Protein engineering handbook 3
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| 020 | |a 9783527331239 |c print |9 978-3-527-33123-9 | ||
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| 049 | |a DE-11 |a DE-355 |a DE-91S |a DE-20 |a DE-91G | ||
| 245 | 1 | 0 | |a Protein engineering handbook |n 3 |c ed. by Stefan Lutz ... |
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2013 | |
| 300 | |a XXI, 479 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 700 | 1 | |a Lutz, Stefan |e Sonstige |4 oth | |
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Datensatz im Suchindex
| DE-BY-TUM_call_number | 1302/CHE 820b 2009 A 8843-3 0304/CHE 820b 2008 A 9640-3 |
|---|---|
| DE-BY-TUM_katkey | 1872893 |
| DE-BY-TUM_media_number | 040030499557 040007699732 |
| _version_ | 1816713799977140224 |
| adam_text | Contents
Prefece
XV
List of Contributors
XVÍÍ
Ί
Dirigent
Effects in Biocatalysis
1
Bettina
M.
Nestl,
Bernd
Α.
Nebel, and Bernhard Hauer
1.1
Introduction I
1.2 Dirigent Proteins 3
1.3
Solvents and Unconventional Reaction Media
4
1.3.1
Ionic Liquids
7
1.3.2
Microemulsions and Reversed Micelles Systems
10
1.4
Structure and Folding
12
1.5
Structured and Unstructured Domains
14
1.6
Isozymes, Moonlighting Proteins, and Promiscuity: Supertalented
Enzymes
19
1.7
Conclusions
22
Acknowledgment
23
References
23
2
Protein Engineering Guided by Natural Diversity
29
James T.
Kratzer,
Megan F. Cole, and Eric
A. Gaucher
2.1
Approaches
29
2.1.1
Ancestral Sequence Reconstruction (ASR)
30
2.1.2
Ancestral Mutation Method
31
2.1.3
Reconstructing Evolutionary Adaptive Paths (REAP)
32
2.2
Protocols
34
2.2.1
Practical Steps to Using ASR
34
2.2.2
Reconstructing Evolutionary Adaptive Paths: A Focused Application
of ASR
36
2.3
Future Directions
38
2.3.1
Industrial Applications
40
2.3.2
Biomedical
41
2.3.3
Drug Discovery
41
2.3.4
Paleobiology
42
VI
Contents
2.3.5
Synthetic Biology
43
2.3.6
Experimental Validation of AS
R
43
2.4
Conclusions
44
References
44
3
Protein Engineering Using Eukaryotic Expression Systems
47
Martina
Geier
and Anton
Glieder
3.1
Introduction
47
3.2
Eukaryotic Expression Systems
48
3.2.1
Yeast Expression Platforms
48
3.2.1.1
Saccharomyces cerevisiae
48
3.2.1.2
Pichia
pastoris
51
3.2.1.3
Pichia
angusta
54
3.2.1.4
Alternative Yeasts
55
3.2.2
Filamentous Fungi
56
3.2.3
Insect Cells
58
3.2.4
Mammalian Cell Cultures
59
3.2.5
Transgenic Animals and Plants
61
3.2.6
Cell-Free Expression Systems
61
3.3
Conclusions
63
References
65
4
Protein Engineering in Microdroplets
73
Yolanda Schaerli,
Balint Kintses,
and
Florian Hollfelder
4.1
Introduction
73
4.2
Droplet Formats
75
4.2.1
Bulk Emulsions
75
4.2.1.1
Catalytic Selections Involving
DNA
Substrates
76
4.2.1.2
Using the Droplet Compartment to Form a Permanent
Genotype-Phenotype Linkage for Selections of Binders
77
4.2.2
Double Bulk Emulsions
78
4.2.3
Microfluidic Droplets
79
4.3
Perspectives
83
Acknowledgments
84
References
84
5
Folding and Dynamics of Engineered Proteins
89
Michelle E. McCully and Valerie Doggett
5.1
Introduction
89
5.2
Proof-of-Principle Protein Designs
90
5.2.1
FSD-1, a Heterogeneous Native State and Complicated Folding
Pathway
91
5.2.2
a3D,
а
Dynamic Core Leads to Fast Folding and Thermal Stability
94
5.2.3
Three-Helix Bundle Thermostabilized Proteins
96
5.2.4
Top7, a Novel Fold Topology
97
Contents
VII
5.2.5
Other
Rosetta
Designs
100
5.3
Proteins Designed for Function
102
5.3.1
Ligands
103
5.3.1.1
Metal-Binding Four-Helix Bundles, the Effectiveness of Negative
Design
103
5.3.1.2
Peptide
Binding
105
5.3.2
Enzymes
106
5.3.2.1
Retro-Aldol Enzyme, Accommodating a Two-Step Reaction
106
5.3.2.2
Kemp Elimination Enzyme, Rigid Active Site Geometry
Promotes Catalysis
108
5.4
Conclusions and Outlook
110
Acknowledgments 111
References
112
6
Engineering Protein Stability
115
Ciarán Ó Fágáin
6.1
Introduction
125
6.2
Power and Scope of Protein Engineering to Enhance Stability
126
6.2.1
Thermal Stabilizations
116
6.2.1.1
Potential Therapeutics: Rational Design with Computational
Support
316
6.2.1.2
Analytical Tools: Green Fluorescent Protein and Luciferase
128
6.2.1.3
Stiffening a Protein by Gly-to-Pro Replacement: Methyl
Parathion Hydrolase
128
6.2.2
Thermal Is Not the Only Stability: Oxidative and Other Chemical
Stabilities
129
6.2.2.1
Oxidative Stability
129
6.2.2.2
Stabilization against Aldehydes and Solvents
130
6.2.2.3
Alkaline Tolerance
131
6.3
Measurement of a Protein s Kinetic Stability
132
6.3.1
Materials and General Hints
132
6.3.2
Thermal Stability
132
6.3.2.1
Thermal Profile
132
6.3.2.2
Thermal Inactivation
133
6.3.3
Measurement of Oxidative Stability
134
6.3.4
Stability Analysis and Accelerated Degradation Testing
135
6.3.4.1
Set-Up
136
6.3.4.2
Analysis of Results
137
6.4
Developments in Protein Stabilization
137
References
139
7
Enzymes from Thermophilic Organisms
245
Tamotsu Kanai and Haruyuki
Atomi
7.1
Introduction
145
7.2
Hyperthermophiles
146
VIII Contents
7.3
Enzymes from Thermophiles and Their Reactions
146
7.4
Production of Proteins from
(Hyper)Thermophiles
148
7.5
Protein Engineering of Thermophffic Proteins
154
7.6
Cell Engineering in Hyperthermophiles
156
7.7
Future Perspectives
157
References
157
8
Enzyme Engineering by Cofactor Redesign
163
Małgorzata
M.
Kopacz,
Frank.
Hollmann,
and Marco
W.
Fraaije
8.1
Introduction
163
8.2
Natural Cofactors: Types, Occurrence, and Chemistry
164
8.3
Inorganic Cofactors
165
8.4
Organic Cofactors
168
8.5
Redox
Cofactors
169
8.5.1
Nicotinamide Cofactor Engineering
170
8.5.2
Heme
Cofactor Engineering
173
8.5.2.1
Reconstitution
of Myoglobin
174
8.5.2.2
Artificial
Metalloproteins
Based on Serum Albumins
175
8.5.3
Flavin Cofactor Engineering
276
8.6
Concluding Remarks
180
References
181
9
Biocatalyst Identification by Anaerobic High-Throughput Screening of
Enzyme Libraries and Anaerobic Microorganisms
193
Helen S. Toogood and Nigel S. Scrutton
9.1
Introduction
193
9.2
Oxygen-Sensitive Biocatalysts
194
9.2.1
Flavoproteins
194
9.2.2
Iron-Sulfur-Containing Proteins
195
9.2.3
Other Causes of Oxygen Sensitivity
197
9.3
Biocatalytic Potential of Oxygen-Sensitive Enzymes and
Microorganisms
198
9.3.1
Old Yellow Enzymes (OYEs)
198
9.3.2
Enoate Reductases
200
9.3.3
Other Enzymes
202
9.3.4
Whole-Cell Anaerobic Fermentations
202
9.4
Anaerobic High-Throughput Screening
203
9.4.1
Semi-Anaerobic Screening Protocols
204
9.4.2
Anaerobic Robotic High-Throughput Screening
205
9.4.2.1
Purified Enzyme versus Whole-Cell Extracts
207
9.4.2.2
Indirect Kinetic Screening versus Direct Product Determination
208
9.4.3
Potential Extensions of Robotic Anaerobic High-Throughput
Screening
209
9.5
Conclusions and Outlook
210
References
210
Contents
IX
10 Organometallic
Chemistry in
Protein
Scaffolds
215
Yvonne M. Wilson, Marc Dürrenberger, and Thomas R. Ward
10.1
Introduction
215
10.1.1
Concept
215
10.1.2
Considerations for Designing an Artificial
Metalloenzyme 216
10.1.2.1
Organometallic Complex
216
10.1.2.2
Biomolecular Scaffold
218
10.1.2.3
Anchoring Strategy
219
10.1.2.4
Advantages and Disadvantages of the Different Anchoring
Modes
221
10.1.2.5
Spacer
222
10.1.3
Other Key Developments in the Field
223
10.1.4
Why Develop Artificial Metalloenzymes?
223
10.2
Protocol/Practical Considerations
226
10.2.1
Protein Scaffold
226
10.2.1.1
Determination of Free Binding Sites
226
10.2.2
Organometallic Catalyst
228
10.2.2.1
Synthesis of [Cp*Ir(biot-p-L)Cl]
229
10.2.2.2 N -(4-Biotinamidophenylsulfonyl)-Ethylenediamine TFA
Salt
230
10.2.3
Combination of Biotinylated Metal Catalyst and Streptavidin
Host
231
10.2.3.1
Binding Affinity of the Biotinylated Complex to Streptavidin
231
10.2.4
Catalysis
232
10.2.4.1
Catalysis Controls
232
10.3
Goals
234
10.3.1
Rate Acceleration
234
10.3.2
High-Throughput Screening
234
10.3.2.1
Considerations for Screening of Artificial Metalloenzymes
235
10.3.3
Expansion of Substrate Scope
236
10.3.4
Upscaling
236
10.3.5
Potential Applications
237
10.4
Summary
237
Acknowledgments
237
References
238
ΊΊ
Engineering Protease Specificity
243
Philip
N.
Bryan
11.1
Introduction
243
11.1.1
Overview
243
11.1.2
Some Basic Points
244
11.1.2.1
Mechanism for
a Serine
Protease
244
11.1.2.2
Measuring Specificity
244
11.1.2.3
Binding Interactions
245
11.1.3
Nature versus Researcher
247
X
Contents
11.1.3.1
Pl
Specificity of Chymotrypsin-like Proteases
247
11.1.3.2
The SI Site of Subtilisin
247
11.1.3.3
The S4 Site of Subtilisin
250
11.1.3.4
Other
Subsites
in Subtilisin
250
11.1.3.5
Kinetic Coupling and Specificity
251
11.2
Protocol and Practical Considerations
253
11.2.1
Remove and Regenerate
251
11.2.2
Engineering Highly Stable and Independently Folding Subtilisins
252
11.2.3
Engineering of P4 Pocket to Increase Substrate Specificity
253
11.2.4
Destroying the Active Site in Order to Save It
254
11.2.5
Identifying a Cognate Sequence for Anion-Triggered Proteases Using
the Subtilisin
Prodomain 255
11.2.6
Tunable Chemistry and Specificity
257
11.2.7
Purification Proteases Based on Prodomain-Subtilisin Interactions
and Triggered Catalysis
258
11.2.8
Design of a Mechanism-Based Selection System
259
11.2.8.1
Step
1:
Ternary Complex Formation
259
11.2.8.2
Step
2:
Acylation
263
11.2.8.3
Steps
3
and
4:
Deacylation and Product Release
265
11.2.9
Evolving Protease Specificity Regulated with
Anion Cofactors
by
Phage Display
266
11.2.9.1
Construction and Testing of Subtilisin Phage
266
11.2.9.2
Random Mutagenesis and Transformation
267
11.2.9.3
Selection of Anions
267
11.2.9.4
Evolving the
Anion
Site
267
11.2.9.5
Catch-and-Release Phage Display
267
11.2.9.6
Conclusions
269
11.2.10
Evolving New Specificities at P4
269
11.3
Concepts, Challenges, and Visions on Future Developments
270
11.3.1
Design Challenges
270
11.3.2
Challenges in Directed Evolution
271
11.3.2.1
One Must Go Deep into Sequence Space
271
11.3.2.2
Methods Which Maximize Substrate Binding Affinity Are Not
Productive
272
11.3.2.3
The Desired Protease May Be Toxic to Cells
272
11.3.3
The Quest for Restriction Proteases
272
11.3.3.1
Not All Substrate Sequences Are Created Equal
273
11.3.4
Final Thoughts: Gilded or Golden?
273
Acknowledgments
274
References
274
12
Polymerase Engineering: From PCR and Sequencing to Synthetic
Biology
279
Vítor
В.
Pinheiro,
Jennifer
L
Ong, and
Philipp Holliger
12.1
Introduction
279
12.2
PCR
281
Contents
XI
12.3
Sequencing
281
12.3.1
First-Generation Sequencing
282
12.3.2
Next-Generation Sequencing Technologies
284
12.4
Polymerase Engineering Strategies
288
12.5
Synthetic Informational Polymers
291
References
295
Ί3
Engineering Glycosyltransferases
303
John McArthur and Gavin J. Williams
13.1
Introduction to Glycosyltransferases
303
13.2
Glycosyltransferase Sequence, Structure, and Mechanism
304
13.3
Examples of Glycosyltransferase Engineering
307
13.3.1
Chimeragenesis and Rational Design
307
13.3.2
Directed Evolution
310
13.3.2.1
Fluorescence-Based Screening
311
13.3.2.2
Reverse Glycosylation Reactions
312
13.3.2.3
ELISA-Based Screens
313
13.3.2.4 pH
Indicator Assays
314
13.3.2.5
Chemical Complementation
314
13.3.2.6
Low-Throughput Assays
314
13.4
Practical Considerations for Screening Glycosyltransferases
325
13.4.1
Enzyme Expression and Choice of Expression Vector
315
13.4.2
Provision of Acceptor and NDP-donor Substrate
315
13.4.3
General Considerations for Microplate-Based Screens
317
13.4.4
Promiscuity, Proficiency, and Specificity
337
13.5
Future Directions and Outlook
318
References
319
14
Protein Engineering of Cytochrome P450 Monooxygenases
327
Katja Koschorreck,
Clemens
J.
von Bühler, Sebastian Schulz,
and Vlada B. Urlacher
14.1
Cytochrome P450
Monooxygenases 327
14.1.1
Introduction
327
14.1.2
Catalytic Cycle of
Cytochrome P450 Monooxygenases 328
14.1.3
Redox Partner Proteins
329
14.2 Engineering
of P450
Monooxygenases
330
14.2.1
Molecular Background for P450 Engineering
330
14.2.2
Altering Substrate Selectivity and Improving Enzyme Activity
332
14.2.2.1
Rational and Semi-Rational Design
332
14.2.2.2
Directed Evolution and Its Combination with Computational
Design
336
14.2.2.3
Decoy Molecules
338
14.2.3
Improving Solvent and Temperature Stability of P450
Monooxygenases
340
14.2.3.1
Solvent Stability
341
14.2.3.2
Thermostability
342
XII
I Contents
14.2.4
Improving
Recombinant
Expression and Solubility of P450
Monooxygenases
343
14.2.4.1
N-Terminal Modifications
344
14.2.4.2
Modifications within the F-G Loop
346
14.2.4.3
Improving Expression by Rational Protein Design and Directed
Evolution
348
14.2.5
Engineering the Electron Transport Chain and Cofactors of
P450S
349
14.2.5.1
Genetic Fusion of Proteins
349
14.2.5.2
Enzymatic Fusion and Self-Assembling
Oligomers
352
14.3
Conclusions
354
References
355
15
Progress and Challenges in Computational Protein Design
363
Yih-En Andrew Ban,
Daniela
Röthlisberger-Grabs,
Eric
Α.
Althoff,
and Alexandre Zanghellim
15.1
Introduction
363
15.2
The Technique of Computational Protein Design
363
15.2.1
Principles of Protein Design
363
15.2.2
A Brief Review of Force-Fields for CPD
364
15.2.3
Optimization Algorithms for Fixed-Backbone Protein Design (PI )
368
15.3
Protein Core Redesign, Structural Alterations, and
Thermostabilization
371
15.3.1
Protein Core Redesign and
de novo
Fold Design
372
15.3.2
Computational Alteration of Protein Folds
373
15.3.2.1
Loop Grafting
374
15.3.2.2
de novo
Loop Design
375
15.3.2.3
Fold Switching
376
15.3.2.4
Fold Alteration: Looking Ahead
377
15.3.2.5
Computational Optimization of the Thermostability of Proteins
377
15.4
Computational Enzyme Design
380
15.4.1
de novo
Enzyme Design
380
15.4.1.1
Initial Proofs-of-Concept
380
15.4.1.2
Review of Recent Developments
382
15.4.2
Computational Redesign of the Substrate Specificity of Enzymes
383
15.4.2.1
Fixed-Backbone and Flexible-Backbone Substrate Specificity
Switches
383
15.4.2.2
Limitations and Feedback Obtained from Experimental Optimization
Attempts
385
15.4.3
Frontiers in Computational Enzyme Design
386
15.5
Computational Protein-Protein Interface Design
388
15.5.1
Natural Protein-Protein Interfaces Redesign
389
15.5.2
Two-Sided
de novo
Design of Protein Interfaces
390
15.5.3
One-Sided
de novo
Design of Protein Interfaces
392
15.5.4
Frontiers in Protein-Protein Interaction Design
393
Contents
і
XIII
15.6
Computational Redesign of
DNA
Binding and Specificity
394
15.7
Conclusions
396
References
396
16
Simulation of Enzymes in Organic Solvents
407
Tobias Kulschewski and
Jürgen Pleiss
16.1
Enzymes in Organic Solvents
407
16.2
Molecular Dynamics Simulations of Proteins and Solvents
408
16.3
The Role of the Solvent
410
16.4
Simulation of Protein Structure and Flexibility
411
16.5
Simulation of Catalytic Activity and Enantioselectivity
413
16.6
Simulation of Solvent-Induced Conformational Transitions
414
16.7
Challenges
415
16.8
The Future of Biocatalyst Design
416
References
417
17
Engineering of Protein Tunnels: The Keyhole-Lock-Key Model for
Catalysis by Enzymes with Buried Active Sites
421
Zbyněk Prokop, Artur
Cora, Jan
Brezovský, Radka Chaloupkova,
Veronika
Štěpánková,
andjiri Damborsky
17.1
Traditional Models of Enzymatic Catalysis
421
17.2
Definition of the Keyhole-Lock-Key Model
422
17.3
Robustness and Applicability of the Keyhole-Lock-Key Model
424
17.3.1
Enzymes with One Tunnel Connecting a Buried Active Site to the
Protein Surface
424
17.3.2
Enzymes with More than One Tunnel Connecting a Buried Active Site
to the Protein Surface
433
17.3.3
Enzymes with One Tunnel Between Two Distinct Active Sites
436
17.4
Evolutionary and Functional Implications of the Keyhoh-Lock-Key
Model
437
17.5
Engineering Implications of the Keyhole-Lock-Kef Model
438
17.5.1
Engineering Activity
442
17.5.2
Engineering Specificity
443
17.5.3
Engineering Stereoselectivity
443
17.5.4
Engineering Stability
443
17.6
Software Tools for the Rational Engineering of Keyholes
444
17.6.1
Analysis of Tunnels in a Single Protein Structure
445
17.6.2
Analysis of Tunnels in the Ensemble of Protein Structures
445
17.6.3
Analysis of Tunnels in the Ensemble of Protein-ligand
Complexes
447
17.7
Case Studies with Haloalkane Dehalogenases
448
17.8
Conclusions
450
References
452
Index
465
|
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| building | Verbundindex |
| bvnumber | BV025817591 |
| ctrlnum | (OCoLC)812183863 (DE-599)BVBBV025817591 |
| format | Book |
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| id | DE-604.BV025817591 |
| illustrated | Illustrated |
| indexdate | 2024-11-25T17:37:10Z |
| institution | BVB |
| isbn | 9783527331239 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-019417691 |
| oclc_num | 812183863 |
| open_access_boolean | |
| owner | DE-11 DE-355 DE-BY-UBR DE-91S DE-BY-TUM DE-20 DE-91G DE-BY-TUM |
| owner_facet | DE-11 DE-355 DE-BY-UBR DE-91S DE-BY-TUM DE-20 DE-91G DE-BY-TUM |
| physical | XXI, 479 S. graph. Darst. |
| publishDate | 2013 |
| publishDateSearch | 2013 |
| publishDateSort | 2013 |
| publisher | Wiley-VCH |
| record_format | marc |
| spellingShingle | Protein engineering handbook |
| title | Protein engineering handbook |
| title_auth | Protein engineering handbook |
| title_exact_search | Protein engineering handbook |
| title_full | Protein engineering handbook 3 ed. by Stefan Lutz ... |
| title_fullStr | Protein engineering handbook 3 ed. by Stefan Lutz ... |
| title_full_unstemmed | Protein engineering handbook 3 ed. by Stefan Lutz ... |
| title_short | Protein engineering handbook |
| title_sort | protein engineering handbook |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=019417691&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035007048 |
| work_keys_str_mv | AT lutzstefan proteinengineeringhandbook3 |