title: Hierarchical description and extensive classification of protein structural changes by Motion Tree.
abstract: The structures of the same protein, determined under different conditions, provide clues toward understanding the role of structural changes in the protein's function. Structural changes are usually identified as rigid-body motions, which are defined using a particular threshold of rigidity, such as domain motions. However, each protein actually undergoes motions with various size and magnitude ranges. In this study, to describe protein structural changes more comprehensively, we propose a method based on hierarchical clustering. This method enables the illustration of a wide range of protein motions in a single tree diagram, named the "Motion Tree". We applied the method to 432 proteins exhibiting large structural changes and classified their Motion Trees in terms of the characteristic indices of the trees. This classification of the Motion Trees revealed clear relationships to their protein functions. Especially, complex structural changes are significantly correlated with multi-step protein functions.
authors.affiliation: Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan. Electronic address: rkoike@is.nagoya-u.ac.jp.
authors.forename: Ryotaro
authors.initials: R
authors.lastname: Koike
authors.affiliation: Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
authors.forename: Motonori
authors.initials: M
authors.lastname: Ota
authors.affiliation: Graduate School of Medical Life Science, Yokohama City University, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Kidera
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D030562:Databases, Protein; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism
chemical_list: D011506:Proteins
keywords: ADK; CAP; PDB; Protein Data Bank; SCOP; SI; Size Index; Structural Classification of Proteins; TD; Tree Depth; adenylate kinase; catabolite activator protein; domain motion; loop motion; protein contact map; protein function; protein structural change