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Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F12%3A00384278%21RIV13-AV0-61388963
rdf:type
skos:Concept n14:Vysledek
dcterms:description
Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between productive and non-productive contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability. Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between productive and non-productive contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.
dcterms:title
Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications
skos:prefLabel
Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications
skos:notation
RIV/61388963:_____/12:00384278!RIV13-AV0-61388963
n14:predkladatel
n15:ico%3A61388963
n3:aktivita
n5:P n5:I
n3:aktivity
I, P(GAP208/10/0725), P(LH11020)
n3:cisloPeriodika
42
n3:dodaniDat
n6:2013
n3:domaciTvurceVysledku
Fačkovec, Boris n13:7358946
n3:druhVysledku
n18:J
n3:duvernostUdaju
n8:S
n3:entitaPredkladatele
n19:predkladatel
n3:idSjednocenehoVysledku
156792
n3:idVysledku
RIV/61388963:_____/12:00384278
n3:jazykVysledku
n17:eng
n3:klicovaSlova
egg-white lysozyme; force-field; 3-dimensional structure; thermophilic proteins; thermal-stability; mutant
n3:klicoveSlovo
n10:mutant n10:3-dimensional%20structure n10:egg-white%20lysozyme n10:thermal-stability n10:thermophilic%20proteins n10:force-field
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[A5569BC8AA69]
n3:nazevZdroje
Journal of Physical Chemistry B
n3:obor
n16:CF
n3:pocetDomacichTvurcuVysledku
2
n3:pocetTvurcuVysledku
2
n3:projekt
n12:LH11020 n12:GAP208%2F10%2F0725
n3:rokUplatneniVysledku
n6:2012
n3:svazekPeriodika
116
n3:tvurceVysledku
Fačkovec, Boris Vondrášek, Jiří
n3:wos
000310120900002
s:issn
1520-6106
s:numberOfPages
10
n11:doi
10.1021/jp303088n