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Entropy Transfer between Residue Pairs Shows that Allostery is an Intrinsic Property of Proteins: Quantifying Allosteric Communication in Ubiquitin

https://doi.org/10.1101/084756
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What this work says

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

inferredcites →https://doi.org/10.1002/jcc.20919openalex-snapshot
Efficient calculation of configurational entropy from molecular simulations by combining the mutual‐information expansion and nearest‐neighbor methods
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CENCALC: A computational tool for conformational entropy calculations from molecular simulations
inferredcites →https://doi.org/10.1002/prot.20232openalex-snapshot
Is allostery an intrinsic property of all dynamic proteins?
inferredcites →https://doi.org/10.1002/prot.24257openalex-snapshot
Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors
inferredcites →https://doi.org/10.1002/prot.24284openalex-snapshot
A fast approximate method of identifying paths of allosteric communication in proteins
inferredcites →https://doi.org/10.1002/prot.25032openalex-snapshot
Universal features of fluctuations in globular proteins
inferredcites →https://doi.org/10.1007/bf00276625openalex-snapshot
Allostery without conformational change
inferredcites →https://doi.org/10.1016/j.abb.2013.07.025openalex-snapshot
Emerging computational approaches for the study of protein allostery
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Coupled binding–bending–folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations
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Importance of local interactions for the stability of inhibitory helix 1 in apo Ets-1
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Extracting the Causality of Correlated Motions from Molecular Dynamics Simulations
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Predicting Interaction Sites from the Energetics of Isolated Proteins: A New Approach to Epitope Mapping
inferredcites →https://doi.org/10.1016/j.drudis.2014.07.012openalex-snapshot
Recent computational advances in the identification of allosteric sites in proteins
inferredcites →https://doi.org/10.1016/j.jmb.2007.08.059openalex-snapshot
Predicting Allosteric Communication in Myosin via a Pathway of Conserved Residues
inferredcites →https://doi.org/10.1016/j.jmb.2009.04.003openalex-snapshot
Configurational Entropy in Protein–Peptide Binding:
inferredcites →https://doi.org/10.1016/j.jmgm.2015.09.010openalex-snapshot
Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods
inferredcites →https://doi.org/10.1016/j.sbi.2004.10.009openalex-snapshot
Searching for new allosteric sites in enzymes
inferredcites →https://doi.org/10.1016/s0006-3495(87)83303-9openalex-snapshot
Configurational entropy of native proteins
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.5b01217openalex-snapshot
PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems
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/bi200503aopenalex-snapshot
Importance of Domain Closure for the Autoactivation of ERK2
inferredcites →https://doi.org/10.1021/bi201137eopenalex-snapshot
Independent Interactions of Ubiquitin-Binding Domains in a Ubiquitin-Mediated Ternary Complex
inferredcites →https://doi.org/10.1021/ct200216nopenalex-snapshot
Entropy Calculations of Single Molecules by Combining the Rigid–Rotor and Harmonic-Oscillator Approximations with Conformational Entropy Estimations from Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/ct200910zopenalex-snapshot
Balanced and Bias-Corrected Computation of Conformational Entropy Differences for Molecular Trajectories
inferredcites →https://doi.org/10.1021/ct4002784openalex-snapshot
Quantification of Drive-Response Relationships Between Residues During Protein Folding
inferredcites →https://doi.org/10.1021/ct9001812openalex-snapshot
Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles
inferredcites →https://doi.org/10.1021/jp2068123openalex-snapshot
Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation
inferredcites →https://doi.org/10.1021/jp310753zopenalex-snapshot
Investigating Allostery in Molecular Recognition: Insights from a Computational Study of Multiple Antibody–Antigen Complexes
inferredcites →https://doi.org/10.1021/jp503668kopenalex-snapshot
Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer
inferredcites →https://doi.org/10.1038/70057openalex-snapshot
Increased protein backbone conformational entropy upon hydrophobic ligand binding.
inferredcites →https://doi.org/10.1038/nature12595openalex-snapshot
Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
inferredcites →https://doi.org/10.1038/nature13001openalex-snapshot
The ensemble nature of allostery
inferredcites →https://doi.org/10.1038/ncomms4287openalex-snapshot
A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods
inferredcites →https://doi.org/10.1038/ncomms4397openalex-snapshot
Activation pathway of Src kinase reveals intermediate states as targets for drug design
inferredcites →https://doi.org/10.1038/srep37012openalex-snapshot
Intrinsic K-Ras dynamics: A novel molecular dynamics data analysis method shows causality between residue pair motions
inferredcites →https://doi.org/10.1063/1.2746329openalex-snapshot
Extraction of configurational entropy from molecular simulations via an expansion approximation
inferredcites →https://doi.org/10.1063/1.4748104openalex-snapshot
Multibody local approximation: Application to conformational entropy calculations on biomolecules
inferredcites →https://doi.org/10.1093/bioinformatics/btu002openalex-snapshot
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites
inferredcites →https://doi.org/10.1093/database/bau069openalex-snapshot
OMICtools: an informative directory for multi-omic data analysis
inferredcites →https://doi.org/10.1093/glycob/cwv083openalex-snapshot
Preferred conformations ofN-glycan core pentasaccharide in solution and in glycoproteins
inferredcites →https://doi.org/10.1093/nar/gkq1022openalex-snapshot
ASD: a comprehensive database of allosteric proteins and modulators
inferredcites →https://doi.org/10.1093/nar/gkt284openalex-snapshot
MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues
inferredcites →https://doi.org/10.1103/physrevlett.85.461openalex-snapshot
Measuring Information Transfer
inferredcites →https://doi.org/10.1119/1.14986openalex-snapshot
Thermodynamics and an Introduction to Thermostatistics
inferredcites →https://doi.org/10.1142/9781860949920_0019openalex-snapshot
CONFORMATIONAL ENTROPY OF BIOMOLECULES: BEYOND THE QUASI-HARMONIC APPROXIMATION
inferredcites →https://doi.org/10.1142/9789812790736openalex-snapshot
A Farewell to Entropy - Statistical Thermodynamics Based on Information
inferredcites →https://doi.org/10.1158/2159-8290.cd-12-0095openalex-snapshot
The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data
inferredcites →https://doi.org/10.1162/089976603321780272openalex-snapshot
Estimation of Entropy and Mutual Information
inferredcites →https://doi.org/10.1371/journal.pcbi.1003394openalex-snapshot
A Unified View of “How Allostery Works”
inferredcites →https://doi.org/10.1371/journal.pone.0119978openalex-snapshot
Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins
inferredcites →https://doi.org/10.3109/10409238.2012.742856openalex-snapshot
The role of allostery in the ubiquitin–proteasome system
inferredcites →https://doi.org/10.5860/choice.41-5949openalex-snapshot
Information theory, inference, and learning algorithms

What points at this work

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

inferred← citeshttps://doi.org/10.1002/prot.25272openalex-snapshot
Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions
inferred← citeshttps://doi.org/10.1101/2021.03.15.243386openalex-snapshot
A Comprehensive Analysis of Allostery in 14-3-3 ζ Docking Proteins using the Spatial Convolution Model (SCM)
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