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The human "magnesome": detecting magnesium binding sites on human proteins

BACKGROUND: Magnesium research is increasing in molecular medicine due to the relevance of this ion in several important biological processes and associated molecular pathogeneses. It is still difficult to predict from the protein covalent structure whether a human chain is or not involved in magnes...

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Autores principales: Piovesan, Damiano, Profiti, Giuseppe, Martelli, Pier Luigi, Casadio, Rita
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439678/
https://www.ncbi.nlm.nih.gov/pubmed/23095498
http://dx.doi.org/10.1186/1471-2105-13-S14-S10
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author Piovesan, Damiano
Profiti, Giuseppe
Martelli, Pier Luigi
Casadio, Rita
author_facet Piovesan, Damiano
Profiti, Giuseppe
Martelli, Pier Luigi
Casadio, Rita
author_sort Piovesan, Damiano
collection PubMed
description BACKGROUND: Magnesium research is increasing in molecular medicine due to the relevance of this ion in several important biological processes and associated molecular pathogeneses. It is still difficult to predict from the protein covalent structure whether a human chain is or not involved in magnesium binding. This is mainly due to little information on the structural characteristics of magnesium binding sites in proteins and protein complexes. Magnesium binding features, differently from those of other divalent cations such as calcium and zinc, are elusive. Here we address a question that is relevant in protein annotation: how many human proteins can bind Mg(2+)? Our analysis is performed taking advantage of the recently implemented Bologna Annotation Resource (BAR-PLUS), a non hierarchical clustering method that relies on the pair wise sequence comparison of about 14 millions proteins from over 300.000 species and their grouping into clusters where annotation can safely be inherited after statistical validation. RESULTS: After cluster assignment of the latest version of the human proteome, the total number of human proteins for which we can assign putative Mg binding sites is 3,751. Among these proteins, 2,688 inherit annotation directly from human templates and 1,063 inherit annotation from templates of other organisms. Protein structures are highly conserved inside a given cluster. Transfer of structural properties is possible after alignment of a given sequence with the protein structures that characterise a given cluster as obtained with a Hidden Markov Model (HMM) based procedure. Interestingly a set of 370 human sequences inherit Mg(2+ )binding sites from templates sharing less than 30% sequence identity with the template. CONCLUSION: We describe and deliver the "human magnesome", a set of proteins of the human proteome that inherit putative binding of magnesium ions. With our BAR-hMG, 251 clusters including 1,341 magnesium binding protein structures corresponding to 387 sequences are sufficient to annotate some 13,689 residues in 3,751 human sequences as "magnesium binding". Protein structures act therefore as three dimensional seeds for structural and functional annotation of human sequences. The data base collects specifically all the human proteins that can be annotated according to our procedure as "magnesium binding", the corresponding structures and BAR+ clusters from where they derive the annotation (http://bar.biocomp.unibo.it/mg).
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spelling pubmed-34396782012-09-17 The human "magnesome": detecting magnesium binding sites on human proteins Piovesan, Damiano Profiti, Giuseppe Martelli, Pier Luigi Casadio, Rita BMC Bioinformatics Research BACKGROUND: Magnesium research is increasing in molecular medicine due to the relevance of this ion in several important biological processes and associated molecular pathogeneses. It is still difficult to predict from the protein covalent structure whether a human chain is or not involved in magnesium binding. This is mainly due to little information on the structural characteristics of magnesium binding sites in proteins and protein complexes. Magnesium binding features, differently from those of other divalent cations such as calcium and zinc, are elusive. Here we address a question that is relevant in protein annotation: how many human proteins can bind Mg(2+)? Our analysis is performed taking advantage of the recently implemented Bologna Annotation Resource (BAR-PLUS), a non hierarchical clustering method that relies on the pair wise sequence comparison of about 14 millions proteins from over 300.000 species and their grouping into clusters where annotation can safely be inherited after statistical validation. RESULTS: After cluster assignment of the latest version of the human proteome, the total number of human proteins for which we can assign putative Mg binding sites is 3,751. Among these proteins, 2,688 inherit annotation directly from human templates and 1,063 inherit annotation from templates of other organisms. Protein structures are highly conserved inside a given cluster. Transfer of structural properties is possible after alignment of a given sequence with the protein structures that characterise a given cluster as obtained with a Hidden Markov Model (HMM) based procedure. Interestingly a set of 370 human sequences inherit Mg(2+ )binding sites from templates sharing less than 30% sequence identity with the template. CONCLUSION: We describe and deliver the "human magnesome", a set of proteins of the human proteome that inherit putative binding of magnesium ions. With our BAR-hMG, 251 clusters including 1,341 magnesium binding protein structures corresponding to 387 sequences are sufficient to annotate some 13,689 residues in 3,751 human sequences as "magnesium binding". Protein structures act therefore as three dimensional seeds for structural and functional annotation of human sequences. The data base collects specifically all the human proteins that can be annotated according to our procedure as "magnesium binding", the corresponding structures and BAR+ clusters from where they derive the annotation (http://bar.biocomp.unibo.it/mg). BioMed Central 2012-09-07 /pmc/articles/PMC3439678/ /pubmed/23095498 http://dx.doi.org/10.1186/1471-2105-13-S14-S10 Text en Copyright ©2012 Piovesan et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Piovesan, Damiano
Profiti, Giuseppe
Martelli, Pier Luigi
Casadio, Rita
The human "magnesome": detecting magnesium binding sites on human proteins
title The human "magnesome": detecting magnesium binding sites on human proteins
title_full The human "magnesome": detecting magnesium binding sites on human proteins
title_fullStr The human "magnesome": detecting magnesium binding sites on human proteins
title_full_unstemmed The human "magnesome": detecting magnesium binding sites on human proteins
title_short The human "magnesome": detecting magnesium binding sites on human proteins
title_sort human "magnesome": detecting magnesium binding sites on human proteins
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439678/
https://www.ncbi.nlm.nih.gov/pubmed/23095498
http://dx.doi.org/10.1186/1471-2105-13-S14-S10
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