Research graph
References from The protein-water H-bond network for bacterial response regulator REC domain activation. Local targets link to admitted publications; unresolved targets remain external evidence.
The crystal structure of an activated Thermotoga maritima CheY with N-terminal region of FliM
10.1016/j.ijbiomac.2012.12.003 · 2013 · External reference
Phosphate sink containing two-component signaling systems as tunable threshold devices
10.1371/journal.pcbi.1003890 · 2014 · External reference
10.1093/database/baz007
10.1093/database/baz007 · External reference
Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution
10.1126/science.7695699 · 1994 · External reference
Protein-water hydrogen-bond networks of G protein-coupled receptors: graph-based analyses of static structures and molecular dynamics
10.1016/j.jsb.2020.107634 · 2020 · External reference
Conformational barrier of CheY3 and inability of CheY4 to bind FliM control the flagellar motor action in vibrio cholerae
10.1371/journal.pone.0073923 · 2013 · External reference
Graphs of hydrogen-bond networks to dissect protein conformational dynamics
10.1021/acs.jpcb.2c00200 · 2022 · External reference
Proton reactions: from basic science to biomedical applications
10.1016/j.bpj.2024.11.013 · 2024 · External reference
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms
10.1038/s42003-023-04488-9 · 2023 · External reference
Clustering protein functional families at large scale with hierarchical approaches
10.1002/pro.5140 · 2024 · External reference
Molecular insights into quorum sensing in the human pathogen Pseudomonas aeruginosa from the structure of the virulence regulator LasR bound to its autoinducer
10.1074/jbc.m700556200 · 2007 · External reference
Conserved aspartate residues and phosphorylation in signal transduction by the chemotaxis protein CheY
10.1073/pnas.87.1.41 · 1990 · External reference
Insights revealed by the co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer protein Ypd1 and the receiver domain of its downstream response regulator Ssk1
10.1002/pro.3755 · 2019 · External reference
AllohubPy: detecting allosteric signals through an information-theoretic approach
10.1016/j.jmb.2025.168969 · 2025 · External reference
Aspartyl phosphates in the regulatory control of bacterial response
10.1007/bf00805841 · 1994 · External reference
Surveying biomolecular frustration at atomic resolution
10.1038/s41467-020-19560-9 · 2020 · External reference
NMR structure of activated CheY
10.1006/jmbi.2000.3595 · 2000 · External reference
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation
10.1093/bioinformatics/btv398 · 2015 · External reference
AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing
10.1021/jp212541y · 2012 · External reference
Prion and water: tight and dynamical hydration sites have a key role in structural stability
10.1073/pnas.0501748102 · 2005 · External reference
Water molecules as structural determinants among prions of low sequence identity
10.1016/j.febslet.2006.02.083 · 2006 · External reference
A conserved H-bond network in human aquaporin-1 is necessary for native folding and oligomerization
10.1016/j.bpj.2024.10.011 · 2024 · External reference
Structure of the constitutively active double mutant CheYD13K Y106W alone and in complex with a FliM peptide
10.1016/j.jmb.2004.07.084 · 2004 · External reference
Mapping the energetic and allosteric landscapes of protein binding domains
10.1038/s41586-022-04586-4 · 2022 · External reference
Correlated motions are a fundamental property of beta-sheets
10.1038/ncomms5070 · 2014 · External reference
Localizing frustration in native proteins and protein assemblies
10.1073/pnas.0709915104 · 2007 · External reference
Hydrogen bonding and biological specificity analysed by protein engineering
10.1038/314235a0 · 1985 · External reference
Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems
10.1002/prot.25207 · 2017 · External reference
Role of position K+4 in the phosphorylation and dephosphorylation reaction kinetics of the CheY response regulator
10.1021/acs.biochem.1c00246 · 2021 · External reference
Chey’s acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli
10.1111/mmi.12858 · 2015 · External reference
Structural and functional comparison of magnesium transporters throughout evolution
10.1007/s00018-022-04442-8 · 2022 · External reference
Local frustration around enzyme active sites
10.1073/pnas.1819859116 · 2019 · External reference
Local energetic frustration conservation in protein families and superfamilies
10.1038/s41467-023-43801-2 · 2023 · External reference
CD-HIT: accelerated for clustering the next-generation sequencing data
10.1093/bioinformatics/bts565 · 2012 · External reference
Direct imaging of intracellular signaling components that regulate bacterial chemotaxis
10.1126/scisignal.2004963 · 2014 · External reference
CheB localizes to polar receptor arrays during repellent adaptation
10.1126/sciadv.adp5636 · 2024 · External reference
Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.1-a structure of a threonine to isoleucine mutant at position 87 of CheY
10.1074/jbc.270.29.17386 · 1995 · External reference
Bacterial response regulators: versatile regulatory strategies from common domains
10.1016/j.tibs.2007.03.002 · 2007 · External reference
Structural basis of response regulator function
10.1146/annurev-micro-020518-115931 · 2019 · External reference
Water and collagen: a mystery yet to unfold
10.1021/acs.biomac.4c01735 · 2025 · External reference
The solvation of the E. Coli CheY phosphorylation site mapped by XFMS
10.3390/ijms232112771 · 2022 · External reference
Allosteric network analysis toolkit for single-domain phosphoproteins
2026 · External reference
High-resolution solution structure of the beryllofluoride-activated NtrC receiver domain
10.1021/bi0273866 · 2003 · External reference
Dali server: structural unification of protein families
10.1093/nar/gkac387 · 2022 · External reference
Protein structure comparison by alignment of distance matrices
10.1006/jmbi.1993.1489 · 1993 · External reference
Dali: a network tool for protein structure comparison
10.1016/s0968-0004(00)89105-7 · 1995 · External reference
DALI shines a light on remote homologs: one hundred discoveries
10.1002/pro.4519 · 2023 · External reference
A variable active site residue influences the kinetics of response regulator phosphorylation and dephosphorylation
10.1021/acs.biochem.6b00645 · 2016 · External reference
Uncoupled phosphorylation and activation in bacterial chemotaxis. The 2.3 a structure of an aspartate to lysine mutant at position 13 of CheY
10.1074/jbc.272.18.11850 · 1997 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations
10.1021/acs.jcim.1c00794 · 2021 · External reference
A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2
10.1016/j.jsb.2020.107617 · 2020 · External reference
Predicting protein structure using hidden Markov models
10.1002/(sici)1097-0134(1997)1+<134::aid-prot18>3.0.co;2-p · 1997 · External reference
General strategies for using amino acid sequence data to guide biochemical investigation of protein function
10.1042/bst20220849 · 2022 · External reference
Conformational spread drives the evolution of the calcium-calmodulin protein kinase II
10.1038/s41598-022-12090-y · 2022 · External reference
Chemotactic signal integration in bacteria
10.1073/pnas.92.21.9757 · 1995 · External reference
Tryptophan, more than just an interfacial amino acid in the membrane activity of cationic cell-penetrating and antimicrobial peptides
10.1017/s0033583522000105 · 2022 · External reference
Transient water wires mediate selective proton transport in designed channel proteins
10.1038/s41557-023-01210-4 · 2023 · External reference
Conserved hydrogen-bond motifs of membrane transporters and receptors
10.1016/j.bbamem.2022.183896 · 2022 · External reference
Crystal structure of activated CheY. Comparison with other activated receiver domains
10.1074/jbc.m101002200 · 2001 · External reference
Crystal structure of an activated response regulator bound to its target
10.1038/nsb0901-789 · 2001 · External reference
Fentanyl and the fluorinated fentanyl derivative NFEPP elicit distinct hydrogen-bond dynamics of the opioid receptor
10.1021/acs.jcim.3c00197 · 2023 · External reference
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
10.1093/bioinformatics/btl158 · 2006 · External reference
Roles of the highly conserved aspartate and lysine residues in the response regulator of bacterial chemotaxis
10.1016/s0021-9258(18)92982-0 · 1991 · External reference
Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors
10.1073/pnas.89.2.718 · 1992 · External reference
Activation mechanism of a signaling protein at atomic resolution from advanced computations
10.1021/ja073059f · 2007 · External reference
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field
10.1002/jcc.24733 · 2017 · External reference
Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
10.1002/jcc.10117 · 2002 · External reference
Comparing conformational ensembles using the Kullback-Leibler divergence expansion
10.1021/ct300008d · 2012 · External reference
Segmental motions, not a two-state concerted switch, underlie allostery in CheY
10.1016/j.str.2012.05.008 · 2012 · External reference
Colocalization of fast and slow timescale dynamics in the allosteric signaling protein CheY
10.1016/j.jmb.2013.04.029 · 2013 · External reference
Identification of the binding interfaces on CheY for two of its targets, the phosphatase CheZ and the flagellar switch protein fliM
10.1006/jmbi.1999.2830 · 1999 · External reference
Parallelization of MAFFT for large-scale multiple sequence alignments
10.1093/bioinformatics/bty121 · 2018 · External reference
Tyrosine hydrogen bonds make a large contribution to protein stability
10.1006/jmbi.2001.4956 · 2001 · External reference
Experimental analysis of functional variation within protein families: receiver domain autodephosphorylation kinetics
10.1128/jb.00853-15 · 2016 · External reference
Coevolved mutations reveal distinct architectures for two core proteins in the bacterial flagellar motor
10.1371/journal.pone.0142407 · 2015 · External reference
Water in protein structure prediction
10.1073/pnas.0307851100 · 2004 · External reference
In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved
10.1073/pnas.0401038101 · 2004 · External reference
Frustration, dynamics, and catalysis
10.1016/j.sbi.2025.103127 · 2025 · External reference
Protein Frustrameter 2: a tool to localize energetic frustration in protein molecules, now with electrostatics
10.1093/nar/gkw304 · 2016 · External reference
Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
10.1093/nar/gkae244 · 2024 · External reference
Functional stability of water wire-carbonyl interactions in an ion channel
10.1073/pnas.2001083117 · 2020 · External reference
Unraveling the functional dark matter through global metagenomics
10.1038/s41586-023-06583-7 · 2023 · External reference
Matching biochemical reaction kinetics to the timescales of life: structural determinants that influence the autodephosphorylation rate of response regulator proteins
10.1016/j.jmb.2009.07.064 · 2009 · External reference
Chemistry and biology
10.1073/pnas.97.2.538 · 2000 · External reference
New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL viewer to recapture online 3D graphics
10.1002/pro.3786 · 2020 · External reference
Water follows polar and nonpolar protein surface domains
10.1073/pnas.1910225116 · 2019 · External reference
Network centrality: An introduction
2019 · External reference
A new structural arrangement in proteins involving lysine NH(3)(+) group and carbonyl
10.1038/s41598-017-16584-y · 2017 · External reference
Assigning protein function from domain-function associations using DomFun
10.1186/s12859-022-04565-6 · 2022 · External reference
Single-cell E. Coli response to an instantaneously applied chemotactic signal
10.1016/j.bpj.2014.06.017 · 2014 · External reference
Water molecules at protein-drug interfaces: computational prediction and analysis methods
10.1039/d0cs00151a · 2021 · External reference
Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes
10.1038/s41467-018-05769-2 · 2018 · External reference
Conformational coupling in the chemotaxis response regulator CheY
10.1073/pnas.101571298 · 2001 · External reference
Interactive Interface for graph-based analyses of dynamic H-bond networks: application to spike protein S
10.1021/acs.jcim.1c00306 · 2021 · External reference
Bridge: a graph-based algorithm to analyze dynamic H-bond networks in membrane proteins
10.1021/acs.jctc.9b00697 · 2019 · External reference
CATH: increased structural coverage of functional space
10.1093/nar/gkaa1079 · 2021 · External reference
Implications of threonine hydrogen bonding in the glycophorin a transmembrane helix dimer
10.1016/s0006-3495(02)75590-2 · 2002 · External reference
The roles of water in the protein matrix: a largely untapped resource for drug discovery
10.1021/acs.jmedchem.7b00057 · 2017 · External reference
Three-dimensional structure of CheY, the response regulator of bacterial chemotaxis
10.1038/337745a0 · 1989 · External reference
Structure of the Mg(2+)-bound form of CheY and mechanism of phosphoryl transfer in bacterial chemotaxis
10.1021/bi00212a001 · 1993 · External reference
Modulation of response regulator CheY reaction kinetics by two variable residues that affect conformation
10.1128/jb.00089-20 · 2020 · External reference
Water channel structures analysed by electron crystallography
10.1016/j.bbagen.2013.10.007 · 2014 · External reference
Structural analysis and solution studies of the activated regulatory domain of the response regulator ArcA: a symmetric dimer mediated by the alpha4-beta5-alpha5 face
10.1016/j.jmb.2005.03.059 · 2005 · External reference
LuxR-type quorum-sensing regulators that are detached from common scents
10.1111/j.1365-2958.2010.07279.x · 2010 · External reference
Crystal structure of Escherichia coli CheY refined at 1.7-a resolution
10.1016/s0021-9258(18)98646-1 · 1991 · External reference
Mapping allosteric communications within individual proteins
10.1038/s41467-020-17618-2 · 2020 · External reference
Allosteric priming of E. Coli CheY by the flagellar motor protein FliM
10.1016/j.bpj.2020.08.009 · 2020 · External reference
The CheZ-binding surface of CheY overlaps the CheA- and FliM-binding surfaces
10.1074/jbc.272.38.23758 · 1997 · External reference
Crystal structures of CheY mutants Y106W and T87I/Y106W. CheY activation correlates with movement of residue 106
10.1074/jbc.272.8.5000 · 1997 · External reference