Using Amino Acid Correlation and Community Detection Algorithms to Identify Functional Determinants in Protein Families

Autor(es)

Bleicher, Lucas ^[1] ; Lemke, Ney ^[2] ; Garratt, Richard Charles ^[3]

Afiliação do(s) autor(es)

^[1] Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Bioquim & Imunol, Belo Horizonte, MG - Brazil

^[2] Univ Estadual Paulista, Dept Fis & Biofis, Botucatu, SP - Brazil

^[3] Univ Sao Paulo, Inst Fis Sao Carlos, Dept Fis & Informat, Sao Carlos, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: PLoS One; v. 6, n. 12, p. e27786, 2011.
• Citações Web of Science: 17

Resumo

Correlated mutation analysis has a long history of interesting applications, mostly in the detection of contact pairs in protein structures. Based on previous observations that, if properly assessed, amino acid correlation data can also provide insights about functional sub-classes in a protein family, we provide a complete framework devoted to this purpose. An amino acid specific correlation measure is proposed, which can be used to build networks summarizing all correlation and anti-correlation patterns in a protein family. These networks can be submitted to community structure detection algorithms, resulting in subsets of correlated amino acids which can be further assessed by specific parameters and procedures that provide insight into the relationship between different communities, the individual importance of community members and the adherence of a given amino acid sequence to a given community. By applying this framework to three protein families with contrasting characteristics (the Fe/Mn-superoxide dismutases, the peroxidase-catalase family and the C-type lysozyme/alpha-lactalbumin family), we show how our method and the proposed parameters and procedures are related to biological characteristics observed in these protein families, highlighting their potential use in protein characterization and gene annotation. (AU)

• Processo FAPESP: 08/58734-1 - Desenvolvimento e formalizacao da tecnica de analise de acoplamento estatistico e sua aplicacao ao estudo de familias de proteinas em conjunto com estudos estruturais
• Beneficiário: Lucas Bleicher
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 98/14138-2 - Center for Structural Molecular Biotechnology
• Beneficiário: Glaucius Oliva
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs