University of Dundee

Dr Andrei Pisliakov

Computational Biophysics
Position: 
Senior Lecturer in Physics & Dundee Fellow
Affiliation: 
Address: 
School of Life Sciences, University of Dundee, Dundee
Full Telephone: 
+44 (0) 1382 388758, int ext 88758
Email: 

Research

Research Interests

We employ (and develop new) methods for biomolecular simulations:

  • Classical molecular dynamics (MD)
  • Quantum mechanics/molecular mechanics (QM/MM)
  • Empirical valence bond (EVB)
  • Hierarchical multiscale methods

To investigate the molecular mechanisms of:

  • Membrane proteins
  • Proton transfer in biology
  • Bioenergetic systems: proton and ion pumps, respiratory enzymes, photosynthetic complexes

Summary

We conduct computational research to explain and predict the functioning of protein complexes that are important in key biological processes, such as cellular energy conversion, molecular transport, and enzyme catalysis. The action of these complex "biomolecular machines" is often intrinsically coupled to the proton and ion translocations across various membranes. Examples include proton and ion pumps and channels, respiratory and photosynthetic complexes. To tackle these challenging problems, we employ a range of computational methods, extensively use supercomputers, and work in close collaboration with experimental groups.

Proton pumps, one of the foci of our current research, are an essential part of the energy production in living cells. They are membrane protein complexes that move protons from one side of the membrane to the opposite, against the electrochemical gradient, as e.g. in the processes of cellular respiration and photosynthesis. In the respiratory complexes of the electro-transport chain, the proton translocation is driven by redox reactions. Understanding the molecular mechanism of such energy coupling is a fascinating ongoing challenge of modern biophysics, biochemistry and structural biology. The efforts are also of biomedical importance, as the mitochondrial proton pumps are implicated in the most common human neurodegenerative diseases and ageing, while bacterial respiratory complexes have come into focus as a promising new target for the development of antimicrobial drugs.

 

 

Publications

1. Carvalheda, C. A. and Pisliakov, A. V. (2017) Insights into proton translocation in cbb3 oxidase from MD simulations. Biochimica et biophysica acta. 1858, 396-406
DOI: 10.1016/j.bbabio.2017.02.013
PMID: 28259641

2. Varshney, D., Petit, A. P., Bueren-Calabuig, J. A., Jansen, C., Fletcher, D. A., Peggie, M., Weidlich, S., Scullion, P., Pisliakov, A. V. and Cowling, V. H. (2016) Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic acids research. 44, 10423-10436
DOI: 10.1093/nar/gkw637
PMCID: 5137418
PMID: 27422871

3. Pisliakov, A. V., Hino, T., Shiro, Y. and Sugita, Y. (2012) Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase. PLoS computational biology. 8, e1002674
DOI: 10.1371/journal.pcbi.1002674

4. Matsumoto, Y., Tosha, T., Pisliakov, A. V., Hino, T., Sugimoto, H., Nagano, S., Sugita, Y. and Shiro, Y. (2012) Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus. Nature structural & molecular biology. 19, 238-245
DOI: 10.1038/nsmb.2213
PMID: 22266822

5. Lyons, J. A., Aragao, D., Slattery, O., Pisliakov, A. V., Soulimane, T. and Caffrey, M. (2012) Structural insights into electron transfer in caa3-type cytochrome oxidase. Nature. 487, 514-518
DOI: 10.1038/nature11182
PMCID: 3428721
PMID: 22763450

6. Pisliakov, A. V., Cao, J., Kamerlin, S. C. and Warshel, A. (2009) Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proceedings of the National Academy of Sciences of the United States of America. 106, 17359-17364
DOI: 10.1073/pnas.0909150106
PMCID: 2762662
PMID: 19805169

7. Pisliakov, A. V., Sharma, P. K., Chu, Z. T., Haranczyk, M. and Warshel, A. (2008) Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proceedings of the National Academy of Sciences of the United States of America. 105, 7726-7731
DOI: 10.1073/pnas.0800580105
PMCID: 2409407
PMID: 18509049

8. Braun-Sand, S., Sharma, P. K., Chu, Z. T., Pisliakov, A. V. and Warshel, A. (2008) The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. Biochimica et biophysica acta. 1777, 441-452
DOI: 10.1016/j.bbabio.2008.03.001
PMCID: 2443747
PMID: 18387356

9. Warshel, A., Kato, M. and Pisliakov, A. V. (2007) Polarizable Force Fields: History, Test Cases, and Prospects. Journal of chemical theory and computation. 3, 2034-2045
DOI: 10.1021/ct700127w
 
10. Kato, M., Pisliakov, A. V. and Warshel, A. (2006) The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations. Proteins. 64, 829-844
DOI: 10.1002/prot.21012
PMID: 16779836