Investigating protein dynamics in collective coordinate space

被引：405

作者：

Kitao, A ^{[1
]}

Go, N ^{[1
]}

机构：

[1] Kyoto Univ, Grad Sch Sci, Dept Chem, Sakyo Ku, Kyoto 6068502, Japan

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 1999年 / 9卷 / 02期

关键词：

D O I：

10.1016/S0959-440X(99)80023-2

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：

Currently, collective coordinates are commonly employed in order to examine protein dynamics. In recent studies, they have been successfully applied to finding functionally relevant motions, to investigating the physical nature of protein dynamics, to sampling of the conformational space and to the analysis of experimental data. Collective coordinates also have other possible applications.

引用

页码：164 / 169

页数：6

共 71 条

[1] OPTIMAL PROTOCOL AND TRAJECTORY VISUALIZATION FOR CONFORMATIONAL SEARCHES OF PEPTIDES AND PROTEINS [J].

ABAGYAN, R ;

ARGOS, P .

JOURNAL OF MOLECULAR BIOLOGY, 1992, 225 (02) :519-532

[2]

Abseher R, 1998, PROTEINS, V31, P370

[3] ESSENTIAL DYNAMICS OF PROTEINS [J].

AMADEI, A ;

LINSSEN, ABM ;

BERENDSEN, HJC .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1993, 17 (04) :412-425

[4] An efficient method for sampling the essential subspace of proteins [J].

Amadei, A ;

Linssen, ABM ;

deGroot, BL ;

vanAalten, DMF ;

Berendsen, HJC .

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1996, 13 (04) :615-625

[5] Characterizing global substates of myoglobin [J].

Andrews, BK ;

Romo, T ;

Clarage, JB ;

Pettitt, BM ;

Phillips, GN .

STRUCTURE, 1998, 6 (05) :587-594

[6] Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential [J].

Bahar, I ;

Atilgan, AR ;

Erman, B .

FOLDING & DESIGN, 1997, 2 (03) :173-181

[7] Principal component analysis and long time protein dynamics [J].

Balsera, MA ;

Wriggers, W ;

Oono, Y ;

Schulten, K .

JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (07) :2567-2572

[8] Protein electron transfer reorganization energy spectrum from normal mode analysis. 1. Theory [J].

Basu, G ;

Kitao, A ;

Kuki, A ;

Go, N .

JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (11) :2076-2084

[9] Protein electron transfer reorganization energy spectrum from normal mode analysis.: 2.: Application to Ru-modified cytochrome c [J].

Basu, G ;

Kitao, A ;

Kuki, A ;

Go, N .

JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (11) :2085-2094

[10] A COLLECTIVE MOTION DESCRIPTION OF THE 3(10-)/ALPHA-HELIX TRANSITION - IMPLICATIONS FOR A NATURAL REACTION COORDINATE [J].

BASU, G ;

KITAO, A ;

HIRATA, F ;

GO, N .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994, 116 (14) :6307-6315

← 1 2 3 4 5 6 7 8 →