Role of water and protein dynamics in proton pumping by respiratory complex I

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Haapanen , O & Sharma , V 2017 , ' Role of water and protein dynamics in proton pumping by respiratory complex I ' , Scientific Reports , vol. 7 , 7747 . https://doi.org/10.1038/s41598-017-07930-1

Title: Role of water and protein dynamics in proton pumping by respiratory complex I
Author: Haapanen, Outi; Sharma, Vivek
Contributor: University of Helsinki, Department of Physics
University of Helsinki, Department of Physics
Date: 2017-08-10
Language: eng
Number of pages: 12
Belongs to series: Scientific Reports
ISSN: 2045-2322
URI: http://hdl.handle.net/10138/215215
Abstract: Membrane bound respiratory complex I is the key enzyme in the respiratory chains of bacteria and mitochondria, and couples the reduction of quinone to the pumping of protons across the membrane. Recently solved crystal or electron microscopy structures of bacterial and mitochondrial complexes have provided significant insights into the electron and proton transfer pathways. However, due to large spatial separation between the electron and proton transfer routes, the molecular mechanism of coupling remains unclear. Here, based on atomistic molecular dynamics simulations performed on the entire structure of complex I from Thermus thermophilus, we studied the hydration of the quinone-binding site and the membrane-bound subunits. The data from simulations show rapid diffusion of water molecules in the protein interior, and formation of hydrated regions in the three antiporter-type subunits. An unexpected water-protein based connectivity between the middle of the Q-tunnel and the fourth proton channel is also observed. The protonation-state dependent dynamics of key acidic residues in the Nqo8 subunit suggest that the latter may be linked to redox-coupled proton pumping in complex I. We propose that in complex I the proton and electron transfer paths are not entirely separate, instead the nature of coupling may in part be 'direct'.
Subject: NADH-QUINONE OXIDOREDUCTASE
ESCHERICHIA-COLI NDH-1
MOLECULAR-DYNAMICS
MEMBRANE DOMAIN
ND1 SUBUNIT
UBIQUINONE BINDING
ENERGY-CONVERSION
CRYSTAL-STRUCTURE
CBB(3) OXIDASES
MECHANISM
114 Physical sciences
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