using amino acid correlation and community detection algorithms to identify functional determinants in protein families使用氨基酸相关性和社区检测算法识别功能蛋白质家庭的决定因素.pdfVIP

Using Amino Acid Correlation and Community Detection Algorithms to Identify Functional Determinants in Protein Families 1 2 3 Lucas Bleicher *, Ney Lemke , Richard Charles Garratt ´ ˆ ´ 1 Departamento de Bioquımica e Imunologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, 2 Departamento ´ ´ ˜ ´ ´ ´ ˜ de Fısica e Biofısica, Universidade Estadual Paulista, Botucatu, Sao Paulo, Brazil, 3 Departamento de Fısica e Informatica, Instituto de Fısica de Sao Carlos, Universidade de ˜ ˜ ˜ Sao Paulo, Sao Carlos, Sao Paulo, Brazil Abstract 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 character