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Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F10%3A00351179%21RIV11-GA0-61388963
rdf:type
skos:Concept n16:Vysledek
dcterms:description
The interactions between amino acid side chains in proteins are generally considered to be the most important stabilizing factor controlling the precise arrangement of the polypeptide chain into a well-defined spatial structure. We used the RI-DFT-D method to calculate the full 20 20 matrix of interaction energies between all pairs of amino acid side chains. We find that all of the calculated interaction energies between selected pairs of amino acids are attractive in the gas phase with the exception of side chain pairs having the same total charge. We compared these data with those calculated by the parm03 and OPLS-AA/L force fields to investigate the reliability of simple methods in modeling biomolecules and their behavior. The force fields yield good overall interaction energies for our set but have problems in evaluation of some particular interactions which could be of principal importance for protein stability. The interactions between amino acid side chains in proteins are generally considered to be the most important stabilizing factor controlling the precise arrangement of the polypeptide chain into a well-defined spatial structure. We used the RI-DFT-D method to calculate the full 20 20 matrix of interaction energies between all pairs of amino acid side chains. We find that all of the calculated interaction energies between selected pairs of amino acids are attractive in the gas phase with the exception of side chain pairs having the same total charge. We compared these data with those calculated by the parm03 and OPLS-AA/L force fields to investigate the reliability of simple methods in modeling biomolecules and their behavior. The force fields yield good overall interaction energies for our set but have problems in evaluation of some particular interactions which could be of principal importance for protein stability.
dcterms:title
Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins
skos:prefLabel
Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins
skos:notation
RIV/61388963:_____/10:00351179!RIV11-GA0-61388963
n3:aktivita
n10:Z n10:P
n3:aktivity
P(GAP208/10/0725), P(LC512), Z(AV0Z40550506), Z(MSM6198959216)
n3:cisloPeriodika
7
n3:dodaniDat
n4:2011
n3:domaciTvurceVysledku
n13:7358946
n3:druhVysledku
n18:J
n3:duvernostUdaju
n8:S
n3:entitaPredkladatele
n6:predkladatel
n3:idSjednocenehoVysledku
257189
n3:idVysledku
RIV/61388963:_____/10:00351179
n3:jazykVysledku
n17:eng
n3:klicovaSlova
protein structure; DFT method; force fields; interaction energy
n3:klicoveSlovo
n5:interaction%20energy n5:DFT%20method n5:force%20fields n5:protein%20structure
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[465BB2CC89F6]
n3:nazevZdroje
Journal of Chemical Theory and Computation
n3:obor
n14:CF
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
4
n3:projekt
n11:GAP208%2F10%2F0725 n11:LC512
n3:rokUplatneniVysledku
n4:2010
n3:svazekPeriodika
6
n3:tvurceVysledku
Hobza, P. Laskowski, R. A. Vondrášek, Jiří Berka, K.
n3:wos
000279751500026
n3:zamer
n15:AV0Z40550506 n15:MSM6198959216
s:issn
1549-9618
s:numberOfPages
13