Protein interactions: the molecular basis of interactomics
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| Weitere Verfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Weinheim
Wiley-VCH
[2023]
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Literaturangaben und Index |
| Beschreibung: | xvi, 411 Seiten Illustrationen, Diagramme |
| ISBN: | 9783527348640 |
Internformat
MARC
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| 001 | BV048531979 | ||
| 003 | DE-604 | ||
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| 008 | 221026s2023 gw a||| |||| 00||| eng d | ||
| 016 | 7 | |a 1259545458 |2 DE-101 | |
| 020 | |a 9783527348640 |c hbk. |9 978-3-527-34864-0 | ||
| 035 | |a (OCoLC)1369549977 | ||
| 035 | |a (DE-599)DNB1259545458 | ||
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| 049 | |a DE-11 |a DE-19 |a DE-703 | ||
| 084 | |a WD 5100 |0 (DE-625)148194: |2 rvk | ||
| 245 | 1 | 0 | |a Protein interactions |b the molecular basis of interactomics |c edited by Volkhard Helms and Olga V. Kalinina |
| 264 | 1 | |a Weinheim |b Wiley-VCH |c [2023] | |
| 264 | 4 | |c © 2023 | |
| 300 | |a xvi, 411 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Literaturangaben und Index | ||
| 650 | 4 | |a Protein-protein interactions | |
| 650 | 4 | |a Molecular biology | |
| 650 | 4 | |a Cell receptors | |
| 650 | 0 | 7 | |a Protein-Protein-Wechselwirkung |0 (DE-588)4745193-2 |2 gnd |9 rswk-swf |
| 653 | |a Biochemie u. Chemische Biologie | ||
| 653 | |a Biochemistry (Chemical Biology) | ||
| 653 | |a Bioinformatics & Computational Biology | ||
| 653 | |a Bioinformatik u. Computersimulationen in der Biowissenschaften | ||
| 653 | |a Biowissenschaften | ||
| 653 | |a Cell & Molecular Biology | ||
| 653 | |a Chemie | ||
| 653 | |a Chemistry | ||
| 653 | |a Life Sciences | ||
| 653 | |a Zell- u. Molekularbiologie | ||
| 653 | |a CHB0: Biochemie u. Chemische Biologie | ||
| 653 | |a LS30: Zell- u. Molekularbiologie | ||
| 653 | |a LSG0: Bioinformatik u. Computersimulationen in der Biowissenschaften | ||
| 689 | 0 | 0 | |a Protein-Protein-Wechselwirkung |0 (DE-588)4745193-2 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Helms, Volkhard |0 (DE-588)135851246 |4 edt | |
| 700 | 1 | |a Kalinina, Olga V. |0 (DE-588)1072406853 |4 edt | |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, PDF |z 978-3-527-83051-0 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, EPUB |z 978-3-527-83052-7 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe |z 978-3-527-83050-3 |
| 856 | 4 | 2 | |m DNB Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=033908679&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-033908679 | ||
Datensatz im Suchindex
| _version_ | 1804184526046363648 |
|---|---|
| adam_text | CONTENTS
PREFACE
XV
1
PROTEIN
STRUCTURE
AND
CONFORMATIONAL
DYNAMICS
1
VOLKHARD
HELMS
1.1
1.1.1
1.1.2
1.1.3
1.1.4
1.1.5
1.1.6
1.1.7
1.2
1.2.1
1.2.2
1.2.3
1.2.4
1.3
1.3.1
1.3.2
1.3.3
1.3.4
1.4
STRUCTURAL
AND
HIERARCHICAL
ASPECTS
1
SIZE
OF
PROTEINS
1
PROTEIN
DOMAINS
1
PROTEIN
COMPOSITION
2
SECONDARY
STRUCTURE
ELEMENTS
3
ACTIVE
SITES
3
MEMBRANE
PROTEINS
6
FOLDING
OF
PROTEINS
7
CONFORMATIONAL
DYNAMICS
8
LARGE-SCALE
DOMAIN
MOTIONS
8
DYNAMICS
OF
N-TERMINAL
AND
C-TERMINAL
TAILS
9
SURFACE
DYNAMICS
9
DISORDERED
PROTEINS
9
FROM
STRUCTURE
TO
FUNCTION
10
EVOLUTIONARY
CONSERVATION
10
BINDING
INTERFACES
10
SURFACE
LOOPS
11
POSTTRANSLATIONAL
MODIFICATIONS
11
SUMMARY
11
REFERENCES
12
2
PROTEIN-PROTEIN-BINDING
INTERFACES
15
ZEYNEP
ABALI,
DAMLA
OVEK,
SIMGE
SENYUZ,
OZLEM
KESKIN,
AND
ATTILA
GURSOY
2.1
2.2
2.3
2.4
2.5
2.6
DEFINITION
AND
PROPERTIES
OF
PROTEIN-PROTEIN
INTERFACES
15
GROWING
NUMBER
OF
KNOWN
PROTEIN-PROTEIN
INTERFACE
STRUCTURES
18
SURFACE
AREAS
OF
PROTEIN-PROTEIN
INTERFACES
21
GAP
VOLUME
OF
PROTEIN-PROTEIN
INTERFACES
22
AMINO
ACID
COMPOSITION
OF
INTERFACES
22
SECONDARY
STRUCTURE
OF
INTERFACES
23
VI
CONTENTS
2.7
2.8
2.9
2.10
2.11
2.12
2.13
2.14
PROTEIN-PROTEIN-BINDING
ENERGY
24
INTERFACES
OF
HOMO
AND
HETERO-DIMERIC
COMPLEXES
24
INTERFACES
OF
NON-OBLIGATE
AND
OBLIGATE
COMPLEXES
25
INTERFACES
OF
TRANSIENT
AND
PERMANENT
COMPLEXES
25
BIOLOGICAL
VS.
CRYSTAL
INTERFACES
26
TYPE
I,
TYPE
II,
AND
TYPE
III
INTERFACES
27
CONSERVED
RESIDUES
AND
HOT
SPOTS
IN
INTERFACES
28
CONCLUSION
AND
FUTURE
IMPLICATIONS
29
REFERENCES
30
3
CORRELATED
COEVOLVING
MUTATIONS
AT
PROTEIN-PROTEIN
INTERFACES
39
ALEXANDER
SCHUG
3.1
3.2
3.3
3.3.1
3.3.2
INTRODUCTION
39
A
SHORT
INTRODUCTION
INTO
BIOMOLECULAR
MODELING
41
STATISTICAL
INFERENCE
OF
COEVOLUTION
41
LIMITATIONS
OF
LOCAL
STATISTICAL
INFERENCE
41
DIRECT-COUPLING
ANALYSIS-A
POTTS
MODEL
BASED
ON
MULTIPLE
SEQUENCE
ALIGNMENTS
42
3.4
3.5
3.6
3.7
SOLVING
THE
INVERSE
POTTS
MODEL
43
CONTACT
GUIDED
PROTEIN
AND
RNA
STRUCTURE
PREDICTION
45
INTER-MONOMER
INTERACTION
AND
SIGNALING
45
SUMMARY
46
REFERENCES
47
4
COMPUTATIONAL
PROTEIN
-
PROTEIN
DOCKING
53
MARTIN
ZACHARIAS
4.1
4.2
4.3
4.4
INTRODUCTION
53
RIGID
BODY
PROTEIN-PROTEIN
DOCKING
APPROACHES
56
ACCOUNTING
FOR
CONFORMATIONAL
CHANGES
DURING
DOCKING
59
INTEGRATION
OF
BIOINFORMATICS
AND
EXPERIMENTAL
DATA
FOR
PROTEIN-PROTEIN
DOCKING
61
4.5
4.6
4.7
4.8
TEMPLATE-BASED
PROTEIN-PROTEIN
DOCKING
62
FLEXIBLE
REFINEMENT
OF
DOCKED
COMPLEXES
64
SCORING
OF
DOCKED
COMPLEXES
66
CONCLUSIONS
AND
FUTURE
DEVELOPMENTS
67
ACKNOWLEDGMENTS
68
REFERENCES
68
5
IDENTIFICATION
OF
PUTATIVE
PROTEIN
COMPLEXES
IN
PROTEIN-PROTEIN
INTERACTION
NETWORKS
77
SUDHARSHINI
THANGAMURUGAN,
MARKUS
HOLLANDER,
AND
VOLKHARD
HELMS
5.1
5.2
5.3
PROTEIN-PROTEIN
INTERACTION
NETWORKS
77
INTEGRATION
OF
VARIOUS
PPI
RESOURCES
IN
PUBLIC
DATA
REPOSITORIES
79
PROTEIN-PROTEIN
INTERACTION
NETWORKS
OF
MODEL
ORGANISMS
80
CONTENTS
VII
5.3.1
PPIN
OF
SACCHAROMYCES
CEREVISIAE
80
5.3.2
PPIN
OF
HUMAN
83
5.4
ALGORITHMS
TO
IDENTIFY
PROTEIN
COMPLEXES
IN
PPI
NETWORKS
84
5.4.1
MOLECULAR
COMPLEX
DETECTION
(MCODE)
84
5.4.1.1
DEFINITIONS
85
5.4.1.2
ALGORITHM
86
5.4.1.3
EXAMPLES
88
5.4.2
CLUSTERING
WITH
OVERLAPPING
NEIGHBORHOOD
EXPANSION
(CLUSTERONE)
89
5.4.2.1
DEFINITIONS
89
5.4.2.2
ALGORITHM
90
5.4.3
DOMAIN-AWARE
COHESIVENESS
OPTIMIZATION
(DACO)
92
5.5
SUMMARY
94
REFERENCES
95
6
STRUCTURE,
COMPOSITION,
AND
MODELING
OF
PROTEIN
COMPLEXES
101
OLGA
V.
KALININA
6.1
PROTEIN
COMPLEX
STRUCTURE
101
6.1.1
PROTEIN
QUATERNARY
STRUCTURE
101
6.1.2
CLASSIFICATION
OF
PROTEIN-PROTEIN
INTERACTION
INTERFACES
102
6.1.3
CLASSIFICATION
AND
EVOLUTION
OF
PROTEIN
COMPLEXES
105
6.2
METHODS
FOR
AUTOMATED
ASSIGNMENT
OF
BIOLOGICAL
ASSEMBLIES
106
6.2.1
ASSIGNMENT
FROM
CRYSTALLOGRAPHIC
DATA
107
6.2.2
EMPLOYING
MACHINE-LEARNING
METHODS
108
6.2.3
LEVERAGING
EVOLUTIONARY
INFORMATION
109
6.3
COMPUTATIONAL
APPROACHES
TO
PREDICTING
3D
STRUCTURE
OF
PROTEIN
COMPLEXES
110
6.3.1
COMBINATORIAL
DOCKING
110
6.3.2
HOMOLOGY-BASED
COMPLEX
RECONSTRUCTION
114
6.3.3
PREDICTION
FROM
SEQUENCE
115
6.3.4
ASSISTED
DOCKING
116
6.4
CONCLUSION
AND
OUTLOOK
117
ACKNOWLEDGMENTS
118
REFERENCES
118
7
LIVE-CELL
STRUCTURAL
BIOLOGY
TO
SOLVE
MOLECULAR
MECHANISMS:
STRUCTURAL
DYNAMICS
IN
THE
EXOCYST
FUNCTION
127
ALTAIR
C.
HERNANDEZ,
BALDO
OLIVA,
DAMIEN
P.
DEVOS,
AND
ORIOL
GALLEGO
7.1
INTRODUCTION
127
7.2
STRUCTURAL
BIOLOGY
USING
LIGHT
MICROSCOPY
METHODS
129
7.3
HYBRID
METHODS:
INTEGRATIVE
STRUCTURAL
BIOLOGY
131
7.4
INTEGRATIVE
MODELING:
THE
CASE
OF
THE
EXOCYST
COMPLEX
133
7.5
COMPARING
THE
IN
SITU
ARCHITECTURE
OF
THE
EXOCYST
WITH
A
HIGH-RESOLUTION
CRYO-EM
MODEL
136
VIII
CONTENTS
7.6
DISCUSSION
AND
FUTURE
PERSPECTIVES
138
ACKNOWLEDGEMENTS
139
REFERENCES
140
8
KINETICS
AND
THERMODYNAMICS
OF
PROTEIN-PROTEIN
ENCOUNTER
143
NICOLAS
KUNZEL
AND
VOLKHARD
HELMS
8.1
8.2
8.2.1
8.3
INTRODUCTION
143
THERMODYNAMIC
ENSEMBLES
AND
FREE
ENERGY
143
THE
ISOTHERMAL-ISOBARIC
ENSEMBLE
AND
THE
GIBBS
FREE
ENERGY
144
OVERVIEW
OF
COMPUTATIONAL
METHODS
TO
DETERMINE
BINDING
FREE
ENERGIES
146
8.3.1
8.3.1.1
8.3.2
8.3.2.1
8.3.3
8.3.3.1
8.3.3.2
8.3.3.3
8.3.3.4
8.3.3.5
8.3.4
8.3.4.1
8.3.4.2
8.3.5
8.3.6
COARSE
GRAINING
147
BROWNIAN
DYNAMICS
147
ENDPOINT
METHODS
149
MM/PBSA/MM/GBSA
149
POTENTIAL
OF
MEAN
FORCE/PATHWAY
METHODS
150
THERMODYNAMIC
INTEGRATION
151
UMBRELLA
SAMPLING
(US)
151
STEERED
MD
(SMD)
153
METADYNAMICS
153
ADAPTIVE
BIASING
FORCE
(ABF)
155
REPLICA-EXCHANGE
METHODS
155
PARALLEL
TEMPERING
155
GENERALIZED/HAMILTONIAN
REPLICA-EXCHANGE
METHODS
156
ADDITIONAL
PATHWAY
METHODS
156
RELATIVE
BINDING
FREE
ENERGIES
156
REFERENCES
157
9
MARKOV
STATE
MODELS
OF
PROTEIN
-
PROTEIN
ENCOUNTERS
163
SIMON
OLSSON
NOTATION
163
9.1
9.2
9.2.1
9.3
9.3.1
INTRODUCTION
163
MOLECULAR
DYNAMICS
AND
MARKOV
STATE
MODELS
164
MARKOV
STATE
MODELS:
THEORY
AND
PROPERTIES
165
STRATEGIES
FOR
MSM
ESTIMATION,
VALIDATION,
AND
ANALYSIS
169
VARIATIONAL
APPROACH
FOR
CONFORMATIONAL
DYNAMICS
AND
MARKOV
PROCESSES
(VAC
AND
VAMP)
169
9.3.2
9.3.3
9.3.4
9.3.5
9.3.6
9.3.7
9.3.8
FEATURE
SELECTION
170
DIMENSIONALITY
REDUCTION
171
CLUSTERING
172
MODEL
ESTIMATION
AND
VALIDATION
173
SPECTRAL
GAPS
AND
COARSE
GRAINING
174
ADAPTIVE
AND
ENHANCED
SAMPLING
STRATEGIES
175
PRACTICAL
CONSIDERATION
FOR
STUDYING
PROTEIN-PROTEIN
ENCOUNTERS
176
CONTENTS
IX
9.3.9
9.4
9.4.1
9.4.1.1
9.4.2
9.4.3
ANALYSIS
OF
THE
ASSOCIATION-DISSOCIATION
PATH
ENSEMBLE
1
77
THE
CONNECTION
TO
EXPERIMENTS
178
EXPERIMENTAL
OBSERVABILITY,
FORWARD
MODELS,
AND
ERRORS
178
SOURCES
OF
ERRORS
AND
UNCERTAINTY
179
PREDICTING
EXPERIMENTAL
OBSERVABLES
USING
MSMS
180
INTEGRATING
EXPERIMENTAL
AND
SIMULATION
DATA
INTO
AUGMENTED
MARKOV
MODELS
181
9.5
9.6
PROTEIN-PROTEIN AND
PROTEIN-PEPTIDE
ENCOUNTERS
182
EMERGING
TECHNOLOGIES
184
ACKNOWLEDGMENTS
186
REFERENCES
186
10
TRANSCRIPTION
FACTOR
-
DNA
COMPLEXES
195
VOLKHARD
HELMS
10.1
10.2
10.3
10.4
10.5
10.6
10.7
10.8
10.8.1
10.8.2
10.8.3
10.9
10.10
10.11
10.12
10.13
INTRODUCTION
195
PRINCIPLES
OF
SEQUENCE
RECOGNITION
197
DIMERIZATION OF
EUKARYOTIC
TFS
198
DETECTION
OF
EPIGENETIC
MODIFICATIONS
199
DETECTION
OF
DNA
CURVATURE/BENDING
200
MODIFICATIONS
OF
TRANSCRIPTION
FACTORS
200
TRANSCRIPTION
FACTOR
BINDING
SITES
201
EXPERIMENTAL
DETECTION
OF
TFBS
201
PROTEIN-BINDING
MICROARRAYS
202
CHROMATIN
IMMUNOPRECIPITATION
ASSAYS
203
DAMID
PROFILING
OF
PROTEIN-DNA
INTERACTIONS
204
POSITION-SPECIFIC
SCORING
MATRICES
204
MOLECULAR
MODELING
OF
TF-DNA
COMPLEXES
204
CIS-REGULATORY
MODULES
205
RELATING
GENE
EXPRESSION
TO
BINDING
OF
TRANSCRIPTION
FACTORS
207
SUMMARY
208
REFERENCES
208
11
THE
CHROMATIN
INTERACTION
SYSTEM
213
SARAH
KREUZ,
STEFAN-SEBASTIAN
DAVID,
LORENA
VIRIDIANA
CORTES
MEDINA,
AND
WOLFGANG
FISCHLE
11.1
11.2
CHROMATIN
IS
A
SPECIAL
INTERACTION
PLATFORM
213
INTERACTION
OF
PROTEINS
WITH
HISTONE
POSTTRANSLATIONAL
MODIFICATIONS
215
11.2.1
THE
HISTORY
OF
HISTONE
POSTTRANSLATIONAL
MODIFICATIONS
AND
THE
HISTONE
CODE
215
11.2.2
11.2.3
11.2.3.1
11.2.3.2
11.2.4
PEPTIDES
AND
NUCLEOSOMAL
TEMPLATES
FOR
STUDYING
HISTONE
PTMS
222
QUALITATIVE
ANALYSIS
OF
HISTONE
PTM
READOUT
224
CHARACTERIZING
BINDING
SPECIFICITIES
OF
KNOWN
READERS
224
IDENTIFICATION
OF
NEW
READER
PROTEINS
225
MOLECULAR
PARAMETERS
OF
HISTONE
PTM-READER
INTERACTION
226
X
CONTENTS
11.2.5
11.2.5.1
11.2.5.2
11.2.5.3
11.3
11.3.1
11.3.2
11.3.3
11.3.4
11.3.4.1
11.3.4.2
11.3.5
CELLULAR
ASSAYS
TO
CHARACTERIZE HISTONE
PTM-READER
INTERACTIONS
227
VISUALIZING
HISTONE-READER
INTERACTIONS
227
CHROMATIN
IMMUNOPRECIPITATION
229
CELLULAR
LABELING
AND
AFFINITY
ENRICHMENT
231
INTERACTION
OF
PROTEINS
WITH
MODIFIED
NUCLEIC
ACIDS
231
DISCOVERY
OF
DNA
METHYLATION
AND
THE
FIRST
READER
PROTEINS
231
RNA
MODIFICATIONS
234
MODIFIED
DNA
AND
RNA
TEMPLATES
234
IN
VITRO
ASSAYS
FOR
IDENTIFYING
READERS
OF
NUCLEIC
ACID
METHYLATION
235
AFFINITY
PURIFICATION
TO
IDENTIFY
NOVEL
MODIFICATION
READERS
235
CHARACTERIZING
BINDING
SPECIFICITIES
OF
KNOWN
READERS
235
CELLULAR
ASSAYS
FOR
IDENTIFYING
READERS
OF
NUCLEIC
ACID
MODIFICATIONS
236
11.4
UHRF1
AS
AN
EXAMPLE
OF
A
MULTIDOMAIN
READER/WRITER
PROTEIN
OF
HISTONE
AND
DNA
MODIFICATIONS
239
11.5
11.5.1
11.5.2
11.5.3
HISTONE
CHAPERONES
AND
CHROMATIN
REMODELING
COMPLEXES
241
CHROMATIN
ASSEMBLY
AND
REMODELING
241
DISCOVERY
OF
HISTONE
CHAPERONES
AND
CHROMATIN
REMODELERS
242
METHODS
FOR
IDENTIFYING
HISTONE
CHAPERONES
AND
REMODELING
FACTORS
244
11.5.3.1
11.5.3.2
11.5.4
11.5.5
11.6
IMMUNOPRECIPITATION
ASSAYS
244
COMPUTATIONAL
METHODS
244
ASSAYS
TO
STUDY
CHAPERONE
AND
REMODELER
ACTIVITIES
245
CELLULAR
ASSAYS
245
CHALLENGES
IN
CHROMATIN
INTERACTOMICS
247
REFERENCES
248
12
RNA-PROTEIN
INTERACTOMICS
271
CORNELIA
KILCHERT
12.1
12.2
12.3
12.3.1
12.3.2
12.4
12.4.1
12.4.1.1
12.4.1.2
12.4.2
12.4.2.1
12.4.2.2
12.5
INTRODUCTION
271
INTERACTIONS
OF
PROTEINS
WITH
MRNA
AND
NCRNA
272
THE
BASIC
TOOLBOX
273
METABOLIC
RNA
LABELING
WITH
MODIFIED
NUCLEOBASES
273
RNA-PROTEIN
CROSSLINKING
274
RNA-PROTEIN
INTERACTOMICS
276
WHAT
PROTEINS
ARE
BOUND
TO
MY
RNA
(OR
RNA
IN
GENERAL)?
276
CATALOGING
THE
RBPOME
276
INTERACTOMES OF
SPECIFIC
RNAS
278
WHICH
RNA
SPECIES
ARE
BOUND
BY
MY
RBP?
280
COPURIFICATION
METHODS:
CLIP
AND
DERIVATIVES
280
PROXIMITY-DEPENDENT
LABELING
METHODS
280
OUTLOOK
282
NOTES
283
REFERENCES
283
CONTENTS
XI
13
INTERACTION
BETWEEN
PROTEINS
AND
BIOLOGICAL
MEMBRANES
293
LORANT
JANOSI
AND
ALEMAYEHU
A.
GORFE
13.1
13.2
INTRODUCTION
293
THE
PLASMA
MEMBRANE:
OVERVIEW
OF
ITS
STRUCTURE,
COMPOSITION,
AND
FUNCTION
294
13.3
LIPID-BASED
AND
PROTEIN-BASED
SORTING
OF
PLASMA
MEMBRANE
COMPONENTS
295
13.3.1
13.3.2
13.3.3
13.4
LIPID-BASED
SORTING
AND
DOMAIN
FORMATION
295
PROTEIN-BASED
SORTING
AND
MEMBRANE
CURVATURE
296
PROTEOLIPID
SORTING
AND
MEMBRANE
DOMAIN
STABILIZATION
297
INTERACTION
OF
PERIPHERAL
MEMBRANE
PROTEINS
WITH
MEMBRANE
LIPIDS
297
13.4.1
13.4.2
13.5
PROTEIN-BASED
MEMBRANE-TARGETING
MOTIFS
298
LIPID-BASED
MEMBRANE-TARGETING
MOTIFS
301
INTERACTIONS
AND
CONFORMATIONS
OF
TRANSMEMBRANE
PROTEINS
IN
LIPID
MEMBRANES
303
13.5.1
GLYCOPHORIN
A
AND
EGFR
AS
EXAMPLES
OF
SINGLE-PASS
TRANSMEMBRANE
PROTEINS
303
13.5.2
13.5.3
13.5.4
13.6
GPCR
AS
AN
EXAMPLE
OF
MULTI-PASS
TM
HELICAL
PROTEINS
306
AQUAPORIN
AS
AN
EXAMPLE
OF
OLIGOMERIC
MULTI-PASS
TM
PROTEINS
306
ANTIMICROBIAL
PEPTIDES:
PERIPHERAL
OR
INTEGRAL?
307
SUMMARY
308
ACKNOWLEDGMENT
308
REFERENCES
309
14
INTERACTIONS
OF
PROTEINS
WITH
SMALL
MOLECULES,
ALLOSTERIC
EFFECTS
315
MICHAEL
C.
HUTTER
ABBREVIATIONS
315
14.1
14.2
14.3
14.3.1
14.3.2
14.3.3
14.3.3.1
14.3.3.2
INTRODUCTION
315
MODES
OF
BINDING
TO
PROTEINS
316
TYPES
OF
INTERACTION
BETWEEN
PROTEIN
AND
LIGAND
317
SALT
BRIDGES
317
COORDINATION
OF
IONS
VIA
LONE
PAIRS
318
HYDROGEN
BONDS
319
DEFINITION
319
OCCURRENCE
AND
FUNCTIONALITY
OF
HYDROGEN
BONDS
IN
BIOLOGICAL
SYSTEMS
320
14.3.3.3
14.3.3.4
14.3.3.5
14.3.3.6
14.3.3.7
14.3.4
CLASSIFICATION
OF
HYDROGEN
BONDS
321
WEAK
HYDROGEN
BONDS
321
HYDROGEN
BONDS
TO
FLUORINE
322
NITROGEN
VS.
OXYGEN
AS
COMPETING
HYDROGEN
BOND
ACCEPTORS
322
BIFURCATED
HYDROGEN
BONDS
322
HALOGEN
BONDS
323
XII
CONTENTS
14.3.5
14.3.6
14.3.7
14.3.8
14.3.9
14.4
VAN
DER
WAALS
INTERACTIONS
324
MUTUAL
INTERACTIONS
OF
DELOCALIZED
-ELECTRON
SYSTEMS
325
CATION-N
INTERACTION
325
ANION-A
INTERACTION
325
UNUSUAL
PROTEIN-LIGAND
CONTACTS
326
MODELING
INTERMOLECULAR
INTERACTIONS
BY
FORCE
FIELDS
AND
DOCKING
SIMULATIONS
326
14.5
14.6
14.7
14.8
ENTROPIC
ASPECTS
327
ALLOSTERIC
EFFECTS:
CONFORMATIONAL
CHANGES
UPON
LIGAND
BINDING
327
ASPECTS
OF
LIGAND
DESIGN
BEYOND
PROTEIN-LIGAND
INTERACTIONS
329
CONCLUSIONS
330
REFERENCES
330
15
EFFECTS
OF
MUTATIONS
IN
PROTEINS
ON
THEIR
INTERACTIONS
333
ALEXANDER
GRESS
AND
OLGA
V,
KALININA
15.1
15.2
15.2.1
15.2.2
15.3
15.3.1
15.3.2
INTRODUCTION
333
STRUCTURAL
ANNOTATION
OF
MUTATIONS IN
PROTEINS
334
DATABASES
FOR
STRUCTURAL
ANNOTATION
OF
MUTATIONS
335
DYNAMIC
STRUCTURAL
ANNOTATION
PIPELINES
340
METHODS
FOR
PREDICTING
EFFECT
OF
PROTEIN
MUTATIONS
342
PREDICTION
OF
PHENOTYPIC
EFFECT
343
ESTIMATION
OF
MUTATION
EFFECTS
BY
MODELING
BIOPHYSICAL
PROPERTIES
OF
PROTEINS
344
15.3.3
PREDICTION
OF
MECHANISTIC
EFFECTS
OF
MUTATIONS
ON
INTERACTIONS
OF
PROTEINS
345
15.4
CONCLUSION
348
ACKNOWLEDGMENTS
349
REFERENCES
349
16
NOT
QUITE
THE
SAME:
HOW
ALTERNATIVE
SPLICING
AFFECTS
PROTEIN
INTERACTIONS
359
ZAKARIA
LOUADI,
OLGA
TSOY
F
JAN
BAUMBACH,
TIM
KACPROWSKI,
AND
MARKUS
LIST
LIST
OF
ABBREVIATIONS
359
16.1
16.2
16.2.1
16.2.2
16.3
INTRODUCTION
359
EFFECTS
OF
ALTERNATIVE
SPLICING
ON
INDIVIDUAL
PROTEINS
362
ALTERNATIVE
SPLICING
AND
PROTEIN
STRUCTURE
362
ALTERNATIVE
SPLICING
AND
INTRINSICALLY
DISORDERED
REGIONS
362
EFFECTS
OF
ALTERNATIVE
SPLICING
ON
PROTEIN-PROTEIN
INTERACTION
NETWORKS
367
16.3.1
16.3.2
16.3.3
ALTERNATIVE
SPLICING
REWIRES
PROTEIN-PROTEIN
INTERACTIONS
367
ALTERNATIVE
SPLICING
IN
DISEASES
368
RESOURCES
FOR
STUDYING
THE
EFFECT
OF
ALTERNATIVE
SPLICING
ON
PROTEIN-PROTEIN
INTERACTIONS
369
16.4
CONCLUSION
AND
FUTURE
WORK
373
REFERENCES
374
CONTENTS
XIII
INDEX
405
17
PHOSPHORYLATION-BASED
MOLECULAR
SWITCHES
381
ATTILA
REMENYI
17.1
17.1.1
17.2
INTRODUCTION
381
STRUCTURAL
AND
FUNCTIONAL
EFFECTS
OF
PROTEIN
PHOSPHORYLATION
383
REVERSIBLE
PROTEIN
PHOSPHORYLATION IN
CELLULAR
SIGNALING:
WRITERS,
READERS,
AND
ERASERS
386
17.3
PROTEIN
KINASES
AS
MOLECULAR
SWITCHES
AND
AS
COMPONENTS OF
SIGNALING
CASCADES
388
17.4
MECHANISMS
OF
PHOSPHORYLATION
SPECIFICITY:
THE
IMPORTANCE
OF
SHORT
LINEAR
MOTIFS
390
17.5
17.6
EXAMPLES
OF
PHOSPHO-SWITCH-BASED
BIOLOGICAL
REGULATION
392
CONCLUSION
395
ACKNOWLEDGMENTS
397
REFERENCES
397
18
SUMMARY
AND
OUTLOOK
401
VOLKHARD
HELMS
AND
OLGA
V.
KALININA
18.1
18.2
18.3
18.4
TECHNICAL
STATE
OF
THE
ART
401
ROLE
OF
MACHINE
LEARNING
401
CHALLENGES
402
WHAT
PICTURE(S)
MAY
EVOLVE?
403
REFERENCES
404
|
| adam_txt |
CONTENTS
PREFACE
XV
1
PROTEIN
STRUCTURE
AND
CONFORMATIONAL
DYNAMICS
1
VOLKHARD
HELMS
1.1
1.1.1
1.1.2
1.1.3
1.1.4
1.1.5
1.1.6
1.1.7
1.2
1.2.1
1.2.2
1.2.3
1.2.4
1.3
1.3.1
1.3.2
1.3.3
1.3.4
1.4
STRUCTURAL
AND
HIERARCHICAL
ASPECTS
1
SIZE
OF
PROTEINS
1
PROTEIN
DOMAINS
1
PROTEIN
COMPOSITION
2
SECONDARY
STRUCTURE
ELEMENTS
3
ACTIVE
SITES
3
MEMBRANE
PROTEINS
6
FOLDING
OF
PROTEINS
7
CONFORMATIONAL
DYNAMICS
8
LARGE-SCALE
DOMAIN
MOTIONS
8
DYNAMICS
OF
N-TERMINAL
AND
C-TERMINAL
TAILS
9
SURFACE
DYNAMICS
9
DISORDERED
PROTEINS
9
FROM
STRUCTURE
TO
FUNCTION
10
EVOLUTIONARY
CONSERVATION
10
BINDING
INTERFACES
10
SURFACE
LOOPS
11
POSTTRANSLATIONAL
MODIFICATIONS
11
SUMMARY
11
REFERENCES
12
2
PROTEIN-PROTEIN-BINDING
INTERFACES
15
ZEYNEP
ABALI,
DAMLA
OVEK,
SIMGE
SENYUZ,
OZLEM
KESKIN,
AND
ATTILA
GURSOY
2.1
2.2
2.3
2.4
2.5
2.6
DEFINITION
AND
PROPERTIES
OF
PROTEIN-PROTEIN
INTERFACES
15
GROWING
NUMBER
OF
KNOWN
PROTEIN-PROTEIN
INTERFACE
STRUCTURES
18
SURFACE
AREAS
OF
PROTEIN-PROTEIN
INTERFACES
21
GAP
VOLUME
OF
PROTEIN-PROTEIN
INTERFACES
22
AMINO
ACID
COMPOSITION
OF
INTERFACES
22
SECONDARY
STRUCTURE
OF
INTERFACES
23
VI
CONTENTS
2.7
2.8
2.9
2.10
2.11
2.12
2.13
2.14
PROTEIN-PROTEIN-BINDING
ENERGY
24
INTERFACES
OF
HOMO
AND
HETERO-DIMERIC
COMPLEXES
24
INTERFACES
OF
NON-OBLIGATE
AND
OBLIGATE
COMPLEXES
25
INTERFACES
OF
TRANSIENT
AND
PERMANENT
COMPLEXES
25
BIOLOGICAL
VS.
CRYSTAL
INTERFACES
26
TYPE
I,
TYPE
II,
AND
TYPE
III
INTERFACES
27
CONSERVED
RESIDUES
AND
HOT
SPOTS
IN
INTERFACES
28
CONCLUSION
AND
FUTURE
IMPLICATIONS
29
REFERENCES
30
3
CORRELATED
COEVOLVING
MUTATIONS
AT
PROTEIN-PROTEIN
INTERFACES
39
ALEXANDER
SCHUG
3.1
3.2
3.3
3.3.1
3.3.2
INTRODUCTION
39
A
SHORT
INTRODUCTION
INTO
BIOMOLECULAR
MODELING
41
STATISTICAL
INFERENCE
OF
COEVOLUTION
41
LIMITATIONS
OF
LOCAL
STATISTICAL
INFERENCE
41
DIRECT-COUPLING
ANALYSIS-A
POTTS
MODEL
BASED
ON
MULTIPLE
SEQUENCE
ALIGNMENTS
42
3.4
3.5
3.6
3.7
SOLVING
THE
INVERSE
POTTS
MODEL
43
CONTACT
GUIDED
PROTEIN
AND
RNA
STRUCTURE
PREDICTION
45
INTER-MONOMER
INTERACTION
AND
SIGNALING
45
SUMMARY
46
REFERENCES
47
4
COMPUTATIONAL
PROTEIN
-
PROTEIN
DOCKING
53
MARTIN
ZACHARIAS
4.1
4.2
4.3
4.4
INTRODUCTION
53
RIGID
BODY
PROTEIN-PROTEIN
DOCKING
APPROACHES
56
ACCOUNTING
FOR
CONFORMATIONAL
CHANGES
DURING
DOCKING
59
INTEGRATION
OF
BIOINFORMATICS
AND
EXPERIMENTAL
DATA
FOR
PROTEIN-PROTEIN
DOCKING
61
4.5
4.6
4.7
4.8
TEMPLATE-BASED
PROTEIN-PROTEIN
DOCKING
62
FLEXIBLE
REFINEMENT
OF
DOCKED
COMPLEXES
64
SCORING
OF
DOCKED
COMPLEXES
66
CONCLUSIONS
AND
FUTURE
DEVELOPMENTS
67
ACKNOWLEDGMENTS
68
REFERENCES
68
5
IDENTIFICATION
OF
PUTATIVE
PROTEIN
COMPLEXES
IN
PROTEIN-PROTEIN
INTERACTION
NETWORKS
77
SUDHARSHINI
THANGAMURUGAN,
MARKUS
HOLLANDER,
AND
VOLKHARD
HELMS
5.1
5.2
5.3
PROTEIN-PROTEIN
INTERACTION
NETWORKS
77
INTEGRATION
OF
VARIOUS
PPI
RESOURCES
IN
PUBLIC
DATA
REPOSITORIES
79
PROTEIN-PROTEIN
INTERACTION
NETWORKS
OF
MODEL
ORGANISMS
80
CONTENTS
VII
5.3.1
PPIN
OF
SACCHAROMYCES
CEREVISIAE
80
5.3.2
PPIN
OF
HUMAN
83
5.4
ALGORITHMS
TO
IDENTIFY
PROTEIN
COMPLEXES
IN
PPI
NETWORKS
84
5.4.1
MOLECULAR
COMPLEX
DETECTION
(MCODE)
84
5.4.1.1
DEFINITIONS
85
5.4.1.2
ALGORITHM
86
5.4.1.3
EXAMPLES
88
5.4.2
CLUSTERING
WITH
OVERLAPPING
NEIGHBORHOOD
EXPANSION
(CLUSTERONE)
89
5.4.2.1
DEFINITIONS
89
5.4.2.2
ALGORITHM
90
5.4.3
DOMAIN-AWARE
COHESIVENESS
OPTIMIZATION
(DACO)
92
5.5
SUMMARY
94
REFERENCES
95
6
STRUCTURE,
COMPOSITION,
AND
MODELING
OF
PROTEIN
COMPLEXES
101
OLGA
V.
KALININA
6.1
PROTEIN
COMPLEX
STRUCTURE
101
6.1.1
PROTEIN
QUATERNARY
STRUCTURE
101
6.1.2
CLASSIFICATION
OF
PROTEIN-PROTEIN
INTERACTION
INTERFACES
102
6.1.3
CLASSIFICATION
AND
EVOLUTION
OF
PROTEIN
COMPLEXES
105
6.2
METHODS
FOR
AUTOMATED
ASSIGNMENT
OF
BIOLOGICAL
ASSEMBLIES
106
6.2.1
ASSIGNMENT
FROM
CRYSTALLOGRAPHIC
DATA
107
6.2.2
EMPLOYING
MACHINE-LEARNING
METHODS
108
6.2.3
LEVERAGING
EVOLUTIONARY
INFORMATION
109
6.3
COMPUTATIONAL
APPROACHES
TO
PREDICTING
3D
STRUCTURE
OF
PROTEIN
COMPLEXES
110
6.3.1
COMBINATORIAL
DOCKING
110
6.3.2
HOMOLOGY-BASED
COMPLEX
RECONSTRUCTION
114
6.3.3
PREDICTION
FROM
SEQUENCE
115
6.3.4
ASSISTED
DOCKING
116
6.4
CONCLUSION
AND
OUTLOOK
117
ACKNOWLEDGMENTS
118
REFERENCES
118
7
LIVE-CELL
STRUCTURAL
BIOLOGY
TO
SOLVE
MOLECULAR
MECHANISMS:
STRUCTURAL
DYNAMICS
IN
THE
EXOCYST
FUNCTION
127
ALTAIR
C.
HERNANDEZ,
BALDO
OLIVA,
DAMIEN
P.
DEVOS,
AND
ORIOL
GALLEGO
7.1
INTRODUCTION
127
7.2
STRUCTURAL
BIOLOGY
USING
LIGHT
MICROSCOPY
METHODS
129
7.3
HYBRID
METHODS:
INTEGRATIVE
STRUCTURAL
BIOLOGY
131
7.4
INTEGRATIVE
MODELING:
THE
CASE
OF
THE
EXOCYST
COMPLEX
133
7.5
COMPARING
THE
IN
SITU
ARCHITECTURE
OF
THE
EXOCYST
WITH
A
HIGH-RESOLUTION
CRYO-EM
MODEL
136
VIII
CONTENTS
7.6
DISCUSSION
AND
FUTURE
PERSPECTIVES
138
ACKNOWLEDGEMENTS
139
REFERENCES
140
8
KINETICS
AND
THERMODYNAMICS
OF
PROTEIN-PROTEIN
ENCOUNTER
143
NICOLAS
KUNZEL
AND
VOLKHARD
HELMS
8.1
8.2
8.2.1
8.3
INTRODUCTION
143
THERMODYNAMIC
ENSEMBLES
AND
FREE
ENERGY
143
THE
ISOTHERMAL-ISOBARIC
ENSEMBLE
AND
THE
GIBBS
FREE
ENERGY
144
OVERVIEW
OF
COMPUTATIONAL
METHODS
TO
DETERMINE
BINDING
FREE
ENERGIES
146
8.3.1
8.3.1.1
8.3.2
8.3.2.1
8.3.3
8.3.3.1
8.3.3.2
8.3.3.3
8.3.3.4
8.3.3.5
8.3.4
8.3.4.1
8.3.4.2
8.3.5
8.3.6
COARSE
GRAINING
147
BROWNIAN
DYNAMICS
147
ENDPOINT
METHODS
149
MM/PBSA/MM/GBSA
149
POTENTIAL
OF
MEAN
FORCE/PATHWAY
METHODS
150
THERMODYNAMIC
INTEGRATION
151
UMBRELLA
SAMPLING
(US)
151
STEERED
MD
(SMD)
153
METADYNAMICS
153
ADAPTIVE
BIASING
FORCE
(ABF)
155
REPLICA-EXCHANGE
METHODS
155
PARALLEL
TEMPERING
155
GENERALIZED/HAMILTONIAN
REPLICA-EXCHANGE
METHODS
156
ADDITIONAL
PATHWAY
METHODS
156
RELATIVE
BINDING
FREE
ENERGIES
156
REFERENCES
157
9
MARKOV
STATE
MODELS
OF
PROTEIN
-
PROTEIN
ENCOUNTERS
163
SIMON
OLSSON
NOTATION
163
9.1
9.2
9.2.1
9.3
9.3.1
INTRODUCTION
163
MOLECULAR
DYNAMICS
AND
MARKOV
STATE
MODELS
164
MARKOV
STATE
MODELS:
THEORY
AND
PROPERTIES
165
STRATEGIES
FOR
MSM
ESTIMATION,
VALIDATION,
AND
ANALYSIS
169
VARIATIONAL
APPROACH
FOR
CONFORMATIONAL
DYNAMICS
AND
MARKOV
PROCESSES
(VAC
AND
VAMP)
169
9.3.2
9.3.3
9.3.4
9.3.5
9.3.6
9.3.7
9.3.8
FEATURE
SELECTION
170
DIMENSIONALITY
REDUCTION
171
CLUSTERING
172
MODEL
ESTIMATION
AND
VALIDATION
173
SPECTRAL
GAPS
AND
COARSE
GRAINING
174
ADAPTIVE
AND
ENHANCED
SAMPLING
STRATEGIES
175
PRACTICAL
CONSIDERATION
FOR
STUDYING
PROTEIN-PROTEIN
ENCOUNTERS
176
CONTENTS
IX
9.3.9
9.4
9.4.1
9.4.1.1
9.4.2
9.4.3
ANALYSIS
OF
THE
ASSOCIATION-DISSOCIATION
PATH
ENSEMBLE
1
77
THE
CONNECTION
TO
EXPERIMENTS
178
EXPERIMENTAL
OBSERVABILITY,
FORWARD
MODELS,
AND
ERRORS
178
SOURCES
OF
ERRORS
AND
UNCERTAINTY
179
PREDICTING
EXPERIMENTAL
OBSERVABLES
USING
MSMS
180
INTEGRATING
EXPERIMENTAL
AND
SIMULATION
DATA
INTO
AUGMENTED
MARKOV
MODELS
181
9.5
9.6
PROTEIN-PROTEIN AND
PROTEIN-PEPTIDE
ENCOUNTERS
182
EMERGING
TECHNOLOGIES
184
ACKNOWLEDGMENTS
186
REFERENCES
186
10
TRANSCRIPTION
FACTOR
-
DNA
COMPLEXES
195
VOLKHARD
HELMS
10.1
10.2
10.3
10.4
10.5
10.6
10.7
10.8
10.8.1
10.8.2
10.8.3
10.9
10.10
10.11
10.12
10.13
INTRODUCTION
195
PRINCIPLES
OF
SEQUENCE
RECOGNITION
197
DIMERIZATION OF
EUKARYOTIC
TFS
198
DETECTION
OF
EPIGENETIC
MODIFICATIONS
199
DETECTION
OF
DNA
CURVATURE/BENDING
200
MODIFICATIONS
OF
TRANSCRIPTION
FACTORS
200
TRANSCRIPTION
FACTOR
BINDING
SITES
201
EXPERIMENTAL
DETECTION
OF
TFBS
201
PROTEIN-BINDING
MICROARRAYS
202
CHROMATIN
IMMUNOPRECIPITATION
ASSAYS
203
DAMID
PROFILING
OF
PROTEIN-DNA
INTERACTIONS
204
POSITION-SPECIFIC
SCORING
MATRICES
204
MOLECULAR
MODELING
OF
TF-DNA
COMPLEXES
204
CIS-REGULATORY
MODULES
205
RELATING
GENE
EXPRESSION
TO
BINDING
OF
TRANSCRIPTION
FACTORS
207
SUMMARY
208
REFERENCES
208
11
THE
CHROMATIN
INTERACTION
SYSTEM
213
SARAH
KREUZ,
STEFAN-SEBASTIAN
DAVID,
LORENA
VIRIDIANA
CORTES
MEDINA,
AND
WOLFGANG
FISCHLE
11.1
11.2
CHROMATIN
IS
A
SPECIAL
INTERACTION
PLATFORM
213
INTERACTION
OF
PROTEINS
WITH
HISTONE
POSTTRANSLATIONAL
MODIFICATIONS
215
11.2.1
THE
HISTORY
OF
HISTONE
POSTTRANSLATIONAL
MODIFICATIONS
AND
THE
HISTONE
CODE
215
11.2.2
11.2.3
11.2.3.1
11.2.3.2
11.2.4
PEPTIDES
AND
NUCLEOSOMAL
TEMPLATES
FOR
STUDYING
HISTONE
PTMS
222
QUALITATIVE
ANALYSIS
OF
HISTONE
PTM
READOUT
224
CHARACTERIZING
BINDING
SPECIFICITIES
OF
KNOWN
READERS
224
IDENTIFICATION
OF
NEW
READER
PROTEINS
225
MOLECULAR
PARAMETERS
OF
HISTONE
PTM-READER
INTERACTION
226
X
CONTENTS
11.2.5
11.2.5.1
11.2.5.2
11.2.5.3
11.3
11.3.1
11.3.2
11.3.3
11.3.4
11.3.4.1
11.3.4.2
11.3.5
CELLULAR
ASSAYS
TO
CHARACTERIZE HISTONE
PTM-READER
INTERACTIONS
227
VISUALIZING
HISTONE-READER
INTERACTIONS
227
CHROMATIN
IMMUNOPRECIPITATION
229
CELLULAR
LABELING
AND
AFFINITY
ENRICHMENT
231
INTERACTION
OF
PROTEINS
WITH
MODIFIED
NUCLEIC
ACIDS
231
DISCOVERY
OF
DNA
METHYLATION
AND
THE
FIRST
READER
PROTEINS
231
RNA
MODIFICATIONS
234
MODIFIED
DNA
AND
RNA
TEMPLATES
234
IN
VITRO
ASSAYS
FOR
IDENTIFYING
READERS
OF
NUCLEIC
ACID
METHYLATION
235
AFFINITY
PURIFICATION
TO
IDENTIFY
NOVEL
MODIFICATION
READERS
235
CHARACTERIZING
BINDING
SPECIFICITIES
OF
KNOWN
READERS
235
CELLULAR
ASSAYS
FOR
IDENTIFYING
READERS
OF
NUCLEIC
ACID
MODIFICATIONS
236
11.4
UHRF1
AS
AN
EXAMPLE
OF
A
MULTIDOMAIN
READER/WRITER
PROTEIN
OF
HISTONE
AND
DNA
MODIFICATIONS
239
11.5
11.5.1
11.5.2
11.5.3
HISTONE
CHAPERONES
AND
CHROMATIN
REMODELING
COMPLEXES
241
CHROMATIN
ASSEMBLY
AND
REMODELING
241
DISCOVERY
OF
HISTONE
CHAPERONES
AND
CHROMATIN
REMODELERS
242
METHODS
FOR
IDENTIFYING
HISTONE
CHAPERONES
AND
REMODELING
FACTORS
244
11.5.3.1
11.5.3.2
11.5.4
11.5.5
11.6
IMMUNOPRECIPITATION
ASSAYS
244
COMPUTATIONAL
METHODS
244
ASSAYS
TO
STUDY
CHAPERONE
AND
REMODELER
ACTIVITIES
245
CELLULAR
ASSAYS
245
CHALLENGES
IN
CHROMATIN
INTERACTOMICS
247
REFERENCES
248
12
RNA-PROTEIN
INTERACTOMICS
271
CORNELIA
KILCHERT
12.1
12.2
12.3
12.3.1
12.3.2
12.4
12.4.1
12.4.1.1
12.4.1.2
12.4.2
12.4.2.1
12.4.2.2
12.5
INTRODUCTION
271
INTERACTIONS
OF
PROTEINS
WITH
MRNA
AND
NCRNA
272
THE
BASIC
TOOLBOX
273
METABOLIC
RNA
LABELING
WITH
MODIFIED
NUCLEOBASES
273
RNA-PROTEIN
CROSSLINKING
274
RNA-PROTEIN
INTERACTOMICS
276
WHAT
PROTEINS
ARE
BOUND
TO
MY
RNA
(OR
RNA
IN
GENERAL)?
276
CATALOGING
THE
RBPOME
276
INTERACTOMES OF
SPECIFIC
RNAS
278
WHICH
RNA
SPECIES
ARE
BOUND
BY
MY
RBP?
280
COPURIFICATION
METHODS:
CLIP
AND
DERIVATIVES
280
PROXIMITY-DEPENDENT
LABELING
METHODS
280
OUTLOOK
282
NOTES
283
REFERENCES
283
CONTENTS
XI
13
INTERACTION
BETWEEN
PROTEINS
AND
BIOLOGICAL
MEMBRANES
293
LORANT
JANOSI
AND
ALEMAYEHU
A.
GORFE
13.1
13.2
INTRODUCTION
293
THE
PLASMA
MEMBRANE:
OVERVIEW
OF
ITS
STRUCTURE,
COMPOSITION,
AND
FUNCTION
294
13.3
LIPID-BASED
AND
PROTEIN-BASED
SORTING
OF
PLASMA
MEMBRANE
COMPONENTS
295
13.3.1
13.3.2
13.3.3
13.4
LIPID-BASED
SORTING
AND
DOMAIN
FORMATION
295
PROTEIN-BASED
SORTING
AND
MEMBRANE
CURVATURE
296
PROTEOLIPID
SORTING
AND
MEMBRANE
DOMAIN
STABILIZATION
297
INTERACTION
OF
PERIPHERAL
MEMBRANE
PROTEINS
WITH
MEMBRANE
LIPIDS
297
13.4.1
13.4.2
13.5
PROTEIN-BASED
MEMBRANE-TARGETING
MOTIFS
298
LIPID-BASED
MEMBRANE-TARGETING
MOTIFS
301
INTERACTIONS
AND
CONFORMATIONS
OF
TRANSMEMBRANE
PROTEINS
IN
LIPID
MEMBRANES
303
13.5.1
GLYCOPHORIN
A
AND
EGFR
AS
EXAMPLES
OF
SINGLE-PASS
TRANSMEMBRANE
PROTEINS
303
13.5.2
13.5.3
13.5.4
13.6
GPCR
AS
AN
EXAMPLE
OF
MULTI-PASS
TM
HELICAL
PROTEINS
306
AQUAPORIN
AS
AN
EXAMPLE
OF
OLIGOMERIC
MULTI-PASS
TM
PROTEINS
306
ANTIMICROBIAL
PEPTIDES:
PERIPHERAL
OR
INTEGRAL?
307
SUMMARY
308
ACKNOWLEDGMENT
308
REFERENCES
309
14
INTERACTIONS
OF
PROTEINS
WITH
SMALL
MOLECULES,
ALLOSTERIC
EFFECTS
315
MICHAEL
C.
HUTTER
ABBREVIATIONS
315
14.1
14.2
14.3
14.3.1
14.3.2
14.3.3
14.3.3.1
14.3.3.2
INTRODUCTION
315
MODES
OF
BINDING
TO
PROTEINS
316
TYPES
OF
INTERACTION
BETWEEN
PROTEIN
AND
LIGAND
317
SALT
BRIDGES
317
COORDINATION
OF
IONS
VIA
LONE
PAIRS
318
HYDROGEN
BONDS
319
DEFINITION
319
OCCURRENCE
AND
FUNCTIONALITY
OF
HYDROGEN
BONDS
IN
BIOLOGICAL
SYSTEMS
320
14.3.3.3
14.3.3.4
14.3.3.5
14.3.3.6
14.3.3.7
14.3.4
CLASSIFICATION
OF
HYDROGEN
BONDS
321
WEAK
HYDROGEN
BONDS
321
HYDROGEN
BONDS
TO
FLUORINE
322
NITROGEN
VS.
OXYGEN
AS
COMPETING
HYDROGEN
BOND
ACCEPTORS
322
BIFURCATED
HYDROGEN
BONDS
322
HALOGEN
BONDS
323
XII
CONTENTS
14.3.5
14.3.6
14.3.7
14.3.8
14.3.9
14.4
VAN
DER
WAALS
INTERACTIONS
324
MUTUAL
INTERACTIONS
OF
DELOCALIZED
-ELECTRON
SYSTEMS
325
CATION-N
INTERACTION
325
ANION-A
INTERACTION
325
UNUSUAL
PROTEIN-LIGAND
CONTACTS
326
MODELING
INTERMOLECULAR
INTERACTIONS
BY
FORCE
FIELDS
AND
DOCKING
SIMULATIONS
326
14.5
14.6
14.7
14.8
ENTROPIC
ASPECTS
327
ALLOSTERIC
EFFECTS:
CONFORMATIONAL
CHANGES
UPON
LIGAND
BINDING
327
ASPECTS
OF
LIGAND
DESIGN
BEYOND
PROTEIN-LIGAND
INTERACTIONS
329
CONCLUSIONS
330
REFERENCES
330
15
EFFECTS
OF
MUTATIONS
IN
PROTEINS
ON
THEIR
INTERACTIONS
333
ALEXANDER
GRESS
AND
OLGA
V,
KALININA
15.1
15.2
15.2.1
15.2.2
15.3
15.3.1
15.3.2
INTRODUCTION
333
STRUCTURAL
ANNOTATION
OF
MUTATIONS IN
PROTEINS
334
DATABASES
FOR
STRUCTURAL
ANNOTATION
OF
MUTATIONS
335
DYNAMIC
STRUCTURAL
ANNOTATION
PIPELINES
340
METHODS
FOR
PREDICTING
EFFECT
OF
PROTEIN
MUTATIONS
342
PREDICTION
OF
PHENOTYPIC
EFFECT
343
ESTIMATION
OF
MUTATION
EFFECTS
BY
MODELING
BIOPHYSICAL
PROPERTIES
OF
PROTEINS
344
15.3.3
PREDICTION
OF
MECHANISTIC
EFFECTS
OF
MUTATIONS
ON
INTERACTIONS
OF
PROTEINS
345
15.4
CONCLUSION
348
ACKNOWLEDGMENTS
349
REFERENCES
349
16
NOT
QUITE
THE
SAME:
HOW
ALTERNATIVE
SPLICING
AFFECTS
PROTEIN
INTERACTIONS
359
ZAKARIA
LOUADI,
OLGA
TSOY
F
JAN
BAUMBACH,
TIM
KACPROWSKI,
AND
MARKUS
LIST
LIST
OF
ABBREVIATIONS
359
16.1
16.2
16.2.1
16.2.2
16.3
INTRODUCTION
359
EFFECTS
OF
ALTERNATIVE
SPLICING
ON
INDIVIDUAL
PROTEINS
362
ALTERNATIVE
SPLICING
AND
PROTEIN
STRUCTURE
362
ALTERNATIVE
SPLICING
AND
INTRINSICALLY
DISORDERED
REGIONS
362
EFFECTS
OF
ALTERNATIVE
SPLICING
ON
PROTEIN-PROTEIN
INTERACTION
NETWORKS
367
16.3.1
16.3.2
16.3.3
ALTERNATIVE
SPLICING
REWIRES
PROTEIN-PROTEIN
INTERACTIONS
367
ALTERNATIVE
SPLICING
IN
DISEASES
368
RESOURCES
FOR
STUDYING
THE
EFFECT
OF
ALTERNATIVE
SPLICING
ON
PROTEIN-PROTEIN
INTERACTIONS
369
16.4
CONCLUSION
AND
FUTURE
WORK
373
REFERENCES
374
CONTENTS
XIII
INDEX
405
17
PHOSPHORYLATION-BASED
MOLECULAR
SWITCHES
381
ATTILA
REMENYI
17.1
17.1.1
17.2
INTRODUCTION
381
STRUCTURAL
AND
FUNCTIONAL
EFFECTS
OF
PROTEIN
PHOSPHORYLATION
383
REVERSIBLE
PROTEIN
PHOSPHORYLATION IN
CELLULAR
SIGNALING:
WRITERS,
READERS,
AND
ERASERS
386
17.3
PROTEIN
KINASES
AS
MOLECULAR
SWITCHES
AND
AS
COMPONENTS OF
SIGNALING
CASCADES
388
17.4
MECHANISMS
OF
PHOSPHORYLATION
SPECIFICITY:
THE
IMPORTANCE
OF
SHORT
LINEAR
MOTIFS
390
17.5
17.6
EXAMPLES
OF
PHOSPHO-SWITCH-BASED
BIOLOGICAL
REGULATION
392
CONCLUSION
395
ACKNOWLEDGMENTS
397
REFERENCES
397
18
SUMMARY
AND
OUTLOOK
401
VOLKHARD
HELMS
AND
OLGA
V.
KALININA
18.1
18.2
18.3
18.4
TECHNICAL
STATE
OF
THE
ART
401
ROLE
OF
MACHINE
LEARNING
401
CHALLENGES
402
WHAT
PICTURE(S)
MAY
EVOLVE?
403
REFERENCES
404 |
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| illustrated | Illustrated |
| index_date | 2024-07-03T20:52:31Z |
| indexdate | 2024-07-10T09:40:44Z |
| institution | BVB |
| isbn | 9783527348640 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-033908679 |
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| physical | xvi, 411 Seiten Illustrationen, Diagramme |
| publishDate | 2023 |
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| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Protein interactions the molecular basis of interactomics edited by Volkhard Helms and Olga V. Kalinina Weinheim Wiley-VCH [2023] © 2023 xvi, 411 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Literaturangaben und Index Protein-protein interactions Molecular biology Cell receptors Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd rswk-swf Biochemie u. Chemische Biologie Biochemistry (Chemical Biology) Bioinformatics & Computational Biology Bioinformatik u. Computersimulationen in der Biowissenschaften Biowissenschaften Cell & Molecular Biology Chemie Chemistry Life Sciences Zell- u. Molekularbiologie CHB0: Biochemie u. Chemische Biologie LS30: Zell- u. Molekularbiologie LSG0: Bioinformatik u. Computersimulationen in der Biowissenschaften Protein-Protein-Wechselwirkung (DE-588)4745193-2 s DE-604 Helms, Volkhard (DE-588)135851246 edt Kalinina, Olga V. (DE-588)1072406853 edt Erscheint auch als Online-Ausgabe, PDF 978-3-527-83051-0 Erscheint auch als Online-Ausgabe, EPUB 978-3-527-83052-7 Erscheint auch als Online-Ausgabe 978-3-527-83050-3 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=033908679&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Protein interactions the molecular basis of interactomics Protein-protein interactions Molecular biology Cell receptors Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd |
| subject_GND | (DE-588)4745193-2 |
| title | Protein interactions the molecular basis of interactomics |
| title_auth | Protein interactions the molecular basis of interactomics |
| title_exact_search | Protein interactions the molecular basis of interactomics |
| title_exact_search_txtP | Protein interactions the molecular basis of interactomics |
| title_full | Protein interactions the molecular basis of interactomics edited by Volkhard Helms and Olga V. Kalinina |
| title_fullStr | Protein interactions the molecular basis of interactomics edited by Volkhard Helms and Olga V. Kalinina |
| title_full_unstemmed | Protein interactions the molecular basis of interactomics edited by Volkhard Helms and Olga V. Kalinina |
| title_short | Protein interactions |
| title_sort | protein interactions the molecular basis of interactomics |
| title_sub | the molecular basis of interactomics |
| topic | Protein-protein interactions Molecular biology Cell receptors Protein-Protein-Wechselwirkung (DE-588)4745193-2 gnd |
| topic_facet | Protein-protein interactions Molecular biology Cell receptors Protein-Protein-Wechselwirkung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=033908679&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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