Stabilizing effect of knots on proteins

被引：125

作者：

Sulkowska, Joanna I. ^{[1
,2
]}

Sulkowski, Piotr ^{[3
,4
,5
]}

Szymczak, P. ^{[6
]}

Cieplak, Marek ^{[1
]}

机构：

[1] Polish Acad Sci, Inst Phys, PL-02668 Warsaw, Poland

[2] Univ Calif San Diego, CTBP, La Jolla, CA 92037 USA

[3] Univ Bonn, Inst Phys, D-53115 Bonn, Germany

[4] Bethe Ctr Theoret Phys, D-53115 Bonn, Germany

[5] Soltan Inst Nucl Studies, PL-00681 Warsaw, Poland

[6] Univ Warsaw, Inst Theoret Phys, PL-00681 Warsaw, Poland

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2008年 / 105卷 / 50期

基金：

美国国家科学基金会;

关键词：

molecular dynamics; stretching; topology; atomic force microscope;

D O I：

10.1073/pnas.0805468105

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Molecular dynamics studies within a coarse-grained, structurebased model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.

引用

页码：19714 / 19719

页数：6

共 37 条

[1] Chemistry on a single protein, vascular cell adhesion molecule-1, during forced unfolding [J].

Bhasin, N ;

Carl, P ;

Harper, S ;

Feng, G ;

Lu, H ;

Speicher, DW ;

Discher, DE .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2004, 279 (44) :45865-45874

[2] Forced unfolding modulated by disulfide bonds in the Ig domains of a cell adhesion molecule [J].

Carl, P ;

Kwok, CH ;

Manderson, G ;

Speicher, DW ;

Discher, DE .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (04) :1565-1570

[3] Thermal effects in stretching of go-like models of titin and secondary structures [J].

Cieplak, M ;

Hoang, TX ;

Robbins, MO .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2004, 56 (02) :285-297

[4] Stretching of proteins in the entropic limit [J].

Cieplak, M ;

Hoang, TX ;

Robbins, MO .

PHYSICAL REVIEW E, 2004, 69 (01) :4

[5]

CLEPLAK M, 2005, J CHEM PHYS, V123

[6] Thermal, chemical, and enzymatic stability of the cyclotide kalata B1: The importance of the cyclic cystine knot [J].

Colgrave, ML ;

Craik, DJ .

BIOCHEMISTRY, 2004, 43 (20) :5965-5975

[7] Topological frustration and the folding of interleukin-1β [J].

Gosavi, S ;

Chavez, LL ;

Jennings, PA ;

Onuchic, JN .

JOURNAL OF MOLECULAR BIOLOGY, 2006, 357 (03) :986-996

[8] Extracting function from a β-trefoil folding motif [J].

Gosavi, Shachi ;

Whitford, Paul C. ;

Jennings, Patricia A. ;

Onuchic, Jose N. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (30) :10384-10389

[9] Utility library for structural bioinformatics [J].

Gront, Dominik ;

Kolinski, Andrzej .

BIOINFORMATICS, 2008, 24 (04) :584-585

[10] Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates [J].

Gront, Dominik ;

Kmiecik, Sebastian ;

Kolinski, Andrzej .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2007, 28 (09) :1593-1597

← 1 2 3 4 →