Methods in Protein Sequence Analysis

396 Pages·1991·12.795 MB·English

by  Brigitte Wittmann-Liebold, Lothar Matschull, Ulrike Pilling, Hans-Arthur Bradaczek (auth.), Dr. Hans Jörnvall, Dr. Jan-Olov Höög, Dr. Ann-Margreth Gustavsson (eds.)

ALB
Advances in Life Sciences
Methods in Protein
Sequence Analysis
Edited by
H.Jornvall
J.-O.Hoog
A.-M. Gustavsson
Springer Basel AG
Edltors' addresses:
Dr. Hans Jörnvall
Dr. Jan-Olov Höög
Dr. Ann-Margreth Gustavsson
Department of Chemistry I
Karolinska Institute
S-104 01 Stockholm
SWEDEN
The use of registered names, trademarks, etc. in this publication does not imply, even in the
absence of a specific statement, that such names are exempt from the relevant protective laws
and regulations and therefore free for general use.
The publisher cannot assume any legal responsibility for given data, especially as far as
directions for the use and the handling of chemicals and drugs are concerned. This information
can be obtained from the manufacturers.
Library of Congress Cataloging-in-Putolication Data
Methods in protein sequence analysis / edited by H. Jörnvall, J.-0. Höög, A-M. Gustavsson.
p. cm. - (Advances in life sciences)
Includes bibliographical references and index.
ISBN 978-3-0348-5680-5
1. Amino acid sequence. I. Jornvall, Hans. II. Höög, J.-O. (Jan-Olov) III. Gustavsson, A-M. (Ann-
Margreth) IV Series. QP551.M3885 1991
574.87'328-dcSO
Deutsche Bibliothek Cataloging-in-Publication Data
Methods in protein sequence analysis / ed. by H. Jörnvall... - Basel; Boston; Berlin:
Birkhäuser, 1991
(Advances in life sciences)
ISBN 978-3-0348-5680-5
NE: Jörnvall, Hans [Hrsg.]
This work is subject to copyright. All rights are reserved, whether the whole or part of the
material is concerned, specifically those of translation, reprinting, re-use of illustrations,
broadcasting, reproduction by photocopying machine or similar means, and storage in data
banks. Under § 54 of the German Copyright Law, where copies are made for other than private
use a fee is payable to «Verwertungsgesellschaft Wort», Munich.
© Springer Basel AG 1991
Originally published by Birkhäuser Verlag Basel in 1991
Softcover reprint of the hardcover 1st edition 1991
ISBN 978-3-0348-5680-5 ISBN 978-3-0348-5678-2 (eBook)
DOI 10.1007/978-3-0348-5678-2
v
TABLE OF CONTENTS
Preface 1
The Edman Award . 4
In Memory 6
SEQUENCER METHODOLOGY AND INSTRUMENTATION
Modular Berlin microsequencer for the sequential degradation of proteins and
peptides from the amino-and carboxyl-terminal ends
B. Wittmann-Liebold, L. Matschull, U. Pilling, H.-A. Bradaczek and
H. Graffunder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 9
C-terminal sequence analysis
A. S. Inglis, R. L. Moritz, G. S. Begg, G. E. Reid, R. J. Simpson, H. Graffunder,
L. Matschull and B. Wittmann-Liebold ............................. 23
Chemical C-terminal sequencing
D. H. Hawke and V. L. Boyd 35
Extending the performance of the solid-phase protein sequencer
R. A. Laursen, Th. T. Lee, J. D. Dixon and S.-P. Liang ..... . ............ 47
Direct microsequencing of blotted and covalently attached proteins in
a cross-flow reaction chamber
H. Reinke, S. Fischer, F. Reimann and H. Tschesche ...................... 55
VI
SAMPLE PREPARATION AND ANALYSIS
Current strategies for microscale purification of proteins and peptides for sequence
analysis
R. I. Simpson, R. L. Moritz, G. E. Reid and L. D. Ward .............. . 67
Capillary electrophoresis: A new dimension in the separation sciences
T.Large ............................... . 79
Structural analysis of membrane proteins
I. E. Shiveley .............. . . . .. 91
Protein-electroblotting and microsequencing in establishing integrated human protein
databases
H. H. Rasmussen, I. Van Damme, G. Bauw, M. Puype, B. Gesser, I. E. Celis and
I. Vandekerckhove ....................................... 103
Comparison of the blotting efficiencies of various PVDF membranes
P. Matsudaira ........................... . ..... 115
Highly sensitive determination of amino acid derivatives obtained from N-terminal
sequence analysis
A. Tsugita and M. Kamo .................................... 123
Amino acid analysis and sequencing -What is state-of-the-art?
R. L. Niece, L. H. Ericsson, A. V. Fowler, A. I. Smith, D. W. Speicher, I. W. Crabb
and K. R. Williams ....................................... 133
Realistic expectations for amino acid analysis
L. H. Ericsson, D. Atherton, R. Kutny, A. I. Smith and I. W. Crabb . 143
MODIFIED RESIDUES, CHEMICAL PROBLEMS AND SYNTHETIC PEPTIDES
A protein chemistry approach to the modelling of integral membrane proteins
I. B. C. Findlay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 151
N-terminal acetylated mitochondrial aldehyde dehydrogenase is found in fresh
but not frozen liver tissue
H. Weiner, S. C. Cunningham and R. A. Angelo ........................ 161
VII
Elucidating ligand binding sites in polypeptides by photoaffinity labeling with
aryl azides
H. Ponstingl, L. D. Barnes, C. Granzow, R. H. Himes, G. Maier and G. Nasioulas ...... 169
Use of thiopropyl-Sepharose 6B for isolation and structure-functional analysis of
thiol proteins
T. A. Egorov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . ..... 177
Zinc fingers involved in MHC class I gene regulation: Use of synthetic peptides
for structural analysis
E. Appelia, J. G. Omichinski, G. M. Clore, A. M. Gronenborn and K. Sakaguchi ....... 187
Hydrophobic surfactant proteins SP-B and SP-C: Special analytical problems
1. Johansson, T. Curstedt, P. Persson, B. Robertson, B. LOwenadler and H. Jornvall ..... 197
PROTEOLYSIS
The yeast prohorrnone-processing Kex2 protease, an enzyme with specificity for
paired basic residues
R. S. Fuller, C. Brenner, P. Gluschankof and C. A. Wilcox ................... 205
Structures of three inhibitor complexes of HIV-l protease
A. Wlodawer, M. Miller, A. L. Swain and M. Jaskolski ................... 215
Protease specificity and protein sequence analysis
L. Polgar ................. . . . . . . . . . . . . . . . . . . . . . . . 223
Cleavage-sites in protein targeting signals
G. von Heijne .............. . ............. 231
Studies on a dimeric aspartic protease from a single domain of pepsin
H. Mattras, L. Chiche, M. Bianchi, R.-A. Boigegrain, B. Castro and
M.-A. Coletti-Previero . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
MASS SPECTROMETRY
LC/MS and LC/MS/MS screening for the sites of post-translational modification
in proteins
T. Covey, B. Shushan and R. Bonner .............................. 249
VIII
Protein and peptide sequence analysis by tandem mass spectrometry in combination
with either capillary electrophoresis or micro-capillary HPLC
D. F. Hunt, H. Shabanowitz, M. A. Moseley, A. L. McCormack, H. Michel,
P. A. Martino, K. B. Tomer and J. W. Jorgenson ............... . . . . . . . 257
Plasma desorption mass spectrometry as a tool for characterization of native and
modified forms of recombinant polypeptides
M. Hartmanis ............................... . . . . . . . 267
Plasma desorption mass spectrometry in monitoring peptide synthesis and
phosphorylation reactions
A. G. Craig, A. Engstrom, G. Lindeberg, H. Bennich, M. Serwe, E. Hoffmann-
Posorske, H. Korte and H. E. Meyer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
SYNERGISM WITH DNA ANALYSIS
Repeating domains in the plasma proteins participating in blood coagulation and
fibrinolysis
A. Ichinose and E. W. Davie .................................. 285
Structural analysis of the glucocorticoid receptor protein
J. Carlstedt-Duke, P.-E. Stromstedt, K. Dahlman-Wright, T. Hard, J. Zilliacus,
C. Cairns, A. Wright, I. McEwan, L. Perez, H. Jornvall and J.-A. Gustafsson ........ 293
Cl inhibitor: structure, genetic variants and serpin homologies
S. Magnusson, S. C. Bock and K. Skriver ........................... 301
Genetic strategies for protein purification
S. Stdhl, P.-A. Nygren and M. Uhlen ... . ... 313
PREDICTIONS, DATA BANKS, PATTERNS AND TERTIARY STRUCTURES
The prediction of the secondary structure of proteins
G. D. Fasman .................... .................... 321
A computer method of rmding supersecondary structure
K. Nagano ........................................... 333
Usefulness of the PIR database for protein comparisons
L. T. Hunt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
IX
The structure and post-translational modification of lipoyl domains in 2-oxo acid
dehydrogenase multienzyme complexes
R. N. Perham, F. Dardel, E. D. Laue and L. C. Packman ................... 353
Zinc chemistry in function and structure of zinc proteins
B.L. Vallee andD. S.Auld .............. . . .............. 363
Patterns of sequence variation in families of homologous proteins
T. Blundell, J. Cooper, D. Donnelly, H. Driessen, Y. Edwards, F. Eisenmenger,
C. Frazao, M. Johnson, K. Niefind, M. Newman, J. Overington, A. Sali,
C. Slingsby, V. Nalini and Z. Zhu ................................ 373
Protein folding: Local structures, domains and assemblies
R. Jaenicke . . . . . . . . . . . . . . . . . . . . . . 387
Keyword Index 397