Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.
Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution.
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DOI：
10.1371/journal.pone.0004762
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发表时间：
2009
期刊：
影响因子：
3.7
通讯作者：
Chen L
中科院分区：
文献类型：
--
作者：
Little DY;Chen L
The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1) removes a significant, non-coevolutionary bias and 2) accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations.
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影响因子：
1
作者：
Gouveia-Oliveira, Rodrigo;Pedersen, Anders G
通讯作者：
Pedersen, Anders G
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
3.2
作者：
Buss, KA;Cooper, DR;Hasson, MS
通讯作者：
Hasson, MS
DOI：
10.1007/978-1-59745-398-1_31
发表时间：
2008-01-01
期刊：
FUNCTIONAL PROTEOMICS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Pazos, Florencio;Juan, David;Valencia, Alfonso
通讯作者：
Valencia, Alfonso
DOI：
10.1093/bioinformatics/btn248
发表时间：
2008-07-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Miller CS;Eisenberg D
通讯作者：
Eisenberg D