Dr Andrei Pisliakov
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
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.
- Lyons JA, Aragão D, Slattery O, Pisliakov AV, Soulimane T & Caffrey M (2012). Structural insights into electron transfer in caa3-type cytochrome oxidase. Nature 487, 514-518.
- Pisliakov AV, Hino T, Shiro Y & Sugita Y (2012). Molecular dynamics simulations reveal proton transfer pathways in cytochrome c-dependent nitric oxide reductase. PLOS Comp. Biol. 8, e1002674.
- Matsumoto Y, Tosha T, Pisliakov AV, Hino T, Sugimoto H, Nagano S, Sugita Y & Shiro Y (2012). Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus. Nature Struct. Mol. Biol. 19, 238-245.
- Pisliakov AV, Cao J, Kamerlin SCL & Warshel A (2009). Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc. Nat. Acad. Sci. USA 106, 17359-17364.
- Pisliakov AV, Sharma PK, Chu ZT, Haranczyk M & Warshel A (2008). Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc. Nat. Acad. Sci. USA 105, 7726-7731.
- Braun-Sand S, Sharma PK, Chu ZT, Pisliakov AV & Warshel A (2008). The energetics of the primary proton transfer in bacteriorhodopsin revisited: It is a sequential light induced charge separation after all. Biochim. Biophys. Acta Bioenergetics 1777, 441-452.
- Warshel A, Kato M & Pisliakov AV (2007). Polarizable force fields: History, test cases and prospects. J. Chem. Theory Comput. 3, 2034-2045.
- Kato M, Pisliakov AV & 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: Struct. Funct. Bioinf. 64, 829-844.