Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding

scientific article published on 01 February 2016

Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/ACS.JPCB.5B11767
P698PubMed publication ID26769494

P50authorGuangfeng ZhouQ50911013
P2093author name stringVincent A Voelz
P2860cites workMolecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)Q24631041
Accelerating molecular dynamic simulation on graphics processing unitsQ24654186
Markov state models of biomolecular conformational dynamicsQ26827934
Rational stabilization of enzymes by computational redesign of surface charge-charge interactionsQ27653671
Energetically significant networks of coupled interactions within an unfolded proteinQ27684951
Strength and co-operativity of contributions of surface salt bridges to protein stabilityQ28268109
Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysisQ28541683
Quantitative comparison of alternative methods for coarse-graining biological networksQ28673041
GPU-accelerated molecular modeling coming of ageQ29585161
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitQ29615867
Anticooperativity in a Glu-Lys-Glu salt bridge triplet in an isolated alpha-helical peptide.Q30351155
Combining single-molecule optical trapping and small-angle x-ray scattering measurements to compute the persistence length of a protein ER/K alpha-helix.Q30383024
Enhanced modeling via network theory: Adaptive sampling of Markov state modelsQ30539212
Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solventQ30591583
The effect of charge-charge interactions on the kinetics of alpha-helix formationQ33294390
Alpha-helical stabilization by side chain shielding of backbone hydrogen bondsQ34014321
Exploring the helix-coil transition via all-atom equilibrium ensemble simulationsQ34189691
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR MeasurementsQ34285601
Unusually stable helix formation in short alanine-based peptidesQ34289699
Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo designQ34376818
COMPUTING: Screen Savers of the World Unite!Q34670167
Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modelingQ35031498
Variational cross-validation of slow dynamical modes in molecular kineticsQ35430118
Aggregation of α-synuclein is kinetically controlled by intramolecular diffusionQ35786977
Modeling molecular kinetics with tICA and the kernel trickQ36175542
Do salt bridges stabilize proteins? A continuum electrostatic analysis.Q36278616
Improved coarse-graining of Markov state models via explicit consideration of statistical uncertaintyQ36335364
Fast events in protein folding: helix melting and formation in a small peptide.Q36789506
Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motifQ36869856
Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' modelQ36871997
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.Q37410885
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathwaysQ37582165
The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backboneQ38269925
Computational screening and selection of cyclic peptide hairpin mimetics by molecular simulation and kinetic network models.Q39205851
MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond ScaleQ39373045
EMMA: A Software Package for Markov Model Building and Analysis.Q40296219
Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov modelsQ40776037
Helicity of short E‐R/K peptidesQ41148281
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.Q41585818
Helical peptides with three pairs of Asp-Arg and Glu-Arg residues in different orientations and spacingsQ41811876
Salt bridges: geometrically specific, designable interactionsQ41989888
Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and UnfoldingQ42151733
A competing salt-bridge suppresses helix formation by the isolated C-peptide carboxylate of ribonuclease AQ42246039
Markov models of molecular kinetics: generation and validationQ43633887
Hierarchical Nyström methods for constructing Markov state models for conformational dynamicsQ44539516
Identification of slow molecular order parameters for Markov model constructionQ44985905
Design of a hyperstable protein by rational consideration of unfolded state interactionsQ46979192
FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.Q50769244
Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models.Q50910954
Coarse master equations for peptide folding dynamics.Q51895837
The structure of salt bridges between Arg(+) and Glu(-) in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries.Q53213855
Kinetic network models of tryptophan mutations in β-hairpins reveal the importance of non-native interactions.Q53281393
Denatured State Effects and the Origin of Nonclassical φ Values in Protein FoldingQ59600464
Statistical characterization of salt bridges in proteinsQ80380712
NMR-based protein potentialsQ84749920
Structural origin of slow diffusion in protein foldingQ86258320
Unfolding and folding internal friction of β-hairpins is smaller than that of α-helicesQ86871707
P433issue5
P304page(s)926-935
P577publication date2016-02-01
P1433published inJournal of Physical Chemistry BQ668669
P1476titleUsing Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding
P478volume120

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cites work (P2860)
Q37563730A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter.
Q38611563Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models.
Q37095634Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models
Q64239170Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study
Q37188955Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking.
Q47241787Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin

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