PREDICTION OF PROTEIN-PROTEIN COMPLEX STRUCTURES

被引：0

作者：

Kanamori, Eiji ^{[1
]}

Murakami, Yoichi ^{[2
]}

Sarmiento, Joy ^{[3
]}

Liang, Shide ^{[3
]}

Standley, Daron M. ^{[3
]}

Shirota, Matsuyuki ^{[4
]}

Kinoshita, Kengo ^{[4
]}

Tsuchiya, Yuko ^{[5
]}

Higo, Junichi ^{[5
]}

Nakamura, Haruki ^{[5
]}

机构：

[1] Hitachi Solut Ltd, 1-1-43 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan

[2] Natl Inst Biomed Innovat, Osaka 5670085, Japan

[3] Osaka Univ, Immunol Frontier Res Ctr, Suita, Osaka 5650871, Japan

[4] Tohoku Univ, Grad Sch Informat Sci, Sendai, Miyagi 9808579, Japan

[5] Osaka Univ, Inst Prot Res, Suita, Osaka 5650871, Japan

来源：

BIOMOLECULAR FORMS AND FUNCTIONS: A CELEBRATION OF 50 YEARS OF THE RAMACHANDRAN MAP | 2013年

基金：

日本学术振兴会;

关键词：

MULTICANONICAL ENSEMBLE; MOLECULAR-SURFACES; DOCKING; EVOLUTION; PEPTIDES; DYNAMICS; LESSONS; SITES; CAPRI;

D O I：

暂无

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

A docking method, surFit, was developed that automatically and semi-automatically docks a pair of protein molecular surfaces. It performs the following six procedures: Binding site prediction, Rigid surface docking, Coarse scoring, Refinement, Precise scoring, and Re-refinement by molecular dynamics. simulation. The first four procedures have been automated and implemented in the webserver surFit. The current protocol successfully built many acceptable predicted complex structures with high qualities for the recent CAPRI targets, and accurately estimated the solvent water positions at the interface for CAPRI Target 47. To reveal the complex structure of an intrinsically disordered protein (IDP) with its partner receptor protein, enhanced sampling computations were performed to simulate the free energy landscapes of the IDP with and without the receptor. Consequently, both induced fitting and population shift mechanisms were observed for the NRSF-Sin3 system.

引用

页码：160 / 172

页数：13

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