Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

Xie, Aihua; Meer, A. F. G. van der; Austin, Robert H.

doi:10.1103/physrevlett.88.018102

Cited by 114 publications

(90 citation statements)

References 26 publications

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“…The results of these analytical studies have also been confirmed by numerous computer simulations of discrete systems [12]. Some indirect experimental evidence of soliton's (large polaron's) existence in quasi-one-dimensional systems have been reported in [48][49][50][51][52][53][54][55][56].…”

Section: Hamiltonian Of the System And Dynamic Equationssupporting

confidence: 52%

Donor-acceptor electron transport mediated by solitons

2014

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Readers may view, browse, and/or download material for temporary copying purposes only, provided these uses are for noncommercial personal purposes. Except as provided by law, this material may not be further reproduced, distributed, transmitted, modied, adapted, performed, displayed, published, or sold in whole or part, without prior written permission from the American Physical Society.Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. We study the long-range electron and energy transfer mediated by solitons in a quasi-one-dimensional molecular chain (conjugated polymer, alpha-helical macromolecule, etc.) weakly bound to a donor and an acceptor. We show that for certain sets of parameter values in such systems an electron, initially located at the donor molecule, can tunnel to the molecular chain, where it becomes self-trapped in a soliton state, and propagates to the opposite end of the chain practically without energy dissipation. Upon reaching the end, the electron can either bounce back and move in the opposite direction or, for suitable parameter values of the system, tunnel to the acceptor. We estimate the energy efficiency of the donor-acceptor electron transport depending on the parameter values. Our calculations show that the soliton mechanism works for the parameter values of polypeptide macromolecules and conjugated polymers. We also investigate the donor-acceptor electron transport in thermalized molecular chains.

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Section: Hamiltonian Of the System And Dynamic Equationssupporting

confidence: 52%

Donor-acceptor electron transport mediated by solitons

2014

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“…It is possible that the narrow linewidths observed with CATM result from employing Dabs, which will amplify and sharpen features as is the case for time-resolved optical pump-infrared probe vibrational measurements 38 . We note that a previous far-infrared pump/ probe measurement suggested that extremely long-lived lowfrequency excitations are present for bacteriorhodopsin 39 .…”

Section: Normal Mode Analysismentioning

confidence: 99%

Optical measurements of long-range protein vibrations

et al. 2014

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Protein biological function depends on structural flexibility and change. From cellular communication through membrane ion channels to oxygen uptake and delivery by haemoglobin, structural changes are critical. It has been suggested that vibrations that extend through the protein play a crucial role in controlling these structural changes. While nature may utilize such long-range vibrations for optimization of biological processes, bench-top characterization of these extended structural motions for engineered biochemistry has been elusive. Here we show the first optical observation of long-range protein vibrational modes. This is achieved by orientation-sensitive terahertz near-field microscopy measurements of chicken egg white lysozyme single crystals. Underdamped modes are found to exist for frequencies 410 cm À 1 . The existence of these persisting motions indicates that damping and intermode coupling are weaker than previously assumed. The methodology developed permits protein engineering based on dynamical network optimization.

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“…Because of the advance of laser technology, there have been many experimental studies of VER in proteins (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). These experimental works are impressive, but it is difficult to derive detailed information from the experimental data alone.…”

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confidence: 99%

Vibrational energy relaxation in proteins

Fujisaki

Straub

2005

Proc. Natl. Acad. Sci. U.S.A.

117

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An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied by using two theoretical approaches. One approach is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach, which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in similar estimates of the VER time (subpicoseconds) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with previous experimental data. A perspective on directions for the detailed study of time scales and mechanisms of VER in proteins is presented.W hen a protein is excited by ligand binding, ATP attachment, or laser pulses, vibrational energy relaxation (VER) occurs. Energy initially ''injected'' into a localized region flows to the rest of the protein and surrounding solvent. VER in large molecules (including proteins) is an important problem for chemical physics (1,2). Even more significant is the challenge to relate VER to fundamental reaction processes, such as a conformational change or electron transfer of a protein, associated with protein functions. The development of an accurate understanding of VER in proteins is an essential step toward the goal of controlling protein dynamics (3).Because of the advance of laser technology, there have been many experimental studies of VER in proteins (4-17). These experimental works are impressive, but it is difficult to derive detailed information from the experimental data alone. Theoretical approaches, including atomic-scale simulations, can provide more detailed information. In turn, experimental data can be used to refine simulation methods and empirical force fields. This combination of experimental and theoretical studies of protein structures and dynamics has begun to blossom. As experimental methods develop further and theoretical approaches grow in accuracy, the relationship will become fruitful.There have been many theoretical tools (see Theories) developed to analyze VER in proteins. Some aspects of VER in proteins can be explained by perturbative formulas based on the equilibrium condition of the bath (see Cyt c), but the use of the perturbative formulas may be too restrictive to describe protein dynamics generally at room temperature. In this article, we not only discuss the success of such established methods but also present a perspective on the study of VER in proteins. TheoriesIn this section, we present a selective overview of theories appropriate for the study of VER in proteins. For the most part, these theories have been developed to deal with VER in liquids, solids, or glasses. For recent reviews, see refs. 18-20. We refer to two distinct categories; one is based on equilibrium dynamics and Fermi's golden rule, whereas the other is based on nonequilibrium dynamical models.Fermi's Golden Rule. If (i) there is a clear separation between the system and bath, (...

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Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

Cited by 114 publications

References 26 publications

Donor-acceptor electron transport mediated by solitons

Donor-acceptor electron transport mediated by solitons

Optical measurements of long-range protein vibrations

Vibrational energy relaxation in proteins

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