Related references
Note: Only part of the references are listed.Description of Hydration Water in Protein (Green Fluorescent Protein) Solution
Stefania Perticaroli et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)
The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery
Francesca Spyrakis et al.
JOURNAL OF MEDICINAL CHEMISTRY (2017)
The Multiple Roles of Waters in Protein Solvation
Adam Hospital et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes
Kei Moritsugu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment
Liwen Wang et al.
MOLECULAR & CELLULAR PROTEOMICS (2017)
Ligand diffusion in proteins via enhanced sampling in molecular dynamics
J. Rydzewski et al.
PHYSICS OF LIFE REVIEWS (2017)
Does metabolite channeling accelerate enzyme-catalyzed cascade reactions?
Liubov Poshyvailo et al.
PLOS ONE (2017)
Recent advances in FRET for the study of protein interactions and dynamics
Kenji Okamoto et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
Water Dynamics in the Hydration Shells of Biomolecules
Damien Laage et al.
CHEMICAL REVIEWS (2017)
Redesign of water networks for efficient biocatalysis
Michael J. Fink et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2017)
Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase
Jerome M. Fox et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)
Specific Inter-residue Interactions as Determinants of Human Monoacylglycerol Lipase Catalytic Competency A ROLE FOR GLOBAL CONFORMATIONAL CHANGES
Sergiy Tyukhtenko et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2016)
Protein Binding Pocket Dynamics
Antonia Stank et al.
ACCOUNTS OF CHEMICAL RESEARCH (2016)
Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation
Shinji Iida et al.
BIOCHEMICAL JOURNAL (2016)
Protein Allostery and Conformational Dynamics
Jingjing Guo et al.
CHEMICAL REVIEWS (2016)
Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods
Ulf Ryde et al.
CHEMICAL REVIEWS (2016)
Solution NMR Spectroscopy for the Study of Enzyme Allostery
George P. Lisi et al.
CHEMICAL REVIEWS (2016)
Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design
Maricarmen Hernandez-Rodriguez et al.
CURRENT MEDICINAL CHEMISTRY (2016)
Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods
Xing Du et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2016)
Perspective: Defining and quantifying the role of dynamics in enzyme catalysis
Arieh Warshel et al.
JOURNAL OF CHEMICAL PHYSICS (2016)
Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics
Phani Ghanakota et al.
JOURNAL OF MEDICINAL CHEMISTRY (2016)
Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems
Phani Ghanakota et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II
Srabani Taraphder et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Untangling Heavy Protein and Cofactor Isotope Effects on Enzyme Catalyzed Hydride Transfer
James E. Longbotham et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)
The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology
Marco Faini et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2016)
QM/MM free energy simulations: recent progress and challenges
Xiya Lu et al.
MOLECULAR SIMULATION (2016)
To keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solvent
Jayangika N. Dahanayake et al.
MOLECULAR SIMULATION (2016)
Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection
Joseph J. Maciag et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation
Urmi Doshi et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Dynamics and mechanism of ultrafast water-protein interactions
Yangzhong Qin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function
George P. Lisi et al.
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2016)
Mass spectrometry: a technique of many faces
Maya A. Olshina et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2016)
Surface water retardation around single-chain polymeric nanoparticles: critical for catalytic function?
Patrick J. M. Stals et al.
CHEMICAL SCIENCE (2016)
Conformational heterogeneity of the calmodulin binding interface
Diwakar Shukla et al.
NATURE COMMUNICATIONS (2016)
Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation
Shane E. Gordon et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
Tatiana Maximova et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Enzyme Stability and Activity in Non-Aqueous Reaction Systems: A Mini Review
Shihui Wang et al.
CATALYSTS (2016)
Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies
Chitra Narayanan et al.
CATALYSTS (2016)
Identifying and Visualizing Macromolecular Flexibility in Structural Biology
Martina Palamini et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2016)
Electron Transfer, Decoherence, and Protein Dynamics: Insights from Atomistic Simulations
Christophe Narth et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Markov State Models Provide Insights into Dynamic Modulation of Protein Function
Diwakar Shukla et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation
Themistoklis Zisis et al.
BIOCHEMISTRY (2015)
Enhanced sampling techniques in molecular dynamics simulations of biological systems
Rafael C. Bernardi et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)
Exploring water as building bricks in enzyme engineering
Peter Hendil-Forssell et al.
CHEMICAL COMMUNICATIONS (2015)
Molecular dynamics simulations of large macromolecular complexes
Juan R. Perilla et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
Samuel Genheden et al.
EXPERT OPINION ON DRUG DISCOVERY (2015)
Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation
Benjamin Stauch et al.
JOURNAL OF LIPID RESEARCH (2015)
Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins
Debashree Chakraborty et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Determination of the Reaction Coordinate for a Key Conformational Fluctuation in Human Carbonic Anhydrase II
Sanjib Paul et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway
David Oyen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Substrate tunnels in enzymes: Structure-function relationships and computational methodology
Laura J. Kingsley et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2015)
Two Pathways Mediate Interdomain Allosteric Regulation in Pin1
Jingjing Guo et al.
STRUCTURE (2015)
Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins
Giorgio Schiro et al.
NATURE COMMUNICATIONS (2015)
Role of Substrate Dynamics in Protein Prenylation Reactions
Dhruva K. Chakravorty et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
The Dynamical Nature of Enzymatic Catalysis
Robert Callender et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Role of Dynamics in Enzyme Catalysis: Substantial versus Semantic Controversies
Amnon Kohen
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes
Gira Bhabha et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains
Obaidur Rahaman et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Extended phase-space methods for enhanced sampling in molecular simulations: a review
Hiroshi Fujisaki et al.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2015)
Protein Conformational Populations and Functionally Relevant Substates
Arvind Ramanathan et al.
ACCOUNTS OF CHEMICAL RESEARCH (2014)
Entropy is Key to the Formation of Pentacyclic Terpenoids by EnzymeCatalyzed Polycyclization
Per-Olof Syren et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)
PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering
Hitesh Patel et al.
BIOINFORMATICS (2014)
Essential role of conformational selection in ligand binding
Austin D. Vogt et al.
BIOPHYSICAL CHEMISTRY (2014)
Binding and Channeling of Alternative Substrates in the Enzyme DmpFG: a Molecular Dynamics Study
Natalie E. Smith et al.
BIOPHYSICAL JOURNAL (2014)
Insight into the Redox Partner Interaction Mechanism in Cytochrome P450BM-3 Using Molecular Dynamics Simulations
Rajni Verma et al.
BIOPOLYMERS (2014)
Markov state models of biomolecular conformational dynamics
John D. Chodera et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
Substrate scope and selectivity in offspring to an enzyme subjected to directed evolution
Cecilia Blikstad et al.
FEBS JOURNAL (2014)
Force spectroscopy studies on protein-ligand interactions: A single protein mechanics perspective
Xiaotang Hu et al.
FEBS LETTERS (2014)
Multi-Scale Computational Enzymology: Enhancing Our Understanding of Enzymatic Catalysis
Rami Gherib et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2014)
Evidence for Hysteretic Substrate Channeling in the Proline Dehydrogenaseand Δ1-Pyrroline-5-carboxylate Dehydrogenase Coupled Reaction of Proline Utilization A (PutA)
Michael A. Moxley et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2014)
Analysis of Factors Influencing Hydration Site Prediction Based on Molecular Dynamics Simulations
Ying Yang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin
Elise Duboue-Dijon et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
WATsite: Hydration Site Prediction Program with PyMOL Interface
Bingjie Hu et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
Aoife C. Fogarty et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains
Wenfei Li et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state
Jessica Dielmann-Gessner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Conformational selection in protein binding and function
Thomas R. Weikl et al.
PROTEIN SCIENCE (2014)
From Structure to Catalysis: Recent Developments in the Biotechnological Applications of Lipases
Cristiane D. Anobom et al.
BIOMED RESEARCH INTERNATIONAL (2014)
Conserved Water Molecules in Family 1 Glycosidases: A DXMS and Molecular Dynamics Study
David Teze et al.
BIOCHEMISTRY (2013)
Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology
Marc W. van der Kamp et al.
BIOCHEMISTRY (2013)
Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover
Lauren C. McGowan et al.
BIOPHYSICAL JOURNAL (2013)
Biomolecular hydration dynamics: a jump model perspective
Aoife C. Fogarty et al.
CHEMICAL SOCIETY REVIEWS (2013)
Applications of small-angle X-ray scattering to biomacromolecular solutions
Maxim V. Petoukhov et al.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2013)
Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3
Rajni Verma et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
First and Second One-Electron Reduction of Lumiflavin in Water-A First Principles Molecular Dynamics Study
Murat Kilic et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media
Yanyan Meng et al.
JOURNAL OF MOLECULAR MODELING (2013)
Uncovering a Dynamically Formed Substrate Access Tunnel in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase
Po-hung Wang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics
Li Zhao et al.
PLOS ONE (2013)
Water-Protein Interactions: The Secret of Protein Dynamics
Silvia Martini et al.
SCIENTIFIC WORLD JOURNAL (2013)
Biomolecular Simulation: A Computational Microscope for Molecular Biology
Ron O. Dror et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)
A practical guide to modelling enzyme-catalysed reactions
Richard Lonsdale et al.
CHEMICAL SOCIETY REVIEWS (2012)
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
Ahmet Bakan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Exploring biological electron transfer pathway dynamics with the Pathways Plugin for VMD
Ilya A. Balabin et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)
Effects of Organic Solvent and Crystal Water on γ-Chymotrypsin in Acetonitrile Media: Observations from Molecular Dynamics Simulation and DFT Calculation
Lijuan Zhu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer
Susmita Roy et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Nature of Protein-CO2 Interactions as Elucidated via Molecular Dynamics
Michael L. Drummond et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Site-Specific Coupling of Hydration Water and Protein Flexibility Studied in Solution with Ultrafast 2D-IR Spectroscopy
John T. King et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites
Gregory A. Ross et al.
PLOS ONE (2012)
Calcium-dependent folding of single calmodulin molecules
Johannes Stigler et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Unlocking the mystery behind the activation phenomenon of T1 lipase: A molecular dynamics simulations approach
Mohd Zulhilmi Abdul Rahman et al.
PROTEIN SCIENCE (2012)
The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
Priyanka Prakash et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
Eva Chovancova et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes
Vern L. Schramm
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 80 (2011)
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
Peter Schmidtke et al.
BIOINFORMATICS (2011)
Dynamics of Protein Folding and Cofactor Binding Monitored by Single-Molecule Force Spectroscopy
Yi Cao et al.
BIOPHYSICAL JOURNAL (2011)
Hydrogen exchange mass spectrometry for studying protein structure and dynamics
Lars Konermann et al.
CHEMICAL SOCIETY REVIEWS (2011)
Mass spectrometry: come of age for structural and dynamical biology
Justin L. P. Benesch et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
Tingjun Hou et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Site-Specific Hydration Dynamics in the Nonpolar Core of a Molten Globule by Dynamic Nuclear Polarization of Water
Brandon D. Armstrong et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site
Moran Grossman et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)
Adhesive water networks facilitate binding of protein interfaces
Mazen Ahmad et al.
NATURE COMMUNICATIONS (2011)
A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
Daniel-Adriano Silva et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Global Dynamics of Proteins: Bridging Between Structure and Function
Ivet Bahar et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 39 (2010)
Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
Weinan E et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61 (2010)
Structural and Kinetic Study of the Extended Active Site for Proton Transfer in Human Carbonic Anhydrase II
John F. Domsic et al.
BIOCHEMISTRY (2010)
Role of protein motions on proton transfer pathways in human carbonic anhydrase II
Arijit Roy et al.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2010)
Electrostatic interactions play a significant role in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn2+
Carolina Sepulveda et al.
BIOCHIMIE (2010)
Dynamics of Biological Macromolecules: Not a Simple Slaving by Hydration Water
S. Khodadadi et al.
BIOPHYSICAL JOURNAL (2010)
Computational enzymology
Richard Lonsdale et al.
CHEMICAL COMMUNICATIONS (2010)
Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins
Ivet Bahar et al.
CHEMICAL REVIEWS (2010)
From protein folding to protein function and biomolecular binding by energy landscape theory
Alexander Schug et al.
CURRENT OPINION IN PHARMACOLOGY (2010)
Reaching biological timescales with all-atom molecular dynamics simulations
Matthew C. Zwier et al.
CURRENT OPINION IN PHARMACOLOGY (2010)
The Role of Water Molecules in Computational Drug Design
Stephanie B. A. de Beer et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2010)
Future directions of structural mass spectrometry using hydroxyl radical footprinting
Janna G. Kiselar et al.
JOURNAL OF MASS SPECTROMETRY (2010)
Stabilizing of a Globular Protein by a Highly Complex Water Network: A Molecular Dynamics Simulation Study on Factor Xa
Hannes G. Wallnoefer et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Ultrafast Dynamics and Hydrogen-Bond Structure in Aqueous Solutions of Model Peptides
Kamila Mazur et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Carbamate Transport in Carbamoyl Phosphate Synthetase: A Theoretical and Experimental Investigation
Liliya Lund et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Solvent-induced lid opening in lipases: A molecular dynamics study
Sascha Rehm et al.
PROTEIN SCIENCE (2010)
Protein-protein interactions at an enzyme-substrate interface: Characterization of transient reaction intermediates throughout a full catalytic cycle of Escherichia coli thioredoxin reductase
Ana Negri et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Steering Electrons on Moving Pathways
David N. Beratan et al.
ACCOUNTS OF CHEMICAL RESEARCH (2009)
Theory of Proton-Coupled Electron Transfer in Energy Conversion Processes
Sharon Hammes-Schiffer
ACCOUNTS OF CHEMICAL RESEARCH (2009)
Analysis of Protein Conformation and Dynamics by Hydrogen/Deuterium Exchange MS
John R. Engen
ANALYTICAL CHEMISTRY (2009)
Long-timescale molecular dynamics simulations of protein structure and function
John L. Klepeis et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)
The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin
Benjamin Born et al.
FARADAY DISCUSSIONS (2009)
Dynamics of hydration water in proteins
Jose Teixeira
GENERAL PHYSIOLOGY AND BIOPHYSICS (2009)
Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies
Shina C. L. Kamerlin et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Transition Path Sampling Study of the Conformational Fluctuation of His-64 in Human Carbonic Anhydrase II
Arijit Roy et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Applications of 2D IR Spectroscopy to Peptides, Proteins, and Hydrogen-Bond Dynamics
Yung Sam Kim et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
A Combined Theoretical and Experimental Study of the Ammonia Tunnel in Carbamoyl Phosphate Synthetase
Yubo Fan et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II
C. Mark Maupin et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Enzymatic transition states and dynamic motion in barrier crossing
Steven D. Schwartz et al.
NATURE CHEMICAL BIOLOGY (2009)
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
Tomasz Wlodarski et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
The role of conserved water molecules in the catalytic domain of protein kinases
James D. R. Knight et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Binding of Small-Molecule Ligands to Proteins: What You See Is Not Always What You Get
David L. Mobley et al.
STRUCTURE (2009)
Mechanism for the transport of ammonia within carbamoyl phosphate synthetase determined by molecular dynamics Simulations
Yubo Fan et al.
BIOCHEMISTRY (2008)
Dynamics at the protein-water interface from 17O spin relaxation in deeply supercooled solutions
Carlos Mattea et al.
BIOPHYSICAL JOURNAL (2008)
Water as an active constituent in cell biology
Philip Ball
CHEMICAL REVIEWS (2008)
Transition networks for modeling the kinetics of conformational change in macromolecules
Frank Noe et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)
Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions
Danilo Roccatano
CURRENT PROTEIN & PEPTIDE SCIENCE (2008)
Structural basis of human triosephosphate isomerase deficiency: Mutation E104D is related to alterations of a conserved water network at the dimer interface
Claudia Rodriguez-Almazán et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2008)
Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
Robert Abel et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Allosteric regulation and catalysis emerge via a common route
Nina M. Goodey et al.
NATURE CHEMICAL BIOLOGY (2008)
Water hydrogen bond analysis on hydrophilic and hydrophobic biomolecule sites
Daniela Russo et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
Laboratory evolution of P450BM3 for mediated electron transfer yielding an activity-improved and reductase-independent variant
Jovana Nazor et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2008)
An extended dynamical hydration shell around proteins
Simon Ebbinghaus et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
Katherine A. Henzler-Wildman et al.
NATURE (2007)
Mapping hydration dynamics around a protein surface
Luyuan Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Coupling of protein and hydration-water dynamics in biological membranes
K. Wood et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
H and other transfers in enzymes and in solution: Theory and computations, a unified view. 2. Applications to experiment and computations
R. A. Marcus
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Understanding a mechanism of organic cosolvent inactivation in heme monooxygenase P450BM-3
Jochen Kuper et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents
Nuno M. Micaelo et al.
FEBS JOURNAL (2007)
The dynamics of water-protein interaction studied by ultrafast optical Kerr-effect spectroscopy
Neil T. Hunt et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Classification of water molecules in protein binding sites
Caterina Barillari et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Relevance of phenylalanine 216 in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn(II)
Alejandro Yevenes et al.
PROTEIN JOURNAL (2007)
A comparison of methods to compute the potential of mean force
Daniel Trzesniak et al.
CHEMPHYSCHEM (2007)
Protein dynamics and function: Insights from the energy landscape and solvent slaving
Hans Frauenfelder et al.
IUBMB LIFE (2007)
Roles of Asp75, Asp78, and Glu83 of GTP-dependent phosphoenolpyruvate carboxykinase from Mycobacterium smegmatis
Christopher L. Case et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2006)
Toward understanding the inactivation mechanism of monooxygenase P450BM-3 by organic cosolvents: A molecular dynamics simulation study
Danilo Roccatano et al.
BIOPOLYMERS (2006)
Tunneling of intermediates in enzyme-catalyzed reactions
Amanda Weeks et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2006)
The dynamic energy landscape of dihydrofolate reductase catalysis
David D. Boehr et al.
SCIENCE (2006)
Computational approaches: Reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency
Thomas C. Bruice
CHEMICAL REVIEWS (2006)
Advances in time-resolved approaches to characterize the dynamical nature of enzymatic catalysis
Robert Callender et al.
CHEMICAL REVIEWS (2006)
Electrostatic basis for enzyme catalysis
Arieh Warshel et al.
CHEMICAL REVIEWS (2006)
Multiple solvent crystal structures: Probing binding sites, plasticity and hydration
C Mattos et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
Water structure and interactions with protein surfaces
TM Raschke
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
A molecular jump mechanism of water reorientation
D Laage et al.
SCIENCE (2006)
Hydrogen tunneling and protein motion in enzyme reactions
S Hammes-Schiffer
ACCOUNTS OF CHEMICAL RESEARCH (2006)
Enzymes: An integrated view of structure, dynamics and function
PK Agarwal
MICROBIAL CELL FACTORIES (2006)
Site-directed mutagenesis study of the microenvironment characteristics of Lys(213) of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase
Alejandro Yevenes et al.
BIOCHIMIE (2006)
Intrinsic dynamics of an enzyme underlies catalysis
EZ Eisenmesser et al.
NATURE (2005)
Role of protein dynamics in reaction rate enhancement by enzymes
PK Agarwal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Structural and dynamic properties of cytochrome P450BM-3 in pure water and in a dimethylsulfoxide/water mixture
D Roccatano et al.
BIOPOLYMERS (2005)
Solution structure of the sulfite reductase flavodoxin-like domain from Escherichia coli
N Sibille et al.
BIOCHEMISTRY (2005)
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
ATR Laurie et al.
BIOINFORMATICS (2005)
Diffraction, crystallography and microscopy beyond three dimensions: structural dynamics in space and time
AH Zewail
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2005)
How do cofactors modulate protein folding?
CL Higgins et al.
PROTEIN AND PEPTIDE LETTERS (2005)
Dynamics of water in biological recognition
SK Pal et al.
CHEMICAL REVIEWS (2004)
Crystal structure of E-coli alcohol dehydrogenase YqhD:: Evidence of a covalently modified NADP coenzyme
G Sulzenbacher et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
Protein hydration dynamics in solution: a critical survey
B Halle
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2004)
Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity
L Yang et al.
BIOPHYSICAL JOURNAL (2004)
Role of cofactors in metalloprotein folding
CJ Wilson et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2004)
Conformational change in substrate binding, catalysis and product release: an open and shut case?
A Gutteridge et al.
FEBS LETTERS (2004)
Biomolecular hydration: From water dynamics to hydrodynamics
B Halle et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
WaterScore:: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes
AT García-Sosa et al.
JOURNAL OF MOLECULAR MODELING (2003)
Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution
MHJ Koch et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2003)
Slaving: Solvent fluctuations dominate protein dynamics and functions
PW Fenimore et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Conserved water molecules in MHC class-1 molecules and their putative structural and functional roles
K Ogata et al.
PROTEIN ENGINEERING (2002)
Dynamic structures of horse liver alcohol dehydrogenase (HLADH):: Results of molecular dynamics simulations of HLADH-NAD+-PhCH2OH, HLADH-NAD+-PhCH2O-, and HLADH-NADH-PhCHO
J Luo et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)
The protein-solvent interface: a big splash
A Purkiss et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2001)
Residence times of water molecules in the hydration sites of myoglobin
VA Makarov et al.
BIOPHYSICAL JOURNAL (2000)
Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
JL Radkiewicz et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)
Share Paper
