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Intramolecular Communication and Allosteric Sites in Enzymes Unraveled by Time-Dependent Linear Response Theory

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What this work says

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

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ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

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Scalable molecular dynamics with NAMD

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A large compressibility change of protein induced by a single amino acid substitution

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

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

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Effect of Solvent on Collective Motions in Globular Protein

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Localized, stereochemically sensitive hydrophobic packing in an early folding intermediate of dihydrofolate reductase from Escherichia coli

inferredcites →https://doi.org/10.1007/bf00276625openalex-snapshot

Allostery without conformational change

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Probing the roles of conserved arginine-44 of Escherichia coli dihydrofolate reductase in its function and stability by systematic sequence perturbation analysis

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Evidence of Protein Collective Motions on the Picosecond Timescale

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Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories

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Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion

inferredcites →https://doi.org/10.1016/j.jmb.2007.08.047openalex-snapshot

Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back

inferredcites →https://doi.org/10.1016/j.jmb.2008.12.032openalex-snapshot

Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle

inferredcites →https://doi.org/10.1016/j.str.2005.03.015openalex-snapshot

Coupling between Catalytic Site and Collective Dynamics: A Requirement for Mechanochemical Activity of Enzymes

inferredcites →https://doi.org/10.1016/s0022-2836(03)00511-4openalex-snapshot

Effects of the Difference in the Unfolded-state Ensemble on the Folding of Escherichia coli Dihydrofolate Reductase

inferredcites →https://doi.org/10.1016/s0022-2836(65)80285-6openalex-snapshot

On the nature of allosteric transitions: A plausible model

inferredcites →https://doi.org/10.1021/acs.jctc.6b00688openalex-snapshot

Protein Dynamics and Contact Topology Reveal Protein–DNA Binding Orientation

inferredcites →https://doi.org/10.1021/acs.jpcb.8b06430openalex-snapshot

Interface Residues That Drive Allosteric Transitions Also Control the Assembly of l -Lactate Dehydrogenase

inferredcites →https://doi.org/10.1021/bi00110a006openalex-snapshot

The function of amino acid residues contacting the nicotinamide ring of NADPH in dihydrofolate reductase from Escherichia coli

inferredcites →https://doi.org/10.1021/bi00110a011openalex-snapshot

Investigation of the functional role of tryptophan-22 in Escherichia coli dihydrofolate reductase by site-directed mutagenesis

inferredcites →https://doi.org/10.1021/bi00155a038openalex-snapshot

Structure and function of alternative proton-relay mutants of dihydrofolate reductase

inferredcites →https://doi.org/10.1021/bi001608nopenalex-snapshot

Interloop Contacts Modulate Ligand Cycling during Catalysis byEscherichia coliDihydrofolate Reductase

inferredcites →https://doi.org/10.1021/bi00204a020openalex-snapshot

Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase

inferredcites →https://doi.org/10.1021/bi00369a034openalex-snapshot

Compressibility-structure relationship of globular proteins

inferredcites →https://doi.org/10.1021/bi00387a052openalex-snapshot

Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli

inferredcites →https://doi.org/10.1021/bi00428a011openalex-snapshot

Probing the functional role of threonine-113 of Escherichia coli dihydrofolate reductase for its effect on turnover efficiency, catalysis, and binding

inferredcites →https://doi.org/10.1021/bi00431a018openalex-snapshot

Effects of multiple replacements at a single position on the folding and stability of dihydrofolate reductase from Escherichia coli

inferredcites →https://doi.org/10.1021/bi00433a043openalex-snapshot

Hydrophobic interactions via mutants of Escherichia coli dihydrofolate reductase: separation of binding and catalysis

inferredcites →https://doi.org/10.1021/bi00442a012openalex-snapshot

Effects of distal point-site mutations on the binding and catalysis of dihydrofolate reductase from Escherichia coli

inferredcites →https://doi.org/10.1021/bi00465a018openalex-snapshot

Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate .cntdot. NADP+ ternary complex. substrate binding and a model for the transition state

inferredcites →https://doi.org/10.1021/bi00865a047openalex-snapshot

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits *

inferredcites →https://doi.org/10.1021/bi010621kopenalex-snapshot

Backbone Dynamics in Dihydrofolate Reductase Complexes: Role of Loop Flexibility in the Catalytic Mechanism

inferredcites →https://doi.org/10.1021/bi026369dopenalex-snapshot

Coupling Interactions of Distal Residues Enhance Dihydrofolate Reductase Catalysis: Mutational Effects on Hydride Transfer Rates

inferredcites →https://doi.org/10.1021/bi400563copenalex-snapshot

A Distal Mutation Perturbs Dynamic Amino Acid Networks in Dihydrofolate Reductase

inferredcites →https://doi.org/10.1021/bi962337copenalex-snapshot

Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase: Crystallographic Evidence,

inferredcites →https://doi.org/10.1021/bi9716231openalex-snapshot

Evidence for a Functional Role of the Dynamics of Glycine-121 ofEscherichia coliDihydrofolate Reductase Obtained from Kinetic Analysis of a Site-Directed Mutant

inferredcites →https://doi.org/10.1021/bi973065wopenalex-snapshot

Strength of an Interloop Hydrogen Bond Determines the Kinetic Pathway in Catalysis byEscherichia coliDihydrofolate Reductase

inferredcites →https://doi.org/10.1021/ci300363copenalex-snapshot

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

inferredcites →https://doi.org/10.1021/ci3003649openalex-snapshot

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

inferredcites →https://doi.org/10.1021/ci500261zopenalex-snapshot

Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs)

inferredcites →https://doi.org/10.1021/ct300400xopenalex-snapshot

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles

inferredcites →https://doi.org/10.1021/ja028487uopenalex-snapshot

Effect of Mutation on Enzyme Motion in Dihydrofolate Reductase

inferredcites →https://doi.org/10.1021/ja209425wopenalex-snapshot

Effects of the Donor–Acceptor Distance and Dynamics on Hydride Tunneling in the Dihydrofolate Reductase Catalyzed Reaction

inferredcites →https://doi.org/10.1021/ja411998hopenalex-snapshot

Extension and Limits of the Network of Coupled Motions Correlated to Hydride Transfer in Dihydrofolate Reductase

inferredcites →https://doi.org/10.1021/ja9913838openalex-snapshot

Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase

inferredcites →https://doi.org/10.1038/emboj.2009.80openalex-snapshot

The structure of Atg4B–LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy

inferredcites →https://doi.org/10.1038/msb4100075openalex-snapshot

Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES

inferredcites →https://doi.org/10.1038/nchembio.98openalex-snapshot

Allosteric regulation and catalysis emerge via a common route

inferredcites →https://doi.org/10.1038/ncomms4076openalex-snapshot

Optical measurements of long-range protein vibrations

inferredcites →https://doi.org/10.1038/nsb0494-226openalex-snapshot

Discovery of new ligand binding pathways in myoglobin by random mutagenesis

inferredcites →https://doi.org/10.1038/nsmb1132openalex-snapshot

Dynamically driven protein allostery

inferredcites →https://doi.org/10.1039/fd9929300217openalex-snapshot

Exploring the molecular mechanism of dihydrofolate reductase

inferredcites →https://doi.org/10.1063/1.1830431openalex-snapshot

Heat flow in proteins: Computation of thermal transport coefficients

inferredcites →https://doi.org/10.1063/1.3130149openalex-snapshot

Frequency-resolved communication maps for proteins and other nanoscale materials

inferredcites →https://doi.org/10.1063/1.3623423openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.0510426103openalex-snapshot

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

inferredcites →https://doi.org/10.1073/pnas.052005999openalex-snapshot

Network of coupled promoting motions in enzyme catalysis

inferredcites →https://doi.org/10.1073/pnas.0608759103openalex-snapshot

Dynamics of allosteric transitions in GroEL

inferredcites →https://doi.org/10.1073/pnas.0611560104openalex-snapshot

Primary protein response after ligand photodissociation in carbonmonoxy myoglobin

inferredcites →https://doi.org/10.1073/pnas.0704459104openalex-snapshot

A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

inferredcites →https://doi.org/10.1073/pnas.0802524105openalex-snapshot

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

inferredcites →https://doi.org/10.1073/pnas.1111471108openalex-snapshot

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

inferredcites →https://doi.org/10.1073/pnas.1230801100openalex-snapshot

Correlated motion and the effect of distal mutations in dihydrofolate reductase

inferredcites →https://doi.org/10.1073/pnas.80.12.3696openalex-snapshot

Dynamics of a small globular protein in terms of low-frequency vibrational modes.

inferredcites →https://doi.org/10.1073/pnas.80.21.6571openalex-snapshot

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.

inferredcites →https://doi.org/10.1074/jbc.r114.565515openalex-snapshot

Evolutionary Aspects of Enzyme Dynamics

inferredcites →https://doi.org/10.1093/bioinformatics/btp023openalex-snapshot

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

inferredcites →https://doi.org/10.1093/jb/mvp034openalex-snapshot

Sequence Perturbation Analysis: Addressing Amino Acid Indices to Elucidate the C-Terminal Role of Escherichia Coli Dihydrofolate Reductase

inferredcites →https://doi.org/10.1093/nar/gki370openalex-snapshot

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

inferredcites →https://doi.org/10.1093/nar/gkq399openalex-snapshot

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

inferredcites →https://doi.org/10.1093/nar/gkx385openalex-snapshot

DynOmics: dynamics of structural proteome and beyond

inferredcites →https://doi.org/10.1101/2021.01.31.429052openalex-snapshot

DRDOCK: A Drug Repurposing platform integrating automated docking, simulations and a log-odds-based drug ranking scheme

inferredcites →https://doi.org/10.1103/physrevlett.80.2733openalex-snapshot

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

inferredcites →https://doi.org/10.1103/physrevlett.94.128101openalex-snapshot

Picosecond Thermometer in the Amide I Band of Myoglobin

inferredcites →https://doi.org/10.1103/revmodphys.15.1openalex-snapshot

Stochastic Problems in Physics and Astronomy

inferredcites →https://doi.org/10.1126/science.1078797openalex-snapshot

Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography

inferredcites →https://doi.org/10.1126/science.1085515openalex-snapshot

A Perspective on Enzyme Catalysis

inferredcites →https://doi.org/10.1126/science.1130258openalex-snapshot

The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis

inferredcites →https://doi.org/10.1126/science.286.5438.295openalex-snapshot

Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families

inferredcites →https://doi.org/10.1371/journal.pcbi.0030172openalex-snapshot

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations

inferredcites →https://doi.org/10.1529/biophysj.106.082180openalex-snapshot

Coupling of Global and Local Vibrational Modes in Dynamic Allostery of Proteins

inferredcites →https://doi.org/10.2142/biophysico.16.0_473openalex-snapshot

Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators

inferredcites →https://doi.org/10.4161/auto.29556openalex-snapshot

ATG4B promotes colorectal cancer growth independent of autophagic flux

inferredcites →https://doi.org/10.7150/thno.22012openalex-snapshot

Drug Repurposing Screening Identifies Tioconazole as an ATG4 Inhibitor that Suppresses Autophagy and Sensitizes Cancer Cells to Chemotherapy

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s12551-024-01209-2openalex-snapshot

Commentary to “Application of Non-equilibrium Physics”: a session of the 21st IUPAB Congress 2024, Kyoto, Japan

inferred← citeshttps://doi.org/10.2142/biophysico.16.0_473openalex-snapshot

Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators

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