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Three-DimensionalWindow Analysis forDetecting PositiveSelection atStructural Regions ofProteins Yoshiyuki Suzuki2004 год

Three-Dimensional Window Analysis for Detecting Positive Selection at Structural Regions of Proteins
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Аннотация: 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 selection 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 α-carbon of an amino acid site. The window size is the radius of the sphere. The sites whose α-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 not only to be more sensitive than single-site analysis and one-dimensional window analysis but also to provide 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.
Год издания: 2004
Авторы: Yoshiyuki Suzuki
Издательство: Oxford University Press
Источник: Molecular Biology and Evolution
Ключевые слова: RNA and protein synthesis mechanisms, Bacteriophages and microbial interactions, RNA modifications and cancer
Другие ссылки: Molecular Biology and Evolution (HTML)
PubMed (HTML)