Web of Science: 17 cites, Scopus: 18 cites, Google Scholar: cites,
GPCRtm : An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors
Rios Azuara, Santiago (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Fernandez, Marta F. (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Caltabiano, Gianluigi 1978- (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Campillo Grau, María Mercedes (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Pardo Carrasco, Leonardo (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Gonzalez, Angel (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)

Data: 2015
Resum: Protein sequence alignments and database search methods use standard scoring matrices calculated from amino acid substitution frequencies in general sets of proteins. These general-purpose matrices are not optimal to align accurately sequences with marked compositional biases, such as hydrophobic transmembrane regions found in membrane proteins. In this work, an amino acid substitution matrix (GPCRtm) is calculated for the membrane spanning segments of the G protein-coupled receptor (GPCR) rhodopsin family; one of the largest transmembrane protein family in humans with great importance in health and disease. The GPCRtm matrix reveals the amino acid compositional bias distinctive of the GPCR rhodopsin family and differs from other standard substitution matrices. These membrane receptors, as expected, are characterized by a high content of hydrophobic residues with regard to globular proteins. On the other hand, the presence of polar and charged residues is higher than in average membrane proteins, displaying high frequencies of replacement within themselves. Analysis of amino acid frequencies and values obtained from the GPCRtm matrix reveals patterns of residue replacements different from other standard substitution matrices. GPCRs prioritize the reactivity properties of the amino acids over their bulkiness in the transmembrane regions. A distinctive role is that charged and polar residues seem to evolve at different rates than other amino acids. This observation is related to the role of the transmembrane bundle in the binding of ligands, that in many cases involve electrostatic and hydrogen bond interactions. This new matrix can be useful in database search and for the construction of more accurate sequence alignments of GPCRs. The online version of this article (doi:10. 1186/s12859-015-0639-4) contains supplementary material, which is available to authorized users.
Ajuts: Ministerio de Economía y Competitividad SAF2013-48271-C2-2-R
Drets: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Llengua: Anglès
Document: Article ; recerca ; Versió publicada
Matèria: Amino acid substitution matrix ; G protein-coupled receptors ; GPCR ; Transmembrane ; Evolution ; Membrane protein
Publicat a: BMC bioinformatics, Vol. 16 (July 2015) , art. 2016, ISSN 1471-2105

DOI: 10.1186/s12859-015-0639-4
PMID: 26134144

Published version
11 p, 3.1 MB

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