About: Essential Motions and Energetic Contributions of Individual Residues in a Peptide Bound to an SH3 Domain.

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About: Essential Motions and Energetic Contributions of Individual Residues in a Peptide Bound to an SH3 Domain. Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	We have studied protein-ligand interactions by molecular dynamics simulations using software designed to exploit parallel computing architectures. The trajectories were analysed to extract the essential motions and to estimate the individual contributions of fragments of the ligand to overall binding enthalpy. Two forms of the bound ligand are compared, one with the termini blocked by cova-lent derivatisation, and one in the underivatised, zwitterionic form. The ends of the peptide tend to bind more loosely in the capped form. We can observe significant motions in the bound ligand and distinguish between mo-tions of the peptide backbone and of the side chains. This could be useful in designing ligands, which fit optimally to the binding protein. We show that it is possible to determine the different contributions of each residue in a peptide to the enthalpy of binding. Proline is a major net contributor to binding en-thalpy, in keeping with the known propensity for this family of proteins to bind prol We have studied protein-ligand interactions by molecular dynamics simulations using software designed to exploit parallel computing architectures. The trajectories were analysed to extract the essential motions and to estimate the individual contributions of fragments of the ligand to overall binding enthalpy. Two forms of the bound ligand are compared, one with the termini blocked by cova-lent derivatisation, and one in the underivatised, zwitterionic form. The ends of the peptide tend to bind more loosely in the capped form. We can observe significant motions in the bound ligand and distinguish between mo-tions of the peptide backbone and of the side chains. This could be useful in designing ligands, which fit optimally to the binding protein. We show that it is possible to determine the different contributions of each residue in a peptide to the enthalpy of binding. Proline is a major net contributor to binding en-thalpy, in keeping with the known propensity for this family of proteins to bind prol (en)
Title	Essential Motions and Energetic Contributions of Individual Residues in a Peptide Bound to an SH3 Domain. Essential Motions and Energetic Contributions of Individual Residues in a Peptide Bound to an SH3 Domain. (en)
skos:prefLabel	Essential Motions and Energetic Contributions of Individual Residues in a Peptide Bound to an SH3 Domain. Essential Motions and Energetic Contributions of Individual Residues in a Peptide Bound to an SH3 Domain. (en)
skos:notation	RIV/67985858:_____/00:27020017!RIV/2003/AV0/A27003/N
http://linked.open.../vavai/riv/strany	646;655
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(IAA4072006), Z(AV0Z4072921)
http://linked.open...iv/cisloPeriodika	N/A
http://linked.open...vai/riv/dodaniDat	2003
http://linked.open...aciTvurceVysledku	Kolafa, Jiří
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Ústav chemických procesů AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	710493
http://linked.open...ai/riv/idVysledku	RIV/67985858:_____/00:27020017
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	protein-ligand interactions; energetic contributions; peptide bound (en)
http://linked.open.../riv/klicoveSlovo	energetic contributions peptide bound protein-ligand interactions
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[D30E6617D0A8]
http://linked.open...i/riv/nazevZdroje	Biophysical Journal
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...ocetUcastnikuAkce	0 (xsd:int)
http://linked.open...nichUcastnikuAkce	0 (xsd:int)
http://linked.open...vavai/riv/projekt	Electron pairing and chemical bonds
http://linked.open...UplatneniVysledku	2000
http://linked.open...v/svazekPeriodika	79
http://linked.open...iv/tvurceVysledku	Kolafa, Jiří Bywater, R. P. Perram, J. W.
http://linked.open...n/vavai/riv/zamer	Theoretical fundamentals of chemical processes: equilibrium and dynamic behavior of multiphase reacting systems
issn	0006-3495
number of pages	10 (xsd:int)

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