Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis

Ishikura, Takakazu; Yamato, Takahisa

doi:10.1016/j.cplett.2006.10.092

Cited by 70 publications

(113 citation statements)

References 29 publications

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“…Such anisotropy has been characterized, e.g., by maps of local conductivities in proteins. 12 The extent to which hot spots, i.e., the regions in the molecule which lie along a channel by which energy transport is facile, depend on individual vibrations is revealed by construction of communication maps broken down by vibrational frequency. Indeed, many vibrational modes of proteins are spatially localized, particularly at higher frequency, and transport energy only locally rather than over longer distances.…”

Section: Discussionmentioning

confidence: 99%

Frequency-resolved communication maps for proteins and other nanoscale materials

Leitner

2009

The Journal of Chemical Physics

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Proteins exhibit highly anisotropic flow of energy. There is presently much interest in locating channels that enable signaling between distant sites, possibly playing a role in protein function such as allostery. We present an approach for computing frequency-resolved local energy diffusivities, which provide a map of communication between protein residues as a function of the vibrational frequencies of the modes that carry energy between them. A network of vibrational energy transport channels can then be identified at select frequencies. Over most frequency ranges the communication maps vary widely with vibrational frequency, as we illustrate for the protein myoglobin. We expect the approach presented here to be useful in mapping frequency-sensitive signaling in a variety of materials on the nanoscale.

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Section: Discussionmentioning

confidence: 99%

Frequency-resolved communication maps for proteins and other nanoscale materials

Leitner

2009

The Journal of Chemical Physics

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“…Since the early 1980s, it is well known that vibrational non-harmonicity [2,3] has to be accounted for to understand intra-structure energy redistribution [4][5][6][7][8]. Among nonlinear effects, long-lived, localized modes were suggested to play a key role both by theoretical [9][10][11] and experimental studies [12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Long-range energy transfer in proteins

Piazza

Sanejouand

2009

Phys. Biol.

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Proteins are large and complex molecular machines. In order to perform their function, most of them need energy, e.g. either in the form of a photon, as in the case of the visual pigment rhodopsin, or through the breaking of a chemical bond, as in the presence of adenosine triphosphate (ATP). Such energy, in turn, has to be transmitted to specific locations, often several tens ofÅ away from where it is initially released. Here we show, within the framework of a coarse-grained nonlinear network model, that energy in a protein can jump from site to site with high yields, covering in many instances remarkably large distances. Following single-site excitations, few specific sites are targeted, systematically within the stiffest regions. Such energy transfers mark the spontaneous formation of a localized mode of nonlinear origin at the destination site, which acts as an efficient energy-accumulating center. Interestingly, yields are found to be optimum for excitation energies in the range of biologically relevant ones.

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“…From a theoretical point of view, the intramolecular vibrational energy flow in biomolecules has also received a great deal of attention 2, 28 through different approaches including harmonic theories, 8,26,[29][30][31][32][33] molecular dynamics (MD) simulations, 28,[34][35][36][37][38][39][40][41][42][43][44][45][46] coarse-grained models, 33,47 and quantum methods. 21,[48][49][50][51][52][53] Despite this diversity of theoretical treatments, comparison between experimental and theoretical studies is still unsatisfactory because it faces the major difficulty that whereas experiments provide information on the energy transport spectroscopically from the vibrational modes which are active in the technique employed, most of the theoretical treatments discuss the energy flow in terms of residuebased models which, although shown to be quite useful in describing the spatial evolution of the energy, 38,39,41,44 are not well suited for direct comparison with observed data since the residues are not the experimentally active units.…”

Section: Introductionmentioning

confidence: 99%

A method for analyzing the vibrational energy flow in biomolecules in solution

Soler

Bastida

Farag

et al. 2011

The Journal of Chemical Physics

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A method is proposed to analyze the intra- and intermolecular vibrational energy flow occurring in biomolecules in solution during relaxation processes. It is based on the assumption that the total energy exchanged between the vibrational modes is minimal and the global process is essentially statistical. This statistical minimum flow method is shown to provide very useful information about the amount and the rate at which energy is transferred between the individual vibrations of the molecule. To demonstrate the performance of the method, an application is made to the relaxation of the amide I mode of N-methylacetamide-d in aqueous D(2)O solution which yields a detailed quantitative description of the process.

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Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis

Cited by 70 publications

References 29 publications

Frequency-resolved communication maps for proteins and other nanoscale materials

Frequency-resolved communication maps for proteins and other nanoscale materials

Long-range energy transfer in proteins

A method for analyzing the vibrational energy flow in biomolecules in solution

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