title: Profile comparison revealed deviation from structural constraint at the positively selected sites.
abstract: The amino acid substitutions at a site are affected by mixture of various constraints. It is also known that the amino acid substitutions are accelerated at sites under positive selection. However, the relationship between the substitutions at positively selected sites and the constraints has not been thoroughly examined. The advances in computational biology have enabled us to divide the mixture of the constraints into the structural constraint and the remainings by using the amino acid sequences and the tertiary structures, which is expressed as the deviation of the mixture of constraints from the structural constraint. Here, two types of profiles, or matrices with the size of 20 x (site length), are compared. One of the profiles represents the mixture of constraints, and is generated from a multiple amino acid sequence alignment, whereas the other is designed to represent the structural constraints. We applied the profile comparison method to proteins under positive selection to examine the relationship between the positive selection and constraints. The results suggested that the constraint at a site under positive selection tends to be deviated from the structural constraint at the site.
authors.affiliation: Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan. Electronic address: hiroyuki.oda1983@gmail.com.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Oda
authors.affiliation: Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya City, Aichi 464-8601, Japan.
authors.forename: Motonori
authors.initials: M
authors.lastname: Ota
authors.affiliation: Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Toh
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics*; D000596:Amino Acids / Q000235:genetics*; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D020134:Catalytic Domain / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004798:Enzymes / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D000072417:Protein Domains; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D000596:Amino Acids; D004798:Enzymes; D011506:Proteins
keywords: 3D-profile; Molecular evolution; Position specific scoring matrices; Positive selection