Multiple alignment of transmembrane protein sequences
Multiple sequence alignment remains one of the most powerful tools for assessing evolutionary sequence relationships and for identifying structurally and functionally important protein regions. Membrane-bound proteins represent a special class of proteins
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Dmitrij Frishman Editor
Structural Bioinformatics of Membrane Proteins
SpringerWienNewYork
Prof. Dmitrij Frishman TU München, Wissenschaftszentrum Weihenstephan, Freising, Germany
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© 2010 Springer-Verlag/Wien Printed in Austria SpringerWienNewYork is part of Springer Science + Business Media springer.at
Typesetting: Thomson Press (India) Ltd., Chennai Printing: Holzhausen Druck und Neue Medien GmbH, 1140 Wien, Austria Printed on acid-free and chlorine-free bleached paper SPIN: 127 63 863
With 63 (partly coloured) Figures
Library of Congress Control Number: 2010929320
ISBN 978-3-7091-0044-8 SpringerWienNewYork
CONTENTS
Evolutionary origins of membrane proteins (Armen Y. Mulkidjanian, Michael Y. Galperin) 1 1 2 3 4 5
Introduction 1 Comparative analysis of F/V-type ATPases: example of function cooption? 3 Emergence of integral membrane proteins 9 Emergence of lipid membranes 10 Scenario for the origin and evolution of membranes and membrane proteins 17
Molecular archeological studies of transmembrane transport systems (Milton H. Saier Jr, Bin Wang, Eric I. Sun, Madeleine Matias, Ming Ren Yen) 29 1 2 3 4 5 6 7
Introduction 29 Molecular transport 30 Techniques to establish homology or the lack of homology 30 Transport protein diversity 31 The ABC superfamily 32 Independent origins for ABC porters 33 The phosphoenolpyruvate-dependent sugar transporting phosphotransferase system (PTS) 35 8 Independent origins for PTS permeases 37 9 Reverse (retro)-evolution 38 10 Conclusions and perspectives 40
Resource for structure related information on transmembrane proteins (Gábor E. Tusnády, István Simon) 45 1 Introduction 45 2 3D structure resources 46 2.1 Protein Data Bank 46 2.2 Manually curated structure resources of TMPs 47 2.3 TMDET algorithm 48 2.4 PDBTM database 51 V
Contents
2.5 OPM database 52 2.6 Modeling protein–lipid assembly 52 3 2D structure resources 53 3.1 TOPDB database 54 3.2 TOPDOM database 55 3.3 Prediction methods incorporating experimental results 56
Topology prediction of membrane proteins: how distantly related homologs come into play (Rita Casadio, Pier Luigi Martelli, Lisa Bartoli, Piero Fariselli) 61 1 Introduction 61 2 From membrane protein sequence to topologic models 62 2.1 Da
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