Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds
- 8 August 2003
- journal article
- research article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 119 (6), 3550-3558
- https://doi.org/10.1063/1.1588293
Abstract
The present work addresses the question of how electron tunneling matrix elements can be quantitatively calculated. In particular, we demonstrate how to go beyond Pathways methods, which have been shown to be qualitatively appropriate to do such calculations. Utilizing a combination of molecular dynamics with semiempirical and ab initio (Hartree–Fock) quantum chemistry calculations, we quantify how the dynamics and quality of the electronic Hamiltonian affect the outcome of the tunneling matrix elements. We show that tunneling is dominated by either one or, at most, a few constructively interfering pathway tubes. Even when equilibrium structures have destructive interference, tunneling is dominated by structures reached by fluctuations, where this interference is destroyed. In this limit, when one or a few constructive pathway tubes dominate, properly selected semiempirical methods are sufficiently powerful to provide quantitative predictions of the tunneling matrix elements. This combined methodology allows us to investigate quite large protein complexes. Calculations involving the electron transfer processes in azurin are used to validate these conclusions.Keywords
This publication has 49 references indexed in Scilit:
- The Nature of Tunneling Pathway and Average Packing Density Models for Protein-Mediated Electron TransferThe Journal of Physical Chemistry A, 2002
- Ab Initio Study of Long-Distance Electron Tunneling in a Model Peptide SystemThe Journal of Physical Chemistry B, 2000
- Electron tunneling in proteins: role of the intervening mediumJBIC Journal of Biological Inorganic Chemistry, 1997
- Electron tunneling in proteins: role of the intervening mediumJBIC Journal of Biological Inorganic Chemistry, 1996
- Electron-transfer reactions in proteins: an artificial intelligence approach to electronic couplingThe Journal of Physical Chemistry, 1993
- Quantum chemical probes of electron-transfer kinetics: the nature of donor-acceptor interactionsChemical Reviews, 1991
- X-ray crystal structure of the two site-specific mutants His35Gln and His35Leu of azurin from Pseudomonas aeruginosaJournal of Molecular Biology, 1991
- Structure of azurin from Alcaligenes denitrificans refinement at 1·8 Å resolution and comparison of the two crystallographically independent moleculesJournal of Molecular Biology, 1988
- Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitalsThe Journal of Chemical Physics, 1985
- Electron transfer in proteinsJournal of the Chemical Society, Faraday Transactions 2: Molecular and Chemical Physics, 1983