System Approach for Building of Calcium-Binding Sites in Proteins

System Approach for Building of Calcium-Binding Sites in Proteins

We introduce five new local metal cation (first of all, Ca<sup>2+</sup>) recognition units in proteins: Clamp<sub>n,(n−2)</sub>, Clamp<sub>n,(n−1)</sub>, Clamp<sub>n,n</sub>, Clamp<sub>n,(n+1)</sub> and Clamp<sub>n,(n+2)</sub>....

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Main Authors: Alexander I. Denesyuk, Sergei E. Permyakov, Mark S. Johnson, Konstantin Denessiouk, Eugene A. Permyakov
Format: Article
Language:English
Published: MDPI AG 2020-04-01
Series:Biomolecules
Subjects:
system approach
protein structure
cation
calcium
sequence-structure motifs
building kit
Online Access:https://www.mdpi.com/2218-273X/10/4/588
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spelling doaj-a060c782615942bfaaaf8340e7a76e3f2020-11-25T03:25:35ZengMDPI AGBiomolecules2218-273X2020-04-011058858810.3390/biom10040588System Approach for Building of Calcium-Binding Sites in ProteinsAlexander I. Denesyuk0Sergei E. Permyakov1Mark S. Johnson2Konstantin Denessiouk3Eugene A. Permyakov4Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, RussiaInstitute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, RussiaStructural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, FinlandStructural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, FinlandInstitute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, RussiaWe introduce five new local metal cation (first of all, Ca<sup>2+</sup>) recognition units in proteins: Clamp<sub>n,(n−2)</sub>, Clamp<sub>n,(n−1)</sub>, Clamp<sub>n,n</sub>, Clamp<sub>n,(n+1)</sub> and Clamp<sub>n,(n+2)</sub>. In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca<sup>2+</sup>-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.https://www.mdpi.com/2218-273X/10/4/588system approachprotein structurecationcalciumsequence-structure motifsbuilding kit
collection DOAJ
language English
format Article
sources DOAJ
author Alexander I. Denesyuk
Sergei E. Permyakov
Mark S. Johnson
Konstantin Denessiouk
Eugene A. Permyakov
spellingShingle Alexander I. Denesyuk
Sergei E. Permyakov
Mark S. Johnson
Konstantin Denessiouk
Eugene A. Permyakov
System Approach for Building of Calcium-Binding Sites in Proteins
Biomolecules
system approach
protein structure
cation
calcium
sequence-structure motifs
building kit
author_facet Alexander I. Denesyuk
Sergei E. Permyakov
Mark S. Johnson
Konstantin Denessiouk
Eugene A. Permyakov
author_sort Alexander I. Denesyuk
title System Approach for Building of Calcium-Binding Sites in Proteins
title_short System Approach for Building of Calcium-Binding Sites in Proteins
title_full System Approach for Building of Calcium-Binding Sites in Proteins
title_fullStr System Approach for Building of Calcium-Binding Sites in Proteins
title_full_unstemmed System Approach for Building of Calcium-Binding Sites in Proteins
title_sort system approach for building of calcium-binding sites in proteins
publisher MDPI AG
series Biomolecules
issn 2218-273X
publishDate 2020-04-01
description We introduce five new local metal cation (first of all, Ca<sup>2+</sup>) recognition units in proteins: Clamp<sub>n,(n−2)</sub>, Clamp<sub>n,(n−1)</sub>, Clamp<sub>n,n</sub>, Clamp<sub>n,(n+1)</sub> and Clamp<sub>n,(n+2)</sub>. In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca<sup>2+</sup>-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.
topic system approach
protein structure
cation
calcium
sequence-structure motifs
building kit
url https://www.mdpi.com/2218-273X/10/4/588
work_keys_str_mv AT alexanderidenesyuk systemapproachforbuildingofcalciumbindingsitesinproteins
AT sergeiepermyakov systemapproachforbuildingofcalciumbindingsitesinproteins
AT marksjohnson systemapproachforbuildingofcalciumbindingsitesinproteins
AT konstantindenessiouk systemapproachforbuildingofcalciumbindingsitesinproteins
AT eugeneapermyakov systemapproachforbuildingofcalciumbindingsitesinproteins
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