Base-sequence-dependent sliding of proteins on DNA

被引：28

作者：

Barbi, M

Place, C

Popkov, V

Salerno, M

机构：

[1] Univ Paris 06, Phys Theor Liquides Lab, F-75252 Paris 05, France

[2] Ecole Normale Super Lyon, Phys Lab, CNRS, UMR 5672, F-69364 Lyon, France

[3] Forschungszentrum Julich, Inst Festkorperforsch, D-52425 Julich, Germany

[4] Univ Salerno, Dipartimento Fis ER Caianiello, I-84081 Baronissi, SA, Italy

[5] Univ Salerno, INFM, I-84081 Baronissi, SA, Italy

来源：

PHYSICAL REVIEW E | 2004年 / 70卷 / 04期

关键词：

D O I：

10.1103/PhysRevE.70.041901

中图分类号：

O35 [流体力学]; O53 [等离子体物理学];

学科分类号：

070204 ; 080103 ; 080704 ;

摘要：

The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.

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页数：6

相关论文

共 22 条

[1]

BARBI M, IN PRESS J BIOL PHYS

[2] DIFFUSION-DRIVEN MECHANISMS OF PROTEIN TRANSLOCATION ON NUCLEIC-ACIDS .1. MODELS AND THEORY [J].

BERG, OG ;

WINTER, RB ;

VONHIPPEL, PH .

BIOCHEMISTRY, 1981, 20 (24) :6929-6948

[3] ANOMALOUS DIFFUSION IN DISORDERED MEDIA - STATISTICAL MECHANISMS, MODELS AND PHYSICAL APPLICATIONS [J].

BOUCHAUD, JP ;

GEORGES, A .

PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 1990, 195 (4-5) :127-293

[4] Physics of protein-DNA interaction [J].

Bruinsma, RF .

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 2002, 313 (1-2) :211-237

[5] Structural basis for initiation of transcription from an RNA polymerase-promoter complex [J].

Cheetham, GMT ;

Jeruzalmi, D ;

Steitz, TA .

NATURE, 1999, 399 (6731) :80-83

[6] Physical constraints and functional characteristics of transcription factor-DNA interaction [J].

Gerland, U ;

Moroz, JD ;

Hwa, T .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (19) :12015-12020

[7] Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling [J].

Gowers, DM ;

Halford, SE .

EMBO JOURNAL, 2003, 22 (06) :1410-1418

[8] Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase [J].

Guthold, M ;

Zhu, XS ;

Rivetti, C ;

Yang, GL ;

Thomson, NH ;

Kasas, S ;

Hansma, HG ;

Smith, B ;

Hansma, PK ;

Bustamante, C .

BIOPHYSICAL JOURNAL, 1999, 77 (04) :2284-2294

[9] How to get from A to B: strategies for analysing protein motion on DNA [J].

Halford, SE ;

Szczelkun, MD .

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2002, 31 (04) :257-267

[10] DIFFUSION IN REGULAR AND DISORDERED LATTICES [J].

HAUS, JW ;

KEHR, KW .

PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 1987, 150 (5-6) :263-406