Protein engineering handbook 2
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245 | 1 | 0 | |a Protein engineering handbook |n 2 |c ed. by Stefan Lutz ... |
264 | 1 | |a Weinheim |b Wiley-VCH |c (2009) | |
300 | |a XLI S., S. 409 - 973 |b Ill., 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 | |
773 | 0 | 8 | |w (DE-604)BV035007048 |g 2 |
856 | 4 | 2 | |m Digitalisierung UB Bayreuth |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016676358&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
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Datensatz im Suchindex
DE-BY-TUM_call_number | 0304 CHE 820b 2008 A 9640 1302 CHE 820b 2009 A 8843 |
---|---|
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_version_ | 1820801045805137920 |
adam_text | Contents XIII
Volume
2
16
A Method for Rapid Directed Evolution
409
Manfred T. Reetz
16.1
Introduction
409
16.2
Focused Libraries Generated by Saturation Mutagenesis
414
16.3
Iterative Saturation Mutagenesis
416
16.3.1
General Concept
416
16.3.2
Combinatorial Active-Site Saturation Test (CAST) as a Means to
Control Substrate Acceptance and/or Enantioselectivity
418
16.3.3
B-Factor Iterative Test (B-FIT) as a Means to Increase
Thermostability
425
16.3.4
Practical Hints for Applying ISM
430
16.4
Conclusions
430
References
431
XIV Contents
17 Evolution
of Enantioselective Bacillus
subtilis
Lipase
441
Thorsten Eggert, Susanne A. Funke, Jennifer N. Andexer, Manfred T. Reetz
and Karl-Erich
Jaeger
17.1
Introduction
441
Yl
.2
Directed Evolution of Enantioselective
Lipase
from Badllus
subtilis
444
17.3
Directed Evolution by Error-Prone PCR
445
17
A Complete Site-Saturation Mutagenesis
446
17.5
Conclusions
448
References
449
18
Circular Permutation of Proteins
453
Clenna E.
Meister,
Manu
Kanwar, and Marc Ostermeier
18.1
Introduction
453
18.2
Evolution of Circular Permutations in Nature
454
18.2.1
Naturally Occurring Circular Permutations
454
18.2.2
Identification of Natural Circular Permutations
455
18.2.3
Mechanisms of Circular Permutation
457
18.3
Artificial Circular Permutations
459
18.3.1
Early Studies
459
18.3.2
Systematic and Random Circular Permutation
460
18.3.3
Protein Folding and Stability
462
18.4
Circular Permutation and Protein Engineering
463
18.4.1
Alteration of the Spatial Arrangement of Protein Fusions
463
18.4.2
Oligomeric State Modification
464
18.4.3
Improvement of Function
465
18.4.4
Creation of Protein Switches
466
18.4.5
Protein Crystallization
467
18.5
Perspective
468
Acknowledgments
468
References
468
19
Incorporating Synthetic Oligonucleotides via
Cene
Reassembly (ISOR):
A Versatile Tool for Generating Targeted Libraries
473
Asael Herman
ond
Dan S. Tawfik
19.1
Introduction
473
19.1.1
Background
473
19.1.2
Overview of the Method
474
19.1.3
Applications
475
19.2
Materials
475
19.2.1
DNasel Digestion
475
19.2.2
Assembly
476
19.2.3
Magnetic Separation and Product Amplification
476
19.3
Methods
476
19.3.1
DNasel Digestion
476
Contents IXV
19.3.2
Assembly
477
19.3.3
Magnetic Separation and Product Amplification
477
19.4
Notes
478
Acknowledgments
479
References
479
20
Protein Engineering by Structure-Guided SCHEMA
Recombination
481
Cloria Saab-Rincon, Yougen Li, Michelle Meyer, Martina
Carbone,
Marco
Landwehr,
and Frances H. Arnold
20.1
Introduction
481
20.1.1
SCHEMA Recombination of Proteins: Theoretical Framework
481
20.1.2
Comparison of SCHEMA with Other Guided-Recombination
Methods
483
20.1.3
Practical Guidelines for SCHEMA Recombination
485
20.2
Examples of Chimeric Libraries Designed Using the SCHEMA
Algorithm
485
20.2.1
SCHEMA Recombination of
ß-Lactamases 485
20.2.2
SCHEMA-Guided Recombination of Cytochrome P450
Heme
Domains
486
20.3
Conclusions
490
References
493
21
Chimeragenesis in Protein Engineering
493
Manuela
Irani and Stefan
Lutz
21.1
Introduction
493
21.1.1
Homology-Independent in vitro Recombination
(Chimeragenesis)
494
21.1.1.1
Homology-Independent Random Gene Fusion
494
21.1.1.2
Homology-Independent Recombination with Multiple
Crossovers
496
21.1.2
Predictive Algorithms in Chimeragenesis
498
21.2
Experimental Aspects of the SCRATCHY Protocol
499
21.2.1
Creation of ITCHY Libraries
499
21.2.2
Size and Reading Frame Selection
502
21.2.3
Enhanced SCRATCHY via Forced Crossovers
503
21.3
Future Trends in Chimeragenesis
506
21.3.1
Combining SCRATCHY and SCHEMA
508
21.3.2
The Future of Chimeragenesis
508
21
A Conclusions
511
Acknowledgments
511
References
511
XVIII
Contents
25.2 Glycosynthases 607
25.3 Glycosyltransferases 608
25.4
Protocol and Practicai
Considerations for Using
HTS
Methodology in
the Directed Evolution of STs
610
25.4.1
Cloning of the Target ST and CMP-NeuSAc-Synthetase
610
25.4.2
Synthesis of Fluorescently Labeled Acceptor Sugar
611
25.4.3
Cell-Based Assay in JM107 Nan A Strain
611
25.4.4
Transformation, Growth and Expression of Plasmids Containing ST
and CMP-syn Genes in JM107 Nan A Strain
612
25.4.5
Cell-Based Assay
613
25.4.6
Validation, Sensitivity and Dynamic Range of the Cell-Based
Assay
613
25.4.7
Model Selection
614
25.4.8
Generation of Genetic Diversity in the Target ST Gene: Strategies for
Constructing Large Mutant Libraries
614
25.4.9
Library Sorting, Rounds of Enrichment and the Stringency of
Selection
615
25.4.10
Identification and Isolation of Improved Mutants
635
25.4.11
Characterization of Improved ST Mutants
616
25.5
Challenges and Prospects of GT Engineering
617
References
617
26
Yeast Surface Display in Protein Engineering and Analysis
621
Benjamin J.
Hackel
and K. Dane Wittrup
26.1
Review
621
26.1.1
Introduction
621
26.1.2
Protein Engineering
622
26.1.2.1
Affinity Engineering
623
26.1.2.2
Stability and Expression Engineering
623
26.1.2.3
Enzyme Engineering
624
26.1.3
Protein Analysis
624
26.1.3.1
Clone Characterization
624
26.1.3.2
Paratope: Epitope Study
625
26.1.3.3
YSD in Bioassays
626
26.2
Protocols and Practical Considerations
626
26.2.1
Materials
627
26.2.1.1
Cells and Plasmids
627
26.2.1.2
Media and Buffers
627
26.2.1.3
Buffers
627
26.2.1.4
Flow Cytometry Reagents
627
26.2.2
Nucleic Acid and Yeast Preparation
628
26.2.2.1 DNA
Preparation
628
26.2.2.2
Yeast Transformation
630
26.2.2.3
Yeast Culture
632
26.2.3
Combinatorial Library Selection
632
Contents XIX
26.2.4 FACS 633
26.2.4.1
Other Selection Techniques
635
26.2.4.2
Stability
636
26.2.4.3
Clone Identification
637
26.2.5
Analysis
637
26.2.5.1
Binding Measurements
637
26.2.5.2
Stability Measurement
641
26.3
The Future of Yeast Surface Display
642
Abbreviations
644
Acknowledgments
644
References
644
27
In Vitro Compartmentalization (IVC) and Other High-Throughput
Screens of Enzyme Libraries
649
Amir Aharoni and Dan S.
Таифк
27.1
Introduction
649
27.2
The Fundamentals of High-Throughput Screens and Selections
650
27.3
Enzyme Selections by Phage-Display
651
27
A HTS of Enzymes Using Cell-Display and FACS
652
27.5
Other FACS-Based Enzyme Screens
653
27.6
In vivo Genetic Screens and Selections
653
27.7
In vitro Compartmentalization (IVC)
654
27.8
IVC in Double Emulsions
657
27.9
What s Next?
659
27.10
Experimental Details
660
Acknowledgments
662
References
662
28
Colorimetrie
and Fluorescence-Based Screening
669
Jean-Louis Reymond
28.1
Introduction
669
28.2
Enzyme-Coupled Assays
670
28.2.1
Alcohol Dehydrogenase (ADHJ-Coupled Assays
671
28.2.2
Peroxidase-Coupled Assays
673
28.2.3
Hydrolase-Coupled Assays
674
28.2.4
Luciferase-Coupled Assays
676
28.3
Fluorogenic and Chromogenic Substrates
678
28.3.1
Release of Aromatic Alcohols
678
28.3.2
Aniline Release
681
28.3.3
FRET
682
28.3.4
Reactions that Modify the Chromophore Directly
685
28.3.5
Separation of Labeled Substrates
685
28.3.6
Precipitation
687
28.4
Chemosensors and Biosensors
688
28.4.1
Quick
-Е
with pH-Indicators
688
XX
Contents
28.4.2
Functional Group-Selective Reagents
689
28.4.3
Antibodies, Aptamers and Lectins
690
28.4.4
Gold Nanopartides
691
28.5
Enzyme Fingerprinting with Multiple Substrates
693
28.5.1
APIZYM
693
28.5.2
Protease Profiling
695
28.5.3
Cocktail Fingerprinting
695
28.5.4
Substrate Microarrays
697
28.6
Conclusions
698
Acknowledgments
699
References
699
29
Confocal and Conventional Fluorescence-Based High Throughput
Screening in Protein Engineering
713
Ulrich Haupts,
Oliver Hesse, Michael Strerath, Peter J. Walla, and
Wayne M. Coco
29.1
General Aspects
713
29.1.1
HTS
and Combinatorial
DNA
Library Strategies in Protein
Engineering
713
29.1.2
HTS
in Protein Engineering: Coupling Genotype and Phenotype and
the Advantages of Clonal Assays
715
29.1.3
Well-Based
HTS
Formats
716
29.2
Fluorescence
718
29.2.1
Overview of Theory and Principles of Fluorescence
719
29.2.1.1
Choice of Fluorophores in
HTS
721
29.2.1.2
Concentration Requirements for Fluorescent Analytes
722
29.2.1.3
Fluorescence Intensity Measurements with a Precautionary Note on
Fluorescent Labeling of Substrates and Binding Partners
722
29.2.1.4
Confocal Versus Bulk Detection Methods
723
29.2.1.5
Advantages of the Confocal Fluorescence Detection Format
724
29.2.1.6
Anisotropy
724
29.2.1.7
FRET/TR-FRET/Iifetime
725
29.2.1.8
Fluorescence Correlation Spectroscopy
726
29.2.1.9
FIDA
726
29.3
Hardware and Instrumentation
727
29.3.1
Confocal and Bulk Concepts
727
29.3.1.1
Light Sources
727
29.3.1.2
Wavelength Selection/Filtering
729
29.3.1.3
Detectors
729
29.3.1.4
Reader Systems
730
29.4
Practical Considerations and Screening Protocol
730
29.4.1
Introduction
730
29.4.2
Fluorescence-Based Assay Design: Practical Considerations
731
29.4.2.1
Choice of Assay Design
731
29.4.2.2
Labeling
731
Contents XXI
29.4.2.3
Choice of
Fluorophore 732
29.4.3
Assay Quality
733
29.4.3.1
What Needs to Be Discriminated?
733
29.4.3.2
Mathematical Description
733
29.4.4
A Specific
HTS
Protein Engineering Program Using a Fluorescence-
Based Screen
735
29.4.5
The Assay
735
29.4.5.1
Expression Host
736
29.4.6
Multiwell Format and Unit Operations in the
HTS
Protocol
738
29.4.6.1
Liquid Handling
738
29.4.6.2
Incubation
738
29.4.6.3
Centrifugation
739
29.4.6.4
Scheduling
739
29.4.6.5
Screening Protocol
739
29.5
Challenges and Future Directions
742
Abbreviations
748
Acknowledgments
748
References
748
30
Alteration of Substrate Specificity and Stereoselectivity of Lipases and
Esterases
753
Dominique
Böttcher,
Marlen
Schmidt, and
Uwe
T.
Bornscheuer
30.1
Introduction
753
30.2
Background of Protein Engineering Methods
754
30.2.1
Directed Evolution
754
30.2.2
Rational Design
756
30.3
Assay Systems
757
30.3.1
Selection
757
30.3.1.1
Display Techniques
757
30.3.1.2
In vivo Selection
758
30.3.2
Screening
759
30.4
Examples
764
30.5
Conclusions
770
References
770
31
Altering Enzyme Substrate and Cofactor Specificity via Protein
Engineering
777
Matthew DeSieno, Jing
Du,
and Huimin Zhao
31.1
Introduction
777
31.1.1
Overview
777
31.1.2
Approaches
779
31.1.2.1
Rational Design
779
31.1.2.2
Directed Evolution
781
31.1.2.3
Semi-Rational Design
781
31.2
Specific Examples
782
XXII Contents
31.2.1
Cofactor
Specificity
782
31.2.1.1
NAD(P)(H)
783
31.2.1.2
ATP
783
31.2.1.3
Summary and Comments for Cofactor Specificity
784
31.2.2
Substrate Specificity
784
31.2.2.1
P450s
785
31.2.2.2
Aldolases
785
31.2.2.3
Transfer-RNA Synthetases
786
31.2.2.4
Restriction Endonudeases
786
31.2.2.5
Homing Endonudeases
788
31.2.2.6
Polymerases
789
31.2.2.7
Summary and Comments for Substrate Specificity
789
31.3
Challenges and Future Prospects
790
31.3.1
New Strategies for Engineering Cofactor/Substrate Specificity
790
31.3.2
Cofactor/Substrate Specificity Engineering for Combinatorial
Biosynthesis
79І
31.3.3
Cofactor/Substrate Specificity Engineering for Metabolic
Engineering
792
31.3.4
Cofactor/Substrate Specificity Engineering for Gene Therapy
793
Acknowledgments
793
References
793
32
Protein Engineering of Modular Polyketide Synthases
797
Alice Y. Chen and Chaitan Khosla
32.1
Introduction
797
32.2
Polyketide Biosynthesis and Engineering
798
32.2.1
Active Sites and Domain Boundaries in Multimodular PKSs
799
32.2.2
Past Achievements in Genetic Reprogramming of Polyketide
Biosynthesis
802
32.2.2.1
Starter Unit Incorporation
802
32.2.2.2
Extender Unit Incorporation
804
32.2.2.3 ß-Carbon
Processing
805
32.2.2.4
Chain Length Control
807
32.2.2.5
Additional Modifications
807
32.2.2.6
Other
PKS
Engineering Opportunities
807
32.2.3
Pre^Post-PRS
Pathway Engineering
809
32.2.3.1
Precursor Production
809
32.2.3.2
Post-PKS Modification
810
32.3
Engineering and Characterization Techniques
810
32.3.1
Common Genetic Techniques for
PKS
Engineering
810
32.3.1.1
Restriction Site Engineering
811
32.3.1.2
Gene SOEing
811
32.3.1.3
Red/ET Homology Recombination
811
32.3.1.4
Gene Synthesis
812
32.3.1.5
Gene Shuffling
813
Contents XXIII
32.3.2 In vitro Characterization 814
32.3.2.1 Protein Expression 814
32.3.2.2 Protein
Purification
814
32.3.2.3 Protein Characterization 815
32.3.3 In vivo Characterization 816
32.3.3.1 Host Engineering 816
32.3.3.2
High-Throughput Screening Assay
817
32.4
The Path Forward
818
Abbreviations
819
References
819
33
Cyanophycin Synthetases
829
Anna
Steinte
and Alexander Steinbiichel
33.1
Introduction
829
33.2
Occurrence of Cyanophycin Synthetases
830
33.3
General Features
830
33.4
Reaction Mechanism
831
33.5
Substrate Specificity
832
33.6
Primary Structure Analysis
836
33.7
Enzyme Engineering
838
33.8 Biotechnical
Applications
843
Acknowledgments
843
References
843
34
Biosynthetic Pathway Engineering Strategies
849
Claudia Schmidt-Dannert and Alexander Pisarchik
34.1
Introduction
849
34.2
Initial Pathway Design
850
34.2.1
Functional Pathway Assembly
850
34.2.2
Selection of the Heterologous Host
854
34.3
Optimization of the Precursor Supply
855
34.3.1
Identification and Overexpression of Rate-limiting Enzymes
856
34.4
Engineering of Control Loops
858
34.5
Engineering of Alternative Precursor Routes
858
34.6
Balancing Gene Expression Levels and Activities of Metabolic
Enzymes
859
34.7
Metabolic Network Integration and Optimization
861
34.8
Engineering Pathways for the Production of Diverse
Compounds
863
34.9
Future Perspectives
866
Abbreviations
867
References
868
XXIV
I Contents
35
Natural Polyester-Related Proteins: Structure, Function, Evolution and
Engineering
877
Seiichi Taguchi and Takeharu Tsuge
35.1
Introduction
877
35.2
Enzymes Related to the Synthesis and Degradation of
PHA
878
35.3
Structure-Based Engineering of PHA Synthase and Monomer-
Supplying Enzymes
879
35.3.1
PHA Synthase (PhaC, PhaEC, PhaRC)
880
35.3.2
S-Ketoacyl-CoA Thiolase (PhaA)
882
35.3.3
Acetoacetyl-CoA
Reducíase
(PhaB)
887
35.3.4
(R)-Specific Enoyl-CoA
Hydratase (PhaJ)
890
35.3.5
(R^-Hydroxyacyl-ACP-CoA
Transferase
(PhaG)
891
35.3.6
3-Ketoacyl-ACP Synthase III (FabH)
891
35.4
Directed Evolution of PHA Synthases
892
35.4.1
Engineering of the Type I Synthases
893
35.4.2
Engineering of the Type II Pseudomonas Species PHA Synthases
897
35.5
Structure-Function Relationship of PHA Depolymerases
899
35.5.1
Domain Structure of Extracellular PHA Depolymerases
899
35.5.2
Intracellular PHA Depolymerase
903
35.5.3
Amino
Acid Residues Related to Binding Affinity
904
35.6
Application of PHA-Protein Binding Affinity
905
35.7
Perspectives
906
References
907
36 Bioengineering
of Sequence-Repetitive Polypeptides: Synthetic Routes
to Protein-Based Materials of Novel Structure and Function
915
Sonha
С.
Payne, Melissa Patterson, and Vincent P. Conticello
36.1
Introduction
915
36.2
Block Copolymers as Targets for Materials Design
918
36.2.1
Amphiphilic Block Copolymers
919
36.2.2
Elastin-Mimetic Block Copolymers
920
36.3
Strategies for the Construction of Synthetic Genes Encoding
Sequence-Repetitive Polypeptides
923
36.3.1 DNA
Cassette Concatemerization
924
36.3.2
Recursive Directional ligation
925
36.3.3
Genetic Assembly of Synthetic Genes Encoding Block
Architectures
926
36.4
A Hybrid Approach to the Controlled Assembly of Complex
Architectures of Sequence-Repetitive Polypeptides
928
36.5
Future Outlook
935
Acknowledgments
936
References
936
Contents XXV
37
Silk
Proteins-Biomaterials and Bioengineering 939
Xiaoqin Wang, Peggy
Cebe,
and David.
L
Kaplan
37.1
Silk Protein Polymers-An Overview
939
37.2
Silk Protein Polymers-Methods of Preparation
947
37.2.1
Preparation of Spider Silks
947
37.2.2
Preparation of Scaffolds
949
37.3
Silk Protein Polymers-Future Perspectives and Challenges
951
Acknowledgments
954
References
954
Index
961
|
any_adam_object | 1 |
building | Verbundindex |
bvnumber | BV035007054 |
ctrlnum | (OCoLC)316292054 (DE-599)BVBBV035007054 |
format | Book |
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id | DE-604.BV035007054 |
illustrated | Illustrated |
indexdate | 2024-12-23T21:10:18Z |
institution | BVB |
language | English |
oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016676358 |
oclc_num | 316292054 |
open_access_boolean | |
owner | DE-91G DE-BY-TUM DE-703 DE-355 DE-BY-UBR DE-29T DE-91S DE-BY-TUM |
owner_facet | DE-91G DE-BY-TUM DE-703 DE-355 DE-BY-UBR DE-29T DE-91S DE-BY-TUM |
physical | XLI S., S. 409 - 973 Ill., graph. Darst. |
publishDate | 2009 |
publishDateSearch | 2009 |
publishDateSort | 2009 |
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 2 ed. by Stefan Lutz ... |
title_fullStr | Protein engineering handbook 2 ed. by Stefan Lutz ... |
title_full_unstemmed | Protein engineering handbook 2 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=016676358&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
volume_link | (DE-604)BV035007048 |
work_keys_str_mv | AT lutzstefan proteinengineeringhandbook2 |