How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

被引：46

作者：

Maisuradze, Gia G. ^{[1
]}

Liwo, Adam ^{[1
]}

Scheraga, Harold A. ^{[1
]}

机构：

[1] Cornell Univ, Baker Lab Chem & Chem Biol, Ithaca, NY 14853 USA

来源：

PHYSICAL REVIEW LETTERS | 2009年 / 102卷 / 23期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

SIMULATIONS; MODEL;

D O I：

10.1103/PhysRevLett.102.238102

中图分类号：

O4 [物理学];

学科分类号：

0702 ;

摘要：

The molecular dynamics trajectories of protein folding or unfolding, generated with the coarse-grained united-residue force field for the B domain of staphylococcal protein A, were analyzed by principal component analysis (PCA). The folding or unfolding process was examined by using free-energy landscapes (FELs) in PC space. By introducing a novel multidimensional FEL, it was shown that the low-dimensional FELs are not always sufficient for the description of folding or unfolding processes. Similarities between the topographies of FELs along low- and high-indexed principal components were observed.

引用

页数：4

共 20 条

[1] Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis [J].

Altis, Alexandros ;

Otten, Moritz ;

Nguyen, Phuong H. ;

Hegger, Rainer ;

Stock, Gerhard .

JOURNAL OF CHEMICAL PHYSICS, 2008, 128 (24)

[2] FIRST-PRINCIPLES CALCULATION OF THE FOLDING FREE-ENERGY OF A 3-HELIX BUNDLE PROTEIN [J].

BOCZKO, EM ;

BROOKS, CL .

SCIENCE, 1995, 269 (5222) :393-396

[3] Statistical thermodynamics - Taking a walk on a landscape [J].

Brooks, CL ;

Onuchic, JN ;

Wales, DJ .

SCIENCE, 2001, 293 (5530) :612-613

[4] Mass fractal dimension and the compactness of proteins [J].

Enright, MB ;

Leitner, DM .

PHYSICAL REVIEW E, 2005, 71 (01)

[5] THE ENERGY LANDSCAPES AND MOTIONS OF PROTEINS [J].

FRAUENFELDER, H ;

SLIGAR, SG ;

WOLYNES, PG .

SCIENCE, 1991, 254 (5038) :1598-1603

[6] 3-DIMENSIONAL SOLUTION STRUCTURE OF THE B-DOMAIN OF STAPHYLOCOCCAL PROTEIN-A - COMPARISONS OF THE SOLUTION AND CRYSTAL-STRUCTURES [J].

GOUDA, H ;

TORIGOE, H ;

SAITO, A ;

SATO, M ;

ARATA, Y ;

SHIMADA, I .

BIOCHEMISTRY, 1992, 31 (40) :9665-9672

[7] How complex is the dynamics of peptide folding? [J].

Hegger, Rainer ;

Altis, Alexandros ;

Nguyen, Phuong H. ;

Stock, Gerhard .

PHYSICAL REVIEW LETTERS, 2007, 98 (02)

[8] Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins [J].

Hyeon, Changbong ;

Thirumalai, D. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2008, 130 (05) :1538-+

[9]

JOLLIFFE IT, 2002, PRINCIPAL COMPONENT, P23402

[10]

Kitao A, 1998, PROTEINS, V33, P496, DOI 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.3.CO

← 1 2 →