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UFS scientists involved in revolutionary protein structure prediction

31 August 2021 | Story Leonie Bolleurs | Photo Supplied

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

SRC Inauguration speech: 22 January 2005

2005-01-22

Campus Head (Prof Peter Mbati). Dean of Students (Dr Natie Luyt). Deputy Director: Student Affairs and my boss (Mr. Teboho Manchu), Members of the University executive and Academic staff members, SRC members, Leaders of trade Unions and Student organizations, Distinguished guests, Ladies and gentlemen, most importantly first entering students and Parents receive my heartfelt revolutionary greetings.

Let me extend my word of appreciation to our distinguished guests for adding value and dignity to this event. Your presence here means a lot to us. Program Director what I bring here with me, assisted by facts, and is therefore just the work of my imagination. Like a love letter addressed to a sweetheart miles away, even though you do not know how she feels, what she wants to hear, and do not even know how her face looks like.

To me a speech is just an honest and intimate conversation. That is why I got into the habit of establishing a dialogue, or a debate, with my acquaintances looking at their faces and trying to persuade them of what I am telling them.

Mr. Speaker and Madam Deputy Speaker of the Student Parliament we are gathering at this ceremony, significantly few weeks after the release of grade 12 results, with the exception of those from Mpumalanga because of fraud. The Grade 12 results also show that only 18% of Black learners matriculated with exemptions, as compared to 53, 6% of white learners. This is an indication that our education system needs an overhaul.

We are also gathered here significantly a day after the management retreat held in Bloemfontein, Masselspoort. The retreat discussed, among other things, the transformation agenda, and some possible solutions to challenges we are facing now.

Most regrettably, we are gathered here when the whole world morns the victims of Tsunami tragedy. Let me therefore tore the line and convey our deepest condolences, from the last robot of my heart, to the affected families. Our hearts and thoughts will always be occupied by this horrified tragedy.

Creating a new Institution

I would submit, for purposes of debate and discussions that this Institution should strive to specialize and excel in regional rural development studies. Since our higher education, institutions in South Africa are generally weak in rural development studies. Instead, most of them tend to have an urban orientation to their programmes. Training everybody for the cities, big business and the private sector. This is a big weakness in a country with such large rural areas and population trapped in poverty, disease and ignorance.

Women’s studies

Program Director, it is only a moron who can argue against the fact that for us to reposition the institution around the regional development challenge, we need to start first with women empowerment. It is a fact that in most of our poor communities and families, it is women who withstand the worst of poverty. They are the ones who daily have to wipe tears from children who are hungry. It is women who look after the sick, the elderly, those dying from AIDS and the jobless. They are the one who have to fetch water, make fire and cook. There can therefore be no rural development studies without women studies, in particular on how to empower them and assist in the provision of basic services, so that they are relieved from some of the burdensome task of the society.

Registration Process

Mr. Speaker and Madam Deputy Speaker of the Student Parliament let me indicate that the registration is a process and not an event, so it cannot be concluded overnight. This huge process demands for people to stay calm, as there is no crisis. People should stop being excited. At the same time, no organization should use its cheap popularity and unilaterally disrupt the continuous and smooth running of the registration process at hand.

Let me strongly indicate, madam deputy speaker, that I am on record for stating that I have forgiven all those who have wronged us. I harbour no bitterness towards the protagonists of our painful and unfortunate events of the past week. And we will overcome this process not by our own devices but by the help of Almighty God and the grace of our Lord Jesus Christ.

Concerning registration of first years, we have programs, concerning that of senior students, we have programs, regarding graduations we have programs, and concerning HIV\AIDS we have programs. So, there is no need for people to press panicking buttons.

Mr. Speaker and Madam Deputy Speaker of the Student Parliament let me be opportunistic and welcome the entire student body on Campus for the academic year 2005. May our lovely first entering students have a happy and momentous year as part of Qwaqwa Campus of University of the Free State. May your studies be fruitful and enjoyable.

Student years are generally the happiest years of your life, so please make the most of them. While you are doing, all your preparations bear in mind that University is not an opportunity, it is just creating opportunities for a person.

On behalf of SRC members, our people, our students and management members I would like to welcome you all. Even though your parents are far away, here at Uniqwa you have more brothers, more sisters and more parents. Since we will love you with the same love as if we are from one family, and I have no doubts that management members will love and care for you as if you are their own children. Should you encounter any problem while studying at the Qwaqwa Campus of University of the Free State do not hesitate to contact us at the SRC offices because we need to ameliorate any factor influencing you negatively while on campus. I wish you well in the attainment of your academic pursuit.

Senior Students: We are not faced with just a new year but another academic year where we all have to work together to achieve our common goal of building our Institution through the development of human power. I urge you to invest your whole selves in this SRC.

For quite some time now, a debate has been ranging as to, whether has there been any progress in this incorporation process, or we are just moving with no direction. This debate is important, but I hasten to add not essential. The SRC is also involved in this debate, but with definite shift in emphasis. For us it is not important to participate in the debate than it is in finding solutions for the challenges of this new chapter in the history of humankind.

To my colleagues: Comrades, we are leading this Institution with a sense of pride and duty, and I know very well that we lead men and women, students who are determined to ensure that we all reach our destination safely and on time.

I said in one of our meetings that there are more enemies on our way, more than we can imagine. I think you witnessed that during the course of this week. The excitement and unnecessary confusions caused by some confused and loosed charlatans bear testimony to my statements. We should not reveal our game plans unless we are ready to slam.

Let me also borrow from the words of the late Albert Lethuli when he said and I quote: “There remains before us the building of the new land, from the ruins of the old narrow groups, a synthesis of the rich cultural strains which we have inherited. The task is immense”. Lastly, a navy divided within its ranks will be vanquished and destroyed by the enemy, but a navy united in purpose and action, loyalty and commitment will not drawn but sail on to victory.

In conclusion, let me call upon all political structures, church denominations, developmental structures, clubs, societies and forums to put aside all their differences, ideological insinuations and forge unity towards transforming Qwaqwa Campus of University of the Free State into an institution that is seen playing vigilant role in developing students academically, politically, socially, spiritually, religiously, culturally and otherwise.

Program Director, let me end my speech by indicating that every drop of my blood is telling me that Uniqwa is my home. I firstly became a student here, I became an activist here, I became a leader here, I became a president here, I will become a graduant here and hopefully I will become an employee here. So never, doubt my commitment towards the community of this campus.

Please be informed, in a central University of Technology’s way, that if there is no UNIQWA in HEAVEN, then I am not GOING.

Let us broaden the social base.

Tello Titus Wa-Motloung President General

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