Energy Transport across Interfaces in Biomolecular Systems

Electrodeposition of Polymer Networks as Conformal and Uniform Ultrathin Coatings

Natural systems, synthetic materials, and devices almost always feature interphases that control the flow of mass and energy or stabilize interfaces between incompatible materials. With technologies transitioning to non-planar and 3D mesoscale architectures, novel deposition methods for realizing ultrathin coatings and interphases are required. Polymer networks are of particular interest for their tunable chemical and physical properties combined with their structural integrity. Here, the electrodeposition of polymer networks (EPoN) is introduced as a general approach to uniformly coat non-planar conductive materials. Conceptually, EPoN utilizes electrochemically activated crosslinkers as polymer end groups to confine their network formation exclusively to the material surface upon charge transfer, yielding a passivating and self-limiting growth of conformal and uniform coatings with tunable submicron thickness on conductive materials. EPoN is found to result in thin functional films of various polymer backbones and side group chemistries as demonstrated for poly(ether) and poly(acrylamide) based polymers as solid electrolyte and thermally responsive interphases, respectively.

Thermal Energy Transport through Nonbonded Native Contacts in Protein

Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.

Ballistic Energy Transport via Long Alkyl Chains: A New Initiation Mechanism

In an effort to increase the speed and efficiency of ballistic energy transport via oligomeric chains, we performed measurements of the transport in compounds featuring long alkyl chains of up to 37 methylene units. Compounds of the N3-(CH2)n-COOMe type (denoted as aznME) were synthesized with n = 5, 10, 15, 19, 28, 37 and studied using relaxation-assisted two-dimensional infrared spectroscopy. The speed of the ballistic transport, initiated by the N3 tag excitation, increased ca. 3-fold for the longer chains (n = 19-37) compared to the shorter chains, from 14.7 to 48 Å/ps, in line with an earlier prediction (Nawagamuwage et al. 2021, J. Phys. Chem. B, 125, 7546). Modeling, based on solving numerically the Liouville equation, was capable of reproducing the experimental data only if three wavepackets are included, involving CH2 twisting (Tw), wagging (W), and rocking (Ro) chain bands. The approaches for designing molecular systems featuring a higher speed and efficiency of energy transport are discussed.

Two stage decoherence of optical phonons in long oligomers

Molecular vibrations are generally responsible for chemical energy transport and dissipation in molecular systems. This transport is fast and efficient if energy is transferred by optical phonons in periodic oligomers, but its efficiency is limited by decoherence emerging due to anharmonic interactions with acoustic phonons. Using a general theoretical model, we show that in the most common case of the optical phonon band being narrower than the acoustic bands, decoherence takes place in two stages. The faster stage involves optical phonon multiple forward scattering due to absorption and emission of transverse acoustic phonons, i.e., collective bending modes with a quadratic spectrum; the transport remains ballistic and the speed can be altered. The subsequent slower stage involves phonon backscattering in multiphonon processes involving two or more acoustic phonons resulting in a switch to diffusive transport. If the initially excited optical phonon possesses a relatively small group velocity, then it is accelerated in the first stage due to its transitions to states propagating faster. This theoretical expectation is consistent with the recent measurements of optical phonon transport velocity in alkane chains, increasing with increasing the chain length.

Vibrational Energy Landscapes and Energy Flow in GPCRs

We construct and analyze disconnectivity graphs to provide the first graphical representation of the vibrational energy landscape of a protein, in this study β2AR, a G-protein coupled receptor (GPCR), in active and inactive states. The graphs, which indicate the relative free energy of each residue and the minimum free energy barriers for energy transfer between them, reveal important composition, structural and dynamic properties that mediate the flow of energy. Prolines and glycines, which contribute to GPCR plasticity and function, are identified as bottlenecks to energy transport along the backbone from which alternative pathways for energy transport via nearby noncovalent contacts emerge, seen also in the analysis of first passage time (FPT) distributions presented here. Striking differences between the disconnectivity graphs and FPT distributions for the inactive and active states of β2AR are found where structural and dynamic changes occur upon activation, contributing to allosteric regulation.

Dynamics of Hydrogen Bonds between Water and Intrinsically Disordered and Structured Regions of Proteins

Recent studies indicate more restricted dynamics of water around intrinsically disordered proteins (IDPs) than structured proteins. We examine here the dynamics of hydrogen bonds between water molecules and two proteins, small ubiquitin-related modifier-1 (SUMO-1) and ubiquitin-conjugating enzyme E2I (UBC9), which we compare around intrinsically disordered regions (IDRs) and structured regions of these proteins. It has been recognized since some time that excluded volume effects, which influence access of water molecules to hydrogen-bonding sites, and the strength of hydrogen bonds between water and protein affect hydrogen bond lifetimes. While we find those two properties to mediate lifetimes of hydrogen bonds between water and protein residues in this study, we also find that the lifetimes are affected by the concentration of charged groups on other nearby residues. These factors are more important in determining the hydrogen bond lifetimes than whether a residue hydrogen bonding with water belongs to an IDR or to a structured region.

Noncovalent π Interactions in Mutated Aquomet-Myoglobin Proteins: A QM/MM and Local Vibrational Mode Study

Protein dynamics and function is strongly connected to the energy flow taking place. Myoglobin (Mb) and its mutations are ideal systems to study the process of vibrational energy transfer (VET) at the molecular level. Anti-Stokes ultraviolet resonance Raman studies using a tryptophan (Trp) probe, introduced at different Mb positions by amino acid replacement, have suggested that the amount of VET depends on the position of the Trp probe relative to the heme group. Inspired by this experimental work, we explored the strength of noncovalent π interactions, as well as covalent interactions for both the axial and distal ligands bound to iron in aquomet-Mb with the local vibrational mode analysis (LMA), originally developed by Konkoli and Cremer. Two sets of noncovalent interactions were investigated: (1) the interaction between the water ligand and Trp rings and (2) the interaction between the Trp and the porphyrin rings of the heme group. We assessed the strength of these noncovalent interactions via a special local mode force constant. Various Trp-modified water-bound ferric Mb proteins in the ground state were studied (6 in total) using gas-phase and QM/MM calculations followed by LMA. Our results disclose that VET is indeed dependent on the position of the Trp probe relative to the heme group but also on the tautomeric nature of distal histidine. They provide new guidelines on how to assess noncovalent π interactions in proteins utilizing LMA and how to use these data to explore VET, and more generally protein dynamics and function.

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.

Locating dynamic contributions to allostery via determining rates of vibrational energy transfer

Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relationship between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β₂-adrenergic receptor, a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist-bound active state. From structures sampled during molecular dynamics (MD) simulations, we find the active state to have, on average, a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in the rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after the transition between states thereby provides information about dynamic contributions to activation and allostery.

Quantum Electrodynamic Behavior of Chlorophyll in a Plasmonic Nanocavity

Plasmonic nanocavities have been used as a novel platform for studying strong light-matter coupling, opening access to quantum chemistry, material science, and enhanced sensing. However, the biomolecular study of cavity quantum electrodynamics (QED) is lacking. Here, we report the quantum electrodynamic behavior of chlorophyll-a in a plasmonic nanocavity. We construct an extreme plasmonic nanocavity using Au nanocages with various linker molecules and Au mirrors to obtain a strong coupling regime. Plasmon resonance energy transfer (PRET)-based hyperspectral imaging is applied to study the electrodynamic behaviors of chlorophyll-a in the nanocavity. Furthermore, we observe the energy level splitting of chlorophyll-a, similar to the cavity QED effects due to the light-matter interactions in the cavity. Our study will provide insight for further studies in quantum biological electron or energy transfer, electrodynamics, the electron transport chain of mitochondria, and energy harvesting, sensing, and conversion in both biological and biophysical systems.

Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation

We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.

Tracking Energy Transfer across a Platinum Center

Rigid, conjugated alkyne bridges serve as important components in various transition-metal complexes used for energy conversion, charge separation, sensing, and molecular electronics. Alkyne stretching modes have potential for modulating charge separation in donor–bridge–acceptor compounds. Understanding the rules of energy relaxation and energy transfer across the metal center in such compounds can help optimize their electron transfer switching properties. We used relaxation-assisted two-dimensional infrared spectroscopy to track energy transfer across metal centers in platinum complexes featuring a triazole-terminated alkyne ligand of two or six carbons, a perfluorophenyl ligand, and two tri(p-tolyl)phosphine ligands. Comprehensive analyses of waiting-time dynamics for numerous cross and diagonal peaks were performed, focusing on coherent oscillation, energy transfer, and cooling parameters. These observables augmented with density functional theory computations of vibrational frequencies and anharmonic force constants enabled identification of different functional groups of the compounds. Computations of vibrational relaxation pathways and mode couplings were performed, and two regimes of intramolecular energy redistribution are described. One involves energy transfer between ligands via high-frequency modes; the transfer is efficient only if the modes involved are delocalized over both ligands. The energy transport pathways between the ligands are identified. Another regime involves redistribution via low-frequency delocalized modes, which does not lead to interligand energy transport.

A Statistical Journey through the Topological Determinants of the β2 Adrenergic Receptor Dynamics

Activation of G-protein-coupled receptors (GPCRs) is mediated by molecular switches throughout the transmembrane region of the receptor. In this work, we continued along the path of a previous computational study wherein energy transport in the β2 Adrenergic Receptor (β2-AR) was examined and allosteric switches were identified in the molecular structure through the reorganization of energy transport networks during activation. In this work, we further investigated the allosteric properties of β2-AR, using Protein Contact Networks (PCNs). In this paper, we report an extensive statistical analysis of the topological and structural properties of β2-AR along its molecular dynamics trajectory to identify the activation pattern of this molecular system. The results show a distinct character to the activation that both helps to understand the allosteric switching previously identified and confirms the relevance of the network formalism to uncover relevant functional features of protein molecules.

Probing Adaptation of Hydration and Protein Dynamics to Temperature

Protein dynamics is strongly influenced by the surrounding environment and physiological conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time scale from femto- to nanosecond. The dielectric spectra reveal several relaxations corresponding to the orientational polarization mechanism, including the dynamics of loosely bound, tightly bound, and bulk water, as well as collective vibrational modes of protein in an aqueous environment. The dynamics of loosely bound and bulk water follow non-Arrhenius behavior; however, the dynamics of water molecules in the tightly bound layer obeys the Arrhenius-type relation. Combining molecular simulations and effective-medium approximation, we have determined the number of water molecules in the tightly bound hydration layer and studied the dynamics of protein as a function of temperature. The results provide the important impact of water on the biochemical functions of proteins.

Biophysical Insight into the SARS-CoV2 Spike-ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational Approach

At the center of the SARS-CoV2 infection, the spike protein and its interaction with the human receptor ACE2 play a central role in the molecular machinery of SARS-CoV2 infection of human cells. Vaccine therapies are a valuable barrier to the worst effects of the virus and to its diffusion, but the need of purposed drugs is emerging as a core target of the fight against COVID19. In this respect, the repurposing of drugs has already led to discovery of drugs thought to reduce the effects of the cytokine storm, but still a drug targeting the spike protein, in the infection stage, is missing. In this work, we present a multifaceted computational approach strongly grounded on a biophysical modeling of biological systems, so to disclose the interaction of the SARS-CoV2 spike protein with ACE2 with a special focus to an allosteric regulation of the spike-ACE2 interaction. Our approach includes the following methodologies: Protein Contact Networks and Network Clustering, Targeted Molecular Dynamics, Elastic Network Modeling, Perturbation Response Scanning, and a computational analysis of energy flow and SEPAS as a protein-softness and monomer-based affinity predictor. We applied this approach to free (closed and open) states of spike protein and spike-ACE2 complexes. Eventually, we analyzed the interactions of free and bound forms of spike with hepcidin (HPC), the major hormone in iron regulation, recently addressed as a central player in the COVID19 pathogenesis, with a special emphasis to the most severe outcomes. Our results demonstrate that, compared with closed and open states, the spike protein in the ACE2-bound state shows higher allosteric potential. The correspondence between hinge sites and the Allosteric Modulation Region (AMR) in the S-ACE complex suggests a molecular basis for hepcidin involvement in COVID19 pathogenesis. We verify the importance of AMR in different states of spike and then study its interactions with HPC and the consequence of the HPC-AMR interaction on spike dynamics and its affinity for ACE2. We propose two complementary mechanisms for HPC effects on spike of SARS-CoV-2; (a) HPC acts as a competitive inhibitor when spike is in a preinfection state (open and with no ACE2), (b) the HPC-AMR interaction pushes the spike structure into the safer closed state. These findings need clear molecular in vivo verification beside clinical observations.

Computational Study on the Thermal Conductivity of a Protein

Protein molecules are thermally fluctuating and tightly packed amino acid residues strongly interact with each other. Such interactions are characterized in terms of heat current at the atomic level. We calculated the thermal conductivity of a small globular protein, villin headpiece subdomain, based on the linear response theory using equilibrium molecular dynamics simulation. The value of its thermal conductivity was 0.3 ± 0.01 [W m^-1 K^-1], which is in good agreement with experimental and computational studies on the other proteins in the literature. Heat current along the main chain was dominated by local vibrations in the polypeptide bonds, with amide I, II, III, and A bands on the Fourier transform of the heat current autocorrelation function.

Energy Transport along α-Helix Protein Chains: External Drives and Multifractal Analysis

Energy transport within biological systems is critical for biological functions in living cells and for technological applications in molecular motors. Biological systems have very complex dynamics supporting a large number of biochemical and biophysical processes. In the current work, we study the energy transport along protein chains. We examine the influence of different factors such as temperature, salt concentration, and external mechanical drive on the energy flux through protein chains. We obtain that energy fluctuations around the average value for short chains are greater than for longer chains. In addition, the external mechanical load is the most effective agent on bioenergy transport along the studied protein systems. Our results can help design a functional nano-scaled molecular motor based on energy transport along protein chains.

Energy Bilocalization Effect and the Emergence of Molecular Functions in Proteins

Proteins are among the most complex molecular structures, which have evolved to develop broad functions, such as energy conversion and transport, information storage and processing, communication, and regulation of chemical reactions. However, the mechanisms by which these dynamical entities coordinate themselves to perform biological tasks remain hotly debated. Here, a physical theory is presented to explain how functional dynamical behavior possibly emerge in complex/macro molecules, thanks to the effect that we term bilocalization of thermal vibrations. More specifically, our approach allows us to understand how structural irregularities lead to a partitioning of the energy of the vibrations into two distinct sets of molecular domains, corresponding to slow and fast motions. This shape-encoded spectral allocation, associated to the genetic sequence, provides a close access to a wide reservoir of dynamical patterns, and eventually allows the emergence of biological functions by natural selection. To illustrate our approach, the SPIKE protein structure of SARS-COV2 is considered.

Activation-Induced Reorganization of Energy Transport Networks in the β2 Adrenergic Receptor

We compute energy exchange networks (EENs) through the β₂ adrenergic receptor (β₂AR), a G-protein coupled receptor (GPCR), in inactive and active states, based on the results of molecular dynamics simulations of this membrane bound protein. We introduce a new definition for the reorganization of EENs upon activation that depends on the relative change in rates of energy transfer across noncovalent contacts throughout the protein. On the basis of the reorganized network that we obtain for β₂AR upon activation, we identify a branched pathway between the agonist binding site and the cytoplasmic region, where a G-protein binds to the receptor when activated. The pathway includes all of the motifs containing molecular switches previously identified as contributing to the allosteric transition of β₂AR upon agonist binding. EENs and their reorganization upon activation are compared with structure-based contact networks computed for the inactive and active states of β₂AR.

Heat flow random walks in biomolecular systems using symbolic transfer entropy and graph theory

This study combines the information- and graph-theoretic measures to investigate the cluster modulation of the amino acid residues and nucleotides at complex biomolecular interfaces. The symbolic transfer entropy is used as an information-theoretic measure. I also used graph theory to obtain information and heat flow weighted digraph models used to study the topology of information and heat flow paths at complex biomolecular interfaces. I introduce the graph-theoretic measures, such as the influence score and betweenness centrality, to identify the most influential amino acid and nucleotide sequences as sources of the information and absorb centers of the structure's heat flow. PageRank-like random walks algorithm is used to analyze the network of amino acid and nucleotide sequences at the protein-RNA interface combined with weighted digraph models. The cluster analysis using graph-theoretic measures revealed the modular molecular structure and the mechanism of the binding interface. In this study, the first benchmark system is an intuitive directed information flow network used to test the algorithms, and the second benchmark is a protein-RNA complex system. The approach was able to identify the most influential amino acid residues and nucleotides. Furthermore, the statistical cluster analysis using graph-theoretic measures revealed the modular molecular structure and the binding mechanism at the interface.

The conundrum of hot mitochondria

The mitochondrion is often referred as the cellular powerhouse because the organelle oxidizes organic acids and NADH derived from nutriments, converting around 40% of the Gibbs free energy change of these reactions into ATP, the major energy currency of cell metabolism. Mitochondria are thus microscopic furnaces that inevitably release heat as a by-product of these reactions, and this contributes to body warming, especially in endotherms like birds and mammals. Over the last decade, the idea has emerged that mitochondria could be warmer than the cytosol, because of their intense energy metabolism. It has even been suggested that our own mitochondria could operate under normal conditions at a temperature close to 50 °C, something difficult to reconcile with the laws of thermal physics. Here, using our combined expertise in biology and physics, we exhaustively review the reports that led to the concept of a hot mitochondrion, which is essentially based on the development and use of a variety of molecular thermosensors whose intrinsic fluorescence is modified by temperature. Then, we discuss the physical concepts of heat diffusion, including mechanisms like phonons scattering, which occur in the nanoscale range. Although most of approaches with thermosensors studies present relatively sparse data and lack absolute temperature calibration, overall, they do support the hypothesis of hot mitochondria. However, there is no convincing physical explanation that would allow the organelle to maintain a higher temperature than its surroundings. We nevertheless proposed some research directions, mainly biological, that might help throw light on this intriguing conundrum.

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.

Energy flow and intersubunit signalling in GSAM: A non-equilibrium molecular dynamics study

Non-equilibrium molecular dynamics simulations of vibrational energy flow induced by the imposition of a thermal gradient have been performed on the μ2-dimeric enzyme glutamate-1-semialdehyde aminomutase (GSAM), the key enzyme in the biosynthesis of chlorophyll, in order to identify energy transport pathways and to elucidate their role as potential allosteric communication networks for coordinating functional dynamics, specifically the negative cooperativity observed in the motion of the two active site gating loops. Fully atomistic MD simulations of thermal diffusion were executed with a GROMACS simulation package on a fully solvated GSAM enzyme by heating various active site target ligands (initially, catalytic intermediates and cofactors) to 300K while holding the remainder of the protein and the solvent bath at 10K and monitoring the temperature T(t) of all the enzyme residues as a function of time over a 1ns observation window. Energy is observed to be deposited in a relatively small number of discrete chains of residues most of which contribute to specific structural or biochemical functionality. Thermal linkages between all thermally active chains were established by isolating a specific pair of chains and performing a thermal diffusion simulation on the pair, one held at 300K and the other at 10K, with the rest of the protein frozen in its initial atomic configuration and thus thermally unresponsive. Proceeding in this way, it was possible to map out multiple pathways of vibrational energy flow leading from one of the active sites through a network of contiguous residues, many of which were evolutionarily conserved and linked by hydrogen bonds, into the other active site and ultimately to the other gating loop.

Ultrafast Vibrational Energy Transfer between Protein and Cofactor in a Flavoenzyme

Protein motions and enzyme catalysis are often linked. It is hypothesized that ultrafast vibrations (femtosecond-picosecond) enhance the rate of hydride transfer catalyzed by members of the old yellow enzyme (OYE) family of ene-reductases. Here, we use time-resolved infrared (TRIR) spectroscopy in combination with stable "heavy" isotopic labeling (2H, 13C, 15N) of protein and/or cofactor to probe the vibrational energy transfer (VET) between pentaerythritol tetranitrate reductase (a member of the OYE family) and its noncovalently bound flavin mononucleotide (FMN) cofactor. We show that when the FMN cofactor is photoexcited with visible light, vibrational energy is transferred from the flavin to the surrounding protein environment on the picosecond timescale. This finding expands the scope of VET investigation in proteins, which are limited by suitable intrinsic probes, and may have implications in the understanding of the mechanism of recently discovered photoactive flavoenzymes.

Role of atomic contacts in vibrational energy transfer in myoglobin

Heme proteins are ideal systems to investigate vibrational energy flow at the atomic level. Upon photoexcitation, a large amount of excess vibrational energy is selectively deposited on heme due to extremely fast internal conversion. This excess energy is redistributed to the surrounding protein moiety and then to water. Vibrational energy flow in myoglobin (Mb) was examined using picosecond time-resolved anti-Stokes ultraviolet resonance Raman (UVRR) spectroscopy. We used the Trp residue directly contacting the heme group as a selective probe for vibrationally excited populations. Trp residues were placed at different position close to the heme by site-directed mutagenesis. This technique allows us to monitor the excess energy on residue-to-residue basis. Anti-Stokes UVRR measurements for Mb mutants suggest that the dominant channel for energy transfer in Mb is the pathway through atomic contacts between heme and nearby amino acid residues as well as that between the protein and solvent water. It is found that energy flow through proteins is analogous to collisional exchange processes in solutions.

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.

Recent developments in the computational study of protein structural and vibrational energy dynamics

Recent developments in the computational study of energy transport in proteins are reviewed, including advances in both methodology and applications. The concept of energy exchange network (EEN) is discussed, and a recent calculation of EENs for the allosteric protein FixL is reviewed, which illustrates how residues and protein regions involved in the allosteric transition can be identified. Recent work has examined relations between EENs and protein dynamics as well as structure. We review some of the computational studies carried out on several proteins that explore connections between energy conductivity across polar contacts in proteins and between proteins and water and equilibrium dynamics of the contacts, and we discuss some of the recent experimental work that addresses this topic.