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Statements

Subject Item
n2:RIV%2F86652036%3A_____%2F13%3A00420825%21RIV14-GA0-86652036
rdf:type
n8:Vysledek skos:Concept
dcterms:description
We describe a computer-based protocol to design protein mutations increasing binding affinity between ligand and its receptor. The method was applied to mutate interferon-gamma receptor 1 (IFN-gamma-Rx) to increase its affinity to natural ligand IFN-gamma, protein important for innate immunity. We analyzed all four available crystal structures of the IFN-gamma-Rx/IFN-gamma complex to identify 40 receptor residues forming the interface with IFN-gamma. For these 40 residues, we performed computational mutation analysis by substituting each of the interface receptor residues by the remaining standard amino acids. The corresponding changes of the free energy were calculated by a protocol consisting of FoldX and molecular dynamics calculations. Based on the computed changes of the free energy and on sequence conservation criteria obtained by the analysis of 32 receptor sequences from 19 different species, we selected 14 receptor variants predicted to increase the receptor affinity to IFN-gamma. These variants were expressed as recombinant proteins in Escherichia coli, and their affinities to IFN-gamma were determined experimentally by surface plasmon resonance (SPR). The SPR measurements showed that the simple computational protocol succeeded in finding two receptor variants with affinity to IFN-gamma increased about fivefold compared to the wild-type receptor. We describe a computer-based protocol to design protein mutations increasing binding affinity between ligand and its receptor. The method was applied to mutate interferon-gamma receptor 1 (IFN-gamma-Rx) to increase its affinity to natural ligand IFN-gamma, protein important for innate immunity. We analyzed all four available crystal structures of the IFN-gamma-Rx/IFN-gamma complex to identify 40 receptor residues forming the interface with IFN-gamma. For these 40 residues, we performed computational mutation analysis by substituting each of the interface receptor residues by the remaining standard amino acids. The corresponding changes of the free energy were calculated by a protocol consisting of FoldX and molecular dynamics calculations. Based on the computed changes of the free energy and on sequence conservation criteria obtained by the analysis of 32 receptor sequences from 19 different species, we selected 14 receptor variants predicted to increase the receptor affinity to IFN-gamma. These variants were expressed as recombinant proteins in Escherichia coli, and their affinities to IFN-gamma were determined experimentally by surface plasmon resonance (SPR). The SPR measurements showed that the simple computational protocol succeeded in finding two receptor variants with affinity to IFN-gamma increased about fivefold compared to the wild-type receptor.
dcterms:title
Increasing Affinity of Interferon-gamma Receptor 1 to Interferon-gamma by Computer-Aided Design Increasing Affinity of Interferon-gamma Receptor 1 to Interferon-gamma by Computer-Aided Design
skos:prefLabel
Increasing Affinity of Interferon-gamma Receptor 1 to Interferon-gamma by Computer-Aided Design Increasing Affinity of Interferon-gamma Receptor 1 to Interferon-gamma by Computer-Aided Design
skos:notation
RIV/86652036:_____/13:00420825!RIV14-GA0-86652036
n8:predkladatel
n14:ico%3A86652036
n4:aktivita
n5:P n5:Z
n4:aktivity
P(GAP305/10/2184), Z(AV0Z50520701)
n4:cisloPeriodika
752514
n4:dodaniDat
n11:2014
n4:domaciTvurceVysledku
n7:5185599 n7:6842690 n7:1076329 n7:5461162 n7:3270505 n7:2785056 n7:6990541 n7:7358946 n7:8449333
n4:druhVysledku
n18:J
n4:duvernostUdaju
n10:S
n4:entitaPredkladatele
n12:predkladatel
n4:idSjednocenehoVysledku
79495
n4:idVysledku
RIV/86652036:_____/13:00420825
n4:jazykVysledku
n16:eng
n4:klicovaSlova
PROTEIN-PROTEIN INTERACTIONS; COMPUTATIONAL DESIGN; BIOLOGICAL-ACTIVITY
n4:klicoveSlovo
n9:PROTEIN-PROTEIN%20INTERACTIONS n9:COMPUTATIONAL%20DESIGN n9:BIOLOGICAL-ACTIVITY
n4:kodStatuVydavatele
US - Spojené státy americké
n4:kontrolniKodProRIV
[FDA207B4994B]
n4:nazevZdroje
BIOMED RESEARCH INTERNATIONAL
n4:obor
n17:EI
n4:pocetDomacichTvurcuVysledku
9
n4:pocetTvurcuVysledku
9
n4:projekt
n20:GAP305%2F10%2F2184
n4:rokUplatneniVysledku
n11:2013
n4:tvurceVysledku
Schneider, Bohdan Mikulecký, Pavel Kuchař, Milan Černý, Jiří Biedermannová, Lada Malý, Petr Vondrášek, Jiří Petroková, Hana Šebo, Peter
n4:wos
000325638500001
n4:zamer
n15:AV0Z50520701
s:issn
2314-6133
s:numberOfPages
10
n19:doi
10.1155/2013/752514