Following the succesful publication of "Proteome and Protein Analysis" in 2000, which was based on a former MPSA (Methods in Protein Structure Analysis) conference, "Methods in Proteome and Protein Analysis" presents the most interesting papers from the 14th MPSA meeting. Selected contributions discuss the latest techniques and approaches for analysing protein and proteome structures. Major topics include: protein and peptide sample preparation and separation new reagent for protein sequence analysis mass spectrometry in protein research analysis of posttranslational modification protein-protein interaction using MALDI-MS manipulation of genome or functional compositon trap structure-function correlation study using optical biosensors of microcolorimetrical techniques structural proteomics as NMR or fluorescence polarization study the classification and prediction of structure or functional sites in silico analysis of proteins and proteomes increasing throughput and data quality for proteomics
Part I Structural Proteomics
1 Helix-helix packing between transmembrane fragments
Mar Orzaez, Francisco J. Taberner, Enrique Perez-Paya and Ismael Mingarro
2 Mobility studies in Proteins by 15N Nuclear Magnetic Resonance: Rusticyanin as an example
Beatrix Jimenez, Jose Maria Moratal, Mario Piccioli and Antonio Donaire
3 Structure and dynamics of proteins in crowded media: A time-resolved fluorescence polarization study
Silvia S. Zorrilla, German Rivas, Maria Pilar Lillo
Part II Proteome Analysis
4 Analyses of wheat seed proteome: exploring protein-protein interactions by manipulating genome composition
Nazrul Islam and Hisashi Hirano
5 Modification-Specific Proteomic Strategy for Identification of Glycosyl-Phosphatidylinosil Anchored Membrane Proteins
Felix Elortza, Leonard J. Foster, Allan Stensballe and Ole Norregaard Jensen
Part III Structure-Function Correlations
6 Diocleinae lectins: clues to delineate structure/function correlation
Francisca Gallego del Sol, Vania M. Ceccatto, Celso S. Nagano, Frederico B.M.B. Moreno, Alexandre H. Sampaio, Thalles B. Grandgeiro, Benildo S. Canada and Juan J. Calvete
7 The contribution of optical biosensors to the analysis of structure-function relationships in proteins
Marc H.V. Van Regenmortel
Part IV Protein-Protein Interaction
8 The Use of Protein-Protein Interaction Networks for Genome Wide Protein Function Comparisons and Predictions
Christine Brun, Anais Baudot, Alain Guenoche and Bernard Jacq
9 Probing ribosomal proteins, capable of interacting with polyamines
Dimitrios L.Kalpaxis, Maria A. Xanplanteri, Iioannis Amarantos, Fotini Leontiadou and Theodora Choli-Papadopoulou
10 Application of Optical Biosensors to Structure-Function Studies on the EGF/EGF Receptor System
Edouard C. Nice, Bruno Catimel, Julie A. Rothacker, Nathan Hall, Anthony W. Burgess, Thomas P.J. Garrett, Neil ;. McKern and Colin W. Ward.
11 The functional Interaction Trap: A novel strategy to study specific protein-protein interactions
Alok Sharma, Susumu Antoku and Bruce J. Mayer
12 Analysis of protein-protein interaction in complex biological samples by MALDI TOF MS. Feasility and use of the Intensity-fading (IF-) approach.
Josep Villanueva, Oscar Yanes, Enrique Querol, Luis Serrano and Francesc X. Aviles
Part V Advanced Technologies
13 Accelerator Mass Spectrometry in Protein Research
John S. Vogel, Darren J. Hillegonds, Magnus Palmblad, Patrick G. Grand and Graham Bench
14 The use microcalorimetric techniques to study the structure and function of the transferrin receptor from Neisseria meningitidis
Tino Krell and Genevieve Renauld-Mongenie
15 The quantitative advantages of an internal standard in multiplexing 2D electrophoresis
John Prime, Andrew Alban, Edward Hawkins and Barry Hughes
16 Genetic engineering of bacterial and eukaryotic ribosomal proteins for investigation on elongation arrest of nascent polypeptides and cell differentiation
Fotini Leontiadou, Christina Matragou, Philippos Kotakis, Dimitrios L. Kalpakis, Ioanis Vizirianakis, Sofia Kouidou, Asterios Tsifsoglou and Theodora Choli-Papadopoulou
17 MALDI-MS Analysis of Peptides Modified Photolabile Arylazido Groups
William Low, James Kang, Michael DiGriccio, Dean Kirby, Marilyn Perrin and Wolfgang H. Fischer
Part VI Protein Sequencing and Amino Acids Analysis
18 A New Edman-Type Reagent for High Sensitive Protein Sequencing
Christian Wurzel, Barbara zu Lynar, Christoph Radeke, Ralf Krüger, Michael Karas and Brigitte Wittmann-Liebold
19 Amino acid sequencing of sulfonic acid-labeled tryptic peptides using post-source decay and quadratic field MALDI-TOF mass spectrometry
Rama Bhikhabhai, Mattias Algotsson, Ulrika Carlsson, John Flensburg, Lena Hörnsten, Camilla Larsson, Jean-Luc Maloisel, Ronnie Palmgren, Mari-Ann Pesul and Maria Liminga
20 Separation of Peptides and Amino Acids using High Performance Capillary Electrophoresis
Hong Jin and Roza Maria Kamp
Part VII Bioinformatics
21 InterPro and Proteome Analysis - in silico Analysis of Proteins and Proteomes
Nicola Jane Mulder, Manuela Pruess and Rolf Apweiler
22 Prediction of Functional Sites in Protein by Evolutionary Methods
Pedro Lopez-Romereo, Manuel J. Gomez, Paulino Gomez-Puertas and Alfonso Valencia
23 Extracting and Searching Structural Information: A Multiresolution Approach
Jiménez-Lozano Natalia, Chagoyen Mónica, De-Alarcón Pedro Antonio and Carazo Jose Maria
24 PeakErazor: A window-based program for improving peptide mass peptide mass searches
Karin Hjernø and Peter Højrup
25 Increasing Throughput and Data Quality for Proteomics
Alfred L. Gaertner, Nicole L. Chow, Beth G. Fryksdale, Paul Jedrzejewski, Brian S. Miller, Sigrid Paech and David L. Wong