day and to dream big.

      “Dream big and don’t let your poor background hold you back,” Makhatho said.

      “Don’t let people say you can’t or that you will fail. Take up one idea. Make that one idea your life, think of it, dream of it, live on that idea, let your brain, muscle, nerves and every part of your body be full of that idea and leave every other idea alone. This is the way to success. If you don’t build your dream, someone else will hire you to help them build theirs,” said Makhatho, the winner of the 2013 Sanlam/Business Partners Entrepreneur of the Year and Job Creator of the Year awards.

      On Saturday, graduates were treated to yet another moving message by eNCA’s news anchor, Mabale Moloi, herself a graduate in Biological sciences.

      “If there is one ability that we should all practice on a daily basis, it is work ethics. This is a value based on hard work and diligence,” Moloi said.

      Moloi further shared her views on what makes excellent work ethics.

      “There are five very important factors of work ethics that we all need to be aware of. One of them is reliability. This means how committed you are to completing a task that is given to you within a particular period of time,” said Moloi.

      “The second one is dedication. This means how prepared you are to go the extra mile in completing a job or your studies. Thirdly, one’s level of productivity is very important in having an excellent work ethic. This refers to giving the best of yourself, even to the extent of surpassing what is expected of you.”

      “Fourthly, there is co-operation. We all must understand the value of team work and how it leads to success. And this, when paired with character, self-discipline and strong personality, will distinguish you from anyone else,” Moloi added.

      Among the more than 800 degrees, diplomas and certificates conferred, were three PhDs in Physics, Polymer Science and Zoology, respectively. Four Masters of Science degrees were conferred cum laude.

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