Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin—Molecular Dynamics Simulations of the Ground State and the M-Intermediate
| Autor: | Georg Büldt, Valentin Gordeliy, A. Baumgaertner, Sergei Grudinin |
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| Přispěvatelé: | Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Moscow Institute of Physics and Technology [Moscow] (MIPT), Research Centre Juelich, Institute of Solid State Research |
| Rok vydání: | 2005 |
| Předmět: |
Halobacterium
Models Molecular Time Factors Proton Protein Conformation Biophysics Biophysical Theory and Modeling Crystallography X-Ray 01 natural sciences chemistry [Bacteriorhodopsins] Diffusion 03 medical and health sciences Molecular dynamics ddc:570 Proton transport 0103 physical sciences Molecule methods [Biophysics] Computer Simulation Exponential decay chemistry [Phosphatidylcholines] 1-palmitoyl-2-oleoylphosphatidylcholine 030304 developmental biology metabolism [Halobacterium] 0303 health sciences Models Statistical 010304 chemical physics biology Hydrogen bond Chemistry chemistry [Water] Water Biological Transport Hydrogen Bonding Bacteriorhodopsin [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation Protein Structure Tertiary Models Chemical Chemical physics Bacteriorhodopsins Phosphatidylcholines biology.protein Physical chemistry Protons Ground state Dimerization Software |
| Zdroj: | Biophysical Journal Biophysical Journal, Biophysical Society, 2005, 88 (5), pp.3252--3261. ⟨10.1529/biophysj.104.047993⟩ Biophysical journal 88, 3252-3261 (2005). doi:10.1529/biophysj.104.047993 |
| ISSN: | 0006-3495 1542-0086 |
| DOI: | 10.1529/biophysj.104.047993 |
| Popis: | International audience; Protein crystallography provides the structure of a protein, averaged over all elementary cells during data collection time. Thus, it has only a limited access to diffusive processes. This article demonstrates how molecular dynamics simulations can elucidate structure-function relationships in bacteriorhodopsin (bR) involving water molecules. The spatial distribution of water molecules and their corresponding hydrogen-bonded networks inside bR in its ground state (G) and late M intermediate conformations were investigated by molecular dynamics simulations. The simulations reveal a much higher average number of internal water molecules per monomer (28 in the G and 36 in the M) than observed in crystal structures (18 and 22, respectively). We found nine water molecules trapped and 19 diffusive inside the G-monomer, and 13 trapped and 23 diffusive inside the M-monomer. The exchange of a set of diffusive internal water molecules follows an exponential decay with a 1/e time in the order of 340 ps for the G state and 460 ps for the M state. The average residence time of a diffusive water molecule inside the protein is ∼95 ps for the G state and 110 ps for the M state. We have used the Grotthuss model to describe the possible proton transport through the hydrogen-bonded networks inside the protein, which is built up in the picosecond-to-nanosecond time domains. Comparing the water distribution and hydrogen-bonded networks of the two different states, we suggest possible pathways for proton hopping and water movement inside bR. |
| Databáze: | OpenAIRE |
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