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MBE Advance Access published online on September 8, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh249
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted August 30, 2004

Research Article

Three-dimensional Window Analysis for Detecting Positive Selection at Structural Regions of proteins

Yoshiyuki Suzuki 1*

1 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima-shi, Shizuoka-ken 411-8540, Japan

* To whom correspondence should be addressed. E-mail: yossuzuk{at}lab.nig.ac.jp.


  Abstract

Detection of natural selection operating at the amino acid sequence level is important in the study of molecular evolution. Single site analysis and one-dimensional window analysis can be used to detect selection when the biological functions of amino acid sites are unknown. Single site analysis is useful when selection operates more or less constantly over evolutionary time, but less so when it operates temporarily. One-dimensional window analysis is more sensitive than single site analysis when the functions of amino acid sites in close proximity in the linear sequence are similar although this is not always the case. Here I present a three-dimensional window analysis method for detecting selection given the three-dimensional structure of the protein of interest. In the three-dimensional structure, the window is defined as the sphere centered on the {alpha}-carbon of an amino acid site. The window size is the radius of the sphere. The sites whose {alpha}-carbons are included in the window are grouped for the neutrality test. The window is moved within the three-dimensional structure by sequentially moving the central site along the primary amino acid sequence. To detect positive selection, it may also be useful to group the surface-exposed sites in the window separately. Three-dimensional window analysis appears to be not only more sensitive than single site analysis and one-dimensional window analysis, but also provides similar specificity for inferring positive selection in the analyses of the hemagglutinin and neuraminidase genes of human influenza A viruses. This method, however, may fail to detect selection when it operates only on a particular site, in which case single site analysis may be preferred although a large number of sequences is required.

Keywords: Three-dimensional structure; window analysis; positive selection; human influenza A virus; hemagglutinin; neuraminidase.
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