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

Made available in DSpace on 2013-08-28T14:09:29Z (GMT). No. of bitstreams: 1 WOS000298666200001.pdf: 402150 bytes, checksum: 3723ce8567931f389f45074a49611911 (MD5) Made available in DSpace on 2013-09-30T18:37:20Z (GMT). No. of bitstreams: 2 WOS000298666200001.pdf: 402150 bytes, checksum: 3723ce8567931f389f45074a49611911 (MD5) WOS000298666200001.pdf.txt: 56655 bytes, checksum: 10d0e581654ecca834117e332f3f69ca (MD5) Previous issue date: 2011-12-20 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T13:49:40Z No. of bitstreams: 2 WOS000298666200001.pdf: 402150 bytes, checksum: 3723ce8567931f389f45074a49611911 (MD5) WOS000298666200001.pdf.txt: 56655 bytes, checksum: 10d0e581654ecca834117e332f3f69ca (MD5) Made available in DSpace on 2014-05-20T13:49:40Z (GMT). No. of bitstreams: 2 WOS000298666200001.pdf: 402150 bytes, checksum: 3723ce8567931f389f45074a49611911 (MD5) WOS000298666200001.pdf.txt: 56655 bytes, checksum: 10d0e581654ecca834117e332f3f69ca (MD5) Previous issue date: 2011-12-20 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 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. Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Bioquim & Imunol, Belo Horizonte, MG, Brazil Univ Estadual Paulista, Dept Fis & Biofis, Botucatu, SP, Brazil Univ São Paulo, Inst Fis Sao Carlos, Dept Fis & Informat, Sao Carlos, SP, Brazil Univ Estadual Paulista, Dept Fis & Biofis, Botucatu, SP, Brazil FAPESP: 08/58734-1 FAPESP: 98/14138-2