MPEx: A tool for exploring membrane proteins

被引：217

作者：

Snider, Craig ^{[1
]}

Jayasinghe, Sajith ^{[2
]}

Hristova, Kalina ^{[3
]}

White, Stephen H. ^{[1
]}

机构：

[1] Univ Calif Irvine, Dept Physiol & Biophys, Ctr Biomembrane Syst, Irvine, CA 92697 USA

[2] Calif State Univ San Marcos, Dept Chem & Biochem, San Marcos, CA 92096 USA

[3] Johns Hopkins Univ, Dept Mat Sci & Engn, Baltimore, MD 21218 USA

来源：

PROTEIN SCIENCE | 2009年 / 18卷 / 12期

关键词：

topology; structure prediction; transmembrane helices; hydropathy plots; hydrophobicity; membrane protein explorer; TRANSMEMBRANE HELICES; SOLVATION ENERGIES; CHARGED RESIDUES; HYDROPHOBICITY; PREDICTION; INTERFACES; STABILITY; TOPOLOGY; RECOGNITION; PRINCIPLES;

D O I：

10.1002/pro.256

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：

Hydropathy plot methods form a cornerstone of membrane protein research, especially in the early stages of biochemical and structural characterization. Membrane Protein Explorer (MPEx), described in this article, is a refined and versatile hydropathy-plot software tool for analyzing membrane protein sequences. MPEx is highly interactive and facilitates the characterization and identification of favorable protein transmembrane regions using experiment-based physical and biological hydrophobicity scales. Besides allowing the consequences of sequence mutations to be examined, it provides tools for aiding the design of membrane-active peptides. MPEx is freely available as a Java Web Start application from our web site at http://blanco.biomol.uci.edu/mpex.

引用

页码：2624 / 2628

页数：5

共 24 条

[1] THE SWISS-PROT PROTEIN-SEQUENCE DATA-BANK [J].

BAIROCH, A ;

BOECKMANN, B .

NUCLEIC ACIDS RESEARCH, 1991, 19 :2247-2248

[2] Prediction of membrane-protein topology from first principles [J].

Bernsel, Andreas ;

Viklund, Hakan ;

Falk, Jenny ;

Lindahl, Erik ;

von Heijne, Gunnar ;

Elofsson, Arne .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (20) :7177-7181

[3] The aromatic residues Trp and Phe have different effects on the positioning of a transmembrane helix in the microsomal membrane [J].

Braun, P ;

von Heijne, G .

BIOCHEMISTRY, 1999, 38 (30) :9778-9782

[4] Folding amphipathic helices into membranes:: Amphiphilicity trumps hydrophobicity [J].

Fernandez-Vidall, Monica ;

Jayasinghe, Sajith ;

Ladokhin, Alexey S. ;

White, Stephen H. .

JOURNAL OF MOLECULAR BIOLOGY, 2007, 370 (03) :459-470

[5] Recognition of transmembrane helices by the endoplasmic reticulum translocon [J].

Hessa, T ;

Kim, H ;

Bihlmaier, K ;

Lundin, C ;

Boekel, J ;

Andersson, H ;

Nilsson, I ;

White, SH ;

von Heijne, G .

NATURE, 2005, 433 (7024) :377-381

[6] Molecular code for transmembrane-helix recognition by the Sec61 translocon [J].

Hessa, Tara ;

Meindl-Beinker, Nadja M. ;

Bernsel, Andreas ;

Kim, Hyun ;

Sato, Yoko ;

Lerch-Bader, Mirjam ;

Nilsson, IngMarie ;

White, Stephen H. ;

von Heijne, Gunnar .

NATURE, 2007, 450 (7172) :1026-U2

[7] An experiment-based algorithm for predicting the partitioning of unfolded peptides into phosphatidylcholine bilayer interfaces [J].

Hristova, K ;

White, SH .

BIOCHEMISTRY, 2005, 44 (37) :12614-12619

[8] Energetics, stability, and prediction of transmembrane helices [J].

Jayasinghe, S ;

Hristova, K ;

White, SH .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 312 (05) :927-934

[9] MPtopo: A database of membrane protein topology [J].

Jayasinghe, S ;

Hristova, K ;

White, SH .

PROTEIN SCIENCE, 2001, 10 (02) :455-458

[10] A SIMPLE METHOD FOR DISPLAYING THE HYDROPATHIC CHARACTER OF A PROTEIN [J].

KYTE, J ;

DOOLITTLE, RF .

JOURNAL OF MOLECULAR BIOLOGY, 1982, 157 (01) :105-132

← 1 2 3 →