Induced fit for mRNA/TIS11d complex

被引：32

作者：

Qin, Fang ^{[1
]}

Chen, Yue ^{[1
]}

Li, Yi-Xue ^{[2
]}

Chen, Hai-Feng ^{[1
,2
]}

机构：

[1] Shanghai Jiao Tong Univ, Coll Life Sci & Biotechnol, Shanghai 200240, Peoples R China

[2] Shanghai Ctr Bioinformat Technol, Shanghai 200235, Peoples R China

来源：

JOURNAL OF CHEMICAL PHYSICS | 2009年 / 131卷 / 11期

基金：

中国国家自然科学基金;

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; ZINC-FINGER PROTEINS; RIBONUCLEASE-P-PROTEIN; AU-RICH ELEMENT; TRANSITION-STATE; SECONDARY STRUCTURE; COUPLED BINDING; MESSENGER-RNA; RECOGNITION; MECHANISMS;

D O I：

10.1063/1.3224126

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

TIS11d tandem zinc finger (TZF) domain can bind the class II AU-rich element of target mRNA and regulate mRNA turnover by promoting or inhibiting degradation. NMR spectra show that TIS11d(TZF) undergoes a transition from disordered to well folded upon binding to Zn and mRNA. To gain an insight into the mechanism, we have performed explicit-solvent molecular dynamics simulations (MD) for both bound and apo-TIS11d(TZF) to study the interdependence of binding and folding in the mRNA-TIS11d(TZF) complex. These results are in qualitative agreement with NMR experiment. Furthermore, this method could be used to other study about protein folding upon ligand binding. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3224126]

引用

页数：6

共 35 条

[1] MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].

BERENDSEN, HJC ;

POSTMA, JPM ;

VANGUNSTEREN, WF ;

DINOLA, A ;

HAAK, JR .

JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690

[2] How do proteins interact? [J].

Boehr, David D. ;

Wright, Peter E. .

SCIENCE, 2008, 320 (5882) :1429-1430

[3] Zinc finger proteins: Getting a grip on RNA [J].

Brown, RS .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2005, 15 (01) :94-98

[4] MOLECULAR-DYNAMICS SIMULATION OF PROTEIN DENATURATION - SOLVATION OF THE HYDROPHOBIC CORES AND SECONDARY STRUCTURE OF BARNASE [J].

CAFLISCH, A ;

KARPLUS, M .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (05) :1746-1750

[5] Feedback inhibition of macrophage tumor necrosis factor-α production by tristetraprolin [J].

Carballo, E ;

Lai, WS ;

Blackshear, PJ .

SCIENCE, 1998, 281 (5379) :1001-1005

[6] Mechanism of coupled folding and binding in the siRNA-PAZ complex [J].

Chen, Hai-Feng .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (08) :1360-1368

[7] Aggregation mechanism investigation of the GIFQINS cross-β amyloid fibril [J].

Chen, Hai-Feng .

COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2009, 33 (01) :41-45

[8] Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations [J].

Chong, LT ;

Snow, CD ;

Rhee, YM ;

Pande, VS .

JOURNAL OF MOLECULAR BIOLOGY, 2005, 345 (04) :869-878

[9] PARTICLE MESH EWALD - AN N.LOG(N) METHOD FOR EWALD SUMS IN LARGE SYSTEMS [J].

DARDEN, T ;

YORK, D ;

PEDERSEN, L .

JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (12) :10089-10092

[10] Ensemble versus single-molecule protein unfolding [J].

Day, R ;

Daggett, V .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (38) :13445-13450

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