Vibrational energy relaxation in proteins

Fujisaki, Hiroya; Straub, John E.

doi:10.1073/pnas.0409083102

Cited by 119 publications

(89 citation statements)

References 69 publications

(85 reference statements)

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“…At the same time, a new contribution from the coherence between the amide-I overtone and the amide-I state becomes possible. This new peak appears at a value of 3 that is 11 cm −1 lower than the original one. The induced absorption part of the cross peak thus shifts to lower 3 with increasing waiting time.…”

Section: -9mentioning

confidence: 97%

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Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Dijkstra¹,

Jansen²,

Bloem³

et al. 2007

The Journal of Chemical Physics

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Two-dimensional infrared spectroscopy is capable of following the transfer of vibrational energy between modes in real time. We develop a method to include vibrational relaxation in simulations of two-dimensional infrared spectra at finite temperature. The method takes into account the correlated fluctuations that occur in the frequencies of the vibrational states and in the coupling between them as a result of interaction with the environment. The fluctuations influence the two-dimensional infrared line shape and cause vibrational relaxation during the waiting time, which is included using second-order perturbation theory. The method is demonstrated by applying it to the amide-I and amide-II modes in N-methylacetamide in heavy water. Stochastic information on the fluctuations is obtained from a molecular dynamics trajectory, which is converted to time dependent frequencies and couplings with a map from a density functional calculation. Solvent dynamics with the same frequency as the energy gap between the two amide modes lead to efficient relaxation between amide-I and amide-II on a 560fs time scale. We show that the cross peak intensity in the two-dimensional infrared spectrum provides a good measure for the vibrational relaxation.

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Section: -9mentioning

confidence: 97%

“…[1][2][3][4] Energy is released into vibrational modes somewhere in a protein, for example, by hydrolysis of adenosine triphosphate ͑ATP͒. This energy then disappears into other vibrational modes, where it can be used to drive chemical reactions.…”

Section: Introductionmentioning

confidence: 99%

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Dijkstra¹,

Jansen²,

Bloem³

et al. 2007

The Journal of Chemical Physics

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“…However, for any realistically sized solution phase molecular systems, one will have to resort to classical mechanics molecular dynamics (MD) simulations [16,[23][24][25][26][27][28]. While the approximation of classical mechanics works extremely well when studying conformational processes of molecular systems, this is not necessarily the case for thermal properties, even in the completely harmonic case.…”

Section: Introductionmentioning

confidence: 99%

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Schade

Hamm

2009

The Journal of Chemical Physics

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Vibrational energy transport in the presence of intrasite vibrational energy redistribution AbstractThe mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e., on length scales of a few chemical bonds and time scales of a few picoseconds. This situation occurs, for example, during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time propagate the system fully quantum mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modeling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and time scales, the latter is governed by intrasite vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.Vibrational energy transport in the presence of intra-site vibrational energy redistribution Marco Schade and Peter HammPhysikalisch-Chemisches Institut, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland (Dated: September 16, 2009) The mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e. on length scales of a few chemical bonds and timescales of a few picoseconds. This situation occurs for example during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time-propagate the system fully quantum-mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modelling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways how classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and timescales, the latter is governed by intra-site vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.

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“…Elegant experiments using Raman detection to follow vibrational energy flow in molecules were performed by Dlott and colleagues (24,25) The IVR process of high-frequency modes in molecules with more than five atoms, in the condensed phase, was found to be very fast, leading to lifetimes of excited vibrations on the order of 0.5-5 ps (12,19,20,26). The relaxation rates are determined by several factors, including the local density of states, the amplitude and rate of frequency fluctuations, and the intermode coupling matrix elements (22,23,26). The complexity of IVR and vibrational energy transport processes originates from the nature of vibrational modes, which are often delocalized in molecules but to a different extent (22,23,27).…”

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confidence: 99%

A relaxation-assisted 2D IR spectroscopy method

Kurochkin

Naraharisetty²,

Rubtsov³

2007

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

148

188

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A method of two-dimensional infrared (2D IR) spectroscopy called relaxation-assisted 2D IR (RA 2DIR) is proposed that utilizes vibrational energy relaxation transport in molecules to enhance crosspeak amplitudes. This method substantially increases the range of distances accessible by 2D IR and is capable of identifying longrange connectivity patterns in molecules. RA 2DIR is illustrated in interactions among CN and CO modes in 3-cyanocoumarin and 4-acetylbenzonitrile, where the distances between the CN and CO groups are Ϸ3.1 and Ϸ6.5 Å, respectively. A 6-fold increase in cross-peak amplitude was observed in 4-acetylbenzonitrile when the dual-frequency RA 2DIR method was used.dual-frequency 2D IR ͉ heat transport ͉ vibrational relaxation D evelopment of new methods for determining the 3D structures of molecules in solution is an important challenge in chemistry. Recently introduced in the pioneering works of Hochstrasser and colleagues (1, 2), two-dimensional infrared (2D IR) spectroscopy has demonstrated its strong potential for measuring molecular structures in solution under physiological conditions (2-10). 2D IR and 2D NMR correlation methods have many analogies (11). The cross-peaks in 2D IR spectra originate from pairwise interactions of vibrational modes (vs. nuclear spins for 2D NMR), offering a measure of the distances between interacting vibrational modes (vs. spins). Readily measurable anisotropy of the cross-peaks in 2D IR reveals another important type of structural information, the mutual orientation of the transition dipoles of interacting modes, vide infra (12). Although 2D IR methods have been successfully applied to the study of small molecules and peptides, the measurement of structural constraints in macromolecules such as proteins remains a challenge. Here, we propose a method that uses vibrational relaxation and vibrational energy transport in molecules to significantly enhance the cross-peaks measured with 2D IR for modes separated by distances Ͼ4-5 Å. This approach substantially increases the range of distances accessible by 2D IR and is capable of identifying vibrational modes separated by multiple bonds and of delivering the long-range bond connectivity patterns in a way similar to that of the total correlation spectroscopy method of 2D NMR (13) and its heteronuclear version, heteronuclear multiple bond correlation. Relaxation-assisted 2D IR (RA 2DIR) enhances the potential of weak modes in 2D IR and allows their convenient use as structural reporters.In general, as structural labels, vibrational modes have the advantage of being very compact compared with, for example, FRET labels. However, the choice of vibrational labels for structural measurement in macromolecules by using 2D IR is not obvious. Thus far, most 2D IR cross-peak measurements have been performed by using strong IR stretching modes, such as CAO, OOH, NOH, and CON. However, these modes are highly abundant in biopolymers, and isotope substitution is required in order to decouple the label from the rest of the modes. 13 C 1...

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Vibrational energy relaxation in proteins

Cited by 119 publications

References 69 publications

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

A relaxation-assisted 2D IR spectroscopy method

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