conformational ensembles of an intrinsically disordered protein pkid with and without a kix domain in explicit solvent investigated by all-atom multicanonical molecular dynamics内在无序蛋白质的构象集合体pkid和没有kix域显式溶剂调查所有原子multicanonical分子动力学.pdfVIP

Biomolecules 2012, 2, 104-121; doi:10.3390/biom2010104 OPEN ACCESS biomolecules ISSN 2218-273X /journal/biomolecules/ Article Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics Koji Umezawa 1, Jinzen Ikebe 2, Mitsunori Takano 1, Haruki Nakamura 2 and Junichi Higo 2,* 1 Graduate School of Advanced Science and Engineering, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan; E-Mails: k.umezawa@aoni.waseda.jp (K.U.); mtkn@waseda.jp (M.T.) 2 Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan; E-Mails: jinzen@protein.osaka-u.ac.jp (J.I.); harukin@protein.osaka-u.ac.jp (H.N.) * Author to whom correspondence should be addressed; E-Mail: higo@protein.osaka-u.ac.jp; Tel.: +81-6-6872-7252; Fax: +81-6-6872-8219. Received: 28 December 2011; in revised form: 11 February 2012 / Accepted: 12 February 2012 / Published: 22 February 2012 Abstract: The phosphorylated kinase-inducible activation domain (pKID) adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, α and α . We performed all-atom multicanonical A B molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensemble