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Communication Maps: Exploring Energy Transport through Proteins and Water

https://doi.org/10.1002/ijch.201300139

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Heat Transport in Molecules and Reaction Kinetics: The Role of Quantum Energy Flow and Localization

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Introduction

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Vibrational spectroscopy and the development of new force fields for biological molecules

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Is allostery an intrinsic property of all dynamic proteins?

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Pump‐probe molecular dynamics as a tool for studying protein motion and long range coupling

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Free energy landscape of a biomolecule in dihedral principal component space: Sampling convergence and correspondence between structures and minima

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Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis

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Mapping the intramolecular signal transduction of G‐protein coupled receptors

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Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property

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Mutational destabilization of the critical interface water cluster in Scapharca dimeric hemoglobin: structural basis for altered allosteric activity

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Fractal symmetry of protein interior: what have we learned?

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Energy landscapes: topographies, interparticle forces and dynamics, and how they are related

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Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme

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Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings

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Allostery in Disease and in Drug Discovery

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Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis

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Mode damping rates in a protein chromophore

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Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion

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Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein

inferredcites →https://doi.org/10.1016/j.sbi.2006.01.003openalex-snapshot

The changing landscape of protein allostery

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Energy landscapes: some new horizons

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Are Proteins Well-Packed?

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Cooperativity in Scapharca Dimeric Hemoglobin: Simulation of Binding Intermediates and Elucidation of the Role of Interfacial Water

inferredcites →https://doi.org/10.1016/s0092-8674(04)00119-9openalex-snapshot

Structural Determinants of Allosteric Ligand Activation in RXR Heterodimers

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Cooperative hemoglobins: conserved fold, diverse quaternary assemblies and allosteric mechanisms

inferredcites →https://doi.org/10.1021/bi0494424openalex-snapshot

Long-Range Dynamic Effects of Point Mutations Propagate through Side Chains in the Serine Protease Inhibitor Eglin c

inferredcites →https://doi.org/10.1021/bi060652lopenalex-snapshot

Dynamic Coupling and Allosteric Behavior in a Nonallosteric Protein

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Asymmetric DNA-Search Dynamics by Symmetric Dimeric Proteins

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Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations

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Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy

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Long-Range Influence of Carbohydrates on the Solvation Dynamics of Water—Answers from Terahertz Absorption Measurements and Molecular Modeling Simulations

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Proteins: Energy, Heat, and Signal Flow

inferredcites →https://doi.org/10.1021/ja200566uopenalex-snapshot

Dielectric Spectroscopy of Proteins as a Quantitative Experimental Test of Computational Models of Their Low-Frequency Harmonic Motions

inferredcites →https://doi.org/10.1021/ja9083545openalex-snapshot

Rattling in the Cage: Ions as Probes of Sub-picosecond Water Network Dynamics

inferredcites →https://doi.org/10.1021/jp0107917openalex-snapshot

Directed Energy “Funneling" Mechanism for Heme Cooling Following Ligand Photolysis or Direct Excitation in Solvated Carbonmonoxy Myoglobin

inferredcites →https://doi.org/10.1021/jp026462bopenalex-snapshot

Vibrational Energy Transfer and Heat Conduction in a Protein

inferredcites →https://doi.org/10.1021/jp0351728openalex-snapshot

Simulating Vibrational Energy Flow in Proteins: Relaxation Rate and Mechanism for Heme Cooling in Cytochrome c

inferredcites →https://doi.org/10.1021/jp035471xopenalex-snapshot

Thermodynamics of Protein Hydration Computed by Molecular Dynamics and Normal Modes

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Dynamics of Water Clusters Confined in Proteins: A Molecular Dynamics Simulation Study of Interfacial Waters in a Dimeric Hemoglobin

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Thermal Boundary Conductance and Thermal Rectification in Molecules

inferredcites →https://doi.org/10.1021/jp711046eopenalex-snapshot

Energy Transport in Peptide Helices: A Comparison between High- and Low-Energy Excitations

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Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study

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Molecules: What Kind of a Bag of Atoms?

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Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

inferredcites →https://doi.org/10.1021/nl101580wopenalex-snapshot

Vibrational Energy Transport through a Capping Layer of Appropriately Designed Peptide Helices over Gold Nanoparticles

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The hinge-bending mode in lysozyme

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Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy

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Evolutionarily conserved networks of residues mediate allosteric communication in proteins

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Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

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Heat transfer in protein–water interfaces

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Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function

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Density of states on fractals : « fractons »

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Random walks on fractal structures and percolation clusters

inferredcites →https://doi.org/10.1063/1.1603211openalex-snapshot

Thermal conductance through molecular wires

inferredcites →https://doi.org/10.1063/1.1626636openalex-snapshot

Anomalous diffusion of vibrational energy in proteins

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Heat flow in proteins: Computation of thermal transport coefficients

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Influence of vibrational energy flow on isomerization of flexible molecules: Incorporating non-Rice-Ramsperger-Kassel-Marcus kinetics in the simulation of dipeptide isomerization

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Frequency-resolved communication maps for proteins and other nanoscale materials

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Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix

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Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins

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Spatio-temporal hierarchy in the dynamics of a minimalist protein model

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Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin

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Solute-induced retardation of water dynamics probed directly by terahertz spectroscopy

inferredcites →https://doi.org/10.1073/pnas.0701762104openalex-snapshot

Energy transport in peptide helices

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Multiscale complex network of protein conformational fluctuations in single-molecule time series

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An extended dynamical hydration shell around proteins

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Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure

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Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures

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The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

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Long-range protein–water dynamics in hyperactive insect antifreeze proteins

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Kinetic response of a photoperturbed allosteric protein

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Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

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Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin

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Allosteric Hemoglobin Assembly: Diversity and Similarity

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Biomolecule large-amplitude motion and solvation dynamics: modelling and probes from THz to X-rays

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Quantum localization and protein-assisted vibrational energy flow in cofactors

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Long-range energy transfer in proteins

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Thermal conductivity of disordered harmonic solids

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Thermal conductivity computed for vitreous silica and methyl-doped silica above the plateau

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Heat flow through an insulating nanocrystal

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Mass fractal dimension and the compactness of proteins

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Hydration dependence of the mass fractal dimension and anomalous diffusion of vibrational energy in proteins

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Proteins as fractals: Role of the hydrodynamic interaction

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Proteins: Coexistence of Stability and Flexibility

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Dynamic Structure Factor of Vibrating Fractals

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Fractal Form of Proteins

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Low-frequency modes in proteins: Use of the effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements

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Fractons in Proteins: Can They Lead to Anomalously Decaying Time Autocorrelations?

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Dynamical properties of fractal networks: Scaling, numerical simulations, and physical realizations

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Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy

inferredcites →https://doi.org/10.1126/science.1169377openalex-snapshot

Sending Signals Dynamically

inferredcites →https://doi.org/10.1126/science.1749933openalex-snapshot

The Energy Landscapes and Motions of Proteins

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Structural Transitions Upon Ligand Binding in a Cooperative Dimeric Hemoglobin

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Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families

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Energy Flow in Proteins

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Normal Mode Analysis

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Proteins

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Thermal conduction through a molecule

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Hydration Dependence of Conformational Dielectric Relaxation of Lysozyme

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A Milestoning Study of the Kinetics of an Allosteric Transition: Atomically Detailed Simulations of Deoxy Scapharca Hemoglobin

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Examining the Impact of Water Molecules in Regulating Amicyanin Protein's Function: A Computational Study

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MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS

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Locating and Navigating Energy Transport Networks in Proteins

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Vibrational energy flow across heme–cytochrome c and cytochrome c–water interfaces

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

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

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Water-Mediated Energy Dynamics in a Homodimeric Hemoglobin

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Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study

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Scaling of Rates of Vibrational Energy Transfer in Proteins with Equilibrium Dynamics and Entropy

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Energy Transport across Interfaces in Biomolecular Systems

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Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin

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Vibrational energy flow in the villin headpiece subdomain: Master equation simulations

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Water-mediated biomolecular dynamics and allostery

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Site-selective heat current analysis of α-helical protein with linear-homopolymer-like model

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Quantum ergodicity and energy flow in molecules

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Structural relationships between members of the Ras superfamily of small GTPases and their roles in functional diversity

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Mapping energy transport networks in proteins

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