Cargando…

Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics

Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties...

Descripción completa

Detalles Bibliográficos
Autores principales: Rosato, Antonio, Valasatava, Yana, Andreini, Claudia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881497/
https://www.ncbi.nlm.nih.gov/pubmed/27153067
http://dx.doi.org/10.3390/ijms17050671
_version_ 1782433971159695360
author Rosato, Antonio
Valasatava, Yana
Andreini, Claudia
author_facet Rosato, Antonio
Valasatava, Yana
Andreini, Claudia
author_sort Rosato, Antonio
collection PubMed
description Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity.
format Online
Article
Text
id pubmed-4881497
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-48814972016-05-27 Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics Rosato, Antonio Valasatava, Yana Andreini, Claudia Int J Mol Sci Review Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity. MDPI 2016-05-04 /pmc/articles/PMC4881497/ /pubmed/27153067 http://dx.doi.org/10.3390/ijms17050671 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Rosato, Antonio
Valasatava, Yana
Andreini, Claudia
Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
title Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
title_full Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
title_fullStr Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
title_full_unstemmed Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
title_short Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
title_sort minimal functional sites in metalloproteins and their usage in structural bioinformatics
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881497/
https://www.ncbi.nlm.nih.gov/pubmed/27153067
http://dx.doi.org/10.3390/ijms17050671
work_keys_str_mv AT rosatoantonio minimalfunctionalsitesinmetalloproteinsandtheirusageinstructuralbioinformatics
AT valasatavayana minimalfunctionalsitesinmetalloproteinsandtheirusageinstructuralbioinformatics
AT andreiniclaudia minimalfunctionalsitesinmetalloproteinsandtheirusageinstructuralbioinformatics