Biocatalysis and Structural Biochemistry

Principal Investigators

Biocatalysis 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.  The Biocatalysis Group at UFS strives to convert alkanes, alcohols, fatty acids or monoterpenes into value added building blocks of pharmaceuticals, bio-plastics, cosmetics, flavours or fragrances.

Dr Carmien Tolmie with Crystalograph
Dr Carmien Tolmie working with X-ray Crystallograph

The research has a strong focus on solving the three-dimensional structures of relevant biocatalysts through X-ray crystallography to investigate structure-function relationships.

The research also involves catalyst improvement through rational design and directed evolution as well as metabolic engineering and process development to further improve the industrial applicability of specific biocatalysts.

Research and Recent Featured Publications

Combining Heterogeneous Catalysis and Biocatalysis

 

Freakly, SJ, Kochius, S, van Marwijk, J, Fenner, C, Lewis, RJ, Baldenius, K, Marias, SS, Opperman, DJ, Harrison, ST, Alcalde, M, Smit, MS and Hutchings, GJ (2019) A chemo-enzymatic oxidation cascade to activate C-H bonds with in situ generation of H2O2. Nature Communications 10:4178 PDF

Freakly et al

Baeyer-Villiger monooxygenases

Tolmie C, Smit MS and Opperman DJ (2019) Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Natural Product Reports. 36:326-353 PDF


 Get

Ferroni FM, Tolmie C, Smit MS and Opperman DJ (2016) Structural and catalytic characterization of a fungal Baeyer-Villiger monooxygenase. PloS one 11:e0160186 PDF

    BVMOAFL838 crystal structure

Cytochrome P450 Monooxygenases

Pennec A, Jacobs CL, Opperman DJ and Smit MS (2015) Revisiting cytochrome P450 mediated oxyfunctionalization of linear and cyclic alkanes. Advanced Synthesis and Catalysis. 357:118-13 Abstract

Cytochrome P450 monooxygenases

Kochius S, van Marwijk J, Ebrecht AC, Opperman DJ and Smit MS (2018) Deconstruction of the CYP153A6 Alkane Hydroxylase System: Limitations and Optimization of In Vitro Alkane Hydroxylation. Catalysts. 8:531
PDF



Terminal hydroxylation of n-octane to 1-octanol by CYP153A6

Cascade Reactions

Pennec A, Hollmann F, Smit MS and Opperman DJ (2015) One-pot conversion of cycloalkanes to lactones. ChemCatChem. 7:236-239 Abstract

One-pot conversion of cycloalkanes to lactones

Vorster A, Smit MS and Opperman DJ (2019) One-pot conversion of cinnamaldehyde to 2-phenylethanol via a biosynthetic cascade reaction. Organic Letters 21:7024-7027 PDF

 Biosynthetic Pathway of 2-Phenylethanol

Research Highlights / News

Biotrans

 

Biotrans2019, Groningen, the Netherlands

 

Jasmin Aschenbrenner, Dr Ana Ebrecht and Dr Rodolpho do Aido-Machado attended the 14th International Symposium on Biocatalysis and Biotransformations (BioTrans) in Groningen, Netherlands, which took place from the 7th to the 11th of July. The focus of the conference this year was the evolution and re-design of natural enzymes for either higher stability and/or new (chemo)enzymatic cascades as well as the design of novel classes of artificial enzymes. Professor Frances Arnold, Nobel prize winner in Chemistry in 2018, was one of the key note speakers.

Diamond data collection workshop, University of Pretoria, SA

The Diamond Light Source Data Collection Workshop was held at the University of Pretoria from the 10th to 11th of July 2019. This workshop was held specifically to teach more advanced data collection strategies via the remote access system at Diamond Light Source (UK) to young and upcoming African scientists interested in structural biology. Dr Dave Hall (leader of the MX science group), Dr Ralf Flaig (Principal Beamline Scientist of I04) and Dr Alice Douangamath (Senior Beamline Scientist of I04-1) presented a series of lectures on the proper use of the sophisticated software to ensure timely transport and delivery of crystals indented for remote data collection, as well as different experimental methods that are available to the remote access user. Staff members, postdoctoral researchers and postgraduate students from universities across South Africa participated, many of whom are currently collecting remote data at Diamond as part of the South African Structural Biology Consortium.

The workshop was attended by Dr Carmien Tolmie from the Biocatalysis and Structural Biology research group of the Department of Microbial, Biochemical and Food Biotechnology and Mr Francois Jacobs from the Inorganic Chemistry group of the Department Chemistry.


Diamond data collection

Research visit to the Structural Genomics Consortium, University of Oxford

Dr Carmien Tolmie is a postdoctoral researcher within the GCRF-START collaboration (Global Challenges Research Fund – Synchrotron Techniques for African Research and Technology) between the Diamond Light Source, United Kingdom, and several research groups at South African universities. Dr Tolmie was hosted for at Structural Genomics Consortium (SGC), University of Oxford, UK, for a two-month research visit between May and June 2019, enabled by GCRF-START. The SGC is a not-for-profit, public-private partnership with the directive to carry out basic science of relevance to drug discovery. The core mandate of the SGC is to determine 3D structures on a large scale and cost-effectively - targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.

Dr Tolmie was hosted in the Biotechnology research group, headed by Dr Nicola Burgess-Brown, under the guidance of Dr Alejandra Fernández-Cid, where she performed high-throughput cloning and expression experiments to prepare DNA constructs of genes encoding for fungal drug targets. Dr Tolmie was also hosted in the Protein Crystallography (Px) group, headed by Dr Frank von Delft, under the guidance of Dr Lizbé Koekemoer, where she performed high-throughput protein purification and crystallization trials of the fungal proteins.

During this period, Dr Tolmie also attended the BAG workshop at Diamond Light Source, Didcot, UK, which is held to train researchers that is part of a Block-Allocated Grant of beamtime on the macromolecular beamlines at Diamond.

SGC1

SGC2

SGC3

SGC4

GCRF-START Launch event, Oxford, UK


GCRF – START (Global Challenges Research Fund – Synchrotron Techniques for African Research and Technology) is a collaborative funding stream between South Africa and Diamond Lightsource, as part of the United Kingdom’s Official Development Assistance to support cutting-edge research to address the problems facing developing countries. This grant aims to establish collaboration between world-leading researchers in the UK and emerging talent in Africa in the fields of Structural Biology and Energy Materials. Carmien Tolmie attended the United Kingdom’s START launch event, held at St Catherine’s College, Oxford, from 27 – 28 March 2019, on behalf of the Biocatalysis and Structural Biology research group at Department of Biotechnology, University of the Free State. The launch event aimed to bring together members of the START participating research groups from South Africa and the UK, including principal investigators and post-doctoral research assistants (PDRAs), as well as other guests, to discuss updates and news on the project in order to facilitate greater collaboration and learning on synchrotron, cryo-electron microscopy and other associated techniques. Carmien presented the progress of the Biocatalysis and Structural Biology group, and also led the brainstorming session of the START Opportunities Committee to discuss the PDRA needs, research and other opportunities such as workshops, and how to structure outreach events in future.

START ox

Biophysics and Structural Biology at Synchrotrons, Cape Town, SA

The Biophysics & Structural Biology at Synchrotrons workshop was held at the University of Cape Town from 17 – 24 January 2019. The workshop was aimed at introducing young, mostly African, bioscience researchers to the power of synchrotron-based facilities. The workshop comprised of lectures by international experts on all aspects of structural biology projects and techniques for structural biology at synchrotrons, a remote X-ray diffraction data collection session on Diamond Lightsource (UK), as well as hands-on experimental session and software tutorials.

The workshop was attended by Dr Ana Ebrecht, Dr Rodolpho do Aido Machado, Jasmin Aschenbrenner and Carmien Tolmie from the Biocatalysis and Structural Biology research group of the Department of Microbial, Biochemical and Food Biotechnology; Dr Alice Brink and Francois Jacobs from the Inorganic Chemistry group of the Department Chemistry. The attendees had the opportunity to present their work to the lecturers and students as both a presentation and a poster to discuss progress and future experimental work. This workshop was funded by GCRF-START, the International Union for Pure and Applied Biophysics and the National Research Foundation. Carmien Tolmie and Francois Jacobs both won Outstanding Poster Prizes for the presentation of their research.

BPSB2

BPSB4

BPSB

BPSB3

cchange

 
C*Change2018, Bela Bela, SA

 

Prof Martie Smit and postgraduate fellows from the Biocatalysis Laboratory attended the C*Change Symposium 2018 from 9-11 November 2018 in Bela Bela. There they discussed the recent advances on alkane activation research and the impact of these results on the local industry and economy.


CCP4/MX2018 Macromolecular crystallography school, San Carlos, Brazil


The CCP4/MX2018 Macromolecular Crystallography School was held at the Institute of Physics of the University of Sao Paulo, Brazil, from 14-24 November 2018, on the topic "From data processing to structure refinement and beyond". Carmien Tolmie attended this workshop, which consisted of lectures by experts on protein crystallography and data processing, as well as hands-on tutorials, giving students the opportunity to work on their own data with the lecturers. A poster session provided the opportunity to present your research to the fellow participants and lecturers, who in turn gave useful suggestions on how to improve not only the quality of your research, but also the presentation of your work. The content of the workshop was of extremely high quality, but also provided ample time to speak to the lecturers and participants in a more informal setting, which allows networking that may lead to future international collaborations.

CCP4



Start 2

START joint launch event at the University of Witwatersrand, Johannesburg, SA

Carmien Tolmie attended the first joint GCRF-START meeting for Structural Biology and Material Science, held from 18-19 September 2018 at the University of Witwatersrand, Johannesburg, South Africa. Principal investigators, post-doctoral researchers and post-graduate students from numerous groups in both disciplines attended and presented an overview of their research, and how their work ties in with the START initiative. Chris Nicklin, the head PI of the START initiative at the Diamond synchrotron, attended the meeting and led strategic discussions on the layout of the grant, and on navigating funding, future collaborations, education and outreach.  While researchers from both Structural Biology and Material Science use synchrotron techniques, the two fields mainly operate in isolation. This meeting provided an interface for researchers from various institutions and from both disciplines not only to learn about each other's work, but also to get to know the researchers in person.  From the perspective of a Structural Biologist, the presentations on the projects of Material Science, and the diversity of the synchrotron techniques that are being used, were very insightful. The meeting also provided an opportunity for the PI's, postgraduate students and post-doctoral researchers in Structural Biology to liaise and discuss future data collections at the Diamond Synchrotron.

Fifth European Crystallographic School, Stellenbosch, SA

Cheri Jacobs, Jasmin Aschenbrenner and Dr Ana Ebrecht attended the 5th European Crystallographic School held in Stellenbosch, from 8-14 July 2018.




5th European Crystallographic School

Research visit to Cardiff University School of Chemistry, UK

Dr Jacqueline van Marwijk visited Cardiff University School of Chemistry from 2-18 April 2018. During the visit, experiments were conducted in an effort to bridge the gap between chemo- and biocatalysis. The experiments were done in the Cardiff Catalysis Institute, hosted by Prof Graham Hutchings.

Cardiff University Visit

2018 DAAD Visiting students

The Biocatalysis Lab hosted two German students for internships in 2018. Andreas Schäffler, an under-graduate student from Eberhard Karls Universität, Tübingen, spent two months (August to October) working on the ADH-mediated lactonization of 1,6-diols during his DAAD RISE internship (German Academic Exchange Service - Research Internship in Science and Engineering). He was later joined by Leon Hennecke, an MSc student from Hamburg University of Technology, for two weeks during October, working on the same project.

Leon Hennecke
Leon Hennecke

Andreas Schäffler
Andreas Schäffler


FACULTY CONTACT

Faculty Manager: Velaphi Makgwahla
T: + 27 51 401 3199
E: makgwahlamvt@ufs.ac.za

Marketing Manager: Elfrieda Lötter
T: +27 51 401 2531
E: lottere@ufs.ac.za

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