Protein folding kinetics: biophysical methods ; with 15 tables
Gespeichert in:
| Format: | Elektronisch E-Book |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2006
|
| Ausgabe: | 2. ed. |
| Schlagworte: | |
| Online-Zugang: | UBR01 Volltext Inhaltsverzeichnis |
| Beschreibung: | 1 Online-Ressource |
| ISBN: | 9783540272779 9783540272786 |
| DOI: | 10.1007/b138868 |
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| 245 | 1 | 0 | |a Protein folding kinetics |b biophysical methods ; with 15 tables |c Bengt Nölting |
| 250 | |a 2. ed. | ||
| 264 | 1 | |a Berlin [u.a.] |b Springer |c 2006 | |
| 300 | |a 1 Online-Ressource | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b c |2 rdamedia | ||
| 338 | |b cr |2 rdacarrier | ||
| 650 | 0 | 7 | |a Proteinfaltung |0 (DE-588)4324567-5 |2 gnd |9 rswk-swf |
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| 689 | 0 | 1 | |a Reaktionskinetik |0 (DE-588)4048655-2 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Nölting, Bengt |d 1962- |e Sonstige |0 (DE-588)113522673 |4 oth | |
| 776 | 0 | 8 | |i Erscheint auch als |n Druck-Ausgabe, Hardcover |z 3-540-27277-1 |
| 856 | 4 | 0 | |u https://doi.org/10.1007/b138868 |x Verlag |3 Volltext |
| 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=016232215&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
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Datensatz im Suchindex
| _version_ | 1804137251488137216 |
|---|---|
| adam_text | CONTENTS
1
INTRODUCTION
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
2
STRUCTURES OF PROTEINS
. . . . . . . . . . . . . . . . . . . . . . . .
5
2.1
PRIMARY STRUCTURE
. . . . . . . . . . . . . . . . . . . . . . . . .
5
2.2
SECONDARY STRUCTURE
. . . . . . . . . . . . . . . . . . . . . . .
9
2.3
TERTIARY STRUCTURE
. . . . . . . . . . . . . . . . . . . . . . . . .
11
3
PHYSICAL INTERACTIONS THAT DETERMINE
THE PROPERTIES OF PROTEINS
. . . . . . . . . . . . . .
17
3.1
ELECTROSTATIC INTERACTIONS
. . . . . . . . . . . . . . . . . . . . .
17
3.1.1
POINT CHARGES
. . . . . . . . . . . . . . . . . . . . . .
17
3.1.2
POINT CHARGE
YY
DIPOLE AND DIPOLE
YY
DIPOLE INTERACTIONS
. . .
19
3.2
QUANTUM-MECHANICAL SHORT-RANGE REPULSION
. . . . . . . . . . .
19
3.3
HYDROGEN BONDING
. . . . . . . . . . . . . . . . . . . . . . . .
21
3.4
HYDROPHOBIC INTERACTION
. . . . . . . . . . . . . . . . . . . . .
22
4
CALCULATION OF THE KINETIC RATE CONSTANTS
. . . . . . . . . . . .
27
4.1
TRANSITION STATE THEORY
. . . . . . . . . . . . . . . . . . . . . .
28
4.2
TWO-STATE TRANSITIONS
. . . . . . . . . . . . . . . . . . . . . .
29
4.2.1
REVERSIBLE TWO-STATE TRANSITION
. . . . . . . . . . . . .
29
4.2.2
IRREVERSIBLE TWO-STATE TRANSITION
. . . . . . . . . . . .
30
4.3
THREE-STATE TRANSITIONS
. . . . . . . . . . . . . . . . . . . . . .
31
4.3.1
REVERSIBLE THREE-STATE TRANSITIONS
. . . . . . . . . . . .
31
4.3.1.1
REVERSIBLE SEQUENTIAL THREE-STATE TRANSITION
. . . . . . .
31
4.3.1.2
REVERSIBLE TWO-PATHWAY THREE-STATE TRANSITION
. . . . .
34
4.3.1.3
REVERSIBLE OFF-PATHWAY INTERMEDIATE
. . . . . . . . . . .
37
4.3.2
IRREVERSIBLE THREE-STATE TRANSITIONS
. . . . . . . . . . .
38
4.3.2.1
IRREVERSIBLE CONSECUTIVE THREE-STATE TRANSITION
. . . . . .
38
4.3.2.2
IRREVERSIBLE PARALLEL DECAY
. . . . . . . . . . . . . . .
39
4.4
REVERSIBLE SEQUENTIAL FOUR-STATE TRANSITION
. . . . . . . . . . . .
40
4.5
REACTIONS WITH MONOMER
YY
DIMER TRANSITIONS
. . . . . . . . . . .
41
4.5.1
MONOMER
YY
DIMER TRANSITION
. . . . . . . . . . . . . . .
41
CONTENTS
XII
4.5.2
REVERSIBLE TWO-STATE FOLDING TRANSITION LINKED
WITH A MONOMER
YY
DIMER TRANSITION
. . . . . .
43
4.6
KINETIC RATE CONSTANTS FOR PERTURBATION METHODS
. . . . . . . . .
44
4.7
SUMMARY
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
47
5
HIGH KINETIC RESOLUTION OF PROTEIN FOLDING EVENTS
. . . . . . .
51
5.1
ULTRAFAST MIXING
. . . . . . . . . . . . . . . . . . . . . . . . .
51
5.2
TEMPERATURE-JUMP
. . . . . . . . . . . . . . . . . . . . . . . .
55
5.2.1
ELECTRICAL-DISCHARGE-INDUCED T-JUMP
. . . . . . . . . .
55
5.2.1.1
T-JUMP APPARATUS
. . . . . . . . . . . . . . . . . . . .
55
5.2.1.2
OBSERVATION OF EARLY FOLDING EVENTS: REFOLDING
FROM THE COLD-UNFOLDED STATE
. . . . . .
58
5.2.1.3
OBSERVATION OF UNFOLDING INTERMEDIATES
. . . . . . . . .
61
5.2.2
LASER-INDUCED T-JUMP
. . . . . . . . . . . . . . . .
62
5.2.3
MAXIMUM TIME RESOLUTION IN T-JUMP EXPERIMENTS
. . . .
64
5.3
OPTICAL TRIGGERS
. . . . . . . . . . . . . . . . . . . . . . . . . .
65
5.3.1
LASER FLASH PHOTOLYSIS
. . . . . . . . . . . . . . . .
65
5.3.2
ELECTRON-TRANSFER-INDUCED REFOLDING
. . . . . . . . . . .
69
5.4
ACOUSTIC RELAXATION
. . . . . . . . . . . . . . . . . . . . . . . .
69
5.5
PRESSURE-JUMP
. . . . . . . . . . . . . . . . . . . . . . . . . .
72
5.6
DIELECTRIC RELAXATION AND ELECTRIC-FIELD-JUMP
. . . . . . . . . . .
73
5.7
NMR LINE BROADENING
. . . . . . . . . . . . . . . . . . . . . .
75
5.8
SUMMARY
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
76
6
KINETIC METHODS FOR SLOW REACTIONS
. . . . . . . . . . . . . . .
79
6.1
STOPPED-FLOW NUCLEAR MAGNETIC RESONANCE (NMR)
. . . . . . . .
79
6.2
FLUORESCENCE- AND ISOTOPE-LABELING
. . . . . . . . . . . . . . . .
80
6.2.1
FOLDING REACTIONS
. . . . . . . . . . . . . . . . . . . .
80
6.2.2
DISSOCIATION REACTIONS
. . . . . . . . . . . . . . . . . .
81
7
RESOLUTION OF PROTEIN STRUCTURES IN SOLUTION
. . . . . . . . . .
83
7.1
NUCLEAR MAGNETIC RESONANCE
. . . . . . . . . . . . . . . . . . .
83
7.2
CIRCULAR DICHROISM
. . . . . . . . . . . . . . . . . . . . . . . .
89
8
HIGH STRUCTURAL RESOLUTION OF TRANSIENT
PROTEIN CONFORMATIONS
. . . . . . . . . . . . . .
95
8.1
NMR DETECTION OF H/D EXCHANGE KINETICS
. . . . . . . . . . . .
95
8.2
TIME-RESOLVED CIRCULAR DICHROISM
. . . . . . . . . . . . . . . . .
98
8.3
YY
-VALUE ANALYSIS
. . . . . . . . . . . . . . . . . . . . . . . . .
105
CONTENTS
XIII
8.3.1
PROTEIN ENGINEERING
. . . . . . . . . . . . . . . . . . .
107
8.3.1.1
CASSETTE MUTAGENESIS
. . . . . . . . . . . . . . . . . .
108
8.3.1.2
PCR MUTAGENESIS
. . . . . . . . . . . . . . . . . . . .
108
8.3.2
DETERMINATION OF THE PROTEIN STABILITY
IN EQUILIBRIUM
. . . . . . . . . .
111
8.3.3
MEASUREMENT OF KINETIC RATE CONSTANTS OF FOLDING
AND UNFOLDING
. . . .
115
8.3.3.1
TWO-STATE KINETICS
. . . . . . . . . . . . . . . . . . .
116
8.3.3.2
THREE-STATE KINETICS
. . . . . . . . . . . . . . . . . . .
117
8.3.3.3
KINETIC IMPLICATIONS OF THE OCCURRENCE OF INTERMEDIATES
.
117
8.3.3.4
DISCRIMINATION BETWEEN FOLDING AND ASSOCIATION EVENTS
.
119
8.3.4
CALCULATION AND INTERPRETATION OF
YY
-VALUES
. . . . . . .
120
8.3.4.1
TWO-STATE TRANSITION
. . . . . . . . . . . . . . . . . .
120
8.3.4.2
MULTI-STATE TRANSITION
. . . . . . . . . . . . . . . . . .
121
8.3.4.3
RESIDUAL STRUCTURE IN THE UNFOLDED STATE
. . . . . . . . .
123
9
EXPERIMENTAL PROBLEMS OF THE KINETIC AND STRUCTURAL
RESOLUTION OF REACTIONS THAT INVOLVE PROTEINS
. . . . .
125
9.1
PROTEIN EXPRESSION PROBLEMS
. . . . . . . . . . . . . . . . . . .
125
9.1.1
LOW EXPRESSION LEVEL
. . . . . . . . . . . . . . . . . .
125
9.1.2
EXPRESSION ERRORS
. . . . . . . . . . . . . . . . . . . .
126
9.2
AGGREGATION
. . . . . . . . . . . . . . . . . . . . . . . . . . .
129
9.2.1
DETECTION
. . . . . . . . . . . . . . . . . . . . . . . .
129
9.2.2
AVOIDANCE OF AGGREGATION
. . . . . . . . . . . . . . . .
131
9.3
MISFOLDING
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
133
9.4
UNSTABLE CURVE FIT
. . . . . . . . . . . . . . . . . . . . . . . . .
135
10
THE FOLDING PATHWAY OF A PROTEIN (BARSTAR) AT THE
RESOLUTION OF INDIVIDUAL RESIDUES
FROM MICROSECONDS TO SECONDS
. . . . . . . .
137
10.1
INTRODUCTION
. . . . . . . . . . . . . . . . . . . . . . . . . . .
137
10.2
MATERIALS AND METHODS
. . . . . . . . . . . . . . . . . . . . . .
138
10.3
STRUCTURE OF NATIVE BARSTAR
. . . . . . . . . . . . . . . . . . . .
140
10.4
RESIDUAL STRUCTURE IN THE COLD-UNFOLDED STATE
. . . . . . . . . .
141
10.5
GROSS FEATURES OF THE FOLDING PATHWAY OF BARSTAR
. . . . . . . . .
143
10.5.1
EQUILIBRIUM STUDIES
. . . . . . . . . . . . . . . . . . .
143
10.5.2
KINETIC STUDIES
. . . . . . . . . . . . . . . . . . . . .
145
10.6
YY
-VALUE ANALYSIS
. . . . . . . . . . . . . . . . . . . . . . . . .
149
10.7
INTER-RESIDUE CONTACT MAPS
. . . . . . . . . . . . . . . . . . . .
152
10.8
THE HIGHLY RESOLVED FOLDING PATHWAY OF BARSTAR
. . . . . . . . . .
155
10.8.1
MICROSECOND TRANSITION STATE
. . . . . . . . . . . . . . .
157
CONTENTS
XIV
10.8.2
INTERMEDIATE
. . . . . . . . . . . . . . . . . . . . . .
157
10.8.3
LATE TRANSITION STATE
. . . . . . . . . . . . . . . . . . .
157
10.8.4
DIRECTIONAL PROPAGATION OF FOLDING
. . . . . . . . . . . .
157
10.8.5
CIS
YY
TRANS
ISOMERIZATION
. . . . . . . . . . . . . . . . .
158
10.8.6
ARE THERE FURTHER FOLDING EVENTS?
. . . . . . . . . . . . .
159
10.9
STRUCTURAL DISORDER AND MISFOLDING
. . . . . . . . . . . . . . . .
160
10.10
STRUCTURE OF PEPTIDES OF BARSTAR
. . . . . . . . . . . . . . . . .
162
10.11
NUCLEATION
YY
CONDENSATION MECHANISM OF FOLDING
. . . . . . . . .
162
11
HIGHLY RESOLVED FOLDING PATHWAYS AND MECHANISMS
OF SIX PROTEINS
. . . . .
165
11.1
GENERAL FEATURES OF THE MAIN TRANSITION STATES FOR THE
FORMATION OF THE NATIVE STRUCTURES
. . . . . .
165
11.2
NUCLEATION
YY
CONDENSATION . . . . . . . . . . . . . . . . . . . . .
176
11.3
FRAMEWORK-MODEL-LIKE PROPERTIES . . . . . . . . . . . . . . . .
179
11.4
CONCLUSIONS
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
179
12
STRUCTURAL DETERMINANTS OF THE RATE OF PROTEIN FOLDING
. . . . .
181
12.1
CHAIN TOPOLOGY AS A MAJOR STRUCTURAL DETERMINANT OF TWO-STATE
FOLDING
. .
181
12.2
CHAIN TOPOLOGY OF THE TRANSITION STATE AND IMPLICATIONS FOR THE
MECHANISM OF FOLDING
. .
184
12.3
FURTHER FACTORS
. . . . . . . . . . . . . . . . . . . . . . . . . .
184
12.4
ULTRAFAST FOLDING
. . . . . . . . . . . . . . . . . . . . . . . . . .
185
13
EVOLUTIONARY COMPUTER PROGRAMMING OF PROTEIN STRUCTURE
AND FOLDING
. .
187
13.1
EVOLUTION METHOD
. . . . . . . . . . . . . . . . . . . . . . . . .
188
13.2
PROTEIN FOLDING AND STRUCTURE PREDICTIONS
. . . . . . . . . . . . .
189
13.3
FURTHER POTENTIAL APPLICATIONS OF THE EVOLUTION METHOD
. . . . . .
194
14
CONCLUSIONS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
195
REFERENCES
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
197
INDEX
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
215
|
| adam_txt |
CONTENTS
1
INTRODUCTION
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
2
STRUCTURES OF PROTEINS
. . . . . . . . . . . . . . . . . . . . . . . .
5
2.1
PRIMARY STRUCTURE
. . . . . . . . . . . . . . . . . . . . . . . . .
5
2.2
SECONDARY STRUCTURE
. . . . . . . . . . . . . . . . . . . . . . .
9
2.3
TERTIARY STRUCTURE
. . . . . . . . . . . . . . . . . . . . . . . . .
11
3
PHYSICAL INTERACTIONS THAT DETERMINE
THE PROPERTIES OF PROTEINS
. . . . . . . . . . . . . .
17
3.1
ELECTROSTATIC INTERACTIONS
. . . . . . . . . . . . . . . . . . . . .
17
3.1.1
POINT CHARGES
. . . . . . . . . . . . . . . . . . . . . .
17
3.1.2
POINT CHARGE
YY
DIPOLE AND DIPOLE
YY
DIPOLE INTERACTIONS
. . .
19
3.2
QUANTUM-MECHANICAL SHORT-RANGE REPULSION
. . . . . . . . . . .
19
3.3
HYDROGEN BONDING
. . . . . . . . . . . . . . . . . . . . . . . .
21
3.4
HYDROPHOBIC INTERACTION
. . . . . . . . . . . . . . . . . . . . .
22
4
CALCULATION OF THE KINETIC RATE CONSTANTS
. . . . . . . . . . . .
27
4.1
TRANSITION STATE THEORY
. . . . . . . . . . . . . . . . . . . . . .
28
4.2
TWO-STATE TRANSITIONS
. . . . . . . . . . . . . . . . . . . . . .
29
4.2.1
REVERSIBLE TWO-STATE TRANSITION
. . . . . . . . . . . . .
29
4.2.2
IRREVERSIBLE TWO-STATE TRANSITION
. . . . . . . . . . . .
30
4.3
THREE-STATE TRANSITIONS
. . . . . . . . . . . . . . . . . . . . . .
31
4.3.1
REVERSIBLE THREE-STATE TRANSITIONS
. . . . . . . . . . . .
31
4.3.1.1
REVERSIBLE SEQUENTIAL THREE-STATE TRANSITION
. . . . . . .
31
4.3.1.2
REVERSIBLE TWO-PATHWAY THREE-STATE TRANSITION
. . . . .
34
4.3.1.3
REVERSIBLE OFF-PATHWAY INTERMEDIATE
. . . . . . . . . . .
37
4.3.2
IRREVERSIBLE THREE-STATE TRANSITIONS
. . . . . . . . . . .
38
4.3.2.1
IRREVERSIBLE CONSECUTIVE THREE-STATE TRANSITION
. . . . . .
38
4.3.2.2
IRREVERSIBLE PARALLEL DECAY
. . . . . . . . . . . . . . .
39
4.4
REVERSIBLE SEQUENTIAL FOUR-STATE TRANSITION
. . . . . . . . . . . .
40
4.5
REACTIONS WITH MONOMER
YY
DIMER TRANSITIONS
. . . . . . . . . . .
41
4.5.1
MONOMER
YY
DIMER TRANSITION
. . . . . . . . . . . . . . .
41
CONTENTS
XII
4.5.2
REVERSIBLE TWO-STATE FOLDING TRANSITION LINKED
WITH A MONOMER
YY
DIMER TRANSITION
. . . . . .
43
4.6
KINETIC RATE CONSTANTS FOR PERTURBATION METHODS
. . . . . . . . .
44
4.7
SUMMARY
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
47
5
HIGH KINETIC RESOLUTION OF PROTEIN FOLDING EVENTS
. . . . . . .
51
5.1
ULTRAFAST MIXING
. . . . . . . . . . . . . . . . . . . . . . . . .
51
5.2
TEMPERATURE-JUMP
. . . . . . . . . . . . . . . . . . . . . . . .
55
5.2.1
ELECTRICAL-DISCHARGE-INDUCED T-JUMP
. . . . . . . . . .
55
5.2.1.1
T-JUMP APPARATUS
. . . . . . . . . . . . . . . . . . . .
55
5.2.1.2
OBSERVATION OF EARLY FOLDING EVENTS: REFOLDING
FROM THE COLD-UNFOLDED STATE
. . . . . .
58
5.2.1.3
OBSERVATION OF UNFOLDING INTERMEDIATES
. . . . . . . . .
61
5.2.2
LASER-INDUCED T-JUMP
. . . . . . . . . . . . . . . .
62
5.2.3
MAXIMUM TIME RESOLUTION IN T-JUMP EXPERIMENTS
. . . .
64
5.3
OPTICAL TRIGGERS
. . . . . . . . . . . . . . . . . . . . . . . . . .
65
5.3.1
LASER FLASH PHOTOLYSIS
. . . . . . . . . . . . . . . .
65
5.3.2
ELECTRON-TRANSFER-INDUCED REFOLDING
. . . . . . . . . . .
69
5.4
ACOUSTIC RELAXATION
. . . . . . . . . . . . . . . . . . . . . . . .
69
5.5
PRESSURE-JUMP
. . . . . . . . . . . . . . . . . . . . . . . . . .
72
5.6
DIELECTRIC RELAXATION AND ELECTRIC-FIELD-JUMP
. . . . . . . . . . .
73
5.7
NMR LINE BROADENING
. . . . . . . . . . . . . . . . . . . . . .
75
5.8
SUMMARY
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
76
6
KINETIC METHODS FOR SLOW REACTIONS
. . . . . . . . . . . . . . .
79
6.1
STOPPED-FLOW NUCLEAR MAGNETIC RESONANCE (NMR)
. . . . . . . .
79
6.2
FLUORESCENCE- AND ISOTOPE-LABELING
. . . . . . . . . . . . . . . .
80
6.2.1
FOLDING REACTIONS
. . . . . . . . . . . . . . . . . . . .
80
6.2.2
DISSOCIATION REACTIONS
. . . . . . . . . . . . . . . . . .
81
7
RESOLUTION OF PROTEIN STRUCTURES IN SOLUTION
. . . . . . . . . .
83
7.1
NUCLEAR MAGNETIC RESONANCE
. . . . . . . . . . . . . . . . . . .
83
7.2
CIRCULAR DICHROISM
. . . . . . . . . . . . . . . . . . . . . . . .
89
8
HIGH STRUCTURAL RESOLUTION OF TRANSIENT
PROTEIN CONFORMATIONS
. . . . . . . . . . . . . .
95
8.1
NMR DETECTION OF H/D EXCHANGE KINETICS
. . . . . . . . . . . .
95
8.2
TIME-RESOLVED CIRCULAR DICHROISM
. . . . . . . . . . . . . . . . .
98
8.3
YY
-VALUE ANALYSIS
. . . . . . . . . . . . . . . . . . . . . . . . .
105
CONTENTS
XIII
8.3.1
PROTEIN ENGINEERING
. . . . . . . . . . . . . . . . . . .
107
8.3.1.1
CASSETTE MUTAGENESIS
. . . . . . . . . . . . . . . . . .
108
8.3.1.2
PCR MUTAGENESIS
. . . . . . . . . . . . . . . . . . . .
108
8.3.2
DETERMINATION OF THE PROTEIN STABILITY
IN EQUILIBRIUM
. . . . . . . . . .
111
8.3.3
MEASUREMENT OF KINETIC RATE CONSTANTS OF FOLDING
AND UNFOLDING
. . . .
115
8.3.3.1
TWO-STATE KINETICS
. . . . . . . . . . . . . . . . . . .
116
8.3.3.2
THREE-STATE KINETICS
. . . . . . . . . . . . . . . . . . .
117
8.3.3.3
KINETIC IMPLICATIONS OF THE OCCURRENCE OF INTERMEDIATES
.
117
8.3.3.4
DISCRIMINATION BETWEEN FOLDING AND ASSOCIATION EVENTS
.
119
8.3.4
CALCULATION AND INTERPRETATION OF
YY
-VALUES
. . . . . . .
120
8.3.4.1
TWO-STATE TRANSITION
. . . . . . . . . . . . . . . . . .
120
8.3.4.2
MULTI-STATE TRANSITION
. . . . . . . . . . . . . . . . . .
121
8.3.4.3
RESIDUAL STRUCTURE IN THE UNFOLDED STATE
. . . . . . . . .
123
9
EXPERIMENTAL PROBLEMS OF THE KINETIC AND STRUCTURAL
RESOLUTION OF REACTIONS THAT INVOLVE PROTEINS
. . . . .
125
9.1
PROTEIN EXPRESSION PROBLEMS
. . . . . . . . . . . . . . . . . . .
125
9.1.1
LOW EXPRESSION LEVEL
. . . . . . . . . . . . . . . . . .
125
9.1.2
EXPRESSION ERRORS
. . . . . . . . . . . . . . . . . . . .
126
9.2
AGGREGATION
. . . . . . . . . . . . . . . . . . . . . . . . . . .
129
9.2.1
DETECTION
. . . . . . . . . . . . . . . . . . . . . . . .
129
9.2.2
AVOIDANCE OF AGGREGATION
. . . . . . . . . . . . . . . .
131
9.3
MISFOLDING
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
133
9.4
UNSTABLE CURVE FIT
. . . . . . . . . . . . . . . . . . . . . . . . .
135
10
THE FOLDING PATHWAY OF A PROTEIN (BARSTAR) AT THE
RESOLUTION OF INDIVIDUAL RESIDUES
FROM MICROSECONDS TO SECONDS
. . . . . . . .
137
10.1
INTRODUCTION
. . . . . . . . . . . . . . . . . . . . . . . . . . .
137
10.2
MATERIALS AND METHODS
. . . . . . . . . . . . . . . . . . . . . .
138
10.3
STRUCTURE OF NATIVE BARSTAR
. . . . . . . . . . . . . . . . . . . .
140
10.4
RESIDUAL STRUCTURE IN THE COLD-UNFOLDED STATE
. . . . . . . . . .
141
10.5
GROSS FEATURES OF THE FOLDING PATHWAY OF BARSTAR
. . . . . . . . .
143
10.5.1
EQUILIBRIUM STUDIES
. . . . . . . . . . . . . . . . . . .
143
10.5.2
KINETIC STUDIES
. . . . . . . . . . . . . . . . . . . . .
145
10.6
YY
-VALUE ANALYSIS
. . . . . . . . . . . . . . . . . . . . . . . . .
149
10.7
INTER-RESIDUE CONTACT MAPS
. . . . . . . . . . . . . . . . . . . .
152
10.8
THE HIGHLY RESOLVED FOLDING PATHWAY OF BARSTAR
. . . . . . . . . .
155
10.8.1
MICROSECOND TRANSITION STATE
. . . . . . . . . . . . . . .
157
CONTENTS
XIV
10.8.2
INTERMEDIATE
. . . . . . . . . . . . . . . . . . . . . .
157
10.8.3
LATE TRANSITION STATE
. . . . . . . . . . . . . . . . . . .
157
10.8.4
DIRECTIONAL PROPAGATION OF FOLDING
. . . . . . . . . . . .
157
10.8.5
CIS
YY
TRANS
ISOMERIZATION
. . . . . . . . . . . . . . . . .
158
10.8.6
ARE THERE FURTHER FOLDING EVENTS?
. . . . . . . . . . . . .
159
10.9
STRUCTURAL DISORDER AND MISFOLDING
. . . . . . . . . . . . . . . .
160
10.10
STRUCTURE OF PEPTIDES OF BARSTAR
. . . . . . . . . . . . . . . . .
162
10.11
NUCLEATION
YY
CONDENSATION MECHANISM OF FOLDING
. . . . . . . . .
162
11
HIGHLY RESOLVED FOLDING PATHWAYS AND MECHANISMS
OF SIX PROTEINS
. . . . .
165
11.1
GENERAL FEATURES OF THE MAIN TRANSITION STATES FOR THE
FORMATION OF THE NATIVE STRUCTURES
. . . . . .
165
11.2
NUCLEATION
YY
CONDENSATION . . . . . . . . . . . . . . . . . . . . .
176
11.3
FRAMEWORK-MODEL-LIKE PROPERTIES . . . . . . . . . . . . . . . .
179
11.4
CONCLUSIONS
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
179
12
STRUCTURAL DETERMINANTS OF THE RATE OF PROTEIN FOLDING
. . . . .
181
12.1
CHAIN TOPOLOGY AS A MAJOR STRUCTURAL DETERMINANT OF TWO-STATE
FOLDING
. .
181
12.2
CHAIN TOPOLOGY OF THE TRANSITION STATE AND IMPLICATIONS FOR THE
MECHANISM OF FOLDING
. .
184
12.3
FURTHER FACTORS
. . . . . . . . . . . . . . . . . . . . . . . . . .
184
12.4
ULTRAFAST FOLDING
. . . . . . . . . . . . . . . . . . . . . . . . . .
185
13
EVOLUTIONARY COMPUTER PROGRAMMING OF PROTEIN STRUCTURE
AND FOLDING
. .
187
13.1
EVOLUTION METHOD
. . . . . . . . . . . . . . . . . . . . . . . . .
188
13.2
PROTEIN FOLDING AND STRUCTURE PREDICTIONS
. . . . . . . . . . . . .
189
13.3
FURTHER POTENTIAL APPLICATIONS OF THE EVOLUTION METHOD
. . . . . .
194
14
CONCLUSIONS
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
195
REFERENCES
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
197
INDEX
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
215 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author_GND | (DE-588)113522673 |
| building | Verbundindex |
| bvnumber | BV023028279 |
| classification_rvk | WD 5100 |
| classification_tum | CHE 802f PHY 821f CHE 820f |
| collection | ZDB-2-SBL |
| ctrlnum | (OCoLC)762184592 (DE-599)BVBBV023028279 |
| discipline | Chemie / Pharmazie Physik Biologie Chemie |
| discipline_str_mv | Chemie / Pharmazie Physik Biologie Chemie |
| doi_str_mv | 10.1007/b138868 |
| edition | 2. ed. |
| format | Electronic eBook |
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| id | DE-604.BV023028279 |
| illustrated | Not Illustrated |
| index_date | 2024-07-02T19:15:59Z |
| indexdate | 2024-07-09T21:09:19Z |
| institution | BVB |
| isbn | 9783540272779 9783540272786 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016232215 |
| oclc_num | 762184592 |
| open_access_boolean | |
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| owner_facet | DE-355 DE-BY-UBR |
| physical | 1 Online-Ressource |
| psigel | ZDB-2-SBL |
| publishDate | 2006 |
| publishDateSearch | 2006 |
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| publisher | Springer |
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| spelling | Protein folding kinetics biophysical methods ; with 15 tables Bengt Nölting 2. ed. Berlin [u.a.] Springer 2006 1 Online-Ressource txt rdacontent c rdamedia cr rdacarrier Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Reaktionskinetik (DE-588)4048655-2 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 s Reaktionskinetik (DE-588)4048655-2 s DE-604 Nölting, Bengt 1962- Sonstige (DE-588)113522673 oth Erscheint auch als Druck-Ausgabe, Hardcover 3-540-27277-1 https://doi.org/10.1007/b138868 Verlag Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016232215&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Protein folding kinetics biophysical methods ; with 15 tables Proteinfaltung (DE-588)4324567-5 gnd Reaktionskinetik (DE-588)4048655-2 gnd |
| subject_GND | (DE-588)4324567-5 (DE-588)4048655-2 |
| title | Protein folding kinetics biophysical methods ; with 15 tables |
| title_auth | Protein folding kinetics biophysical methods ; with 15 tables |
| title_exact_search | Protein folding kinetics biophysical methods ; with 15 tables |
| title_exact_search_txtP | Protein folding kinetics biophysical methods ; with 15 tables |
| title_full | Protein folding kinetics biophysical methods ; with 15 tables Bengt Nölting |
| title_fullStr | Protein folding kinetics biophysical methods ; with 15 tables Bengt Nölting |
| title_full_unstemmed | Protein folding kinetics biophysical methods ; with 15 tables Bengt Nölting |
| title_short | Protein folding kinetics |
| title_sort | protein folding kinetics biophysical methods with 15 tables |
| title_sub | biophysical methods ; with 15 tables |
| topic | Proteinfaltung (DE-588)4324567-5 gnd Reaktionskinetik (DE-588)4048655-2 gnd |
| topic_facet | Proteinfaltung Reaktionskinetik |
| url | https://doi.org/10.1007/b138868 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016232215&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT noltingbengt proteinfoldingkineticsbiophysicalmethodswith15tables |