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Author:

Sun, TG (Sun, TG.) | Hu, JP (Hu, JP.) | Li, CH (Li, CH.) | Chen, WZ (Chen, WZ.) | Wang, CX (Wang, CX.)

Indexed by:

Scopus SCIE

Abstract:

Glutamine-binding protein (GlnBP) is one of the periplastic binding proteins from Gram-negative bacteria, whose crystal structure has been solved in both open and closed forms. GlnBP shares the common architecture with the other periplastic binding proteins composed of two domains linked by a hinge region. Molecular dynamics (MD) simulations were performed with the GROMOS96 program package to study the characters of GlnBP in both ligand-free and ligand-binding states. We also expected to provide some useful hints for understanding the mechanisms of inter-domain motions and ligand binding by analyzing the flexibility of the GlnBP. MD simulations reproduced most of the key hydrogen bonds observed in crystal structure. Binding of the ligand induced the formation of some stable hydrogen bonds, which made the hinge strands more rigid and further stabilized the complex. The analysis of MD trajectories of 2 ns showed that the open-close motion was coupled with inter-domain twisting motion in the ligand-free state, and some loop regions in the small domain contributed primarily to the flexibility of this protein while the main secondary structures maintained the fairly stable conformation. These motions seemed to shed some light on the mechanisms of ligand binding and releasing. All the results kept in good consistence with experimental data. (c) 2005 Elsevier B.V. All rights reserved.

Keyword:

flexibility MD simulation open-close motion glutamine-binding protein

Author Community:

  • [ 1 ] Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100022, Peoples R China

Reprint Author's Address:

  • [Wang, CX]Beijing Univ Technol, Coll Life Sci & Bioengn, Beijing 100022, Peoples R China

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Source :

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

ISSN: 0166-1280

Year: 2005

Issue: 1-3

Volume: 725

Page: 9-16

JCR Journal Grade:3

Cited Count:

WoS CC Cited Count: 15

SCOPUS Cited Count: 15

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 9

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