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On the coupling of protein and water dynamics in confinement: Spatially resolved molecular dynamics simulation studies

https://doi.org/10.1063/1.5097777
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What this work says

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

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An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
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GROMACS: Fast, flexible, and free
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Molecular dynamics simulation of hydration in myoglobin
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Hydration dependent dynamics in sol–gel encapsulated myoglobin
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The dynamical transition of proteins, concepts and misconceptions
inferredcites →https://doi.org/10.1016/0014-5793(92)80252-copenalex-snapshot
Rhizomucor miehei lipase remains highly active at water activity below 0.0001
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Esterase catalysis of substrate vapour: enzyme activity occurs at very low hydration
inferredcites →https://doi.org/10.1016/j.biomaterials.2017.01.041openalex-snapshot
Computational smart polymer design based on elastin protein mutability
inferredcites →https://doi.org/10.1016/j.bpj.2009.12.4284openalex-snapshot
Dynamics of Biological Macromolecules: Not a Simple Slaving by Hydration Water
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Elastin‐like polypeptides as models of intrinsically disordered proteins
inferredcites →https://doi.org/10.1016/j.jnoncrysol.2010.08.002openalex-snapshot
The two-step scenario of the protein dynamical transition
inferredcites →https://doi.org/10.1016/j.sbi.2017.09.003openalex-snapshot
How does solvation in the cell affect protein folding and binding?
inferredcites →https://doi.org/10.1016/j.ymeth.2010.05.007openalex-snapshot
Combining THz spectroscopy and MD simulations to study protein-hydration coupling
inferredcites →https://doi.org/10.1016/s0006-3495(00)76557-xopenalex-snapshot
The Dynamics of Protein Hydration Water: A Quantitative Comparison of Molecular Dynamics Simulations and Neutron-scattering Experiments
inferredcites →https://doi.org/10.1016/s0006-3495(03)74614-1openalex-snapshot
Translational Hydration Water Dynamics Drives the Protein Glass Transition
inferredcites →https://doi.org/10.1016/s0006-3495(94)80835-5openalex-snapshot
A global model of the protein-solvent interface
inferredcites →https://doi.org/10.1016/s0092-8674(01)00517-7openalex-snapshot
Dual Function of Protein Confinement in Chaperonin-Assisted Protein Folding
inferredcites →https://doi.org/10.1016/s0301-4622(02)00283-1openalex-snapshot
A microscopic view of peptide and protein solvation
inferredcites →https://doi.org/10.1016/s0959-440x(99)00045-7openalex-snapshot
Implications of macromolecular crowding for protein assembly
inferredcites →https://doi.org/10.1021/acs.chemrev.6b00765openalex-snapshot
Water Dynamics in the Hydration Shells of Biomolecules
inferredcites →https://doi.org/10.1021/acs.jpcb.7b10448openalex-snapshot
Complex Dynamics of Water in Protein Confinement
inferredcites →https://doi.org/10.1021/acs.jpclett.6b01858openalex-snapshot
Anomalous Dynamics of Water Confined in Protein–Protein and Protein–DNA Interfaces
inferredcites →https://doi.org/10.1021/bi00340a034openalex-snapshot
Carbon-13 NMR relaxation studies demonstrate an inverse temperature transition in the elastin polypentapeptide
inferredcites →https://doi.org/10.1021/bm4007166openalex-snapshot
A Unified Model for De Novo Design of Elastin-like Polypeptides with Tunable Inverse Transition Temperatures
inferredcites →https://doi.org/10.1021/cr040426mopenalex-snapshot
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
inferredcites →https://doi.org/10.1021/cr068037aopenalex-snapshot
Water as an Active Constituent in Cell Biology
inferredcites →https://doi.org/10.1021/ct500569bopenalex-snapshot
Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
inferredcites →https://doi.org/10.1021/j100308a038openalex-snapshot
The missing term in effective pair potentials
inferredcites →https://doi.org/10.1021/ja046900nopenalex-snapshot
Protein Encapsulation in Mesoporous Silicate: The Effects of Confinement on Protein Stability, Hydration, and Volumetric Properties
inferredcites →https://doi.org/10.1021/ja200067popenalex-snapshot
Protein Crowding Tunes Protein Stability
inferredcites →https://doi.org/10.1021/ja211115qopenalex-snapshot
Protein Crowding Affects Hydration Structure and Dynamics
inferredcites →https://doi.org/10.1021/jp020100mopenalex-snapshot
Molecular Dynamics of Water at the Protein−Solvent Interface
inferredcites →https://doi.org/10.1021/jp054805aopenalex-snapshot
Inverse Temperature Transition of a Biomimetic Elastin Model: Reactive Flux Analysis of Folding/Unfolding and Its Coupling to Solvent Dielectric Relaxation
inferredcites →https://doi.org/10.1021/jp9116886openalex-snapshot
Water Hydrogen Bond Dynamics in Aqueous Solutions of Amphiphiles
inferredcites →https://doi.org/10.1021/jp9119793openalex-snapshot
Water Hydrogen-Bond Dynamics around Amino Acids: The Key Role of Hydrophilic Hydrogen-Bond Acceptor Groups
inferredcites →https://doi.org/10.1038/35051719openalex-snapshot
Improving enzymes by using them in organic solvents
inferredcites →https://doi.org/10.1039/c6cp05601fopenalex-snapshot
Hydrogen-bond dynamics at the bio–water interface in hydrated proteins: a molecular-dynamics study
inferredcites →https://doi.org/10.1063/1.2121687openalex-snapshot
A general purpose model for the condensed phases of water: TIP4P/2005
inferredcites →https://doi.org/10.1063/1.328693openalex-snapshot
Polymorphic transitions in single crystals: A new molecular dynamics method
inferredcites →https://doi.org/10.1063/1.447334openalex-snapshot
A unified formulation of the constant temperature molecular dynamics methods
inferredcites →https://doi.org/10.1063/1.4768046openalex-snapshot
Power-law and logarithmic relaxations of hydrated proteins: A molecular dynamics simulations study
inferredcites →https://doi.org/10.1063/1.4798217openalex-snapshot
Structure and dynamics of supercooled water in neutral confinements
inferredcites →https://doi.org/10.1063/1.4870089openalex-snapshot
Static and dynamic length scales in supercooled liquids: Insights from molecular dynamics simulations of water and tri-propylene oxide
inferredcites →https://doi.org/10.1073/pnas.0608256104openalex-snapshot
Protein folding under confinement: A role for solvent
inferredcites →https://doi.org/10.1073/pnas.0810679105openalex-snapshot
How main-chains of proteins explore the free-energy landscape in native states
inferredcites →https://doi.org/10.1073/pnas.082335099openalex-snapshot
Is the first hydration shell of lysozyme of higher density than bulk water?
inferredcites →https://doi.org/10.1073/pnas.0900336106openalex-snapshot
A unified model of protein dynamics
inferredcites →https://doi.org/10.1073/pnas.212637899openalex-snapshot
Slaving: Solvent fluctuations dominate protein dynamics and functions
inferredcites →https://doi.org/10.1103/physreva.31.1695openalex-snapshot
Canonical dynamics: Equilibrium phase-space distributions
inferredcites →https://doi.org/10.1103/physreve.89.032710openalex-snapshot
Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H 2 NMR studies on perdeuterated C-phycocyanin
inferredcites →https://doi.org/10.1103/physrevlett.100.188103openalex-snapshot
Subdiffusion in Peptides Originates from the Fractal-Like Structure of Configuration Space
inferredcites →https://doi.org/10.1103/physrevlett.88.138101openalex-snapshot
Role of Protein-Water Hydrogen Bond Dynamics in the Protein Dynamical Transition
inferredcites →https://doi.org/10.1103/physrevlett.92.148101openalex-snapshot
Folding and Unfolding of an Elastinlike Oligopeptide: “Inverse Temperature Transition,” Reentrance, and Hydrogen-Bond Dynamics
inferredcites →https://doi.org/10.1110/ps.03288104openalex-snapshot
Protein folding by the effects of macromolecular crowding
inferredcites →https://doi.org/10.1126/science.1312257openalex-snapshot
Encapsulation of Proteins in Transparent Porous Silicate Glasses Prepared by the Sol-Gel Method
inferredcites →https://doi.org/10.1140/epje/i2003-10043-5openalex-snapshot
Low-temperature behavior of water confined by biological macromolecules and its relation to protein dynamics
inferredcites →https://doi.org/10.1146/annurev.biophys.35.040405.102134openalex-snapshot
WATER MEDIATION IN PROTEIN FOLDING AND MOLECULAR RECOGNITION
inferredcites →https://doi.org/10.1146/annurev.biophys.37.032807.125817openalex-snapshot
Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences
inferredcites →https://doi.org/10.1515/zpch-2017-1042openalex-snapshot
Molecular Dynamics Simulations of Water, Silica, and Aqueous Mixtures in Bulk and Confinement
inferredcites →https://doi.org/10.7554/elife.26526openalex-snapshot
The liquid structure of elastin

What points at this work

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

inferred← citeshttps://doi.org/10.2139/ssrn.4766630openalex-extracted
Examining the Impact of Water Molecules in Regulating Amicyanin Protein's Function: A Computational Study
inferred← citeshttps://doi.org/10.1016/j.eml.2023.102114openalex-snapshot
Curvature-enhanced membrane asymmetry slows down protein diffusion
inferred← citeshttps://doi.org/10.1021/acs.jpcc.1c05502openalex-snapshot
Influence of Pore Surface Chemistry on the Rotational Dynamics of Nanoconfined Water
inferred← citeshttps://doi.org/10.1021/acs.langmuir.2c00521openalex-snapshot
Structural and Dynamical Properties of Liquids in Confinements: A Review of Molecular Dynamics Simulation Studies
inferred← citeshttps://doi.org/10.1039/d0cp02803gopenalex-snapshot
Dynamic coupling of a hydration layer to a fluid phospholipid membrane: intermittency and multiple time-scale relaxations
inferred← citeshttps://doi.org/10.1039/d5ra04968gopenalex-snapshot
Water confinement in carbon nanocones: molecular dynamics study
inferred← citeshttps://doi.org/10.1063/5.0047078openalex-snapshot
Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response
inferred← citeshttps://doi.org/10.1063/5.0105062openalex-snapshot
Temperature-dependent dynamics at protein–solvent interfaces
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Exploring the influence of water molecules on modulating the functional dynamics of amicyanin: a computational investigation
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Lab on a Tip: Atomic Force Microscopy as a Versatile Analytical Tool for Nano-bioscience
inferred← citeshttps://doi.org/10.21203/rs.3.rs-9520801/v1openalex-snapshot
Protein Structure Group Velocity Dispersion: A Hydration-Driven Inside-out Rupture Principle
inferred← citeshttps://doi.org/10.3390/biom15050660openalex-snapshot
Residue-Specific Structural and Dynamical Coupling of Protein and Hydration Water Revealed by Molecular Dynamics Simulations
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Entropy and Random Walk Trails Water Confinement and Non-Thermal Equilibrium in Photon-Induced Nanocavities
inferred← citeshttps://doi.org/10.70675/a9cadf06z213ez4cfez8604z59ed8aa55e60openalex-snapshot
Nanostructuration de liquides binaires et d’eau par confinement dans des organosilicates périodiques mésoporeux
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