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Biomolecular Structure and Dynamics

The structure and dynamics of biological systems govern their behaviour, and in turn the central processes in all living organisms. We use a multidisciplinary approach to study the organisation of molecules, macromolecular biological complexes and the dynamic interactions in biological systems.

Our community combines cell and molecular biologists, biochemists, single molecule biophysicists and biomathematicians. We are committed to working collaboratively using established technologies in new ways and developing new approaches to address fundamental biology questions.
Biomolecular Structure and Dynamics Academics
Crystal courtesy of Ehmke Pohl

Research Highlights

  • Biobox is freely available, Python based software developed by a team led by Dr Matteo Degiacomi (Durham Physics) at Durham University. This new tool handles numerous complex pre-processing and molecular structure manipulation tasks, allowing the development of new biomolecular modelling methods. Find out more here.
  • Investigation of the structure-function relationship in two key retinoic acid binding proteins has given insights into the mechanism of action of this important class of proteins. The work of the multidisciplinary team led by Professor Ehmke Pohl (Durham Biosciences and Chemistry) has provided new details about retinoic acid signalling pathways that are implicated in several cancers and neurodegenerative diseases. Find out more here.

  • Professor Tim Blower (Durham Biosciences) and a team of international collegues have reported the first structure of an anti-CRISPR associated protein Aca2. These proteins are synthesised by bacteriophages and other attacking species to counter the CRISPR-Cas defences mounted by bacteria to halt the attacking species. CRISPR proteins are widely used in bioengineering and the discovery of new anti-CRSPR associated proteins would be an important step in the development of more refined CRSPR techniques. Find out more here.

New insights into retinoic acid signalling pathways

Representation of a ligand binding in the retinoic acid binding protein CRABPII, exploration of this binding site has given key information about potential new therapeutic targets.
Representation of a ligand binding in the retinoic acid binding protein CRABPII

The first structure of an anti-CRISPR associated protein Aca2

The image above shows a cartoon overview of the Aca2 dimer DNA-binding transcriptional autorepressor from Pectobacterium carotovorum bacteriophage in complex with DNA.
Cartoon overview of the Aca2 dimer DNA-binding transcriptional autorepressor from Pectobacterium carotovorum bacteriophage in complex with DNA.

Activities

Multi-layered bacterial genome defences 

The £4.6M project Multi-layered bacterial genome defences: linking molecular mechanisms to bacteria-MGE conflicts in single cells, populations, and communities was launched in 2022. Durham Biosciences's Professor Tim Blower is the Durham lead for the project which uses new interdisciplinary approaches and techniques to uncover bacterial defence systems. These systems could be exploited to tackle the spread of drug-resistant genes through the use of phages (viruses that infect bacteria). The project is led by Professor Edze Westra at University of Exeter, and includes researchers from the Universities of Durham, Manchester, Bath, Bristol, Liverpool and St Andrews.

Virus-X Consortium

As part of the EU funded Virus-X project Professor Ehmke Pohl (Durham Biosciences and Chemistry) has been exploring the strange world of viruses, also known as the Virosphere. Researchers in the Virus-X team have probed extreme environments, hunting for previously undiscovered viruses, including volcanic hot springs in Iceland (image right) and deep sea vents in the Atlantic Ocean more than 2300 m below sea level. 50 million new genes from extreme habitats have been found, and close to 1000 enzymes were selected for further characterisation. Several of these enzymes are currently being tested for use in applications ranging from protein production to the detection of pathogenic viruses such as SARS-CoV-2.

  • Multi-layered bacterial genome defences

    An intertwined BrxU dimer, with each monomer coloured in cyans or pinks. This DNA restriction enzyme (the BrxU dimer) is part of the defence system against phage attack in the emerging pathogen Escherichia fergusonii.
    An intertwined BrxU dimer, with each monomer coloured in cyans or pinks
  • Virus-X Consortium

    The image above shows cameraman Terry Winn at Euro News shooting a TV documentary about the Virus-X project (click to view).
    Cameraman Terry Winn at Euro News shooting a TV documentary about the Virus-X project.

Multi-layered bacterial genome defences

An intertwined BrxU dimer, with each monomer coloured in cyans or pinks. This DNA restriction enzyme (the BrxU dimer) is part of the defence system against phage attack in the emerging pathogen Escherichia fergusonii.
An intertwined BrxU dimer, with each monomer coloured in cyans or pinks

Virus-X Consortium

The image above shows cameraman Terry Winn at Euro News shooting a TV documentary about the Virus-X project (click to view).
Cameraman Terry Winn at Euro News shooting a TV documentary about the Virus-X project.

Highlight Publications

Cornish, K.A.S., Lange, J., Aevarsson, A., & Pohl, E., 2022. CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins. Journal of Biological Chemistry, 298, 5.

Jasilionis, A., Plotka, M., Wang, L., Dorawa, S., Lange, J., Watzlawick, H., van den Bergh, T., Vroling, B., Altenbuchner, J., Kaczorowska, A.-K., Pohl, E., Kaczorowski, T., Nordberg, Karlsson, E., & Freitag-Pohl, S., 2023. AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase. Protein Science, 32, 3.

Morris, E.R., Caswell, S.J., Kunzelmann, S., Arnold, L.H., Purkiss, A.G., Kelly, G., & Taylor, I.A., 2020. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Nature Communications, 11, 1.

Picton, D.M., Luyten, Y.A., Morgan, R.D., Nelson, A., Smith, D.L., Dryden, D.T.F., Hinton, J.C.D., & Blower, T.R., 2021. The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses. Nucleic acids research, 49, 19.

Prior, C., Davies, O.R., Bruce, D., & Pohl, E., 2020. Obtaining Tertiary Protein Structures by the ab Initio Interpretation of Small Angle X-ray Scattering Data. Journal of Chemical Theory and Computation, 16, 3.

Ramaswamy, V. K., Musson, S. C., Willcocks, C. G., & Degiacomi, M. T. 2021. Deep learning protein conformational space with convolutions and latent interpolations. Physical Review X, 11, 1.

Rudden, L.S.P., Musson, S.C., Benesch, J.L.P., & Degiacomi, M.T., 2022. Biobox: a toolbox for biomolecular modelling. Bioinformatics, 38, 4.

Tomlinson, C.W.E., Cornish, K.A.S., Whiting, A., & Pohl, E., 2021. Structure-functional relationship of cellular retinoic acid-binding proteins i and II interacting with natural and synthetic ligands. Acta Crystallographica Section D: Structural Biology, 77.

A purple dividing line

Biomolecular Structure and Dynamics Academics

Professor Tim Blower, Department of Biosciences           

Areas of Expertise: Microbiology, Genomics, Biochemistry, X-ray Crystallography 

Research Interests

  • Toxin-antitoxin systems
  • Bacteriophage-resistance
  • Antimicrobial Resistance
  • Bacteriophage biology
  • Phage defence 

 

Dr Liz Morris, Department of Biosciences             

Areas of Expertise: Structural biology, Biophysics, Biochemistry, Virology 

Research Interests

  • Enzyme mechanisms
  • Protein-protein and protein-nucleotide interactions involved in virus replication

 

Dr Matteo T. Degiacomi, Department of Physics               

Areas of Expertise: Molecular Dynamics, Machine Learning, Computational Biophysics    

Research Interests: The development of protein-protein docking methods, and techniques combining machine learning and molecular dynamics simulations to sample protein conformational spaces. 

 

Professor Ehmke Pohl, Departments of Biosciences and Chemistry & Nevrargenics

Areas of Expertise: Structural Biology 

Research Interests

  • Structure-based drug design focusing in infectious diseases
  • High-throughput screening for drug discovery

 

Dr Christopher Prior, Department of Mathematical Sciences       

Areas of Expertise: Magnetohydrodynamics, Topological Constraints 

Research Interests

  • Magnetohydrodynamics
  • Solar physics
  • Protein dynamics
  • Biological filament elasticity and topological constraints