Small Saccharides as a Blanket around Proteins: A Computational Study

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

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.

Simulation toolkits at the molecular scale for trans-scale thermal signaling

Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.

Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations

Molecular dynamics simulations of the villin headpiece subdomain HP36 have been carried out to examine relations between rates of vibrational energy transfer across non-covalently bonded contacts and equilibrium structural fluctuations, with focus on van der Waals contacts. Rates of energy transfer across van der Waals contacts vary inversely with the variance of the contact length, with the same constant of proportionality for all nonpolar contacts of HP36. A similar relation is observed for hydrogen bonds, but the proportionality depends on contact pairs, with hydrogen bonds stabilizing the α-helices all exhibiting the same constant of proportionality, one that is distinct from those computed for other polar contacts. Rates of energy transfer across van der Waals contacts are found to be up to 2 orders of magnitude smaller than rates of energy transfer across polar contacts.

Hydrophobic solvation increases thermal conductivity of water

The interaction of water with small alcohols can be used as a model for understanding hydrophobic solvation of larger and more complex amphiphilic molecules. Despite its apparent simplicity, water/ethanol mixtures show important anomalies in several of their properties, like specific heat or partial molar volume, whose precise origin are still a matter of debate. Here we report high-resolution thermal conductivity, compressibility, and IR-spectroscopy data for water/ethanol solutions showing three distinct regions of solvation, related to changes in the H-bond network. Notably, the thermal conductivity shows a surprising increase of ≈3.1% with respect to pure water at dilute concentrations of ethanol (x = 0.025), which suggests a strengthening of H-bond network of water. Our results prove that the rate of energy transfer in water can be increased by hydrophobic solvation, due to the cooperative nature of the H-bond network.

Temperature relaxation in binary hard-sphere mixture system: Molecular dynamics and kinetic theory study

Computational schemes to describe the temperature relaxation in the binary hard-sphere mixture system are given on the basis of molecular dynamics (MD) simulation and renormalized kinetic theory. Event-driven MD simulations are carried out for three model systems in which the initial temperatures and the ratios of diameter and mass of two components are different to study the temporal evolution of each component temperature in nanoscale molecular conditions mimicking those in living cells. On the other hand, the temperature changes of the two components are also described in terms of a mean-field kinetic theory with the correlation functions calculated in the Percus-Yevick approximation. The calculated results by both the computational approaches have shown fair agreement with each other, whereas slight deviations have been found in the temporal range of femto- to picoseconds when the initial temperatures of the two components are significantly different, such as 300 K vs 1000 K. This discrepancy can be ascribed to the fast intra-component temperature relaxation assumed in the kinetic theory, and its violation in the MD simulations can be evaluated in terms of the Kullback-Leibler divergence between the equilibrated Maxwell-Boltzmann distribution at each temperature and the actual non-equilibrium velocity distribution realized in the MD. Thus, the present analysis provides a quantitative basis for addressing the temperature inhomogeneities experimentally observed in nanoscale crowding conditions.

Nanoscale Quantum Thermal Conductance at Water Interface: Green's Function Approach Based on One-Dimensional Phonon Model

We have derived the fundamental formula of phonon transport in water for the evaluation of quantum thermal conductance by using a one-dimensional phonon model based on the nonequilibrium Green’s function method. In our model, phonons are excited as quantum waves from the left or right reservoir and propagate from left to right of H2O layer or vice versa. We have assumed these reservoirs as being of periodic structures, whereas we can also model the H2O sandwiched between these reservoirs as having aperiodic structures of liquid containing N water molecules. We have extracted the dispersion curves from the experimental absorption spectra of the OH stretching and intermolecular modes of water molecules, and calculated phonon transmission function and quantum thermal conductance. In addition, we have simplified the formulation of the transmission function by employing a case of one water molecule (N=1). From this calculation, we have obtained the characteristic that the transmission probability is almost unity at the frequency bands of acoustic and optical modes, and the transmission probability vanishes by the phonon attenuation reflecting the quantum tunnel effect outside the bands of these two modes. The classical limit of the thermal conductance calculated by our formula agreed with the literature value (order of 10−10 W/K) in high temperature regime (>300 K). The present approach is powerful enough to be applicable to molecular systems containing proteins as well, and to evaluate their thermal conductive characteristics.

Molecules and the Eigenstate Thermalization Hypothesis

We review a theory that predicts the onset of thermalization in a quantum mechanical coupled non-linear oscillator system, which models the vibrational degrees of freedom of a molecule. A system of N non-linear oscillators perturbed by cubic anharmonic interactions exhibits a many-body localization (MBL) transition in the vibrational state space (VSS) of the molecule. This transition can occur at rather high energy in a sizable molecule because the density of states coupled by cubic anharmonic terms scales as N³, in marked contrast to the total density of states, which scales as exp(aN), where a is a constant. The emergence of a MBL transition in the VSS is seen by analysis of a random matrix ensemble that captures the locality of coupling in the VSS, referred to as local random matrix theory (LRMT). Upon introducing higher order anharmonicity, the location of the MBL transition of even a sizable molecule, such as an organic molecule with tens of atoms, still lies at an energy that may exceed the energy to surmount a barrier to reaction, such as a barrier to conformational change. Illustrative calculations are provided, and some recent work on the influence of thermalization on thermal conduction in molecular junctions is also discussed.