Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape

Kurisaki, Ikuo; Tanaka, Seiya; Mori, Ichiro; Umegaki, Toshihito; Mori, Y.; Tanaka, Shigenori

doi:10.1002/jcc.27048

Cited by 8 publications

(1 citation statement)

References 52 publications

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“…A full atomistic description of protein thermal network function (and design) will depend on a better understanding of the mechanisms of long-range heat transfer in proteins. Rapid and long-range heat flow has been characterized in model peptides and a few proteins and is generally understood in the context of coupled anharmonic vibrational modes that are of low frequency. − The speed of heat transmission via such vibrational excitation has been estimated to be as high as ca. 15 Å 2 /ps, , compatible with the length of interrogated thermal networks.…”

Section: Discussionmentioning

confidence: 99%

Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase

Gao,

Wu,

Zhang

et al. 2024

ACS Catal.

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Murine adenosine deaminase (mADA) is a prototypic system for studying the thermal activation of active site chemistry within the TIM barrel family of enzyme reactions. Previous temperature-dependent hydrogen−deuterium exchange studies under various conditions have identified interconnected thermal networks for heat transfer from opposing protein−solvent interfaces to active site residues in mADA. One of these interfaces contains a solvent-exposed helix−loop−helix moiety that presents the hydrophobic face of its long α-helix to the backside of the bound substrate. Herein, we pursue the time and temperature dependence of solvation dynamics at the surface of mADA for comparison to established kinetic parameters that represent active site chemistry. We first created a modified protein devoid of native tryptophans with a close-to-native kinetic behavior. Single sitespecific tryptophan mutants were back-inserted into each of the four positions where native tryptophans reside. Measurements of nanosecond fluorescence relaxation lifetimes and Stokes shift decays that reflect time-dependent environmental reorganization around the photoexcited state of Trp* display minimal temperature dependences. These regions serve as controls for the behavior of a new single tryptophan inserted into a solvent-exposed region near the helix−loop−helix moiety located behind the bound substrate, Lys54Trp. This installed Trp displays a significantly elevated value for E a (k Stokes shift ); further, when Phe61 within the long helix positioned behind the bound substrate is replaced by a series of aliphatic hydrophobic side chains, the trends in E a (k Stokes shift ) mirror the earlier reported impact of the same series of function-altering hydrophobic side chains on the activation energy of catalysis, E a (k cat ). The reported experimental findings implicate a solvent-initiated and rapid (>ns) protein restructuring that contributes to the enthalpic activation barrier to catalysis in mADA.

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Section: Discussionmentioning

confidence: 99%

Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase

Gao,

Wu,

Zhang

et al. 2024

ACS Catal.

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Temperature Dependence of Thermal Conductivity of Proteins: Contributions of Thermal Expansion and Grüneisen Parameter

Leitner

2024

ChemPhysChem

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The thermal conductivity of many materials depends on temperature due to several factors, including variation of heat capacity with temperature, changes in vibrational dynamics with temperature, and change in volume with temperature. For proteins some, but not all, of these influences on the variation of thermal conductivity with temperature have been investigated in the past. In this study, we examine the influence of change in volume, and corresponding changes in vibrational dynamics, on the temperature dependence of the thermal conductivity. Using a measured value for the coefficient of thermal expansion and recently computed values for the Grüneisen parameter of proteins we find that the thermal conductivity increases with increasing temperature due to change in volume with temperature. We compare the impact of thermal expansion on the variation of the thermal conductivity with temperature found in this study with contributions of heat capacity and anharmonic coupling examined previously. Using values of thermal transport coefficients computed for proteins we also model heating of water in a protein solution following photoexcitation.

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Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape

et al. 2022

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Considering the importance of elucidating the heat transfer in living cells, we evaluated the thermal conductivity κ and conductance G of hydrated protein through all-atom non-equilibrium molecular dynamics simulation. Extending the computational scheme developed in earlier studies for spherical protein to cylindrical one under the periodic boundary condition, we enabled the theoretical analysis of anisotropic thermal conduction and also discussed the effects of protein size correction on the calculated results. While the present results for myoglobin and green fluorescent protein (GFP) by the spherical model were in fair agreement with previous computational and experimental results, we found that the evaluations for κ and G by the cylindrical model, in particular, those for the longitudinal direction of GFP, were enhanced substantially, but still keeping a consistency with experimental data. We also studied the influence by salt addition of physiological concentration, finding insignificant alteration of thermal conduction of protein in the present case.

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Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape

Cited by 8 publications

References 52 publications

Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase

Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase

Temperature Dependence of Thermal Conductivity of Proteins: Contributions of Thermal Expansion and Grüneisen Parameter

Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape

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