Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships

scientific article published on 22 February 2018

Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/ACS.JPCLETT.8B00238
P932PMC publication ID6555141
P698PubMed publication ID29461836

P50authorZhi YueQ84135240
Jana ShenQ87827774
P2093author name stringCheng-Chieh Tsai
Yandong Huang
Jack A Henderson
P2860cites workAll-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable WaterQ39317206
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Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors.Q47136224
Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux PumpQ47154372
Conformational dynamics of cathepsin D and binding to a small-molecule BACE1 inhibitorQ48333250
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Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values.Q51550011
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Catalysis by hen egg-white lysozyme proceeds via a covalent intermediateQ27634351
Crystal Structure of an Active Form of BACE1, an Enzyme Responsible for Amyloid   Protein ProductionQ27650198
The pKa Values of Acidic and Basic Residues Buried at the Same Internal Location in a Protein Are Governed by Different FactorsQ27654435
Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nucleaseQ27656001
All-atom empirical potential for molecular modeling and dynamics studies of proteinsQ27860468
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Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculationsQ30399241
THEMATICS: a simple computational predictor of enzyme function from structureQ33947797
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What are the dielectric "constants" of proteins and how to validate electrostatic models?Q34325469
Constant pH molecular dynamics with proton tautomerismQ34350350
Structural basis of perturbed pKa values of catalytic groups in enzyme active sitesQ34670783
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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulationsQ36088442
pH-Dependent Population Shift Regulates BACE1 Activity and InhibitionQ36420889
Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.Q36437502
Calculating pKa values in enzyme active sitesQ36572237
Staphylococcal nuclease: Proposed mechanism of action based on structure of enzyme—thymidine 3′,5′-bisphosphate—calcium ion complex at 1.5-Å resolutionQ37332171
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and ValidationQ37701323
P433issue6
P304page(s)1179-1184
P577publication date2018-02-22
P1433published inJournal of Physical Chemistry LettersQ1768577
P1476titlePredicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships
P478volume9

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cites work (P2860)
Q99710728Alternative proton-binding site and long-distance coupling in Escherichia coli sodium-proton antiporter NhaA
Q92839822Assessing Lysine and Cysteine Reactivities for Designing Targeted Covalent Kinase Inhibitors
Q92423429Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules
Q90348471Electrostatic lock in the transport cycle of the multidrug resistance transporter EmrE
Q90987028GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations
Q89289610Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis
Q90646398Zooming in on a small multidrug transporter reveals details of asymmetric protonation

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