Literature DB >> 20972505

Protein-water electrostatics and principles of bioenergetics.

David N Lebard1, Dmitry V Matyushov.   

Abstract

Despite its diversity, life universally relies on a simple basic mechanism of energy transfer in its energy chains-hopping electron transport between centers of electron localization on hydrated proteins and redox cofactors. Since many such hops connect the point of energy input with a catalytic site where energy is stored in chemical bonds, the question of energy losses in (nearly activationless) electron hops, i.e., energetic efficiency, becomes central for the understanding of the energetics of life. We show here that standard considerations based on rules of Gibbs thermodynamics are not sufficient, and the dynamics of the protein and the protein-water interface need to be involved. The rate of electronic transitions is primarily sensitive to the electrostatic potential at the center of electron localization. Numerical simulations show that the statistics of the electrostatic potential produced by hydration water are strongly non-Gaussian, with the breadth of the electrostatic noise far exceeding the expectations of the linear response. This phenomenon, which dramatically alters the energetic balance of a charge-transfer chain, is attributed to the formation of ferroelectric domains in the protein's hydration shell. These dynamically emerging and dissipating domains make the shell enveloping the protein highly polar, as gauged by the variance of the shell dipole which correlates with the variance of the protein dipole. The Stokes-shift dynamics of redox-active proteins are dominated by a slow component with the relaxation time of 100-500 ps. This slow relaxation mode is frozen on the time-scale of fast reactions, such as bacterial charge separation, resulting in a dramatically reduced reorganization free energy of fast electronic transitions. The electron transfer activation barrier becomes a function of the corresponding rate, self-consistently calculated from a non-ergodic version of the transition-state theory. The peculiar structure of the protein-water interface thus provides natural systems with two "non's"-non-Gaussian statistics and non-ergodic kinetics-to tune the efficiency of the redox energy transfer. Both act to reduce the amount of free energy released as heat in electronic transitions. These mechanisms are shown to increase the energetic efficiency of protein electron transfer by up to an order of magnitude compared to the "standard picture" based on canonical free energies and the linear response approximation. In other words, the protein-water tandem allows both the formation of a ferroelectric mesophase in the hydration shell and an efficient control of the energetics by manipulating the relaxation times.

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Year:  2010        PMID: 20972505     DOI: 10.1039/c0cp01004a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  11 in total

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2.  Photosynthetic diode: electron transport rectification by wetting the quinone cofactor.

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3.  Protein dielectric environment modulates the electron-transfer pathway in photosynthetic reaction centers.

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Journal:  Biophys J       Date:  2012-11-07       Impact factor: 4.033

4.  Electronic Conductance Resonance in Non-Redox-Active Proteins.

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5.  Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex.

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6.  Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer.

Authors:  Mohammadhasan Dinpajooh; Daniel R Martin; Dmitry V Matyushov
Journal:  Sci Rep       Date:  2016-06-16       Impact factor: 4.379

7.  Electron-transfer chain in respiratory complex I.

Authors:  Daniel R Martin; Dmitry V Matyushov
Journal:  Sci Rep       Date:  2017-07-14       Impact factor: 4.379

8.  Effects of nonequilibrium fluctuations on ultrafast short-range electron transfer dynamics.

Authors:  Yangyi Lu; Mainak Kundu; Dongping Zhong
Journal:  Nat Commun       Date:  2020-06-04       Impact factor: 14.919

9.  DelPhi: a comprehensive suite for DelPhi software and associated resources.

Authors:  Lin Li; Chuan Li; Subhra Sarkar; Jie Zhang; Shawn Witham; Zhe Zhang; Lin Wang; Nicholas Smith; Marharyta Petukh; Emil Alexov
Journal:  BMC Biophys       Date:  2012-05-14       Impact factor: 4.778

10.  Modeling the Energy Landscape of Side Reactions in the Cytochrome bc1 Complex.

Authors:  Peter Husen; Ilia A Solov'yov
Journal:  Front Chem       Date:  2021-05-19       Impact factor: 5.221

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