System Approach for Building of Calcium-Binding Sites in Proteins

Alexander I. Denesyuk; Sergei E. Permyakov; Mark S. Johnson; Konstantin Denessiouk; Eugene A. Permyakov

doi:10.3390/biom10040588

System Approach for Building of Calcium-Binding Sites in Proteins

Alexander I. Denesyuk, Sergei E. Permyakov, Mark S. Johnson, Konstantin Denessiouk, Eugene A. Permyakov

Research output: Contribution to journal › Article › Scientific › peer-review

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Abstract

We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n-2), Clampn,(n-1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). 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 "Ca2+-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.

Original language	English
Article number	588
Journal	Biomolecules
Volume	10
Issue number	4
DOIs	https://doi.org/10.3390/biom10040588
Publication status	Published - 2020
MoE publication type	A1 Journal article-refereed

Keywords

system approach
building kit
calcium
cation
InFlames

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10.3390/biom10040588

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title = "System Approach for Building of Calcium-Binding Sites in Proteins",

abstract = "We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n-2), Clampn,(n-1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). 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 {"}Ca2+-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. ",

keywords = "system approach, building kit, calcium, cation, InFlames",

author = "Denesyuk, {Alexander I.} and Permyakov, {Sergei E.} and Johnson, {Mark S.} and Konstantin Denessiouk and Permyakov, {Eugene A.}",

year = "2020",

doi = "10.3390/biom10040588",

language = "English",

volume = "10",

journal = "Biomolecules",

issn = "2218-273X",

publisher = "MDPI",

number = "4",

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TY - JOUR

T1 - System Approach for Building of Calcium-Binding Sites in Proteins

AU - Denesyuk, Alexander I.

AU - Permyakov, Sergei E.

AU - Johnson, Mark S.

AU - Denessiouk, Konstantin

AU - Permyakov, Eugene A.

PY - 2020

Y1 - 2020

N2 - We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n-2), Clampn,(n-1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). 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 "Ca2+-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.

AB - We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n-2), Clampn,(n-1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). 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 "Ca2+-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.

KW - system approach

KW - building kit

KW - calcium

KW - cation

KW - InFlames

U2 - 10.3390/biom10040588

DO - 10.3390/biom10040588

M3 - Article

SN - 2218-273X

VL - 10

JO - Biomolecules

JF - Biomolecules

IS - 4

M1 - 588

ER -

System Approach for Building of Calcium-Binding Sites in Proteins

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Keywords

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