Energy Flow from Solute to Solvent Probed by Femtosecond IR Spectroscopy: Malachite Green and Heme Protein Solutions

Lian, Tianquan; Locke, B.; Kholodenko, Yuriy; Hochstrasser, Robin M.

doi:10.1021/j100096a005

Cited by 197 publications

(266 citation statements)

References 14 publications

Supporting

Mentioning

241

Contrasting

Order By: Relevance

“…5. This scaling is also consistent with the time constant (≈ 20 ps) found at room temperature for the inverse process, the diffusive heating of water after photoexcitation of heme [2].…”

Section: Discussionsupporting

confidence: 88%

“…Heat transport across heme proteins has, in the past, been investigated extensively [1][2][3][4]. Vibrational energy flow from the heme group in hemoglobin or myoglobin into the surrounding solvent could be directly followed using ultrafast spectroscopy because electronic relaxation very quickly converts the energy of an absorbed visible photon into vibrational energy of the heme, leading to an initial local temperature jump of several hundred Kelvin [2].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Temperature Dependence of the Heat Diffusivity of Proteins

et al. 2011

View full text Add to dashboard Cite

In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme protein, the sperm whale myoglobin double mutant L29W-S108L, and its dependence on temperature from 20 to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the protein but is trapped in one of its binding pockets (the Xe4 pocket) was used as the local thermometer. Energy was deposited into the solvent by IR excitation. Experimentally, the energy transfer rate increased from (30 ps)−1 at 20 K to (8 ps)−1 at 70 K. This temperature trend is opposite to what is expected, assuming that the mechanism of heat transport is similar to that in glasses. In order to elucidate the mechanism and its temperature dependence, nonequilibrium molecular dynamics (MD) simulations were performed, which, however, predicted an essentially temperature-independent rate of vibrational energy flow. We tentatively conclude that the MD potentials overestimate the coupling between the protein and the CO molecule, which appears to be the rate-limiting step in the real system at low temperatures. Assuming that this coupling is anharmonic in nature, the observed temperature trend can readily be explained. In a combined experimental-theoretical study, we investigated the transport of vibrational energy from the surrounding solvent into the interior of a heme-protein, the sperm whale myoglobin double mutant L29W-S108L, in dependence of temperature from 20 K to 70 K. The hindered libration of a CO molecule that is not covalently bound to any part of the protein but is trapped in one of its binding pockets (the Xe4 pocket), was used as "local thermometer". Energy was deposited into the solvent by IR excitation. Experimentally, the energy transfer rate increased from (30 ps) −1 at 20 K to (8 ps) −1 at 70 K. This temperature trend is opposite to what is expected, assuming the mechanism of heat transport is similar to that in glasses. In order to elucidate the mechanism and its temperature dependence, non-equilibrium molecular dynamics (MD) simulations were performed, which, however, predicted an essentially temperature independent rate of vibrational energy flow. We tentatively conclude that the MD potentials overestimate the coupling between the protein and the CO molecule, which appears to be the rate limiting step in the real system at low temperatures. Assuming that this coupling is anharmonic in nature, the observed temperature trend can readily be explained.

show abstract

“…5. This scaling is also consistent with the time constant (≈ 20 ps) found at room temperature for the inverse process, the diffusive heating of water after photoexcitation of heme [2].…”

Section: Discussionsupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Temperature Dependence of the Heat Diffusivity of Proteins

et al. 2011

View full text Add to dashboard Cite

show abstract

“…The fundamental process behind vibrational energy transport is intramolecular vibrational energy redistribution (IVR), which is typically discussed in terms of energy or state space [5][6][7][8][9], but it also may have a spatial component [10]. Most studies that emphasize the spatial character concentrated on the vibrational energy flow from a heme group in proteins into the surrounding solvent [11][12][13][14][15], which has been attributed to the transport through the propionate side chain [16,17]. The latter is part of the heme moiety and connects it directly to the protein surface.…”

Section: Introductionmentioning

confidence: 99%

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Schade

Hamm

2009

The Journal of Chemical Physics

View full text Add to dashboard Cite

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.

show abstract

“…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.…”

mentioning

confidence: 99%

Vibrational energy relaxation in proteins

Fujisaki

Straub

2005

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

123

View full text Add to dashboard Cite

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, (...

show abstract

Energy Flow from Solute to Solvent Probed by Femtosecond IR Spectroscopy: Malachite Green and Heme Protein Solutions

Cited by 197 publications

References 14 publications

Temperature Dependence of the Heat Diffusivity of Proteins

Temperature Dependence of the Heat Diffusivity of Proteins

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Vibrational energy relaxation in proteins

Contact Info

Product

Resources

About