Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

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http://www.wikidata.org/entity/Q29547631

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Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA Principles of conduction and hydrophobic gating in K+ channels A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3 Improved side-chain torsion potentials for the Amber ff99SB protein force field Structure and function of an irreversible agonist-β(2) adrenoceptor complex Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study CHARMM: the biomolecular simulation program Computational studies of marine toxins targeting ion channels Synergistic applications of MD and NMR for the study of biological systems Structural analysis of a peptide fragment of transmembrane transporter protein bilitranslocase Intrinsic Localized Modes in Proteins Dynamics of Bcl-xL in water and membrane: molecular simulations Mechanism of eIF6 release from the nascent 60S ribosomal subunit.Two distinct states of the HAMP domain from sensory rhodopsin transducer observed in unbiased molecular dynamics simulations Dynamic Motion and Communication in the Streptococcal C1 Phage Lysin, PlyC Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: computational approaches Canine CNGA3 Gene Mutations Provide Novel Insights into Human Achromatopsia-Associated Channelopathies and Treatment Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability.The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses Complete mapping of substrate translocation highlights the role of LeuT N-terminal segment in regulating transport cycle Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure Exploring volatile general anesthetic binding to a closed membrane-bound bacterial voltage-gated sodium channel via computation Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na+ coupling.Force-induced unfolding simulations of the human Notch1 negative regulatory region: possible roles of the heterodimerization domain in mechanosensing The p7 protein of hepatitis C virus forms structurally plastic, minimalist ion channels Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase Structural and dynamic requirements for optimal activity of the essential bacterial enzyme dihydrodipicolinate synthase Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site.Unveiling the Mechanism of Arginine Transport through AdiC with Molecular Dynamics Simulations: The Guiding Role of Aromatic Residues "Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor.

P2860

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P2860

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

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http://www.wikidata.org/entity/Q29547631

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2004 nî lūn-bûn

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2004 թուականի Օգոստոսին հրատարակուած գիտական յօդուած

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2004 թվականի օգոստոսին հրատարակված գիտական հոդված

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2004年の論文

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2004年論文

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2004年論文

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2004年論文

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2004年論文

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