Implementation of an algorithm for modeling disulfide bond patterns using mass spectrometry

被引：9

作者：

Craig, R ^{[1
]}

Krokhin, O

Wilkins, J

Beavis, RC

机构：

[1] Univ Manitoba, Manitoba Ctr Prote, Winnipeg, MB R3T 2N2, Canada

[2] Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2003年 / 2卷 / 06期

关键词：

disulfide; crosslinking; mass spectrometry; Fenyo algorithm; MALDI; sequence modeling;

D O I：

10.1021/pr034016a

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The paper describes the implementation of a software system based on the Fenyo disulfide bond assignment algorithm. The system allows an investigator to enter data derived from mass spectrum peak assignments, a target protein sequence and other experimental conditions. The output of the system is the set of disulfide bonding pattern models that are consistent with the experimental evidence. The software and code are available through a public web site, which also has a functioning, publicly accessible version of the disulfide bond modeler. This implementation was tested as part of a project to check homology-based assignments disulfide bonding patterns of human integrins.

引用

页码：657 / 661

页数：5

共 26 条

[1] PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].

ANFINSEN, CB .

SCIENCE, 1973, 181 (4096) :223-230

[2]

[Anonymous], 1979, Computers and Intractablity: A Guide to the Theoryof NP-Completeness

[3] CHARACTERIZATION OF DISULFIDE BOND POSITION IN PROTEINS AND SEQUENCE-ANALYSIS OF CYSTINE-BRIDGED PEPTIDES BY TANDEM MASS-SPECTROMETRY [J].

BEAN, MF ;

CARR, SA .

ANALYTICAL BIOCHEMISTRY, 1992, 201 (02) :216-226

[4] Oxidative protein folding in bacteria [J].

Collet, JF ;

Bardwell, JCA .

MOLECULAR MICROBIOLOGY, 2002, 44 (01) :1-8

[5] Formation, isomerisation and reduction of disulphide bonds during protein quality control in the endoplasmic reticulum [J].

Fassio, A ;

Sitia, R .

HISTOCHEMISTRY AND CELL BIOLOGY, 2002, 117 (02) :151-157

[6] The biopolymer markup language [J].

Fenyö, D .

BIOINFORMATICS, 1999, 15 (04) :339-340

[7]

Fenyo D, 1997, COMPUT APPL BIOSCI, V13, P617

[8] Pathways for protein disulphide bond formation [J].

Frand, AR ;

Cuozzo, JW ;

Kaiser, CA .

TRENDS IN CELL BIOLOGY, 2000, 10 (05) :203-210

[9] DISULFIDE STRUCTURES OF HIGHLY BRIDGED PEPTIDES - A NEW STRATEGY FOR ANALYSIS [J].

GRAY, WR .

PROTEIN SCIENCE, 1993, 2 (10) :1732-1748

[10] VLA PROTEINS IN THE INTEGRIN FAMILY - STRUCTURES, FUNCTIONS, AND THEIR ROLE ON LEUKOCYTES [J].

HEMLER, ME .

ANNUAL REVIEW OF IMMUNOLOGY, 1990, 8 :365-400

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