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Prediction of the plant β‐barrel proteome: A case study of the chloroplast outer envelope
Author(s) -
Schleiff Enrico,
Eichacker Lutz Andreas,
Eckart Kerstin,
Becker Thomas,
Mirus Oliver,
Stahl Tanja,
Soll Jürgen
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0237503
Subject(s) - bacterial outer membrane , proteome , arabidopsis thaliana , chloroplast , chloroplast membrane , biology , membrane protein , organelle , genome , membrane , microbiology and biotechnology , biochemistry , gene , mutant , escherichia coli , thylakoid
In the postgenomic era, the transformation of genetic information into biochemical meaning is required. We have analyzed the proteome of the chloroplast outer envelope membrane by an in silico and a proteomic approach. Based on its evolutionary relation to the outer membrane of Gram‐negative bacteria, the outer envelope membrane should contain a large number of β‐barrel proteins. We therefore calculated the probability for the existence of β‐sheet, β‐barrel, and hairpin structures among all proteins of the Arabidopsis thaliana genome. According to the existence of these structures, a number of candidates were selected. This protein pool was analyzed by TargetP to discard sequences with signals that would direct the protein to other organelles different from chloroplasts. In addition, the pool was manually controlled for the presence of proteins known to function outside of the chloroplast envelope. The approach developed here can be used to predict the topology of β‐barrel proteins. For the proteomic approach, proteins of highly purified outer envelope membranes of chloroplasts from Pisum sativum were analyzed by ESI‐MS/MS mass spectrometry. In addition to the known components, four new proteins of the outer envelope membranes were identified in this study.