Methods in proteome and protein analysis: [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain]
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2004
|
| Schriftenreihe: | Principles and practice
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXXII, 404 S. Ill., graph. Darst. |
| ISBN: | 3540202226 |
Internformat
MARC
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| 245 | 1 | 0 | |a Methods in proteome and protein analysis |b [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] |c Roza Maria Kamp, Juan J. Calvete, Theodore Choli-Papadopoulou (eds.) |
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2004 | |
| 300 | |a XXXII, 404 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 0 | |a Principles and practice | |
| 650 | 4 | |a Proteine - Strukturaufklärung - Kongress - Valencia <2002> | |
| 650 | 4 | |a Proteom - Strukturaufklärung - Kongress - Valencia <2002> | |
| 650 | 0 | 7 | |a Proteom |0 (DE-588)4576155-3 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Strukturaufklärung |0 (DE-588)4183788-5 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Proteine |0 (DE-588)4076388-2 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)1071861417 |a Konferenzschrift |y 2002 |z Valencia |2 gnd-content | |
| 689 | 0 | 0 | |a Proteom |0 (DE-588)4576155-3 |D s |
| 689 | 0 | 1 | |a Strukturaufklärung |0 (DE-588)4183788-5 |D s |
| 689 | 0 | |5 DE-604 | |
| 689 | 1 | 0 | |a Proteine |0 (DE-588)4076388-2 |D s |
| 689 | 1 | 1 | |a Strukturaufklärung |0 (DE-588)4183788-5 |D s |
| 689 | 1 | |5 DE-604 | |
| 700 | 1 | |a Kamp, Roza Maria |d 1951- |e Sonstige |0 (DE-588)120965933 |4 oth | |
| 700 | 1 | |a Calvete, Juan J. |e Sonstige |4 oth | |
| 700 | 1 | |a Choli-Papadopoulou, Theodora |e Sonstige |4 oth | |
| 856 | 4 | 2 | |m Digitalisierung TU Muenchen |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010582028&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-010582028 | ||
Datensatz im Suchindex
| _version_ | 1804130349617250304 |
|---|---|
| adam_text | Contents
1
Helix-Helix Packing Between
Transmembrane
Fragments
. 1
Mar Orzáez, Francisco J.
Taberner,
Enrique Pérez-Paya, Ismael Mingarro
Abstract
.................................. 1
1.1
Introduction
........................... 2
1.2
Glycophorin A as a Model System
............... 3
1.3
Influence of the Distance Between the Dimerisation
Motif and the Flanking Charged Residues
on the Packing Process Between TM Helices
......... 5
1.4
Length of the
Hydrophobie
Fragment
and Oligomerisation
Processe
................. 6
1.5 Prolines in
Transmembrane
Helix Packing
.......... 8
1.6
Future Prospects for Membrane Protein Analysis
...... 11
References
.................................. 12
2
Mobility Studies in Proteins by 15N Nuclear
Magnetic Resonance: Rusticyanin as an Example
...... 15
Beatriz Jiménez, José María
Moratal,
Mario Piccioli,
Antonio
Donaire
Abstract
.................................. 15
2.1
Introduction
........................... 15
2.1.1
NMR
Versus
Х
-Ray for the Acquisition
of Dynamic
Information
.................... 16
2.1.2
Dynamics of Proteins and NMR
................ 17
2.1.2.1
Theoretical Considerations
................... 17
2.1.2.2
A Quantitative Analysis of the Model-Free Approach
.... 19
2.1.2.3
Practical Aspects
........................ 21
2.1.3
The System: Rusticyanin
.................... 23
VIII Contents
2.2
Results and
Discussion
..................... 24
2.2.1
Relaxation Properties of Rusticyanin
............. 24
2.2.1.1
Relaxation Data
.........................
24
2.2.1.2
An Analysis of the Generalized Order Parameter in Re
... 26
2.2.2
DjO/HjO Exchange Experiments
............... 27
2.2.3
Dynamics,
Hydration,
and Rusticyanin Stability
....... 27
2.2.4
Mobility, Hydrophobicity, and High
Redox
Potential
..... 29
2.3
Conclusions
........................... 30
References
.................................. 30
3
Structure and Dynamics of Proteins in Crowded Media:
A Time-Resolved Fluorescence Polarization Study
..... 35
Silvia Zorrilla,
German
Rivas,
Maria
Pilar Lillo
3.1
Macromolecular Crowding in Physiological Media
..... 35
3.1.1
Effect of Macromolecular Crowding on Chemical
Equilibrium of Macromolecular Association Reactions
... 36
3.1.2
Experimental Approaches to the Study of the Effect
of Macromolecular Crowding Upon Biochemical Reactions
36
3.2
Application of Time-Resolved Fluorescence
Polarization Spectroscopy in Crowded Media
........ 37
3.3
Volume Fraction and Intermolecular Separations
in a Heterogeneous System
................... 39
3.3.1
Characterization of the Crowded Medium Itself
....... 39
3.3.2
Microscopic Model for Crowded Solutions
.......... 39
3.4
Structure and Dynamics of apoMb Dimer
in Crowded Protein Solutions
................. 41
3.4.1
Preparation of Apomyoglobin and Labelling with
ANS ... 42
3.4.2
Spectroscopic Properties of
ANS
Remain
Essentially Unchanged Upon Dimer Formation
....... 42
3.4.3
Conformational Dynamics of the Dimer of Apomyoglobin
. 44
3.5
Conclusions and Outlook
.................... 46
References
.................................. 47
4
Analyses of Wheat Seed Proteome: Exploring Protein-Protein
Interactions by Manipulating Genome Composition
.... 49
Nazrul
Islamand,
Hisashi Hirano
4.1
Summary
............................. 49
4.2
Introduction
........................... 49
Contents
IX
4.3
Techniques of Protein-Protein Interactions
......... 50
4.4
Chromosome Manipulation: An Alternative Approach
... 51
4.4.1
Principle
............................. 51
4.4.2
Experimentation
........................ 52
4.4.2.1
Plant Materials
.......................... 52
4.4.2.2
Two-Dimensional Electrophoresis
............... 53
4.4.2.3
Quantitative Analysis of Electrophoresis Patterns
...... 54
4.4.2.4
Statistical Analysis
....................... 54
4.4.2.5
Sample Preparation for ICAT-ESI
............... 54
4.4.2.6
Protein Analysis by ESI-MS/MS
................ 55
4.4.3
Results and Discussion
..................... 55
4.4.3.1
Localization of Structural Genes
................ 55
4.4.3.2
Exploring Protein-Protein Interactions
............ 58
4.5
Concluding Remarks
...................... 64
References
.................................. 64
5
Modification-Specific Proteomic Strategy
for Identification of Glycosyl-Phosphatidylinositol
Anchored Membrane Proteins
................. 67
Eelix Elortza, Leonard J. Foster,
Allan Stensballe,
Ole
N.
Jensen
5.1
Summary
............................. 67
5.2
Introduction
........................... 68
5.2.1
Glycosyl-Phosphatidylinositol Anchored Proteins
...... 68
5.3
Results
.............................. 71
5.3.1
Selective Isolation of GPI-Anchored Proteins
........ 71
5.3.2
Identification of GPI-Anchored Proteins
by Mass Spectrometry
..................... 72
5.3.3
Protein Sequence Analysis
.... ............... 73
5.4
Discussion
............................ 73
5.5
Conclusion
............................ 75
5.6
Material and Methods
...................... 76
5.6.1
Lipid
Raft Preparation
..................... 76
5.6.2
Two-Phase Separation
and Phosphoinositol-Phospholipase
С
Treatment
...... 76
5.6.3
Mass Spectrometry
....................... 76
5.6.4
Bioinformatics
.......................... 77
References
.................................. 77
X
Contents
6
Diocleinae Lectins: Clues to Delineate Structure/
Function Correlations
..................... 81
Francisca
Gallego
Del Sol,
Vania M. Ceccatto,
Celso
S.
Nagano,
Frederico
B.M.B.
Moreno,
Alexandre H.
Sampaio,
Thalles
В.
Grangeiro, Benildo S.
Cavada, Juan J. Calvete
6.1
Introduction
........................... 81
6.2
Quaternary
Structure
Variability
............... 82
6.3
Structural
Basis of
pH-Dependent Oligomerisation:
The Crystal
Structures
of the
Lectins
from
Dioclea
grandiflora
and Dioclea guianensis
.......... 83
6.3.1
The Key Role of His-131: The Crystal Structure
of Dioclea
violacea (Dviol)
Seed Lectin
............ 85
6.4
Diocleinae Lectin Sequence Characteristics
as Phylogenetic Markers
.................... 89
References
.................................. 90
7
The Contribution of Optical Biosensors to the
Analysis of Structure-Function Relationships in Proteins
. 93
Marc H.V.Van Regenmortel
7.1
Introduction
........................... 93
7.2
Structures Do Not Cause Function
.............. 94
7.3
Can Protein Functions Be Predicted from Structure
or Should They Be Determined Experimentally?
....... 95
7.4
Analysing Structure-Activity Correlations with Biosensors
. 96
References
.................................. 100
8
The Use of Protein-Protein Interaction Networks
for Genome-Wide Protein Function Comparisons
and Predictions
......................... 103
Christine Brun, Anaïs
Baudot,
Alain Guénoche,
Bernard Jacq
Abstract
..................................
ЮЗ
8.1
Introduction
...........................
Ю4
8.2
How is Protein Function Defined and Represented?
..... 105
8.2.1
The Problem of Function Description
............. 105
8.2.2
Attempts Towards Textual Descriptions of Function
..... 106
8.2.3
Present Limitations of Functional Descriptions
and New Research Directions
................. 108
Contents
XI
8.3
A
Protein
Network-Based Approach
of the Study of Function
.................... 109
8.3.1
Molecular Interactions and Genetic Networks
........ 109
8.3.2
Protein-Protein Interaction Data Acquisition,
Protein Interaction Databases and Maps
........... 110
8.3.3
Protein Networks Studies Allow Us to Revisit
the Notion of Function
..................... 110
8.4
Functional Clustering of Proteins Based on Interactions
. . 112
8.4.1
Principle
............................. 112
8.4.2
Functional Classification of
10%
of the Yeast Proteome
... 114
8.4.3
The Different Types of Functional Clusters
.......... 116
8.4.4
Application to Another Proteome: Helicobacterpylori
.... 117
8.5
Protein-Protein Interactions and Structural Biology
.... 118
8.6
Conclusion
............................ 120
References
.................................. 121
9
Probing Ribosomal Proteins Capable of Interacting with
Polyamines
........................... 125
Dimitrios L. Kalpaxis, Maria A. Xaplanteri,
Ioannis
Amarantos, Fotini
Leontiadou,
Theodora Choli-Papadopoulou
9.1
Introduction
........................... 125
9.2
Fixation of Polyamines to Ribosomal Proteins
with Homobifunctional Cross-Linkers
............ 126
9.3
Labeling of Ribosomal Proteins with Photoreactive
Spermine Analogues
...................... 127
9.4
Functional Implications and Perspectives
........... 128
References
.................................. 130
10
Applications of Optical Biosensors to Structure-Function
Studies on the EGF/EGF Receptor System
.......... 133
Edouard
С.
Nice, Bruno Catimel, Julie A.
Rothacker,
Nathan Hall, Antony W. Burgess, Thomas P. J. Garrett,
Neil M. McKern, Colin W. Ward
10.1
Introduction
........................... 133
10.2
The EGF/EGFR Family
..................... 134
10.3
Biosensor Analysis
....................... 136
10.3.1
Instrumentation
......................... 136
10.3.2
Generation of an Active Biosensor Surface
.......... 139
XII Contents
10.3.3
Kinetic Analysis
.........................
139
10.3.4
Solution Competition Analysis Using Biosensors
...... 140
10.4
Biosensor Analysis of the Interactions
Between EGF and the EGFR
.................. 140
10.4.1
Immobilisation Strategies for EGF
............... 140
10.4.2
Immobilisation Strategies for sEGFR
............. 142
10.4.3
Kinetic Analysis of the Interaction Between hEGF
and the Soluble Extracellular Domain
of the EGF Receptor (sEGFR
1-621).............. 143
10.4.4
Confirmation of the Binding Model
.............. 145
10.4.5
Identification of a Truncated High Affinity Form
of the Soluble Extracellular Domain of the EGF Receptor
. . 147
10.4.6
Kinetic Analysis of the Interaction Between EGF
and sEGFR
1-501 ........................ 148
10.4.7
Analysis of the Receptor/Ligand Interaction Using
Immobilised Receptor
. .................... 149
10.4.8
sEGFR
1-501
and sEGFR
1-621
are Competitive
Inhibitors of EGF Induced Mitogenesis
............ 150
10.4.9
Identification of a Determinant of EGF Receptor
Ligand Binding Specificity (Chickenising
the Human EGF Receptor)
................... 151
10.5
Structural Studies on the EGF Receptor Family
....... 152
10.5.1
Inactivated EGFR Adopts an Autoinhibited Configuration
. 154
10.6.
Regulation of Homo- and Heterodimerisation
........ 154
10.7
Rationalisation of the Structural and Biosensor Data
.... 156
10.8
Conclusion
............................ 157
References
.................................. 158
11
The Functional Interaction Trap: A Novel Strategy
to Study Specific Protein-Protein Interactions
........ 165
Alok Sharma, Susumu Antoku, Bruce J. Mayer
11.1
Protein-Protein Interactions in Cellular Systems
...... 165
11.2
Signal Transduction
....................... 165
11.3
Tyrosine Phosphorylation and the Identification
of Physiologically Relevant Substrates
............. 167
11.4
The Functional Interaction Trap as a Novel Strategy
to Promote Specific Protein-Protein Interactions
and Post-Translational Modifications
............. 169
11.4.1
Coiled-Coil Segments Can Act as a Specific
Artificial Binding Interface Between the Abl Tyrosine
Kinase and Substrates
...................... 170
Contents XIII
11.4.2 Coiled-Coil Segments
can Activate Physiological
Downstream Signaling Events
................. 173
11.4.3
Implications of FIT for Analysis of the Functional
Consequences of Specific Tyrosine Phosphorylation
.... 174
11.5
Broader Uses of the FIT Strategy
................ 176
11.6
Advantages and Disadvantages of FIT
............. 178
11.7
Concluding Remarks
...................... 179
References
.................................. 180
12
Analysis of Protein-Protein Interactions in Complex
Biological Samples by MALDI
TOF
MS. Feasibility
and Use of the Intensity-Fading (IF-) Approach
....... 183
JOSEP VlLLANUEVA, OSCAR YaNES, ENRIQUE QUEROL,
Luis Serrano and Francesc X.
Aviles
12.1
Introduction
........................... 183
12.1.1
Mass Spectrometry as a Modern Approach
to Study Protein-Protein and Protein-Ligand Interactions
. 183
12.1.2
Characterization of Non-Covalent Interactions Using ESI
.. 184
12.1.3
Characterization of Non-Covalent Interactions
UsingMALDI
.......................... 184
12.1.3.1
MALDI-Based Indirect Methods
................ 184
12.1.3.2
MALDI-Based Direct Methods
................. 185
12.1.3.3
The Intensity-Fading (IF) MALDI-T of Approach
...... 186
12.2
Experimental Procedures
.................... 186
12.2.1
Biomolecule
Interaction Experiments
............. 186
12.2.1.1
General Sample Preparation
.................. 186
12.2.1.2
Protease-Inhibitor Interaction
................. 187
12.2.2
MALDI-TOF Mass Spectrometry
............... 187
12.2.2.1
Preparation of Samples for MALDI-TOF Mass Spectrometry
187
12.2.2.2
MALDI-TOF Matrix Preparation
............... 188
12.2.2.3
Sample-Matrix Preparation
.................. 188
12.3
Results and Discussion
..................... 188
12.3.1
Basis for the Detection of Non-Covalent
Complexes by MALDI-TOF MS
................ 188
12.3.2
Suggested Mechanism for Intensity Fading
(IF-) inMALDI-MS
....................... 189
12.3.3 Semiquantitative
Determination
of the Affinities Between the Interacting Partners
...... 190
12.3.4
Detection of Protein Ligands in Complex Samples
...... 192
12.3.4.1
Ion Suppression Effects in MALDI-TOF MS,
and Sample Preparation for Complex Biological Samples
. . 192
XIV Contents
12.3.4.2
Leech
Saliva
ІБ
MALDI-TOF
Analysis
............. 194
12.3.4.3
Sea Anemone Extract IF MALDI-TOF Analysis
........ 196
12.3.4.3.1
Trypsin
as the target molecule
.................
I96
12.3.4.3.2
Carboxypeptidase A as the Target Molecule
......... 197
12.4
General Discussion
....................... 1
References
..................................
200
13
Accelerator Mass Spectrometry in Protein Analysis
..... 203
John S.
Vogel, Darren J.
Hillegonds,
Magnus
Palmblad,
Patrick G. Grant, Graham Bench
13.1
Introduction
........................... 203
13.2
Accelerator Mass Spectrometry
................ 205
13.3
Biomolecular Targets of Labeled Compounds
........ 207
13.4
Specific Binding Affinity
.................... 209
13.5
Attomole
Edman
Sequencing
................. 211
13.6
Conclusion
............................ 214
References
.................................. 214
14
The Use of Microcalorimetric Techniques to Study
the Structure and Function of the Transferrin
Receptor from Neisseria meningitidis
............. 217
Tino Krell,
Geneviève Renauld-Mongénie
14.1
Introduction
........................... 217
14.2
Microcalorimetric Titrations of Individual TbpA,
TbpB and the Meningococcal Receptor Complex with
Human Iron-Free
(apo)
and Iron-Loaded
(holo)
Transferrin
220
14.2.1
Binding of Transferrin to TbpA
................ 220
14.2.2
Binding of Transferrin to TbpB
................ 222
14.2.3
Binding of Transferrin to the Receptor Complex
(TbpA+TbpB)
.......................... 222
14.2.4
Conclusions Concerning the Structure and Function
of the Receptor
......................... 223
14.3
Generation of
Recombinant
N-
and
C-Terminal
Domains of TbpB and the Study of Their Interaction
.... 224
14.3.1
Isothermal
Titration Calorimetry (ITC)
Binding Studies
. . 224
14.3.1.1
Calorimetrie
Titrations of TbpB,N-ter and C-ter
withholo-htf
......................... 224
14.3.1.2
Calorimetrie
Titration
of the N-terminal Domain
of TbpB with its
C-Terminal
Domain
............. 225
Contents
XV
14.3.2
Thermal Denaturation
Studies
Monitored
by Differential Scanning Calorimetry (DSC)
......... 227
14.3.3
Circular Dichroism Spectroscopy
............... 228
14.3.4
Conclusions Concerning the Structure of TbpB
....... 229
References
.................................. 229
15
The Quantitative Advantages of an Internal Standard
in Multiplexing 2D Electrophoresis
.............. 231
John Prime, Andrew
Alban, Edward
Hawkins, Barry Hughes
15.1
Introduction
........................... 231
15.2
Materials and Methods
..................... 234
15.2.1
Sample Preparation and Labelling
............... 234
15.2.2
CyDye Pre-Labelling of Protein Samples
for the
Ettan
DIGE System
................... 236
15.2.3
2-D Gel Electrophoresis
..................... 236
15.2.4
Image Acquisition of
Ettan
DIGE System Gels
........ 237
15.2.5
SYPRO Ruby Post-Staining of Conventional 2-DE Gels
... 237
15.3
Results
.............................. 237
15.3.1
Ettan
DIGE System Analysis
.................. 238
15.3.2
Image Analysis of Conventional One Sample
Per Gel SYPRO Ruby Stained Gels with
Progenesis ..... 242
15.3.3
Comparison of Quantitative Proteome Analysis Results
Between the Two Systems
.................... 245
15.3.3.1
BSA
................................ 245
15.3.3.2
Conalbumin
........................... 246
15.3.3.3
GAPDH
.............................. 246
15.3.3.4
Trypsin
Inhibitor
........................ 247
15.4
Conclusions
........................... 247
References
.................................. 249
16
Genetic Engineering of Bacterial and Eukaryotic
Ribosomal Proteins for Investigation on Elongation
Arrest of Nascent Polypeptides and Cell Differentiation
. . 251
Fotini Leontiadou, Christina Matragkou,
filippos
Kottakis, Dimitrios L. Kalpakis, Ioannis S. Vizirianakis,
Sofia Kouidou,
Asterios S.Tsiftsoglou,
Theodora Choli-Papadopoulou
16.1
Introduction
........................... 251
16.2
The Involvement of L4 Ribosomal Protein
on Ribosome Elongation Arrest
................ 252
XVI Contents
16.3
Down-Regulation of rpS5 and rpL35a Gene Expression
During
Murine Erythroleukemia
(MEL) Cell Differentiation:
Implications for Cell Differentiation and Apoptosis
..... 255
257
References
..................................
17
MALDI-MS Analysis of Peptides Modified
with
Photolabile
Arylazido Groups
.............. 261
William Low, James Rang, Micheal DiGruccio,
Dean Kirby, Marilyn Perrin, and Wolfgang H. Fischer
Abstract
.................................. 261
17.1
Introduction
........................... 261
17.2
Results and Discussion
..................... 262
17.3
Experimental Procedures
.................... 267
17.3.1
Azidobenzoylation of Astressin
................ 267
17.3.2
V8Peptidase Digestion of Modified Peptides
......... 267
17.3.3
MALDI-MS Analysis
...................... 268
17.3.4
UV Spectra
............................ 268
References
.................................. 268
18
A New Edman-iype Reagent for High Sensitive
Protein Sequencing
....................... 269
Christian
Wurzel,
Barbara
zu Lynar,
Christoph
RadckEjRalf
Krüger, Michael
Karas,
Brigitte Wittmann-Liebold
Abstract
.................................. 269
18.1
Introduction
........................... 270
18.2
Materials and Methods
..................... 271
18.3
Results
.............................. 271
18.3.1
Chip-Sequencer
......................... 271
18.3.2
Evaluation of
lß-bis-CTrifluoromethy^-Phenylisothiocyanate
as a New Coupling Reagent in
Edman
Chemistry
...... 272
18.3.3
High Sensitive Detection of Thiohydantoin Derivatives
. . . 273
18.4
Discussion and Outlook
.................... 277
References
........................ 278
Contents XVII
19
Amino
Acid Sequencing of Sulfonic Acid-Labeled
Tryptic Peptides Using Post-Source Decay
and Quadratic Field MALDI-ToF Mass Spectrometry
.... 279
Rama Bhikhabhai,
Mattias Algotsson,
Ulrika Carlsson, John
Flensburg,
Lena Hörnsten,
Camilla Larsson,
Jean-Luc
Maloisel,
Ronnie
Palmgren, Mari-Ann Pesula, Maria Liminga
Abstract
.................................. 279
19.1
Introduction...........................
279
19.2
Material
and Methods
...................... 280
19.2.1
Chemicals
............................ 280
19.2.2
CAF
Labeling Protocol
..................... 281
19.2.3
Analysis of Peptides
by MALDI-ToF Mass
Spectrometry
. . 281
19.2.4
Interpretation
of Spectra
.................... 281
19.2.5
Protein
Identification
...................... 282
19.2.6
Analysis
of Synthetic
Phosphopeptides
............ 282
19.3
Results and Discussion
..................... 282
19.3.1
Sequencing of a Synthetic
Peptide
............... 283
19.4
Identification/Confirmation of
Recombinant
Protein
.... 284
19.4.1
Sensitivity
............................ 286
19.4.2
Sequencing of Phosphopeptides
................ 292
19.4.2.1
Identifcation of Phosphopeptides
............... 293
19.5
Conclusions
........................... 296
References
.................................. 297
20
Separation of Peptides and
Amino
Acids using
High Performance Capillary Electrophoresis
........ 299
Hong Jin,
Roza
Maria Kamp
20.1
Introduction
........................... 299
20.2
Separation of Peptides
..................... 301
20.2.1
Trypsin
Cleavage
........................ 301
20.2.1.1
Digestion of
ß-Lactoglobulin.................. 301
20.2.1.2
Trypsin
Digestion of Cytochrome
С
.............. 301
20.2.2
Separation Conditions for HPCE
............... 301
20.2.2.1
Separation of
ß-Lactoglobulin
Tryptic Peptides
....... 301
20.2.2.2
Separation of Cytochrome
С
After
Trypsin
Digestion
.... 302
20.3
Sequencing of Proteins and PTH
Amino
Acid Analysis
. . . 303
20.3.1
Chemicals
............................ 304
20.3.2
Amino
Acid Standard Preparation
............... 304
20.3.3
Sequencing of Bradykinin
................... 304
XVIII
Contents
20.3.4
HPCE
Separation Conditions
for
РТН
Amino
Acid
..... 305
20.3.5
Optimization of the PTH
Amino
Acid Separation
...... 305
20.4
Conclusion
............................ 305
References
.................................. 306
21
InterPro and Proteome Analysis
-
In silico Analysis
of Proteins and Proteomes
................... 307
Nicola Jane Mulder,
Manuela Pruess,
Rolf Apweiler
21.1
Introduction
........................... 307
21.2
Protein Analysis Tools
..................... 308
21.2.1
InterPro
............................. 308
21.2.1.1
Content and Features
...................... 308
21.2.1.2
Searching InterPro
....................... 310
21.2.1.3
Applications
........................... 310
21.2.2
Proteome Analysis
....................... 312
21.2.2.1
Content and Features
...................... 312
21.2.2.2
Statistical Analysis
....................... 314
21.2.2.3
Applications
........................... 315
21.3
Discussion
............................ 315
References
.................................. 316
22
Prediction of Functional Sites in Proteins
by Evolutionary Methods
....................
Pedro López-Romero,
Manuel J.
Gómez,
Paulino Gómez-Puertas, Alfonso
Valencia
Abstract
.................................. 319
22.1
Protein Function and
Amino
Acids Involved
......... 319
22.2
Interaction Sites and Their Structural
and Chemical Properties
.................... 320
22.3
Functional Role of Conserved Residues
in Multiple Sequence Alignments
............... 320
22.4
Why Predicting Functional Sites?
............... 321
22.5
The Use of Sequence Information for the
Prediction of Functional Sites
................. 322
22.6
Methods for Predicting Tree-Determinant Residues
..... 324
22.7
Methods for Predicting Functional Sites Based
on Structural Information
................... 327
Contents XIX
22.8
Comparisons Between Methods
................ 328
22.9
Main Problems in the Characterization
of Tree-Determinant Residues
................. 331
22.10
The Use of Information on Tree-Determinant
Residues in Molecular Biology
................. 333
References
.................................. 336
23
Extracting and Searching for Structural Information:
A Multiresolution Approach
.................. 341
Natalia Jiménez-Lozano,
Monica Chagoyen,
Pedro Antonio De-alarcón, José María Carazo
23.1
From Protein to Function
.................... 341
23.2
Structural Feature Relevance in Macromolecular Complexes
343
23.3
Extraction and Characterisation of Structural Features
. . . 344
23.4
FEMME
Database: Feature Extraction in a Multi-Resolution
Macromolecular Environment
................. 348
23.5
One of the
FEMME
Utilities: Query by Content
....... 352
23.6
Conclusions
........................... 354
References
.................................. 355
24
Peak Erazor: A Windows-Based Programme
for Improving
Peptide
Mass Searches
............. 359
Karin
Hjern0, Peter H0jrup
24.1
Introduction
........................... 359
24.2
Program Layout
......................... 360
24.2.1
Erazor List
............................ 360
24.2.2
Peak List
............................. 362
24.2.3
Background
........................... 363
24.2.4
Evaluate
............................. 363
24.3
Calibrating for
Peptide
Mass Fingerprinting
......... 363
24.4
Mapping
Peptide
Masses in Known Proteins
......... 365
24.5
Identifying Background Peaks
................. 366
24.6
Evaluation: Extracting Information
on Common Contaminants
................... 366
24.7
Discussion
............................ 368
References
.................................. 369
XX
Contents
25
Increasing Throughput and Data Quality for Proteomics
. . 371
Alfred L. Gaertner, Nicole L. Chow, Beth G. Fryksdale,
Paul Jedrzejewski, Brian S. Miller,
Sigrid Paech,
David L.Wong
Abstract
..................................
371
25.1
Introduction
........................... 372
25.1.1
Prefractionation by Membrane Devices
............ 372
25.1.2
Fractionation of a Fungal Exoproteome
............ 373
25.1.3
Mass Spectrometry Identification After Prefractionation
. . 376
25.2
Deglycosylation as a Means for Improved
Protein Identification
...................... 377
25.2.1
Deglycosylation of a Fungal Proteome
............ 378
25.2.2
Deglycosylation Summary
................... 380
25.3
High-throughput Proteomics Method Optimization
..... 381
25.3.1
Method Development to Increase Sample Consistency
. . . 383
25.3.2
Method Optimization and Results
............... 384
25.3.2.1
Digestion Buffers
........................ 384
25.3.2.2
Extraction Buffers
........................ 386
25.3.2.3
Matrix Spotting Methods
.................... 389
25.3.3
High-throughput Proteomics (ProGest) Optimization
.... 390
25.3.4
High-throughput Proteomics Summary
............ 390
25.4
Protein Identification and Quantification
using N14/N15
Isotopie
Labeling Technique
.......... 391
25.4.1
Identification and Quantification Technique
......... 392
25.4.2
Conclusion
............................ 396
References
.................................. 396
Subject Index
................................ 399
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| genre | (DE-588)1071861417 Konferenzschrift 2002 Valencia gnd-content |
| genre_facet | Konferenzschrift 2002 Valencia |
| id | DE-604.BV017587785 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T19:19:37Z |
| institution | BVB |
| isbn | 3540202226 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-010582028 |
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| physical | XXXII, 404 S. Ill., graph. Darst. |
| publishDate | 2004 |
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| publisher | Springer |
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| series2 | Principles and practice |
| spelling | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] Roza Maria Kamp, Juan J. Calvete, Theodore Choli-Papadopoulou (eds.) Berlin [u.a.] Springer 2004 XXXII, 404 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Principles and practice Proteine - Strukturaufklärung - Kongress - Valencia <2002> Proteom - Strukturaufklärung - Kongress - Valencia <2002> Proteom (DE-588)4576155-3 gnd rswk-swf Strukturaufklärung (DE-588)4183788-5 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf (DE-588)1071861417 Konferenzschrift 2002 Valencia gnd-content Proteom (DE-588)4576155-3 s Strukturaufklärung (DE-588)4183788-5 s DE-604 Proteine (DE-588)4076388-2 s Kamp, Roza Maria 1951- Sonstige (DE-588)120965933 oth Calvete, Juan J. Sonstige oth Choli-Papadopoulou, Theodora Sonstige oth Digitalisierung TU Muenchen application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010582028&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] Proteine - Strukturaufklärung - Kongress - Valencia <2002> Proteom - Strukturaufklärung - Kongress - Valencia <2002> Proteom (DE-588)4576155-3 gnd Strukturaufklärung (DE-588)4183788-5 gnd Proteine (DE-588)4076388-2 gnd |
| subject_GND | (DE-588)4576155-3 (DE-588)4183788-5 (DE-588)4076388-2 (DE-588)1071861417 |
| title | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] |
| title_auth | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] |
| title_exact_search | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] |
| title_full | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] Roza Maria Kamp, Juan J. Calvete, Theodore Choli-Papadopoulou (eds.) |
| title_fullStr | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] Roza Maria Kamp, Juan J. Calvete, Theodore Choli-Papadopoulou (eds.) |
| title_full_unstemmed | Methods in proteome and protein analysis [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] Roza Maria Kamp, Juan J. Calvete, Theodore Choli-Papadopoulou (eds.) |
| title_short | Methods in proteome and protein analysis |
| title_sort | methods in proteome and protein analysis selected papers presented at the 14th meeting on methods in protein structural analysis mpsa september 2002 valencia spain |
| title_sub | [selected papers presented at the 14th Meeting on Methods in Protein Structural Analysis (MPSA), September 2002, Valencia, Spain] |
| topic | Proteine - Strukturaufklärung - Kongress - Valencia <2002> Proteom - Strukturaufklärung - Kongress - Valencia <2002> Proteom (DE-588)4576155-3 gnd Strukturaufklärung (DE-588)4183788-5 gnd Proteine (DE-588)4076388-2 gnd |
| topic_facet | Proteine - Strukturaufklärung - Kongress - Valencia <2002> Proteom - Strukturaufklärung - Kongress - Valencia <2002> Proteom Strukturaufklärung Proteine Konferenzschrift 2002 Valencia |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010582028&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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