From enzyme models to model enzymes:
"Designing artificial systems with catalytic efficiencies to rival those of natural enzymes is one of the great challenges facing science today. Our current level of understanding fails the basic, practical test - designing and making artificial systems with catalytic efficiencies to rival thos...
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge
Royal Society of Chemistry Publ.
2009
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Klappentext |
| Zusammenfassung: | "Designing artificial systems with catalytic efficiencies to rival those of natural enzymes is one of the great challenges facing science today. Our current level of understanding fails the basic, practical test - designing and making artificial systems with catalytic efficiencies to rival those of natural enzymes. Chemists and bio-scientists are well aware of this problem, and 'artificial enzymes' have been a 'hot topic' for many years. However, until now, there has been no book devoted specifically to this subject. This is the first book to provide a critical introduction to, and overview of, this exciting area. It is aimed at students and more senior researchers with specialist or general interests in the field. The book starts with a systematic overview of the most important properties of natural enzymes, with special emphasis on mechanisms and efficiency of catalysis. This is followed by a summary of the mechanisms involved in the major classes of reaction they catalyze, and spells out the logical progression from simple mechanistic models for particular reactions to the first, rudimentary artificial enzymes catalyzing them. Catalytic efficiency is the key criterion for inclusion. An analysis of the strengths and limitations of the classical design-based approach to catalysis by enzyme mimics leads on to a discussion of recent advances which use selection methods coupled with iterative techniques for creating and improving catalysts by natural methods. The comparison of natural and artificial catalysts requires a quantitative understanding based on the interpretation of kinetic measurements. Key skills in data interpretation are introduced in a guided approach that connects the formal treatment of kinetic measurements with their chemical and biological interpretation."--Publisher's description. |
| Beschreibung: | XI, 273 S. Ill., graph. Darst. |
| ISBN: | 9780854041756 |
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| 245 | 1 | 0 | |a From enzyme models to model enzymes |c Anthony J. Kirby ; Florian Hollfelder |
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| 300 | |a XI, 273 S. |b Ill., graph. Darst. | ||
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| 520 | 3 | |a "Designing artificial systems with catalytic efficiencies to rival those of natural enzymes is one of the great challenges facing science today. Our current level of understanding fails the basic, practical test - designing and making artificial systems with catalytic efficiencies to rival those of natural enzymes. Chemists and bio-scientists are well aware of this problem, and 'artificial enzymes' have been a 'hot topic' for many years. However, until now, there has been no book devoted specifically to this subject. This is the first book to provide a critical introduction to, and overview of, this exciting area. It is aimed at students and more senior researchers with specialist or general interests in the field. The book starts with a systematic overview of the most important properties of natural enzymes, with special emphasis on mechanisms and efficiency of catalysis. This is followed by a summary of the mechanisms involved in the major classes of reaction they catalyze, and spells out the logical progression from simple mechanistic models for particular reactions to the first, rudimentary artificial enzymes catalyzing them. Catalytic efficiency is the key criterion for inclusion. An analysis of the strengths and limitations of the classical design-based approach to catalysis by enzyme mimics leads on to a discussion of recent advances which use selection methods coupled with iterative techniques for creating and improving catalysts by natural methods. The comparison of natural and artificial catalysts requires a quantitative understanding based on the interpretation of kinetic measurements. Key skills in data interpretation are introduced in a guided approach that connects the formal treatment of kinetic measurements with their chemical and biological interpretation."--Publisher's description. | |
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Datensatz im Suchindex
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|---|---|
| adam_text |
Contents
Chapter
1
From Models Through Mimics to Artificial Enzymes
1
1.1
Introduction to Enzyme Chemistry
2
1.1.1
Why are Enzymes so Big?
3
1.1.2
Functional Groups Available to Enzymes
4
1.2
Principles of Catalysis by Enzymes
6
1.2.1
Dependence on
pH 7
1.3
General Acid-Base Catalysis
8
1.3.1
Experimental Evidence
8
1.3.2
Mechanisms
9
1.3.3
Kinetic Equivalence
13
1.4
Intramolecularity
14
1.4.1
Efficiency of Intramolecular Catalysis
17
1.5
Energetics
18
1.6
Binding and Recognition
20
1.6.1 Hydrophobie
Binding
22
1.6.2
The Special Environment of the Active Site
24
1.7
Cofactors
24
1.8
Many Enzymes Use the Same Basic Mechanisms
25
1.9
Enzyme Models, Mimics and Pretenders
26
Chapter
2
Evaluation of Catalytic Efficiency in Enzymes and
Enzyme Models
29
2.1
Introduction
29
2.2
Measurement of Uncatalyzed Rate Constants,
kunait
30
2.3
Characterizing the Catalytic Reactivity of an Enzyme
or an Enzyme Model
32
2.3.1
Comparing Catalyzed and Uncatalyzed Rates
34
From Enzyme Models to Model Enzymes
By Anthony J. Kirby and
Florian Hollfelder
£
Anthony
J.
Kirby and
Florian Hollfelder 2009
Published by the Royal Society of Chemistry, www.rsc.org
viii Contents
2.3.2
Calculating Rate Accelerations
35
2.4
Catalytic Efficiencies of Representative Enzymes:
The Size of the Challenge
41
Chapter
3
Constructing Enzyme Models
-
Building up Complexity
42
3.1
Solvents
-
Catalysis Without Functional Groups?
43
3.2
Introducing Catalytic Groups Without
Positioning Them
46
3.3
Positioning of Substrate and Catalytic Groups
by Covalent Design
47
3.4
Binding the Ground State by Noncovalent
Interactions
47
3.5
Binding the TS More Strongly than the GS by
Noncovalent Interactions
50
3.6
Existing Enzymes as Catalytic Scaffolds
to Accommodate New Functions
52
3.6.1
Enzymes Modified by Addition of
Functionality
54
3.6.1.1
Exploiting Modular Build-Up
of Binding and Catalytic Features:
Chimeras of Binding Proteins and
Reactive Chemical Functionality
54
3.6.1.2
Noncovalent Introduction of
Reactive Cofactors: Transition-Metal
Catalysts in a Protein
55
3.6.1.3
Covalent Derivatization of
Active-Site Residues
to Introduce Reactive Cofactors
56
3.6.2
Site-Directed Mutants of Enzymes: Minimalist
Protein Redesign
56
3.6.3
Exploring Enzyme Promiscuity
57
Chapter
4
Enzyme Models Classified by Reaction
61
4.1
Acyl
Transfer
61
4.1.1
The
Serine
Proteases. Typical Active Sites
62
4.1.1.1
The Active-Site Environment
. . .
and Mechanism
64
4.1.1.2
Intramolecular Models
66
4.1.1.3
Supramolecular Models
69
4.1.1.3.1
Cyclodextrins
69
4.1.1.3.2
Synthetic Models
72
4.1.2
SH Hydrolases
75
4.1.2.1
Models
76
Contents ix
4.1.2.2
Intramolecular
Models 78
4.1.2.3 Supramolecular Models 79
4.1.3 Aspartic
Proteinases
79
4.1.3.1
Intramolecular
Models 80
4.1.4 Metallopeptidases/
Amide
Hydrolases 83
4.1.4.1
Enzymes
86
4.1.4.2 Model Systems
with One
Metal
Centre
86
4.1.4.2.1
Intramolecular
Reactions
88
4.1.4.2.2
Supramolecular
Metalloprotease/Peptidase Models
88
4.1.4.3
Model Systems with Two Metal
Centres
90
4.1.4.3.1
Aminopeptidase and
Lactamase Models
92
4.2
Phosphoryl Transfer
95
4.2.1
Phosphoryl Group Transfer from
Monoesters
96
4.2.1.1
Enzymes I. Phosphoryl Transfer
Without Metals: PTPases
98
4.2.1.1.1
Models
100
4.2.1.1.2
Intramolecular Models
100
4.2.1.1.3
Supramolecular Models
101
4.2.1.2
Enzymes II. Metalloenzymes
102
4.2.1.2.1
Models
102
4.2.2
Phosphoryl Group Transfer from
Phosphodiesters
105
4.2.2.1
Intramolecular Reactions
106
4.2.2.1.1
Intramolecular Attack
by OH
108
4.2.2.2
Enzymes I. Phosphoryl Group
Transfer Without Metals
111
4.2.2.2.1
Transfer to
Neighbouring OH
113
4.2.2.2.2
Supramolecular Models
114
4.2.2.3
Enzymes II. Metalloenzymes
117
4.2.2.3.1
Supramolecular Models:
RNA
Cleavage
118
4.2.2.3.2
Supramolecular Models:
DNA-Cleavage
122
4.3
Glycosyl Transfer
126
4.3.1
Simple Models
129
4.3.2
Enzymes
132
4.3.2.1
Glycoside Hydrolases
133
4.3.2.2
Glycoside
Transferases
135
4.3.3
Intramolecular Models
138
4.3.4
Enzyme Mimics
142
Contents
4.4
Hydrogen
Transfer 145
Introduction
145
4.4.1 Enolization: Proton Transfer
from
Carbon 146
4.4.1.1 Simple Models 148
4.4.1.2
Intramolecular
Models 149
4.4.1.3
Catalysis by
Metal
Ions 151
4.4.1.4
Enzymes Catalyzing Enolization
152
4.4.
4.4.
4.4.
4.4.
4.4.
.4.1
Triose
Phosphate Isomerase
152
.4.2
Citrate Synthase
155
.4.3
The Enolase Superfamily
155
.4.4
Mandelate Racemase
157
1.4.5
Models
157
4.4.2
Hydride Transfer
159
4.4.2.1
Uridine Diphosphate-galactose-4-
epimerase
160
4.4.2.2
Dehydrogenases
161
4.4.2.3
Models
161
4.4.2.4
Intramolecular Models
165
4.4.3
Hydrogen-Atom Transfer
165
4.5
Radical Reactions
168
4.5.1
Coenzyme Initiators Based on
Adenosylcobalamin
168
4.5.2
Radicals in Enzyme-Active Sites
171
4.5.2.1
Pyruvate-formate Lyase
171
4.5.2.2
Ribonucleotide Reductases
172
4.5.3
Models
174
4.5.3.1
Initiation Stages
176
4.5.3.2
Hydrogen-Atom Transfers
176
4.6
Pericyclic Reactions
180
4.6.1
Chorismate
Mutase
181
4.6.1.1
Models: Catalysis by Antibodies
182
4.6.2
Antibodies Catalyzing the Diels-Alder
Reaction
185
4.6.2.1
Supramolecular Catalysis of the
Diels-Alder Reaction
187
4.6.3
Catalysis by
RNA
191
Chapter
5
Design vs. Iterative Methods
-
Mimicking the Way Nature
Generates Catalysts
195
Introduction
195
5.1
Catalytic Polymers
197
5.1.1
Synzymes
199
5.1.2
Dendrimers
202
5.1.2.1
Peptide
Dendrimers
204
5.1.3
Molecular Imprinting
209
Contents
5.2
5.3
5.4
Catalytic Antibodies
5.2.1
Other Approaches
5.2.2
Proton Transfer from Carbon
5.2.3
Conclusions
Nucleic Acids as Catalysts
5.3.1
Mechanisms of Nucleic-acid Catalysis
5.3.2
Selection as an Alternative to Design Strategies
5.3.3
Access to New Catalysts Using SELEX
5.3.4
Changing the Catalyst Backbone: DNAzymes
5.3.5
Nucleic-Acid Catalysis of Other Reactions
Improving Protein Enzymes
5.4.1
Challenges in Exploring Protein Catalysts
5.4.2
What Fraction of Diversity Space is Practically
Accessible?
5.4.3
Mapping Enzyme Function in the Proteome:
Protein Superfamilies as a Basis for
Understanding Functional Links
5.4.3.1
The Enolase Superfamily
5.4.3.2
The Alkaline Phosphatase
Superfamily
5.4.4
Challenging Chance by Design and
Directed Evolution
References
Subject Index
212
214
216
219
220
220
225
227
228
229
231
231
233
236
236
238
243
248
266
Enzymes
are the (impeccably green) catalysts that make the Chemistry
of Life run smoothly and efficiently, and understanding how they
work has been a major challenge for Biological Science for many years.
Despite tremendous progress our understanding still fails the ultimate,
practical test
-
of designing and making artificial systems with catalytic
efficiencies to rival those of natural enzymes."Artificial enzymes" has been
a hot topic for many years, but until now no textbook has been devoted
specifically to this subject. From Enzyme Models to Model Enzymes is
the first to provide a critical introduction to, and overview of, this exciting
area. It is aimed at both students and more senior researchers with
interests in this and the many related fields.
The book starts with a systematic overview of the most important
properties of natural enzymes, with special emphasis on mechanisms
and catalytic efficiency. There follows a summary of the mechanisms
involved in the major classes of reaction they catalyze, and of the logical
progression from simple mechanistic models for particular reactions
to the first, rudimentary model enzymes. Catalytic efficiency is the key
criterion for inclusion. A careful analysis of the strengths and limitations of
the classical design-based approach to catalysis by enzyme mimics leads
on to a critical discussion of recent advances, which combine selection
routines with iterative techniques for creating and improving catalysts
by biomimetic methods.The meaningful comparison of natural and
artificial catalysts requires a quantitative understanding based on the
interpretation of kinetic measurements. Key skills in data interpretation
are introduced in a guided approach that connects the formal treatment
of kinetic measurements with their chemical and biological mechanistic
interpretation.
This book provides a convenient entry point into the chemistry for the
biochemist and molecular biologist, and for the chemist an
entrée
into
the biological methods that are of rapidly growing importance in this
and a number of other topical areas. |
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| id | DE-604.BV035725370 |
| illustrated | Illustrated |
| indexdate | 2024-11-11T09:11:19Z |
| institution | BVB |
| isbn | 9780854041756 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-018002067 |
| oclc_num | 421807269 |
| open_access_boolean | |
| owner | DE-19 DE-BY-UBM DE-91S DE-BY-TUM |
| owner_facet | DE-19 DE-BY-UBM DE-91S DE-BY-TUM |
| physical | XI, 273 S. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Royal Society of Chemistry Publ. |
| record_format | marc |
| spelling | Kirby, Anthony John Verfasser aut From enzyme models to model enzymes Anthony J. Kirby ; Florian Hollfelder Cambridge Royal Society of Chemistry Publ. 2009 XI, 273 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier "Designing artificial systems with catalytic efficiencies to rival those of natural enzymes is one of the great challenges facing science today. Our current level of understanding fails the basic, practical test - designing and making artificial systems with catalytic efficiencies to rival those of natural enzymes. Chemists and bio-scientists are well aware of this problem, and 'artificial enzymes' have been a 'hot topic' for many years. However, until now, there has been no book devoted specifically to this subject. This is the first book to provide a critical introduction to, and overview of, this exciting area. It is aimed at students and more senior researchers with specialist or general interests in the field. The book starts with a systematic overview of the most important properties of natural enzymes, with special emphasis on mechanisms and efficiency of catalysis. This is followed by a summary of the mechanisms involved in the major classes of reaction they catalyze, and spells out the logical progression from simple mechanistic models for particular reactions to the first, rudimentary artificial enzymes catalyzing them. Catalytic efficiency is the key criterion for inclusion. An analysis of the strengths and limitations of the classical design-based approach to catalysis by enzyme mimics leads on to a discussion of recent advances which use selection methods coupled with iterative techniques for creating and improving catalysts by natural methods. The comparison of natural and artificial catalysts requires a quantitative understanding based on the interpretation of kinetic measurements. Key skills in data interpretation are introduced in a guided approach that connects the formal treatment of kinetic measurements with their chemical and biological interpretation."--Publisher's description. Enzymes Enzymes Synthesis Enzym (DE-588)4014988-2 gnd rswk-swf Enzymkatalyse (DE-588)4152480-9 gnd rswk-swf Modell (DE-588)4039798-1 gnd rswk-swf Enzymkatalyse (DE-588)4152480-9 s DE-604 Enzym (DE-588)4014988-2 s Modell (DE-588)4039798-1 s Hollfelder, Florian Sonstige oth Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018002067&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018002067&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext |
| spellingShingle | Kirby, Anthony John From enzyme models to model enzymes Enzymes Enzymes Synthesis Enzym (DE-588)4014988-2 gnd Enzymkatalyse (DE-588)4152480-9 gnd Modell (DE-588)4039798-1 gnd |
| subject_GND | (DE-588)4014988-2 (DE-588)4152480-9 (DE-588)4039798-1 |
| title | From enzyme models to model enzymes |
| title_auth | From enzyme models to model enzymes |
| title_exact_search | From enzyme models to model enzymes |
| title_full | From enzyme models to model enzymes Anthony J. Kirby ; Florian Hollfelder |
| title_fullStr | From enzyme models to model enzymes Anthony J. Kirby ; Florian Hollfelder |
| title_full_unstemmed | From enzyme models to model enzymes Anthony J. Kirby ; Florian Hollfelder |
| title_short | From enzyme models to model enzymes |
| title_sort | from enzyme models to model enzymes |
| topic | Enzymes Enzymes Synthesis Enzym (DE-588)4014988-2 gnd Enzymkatalyse (DE-588)4152480-9 gnd Modell (DE-588)4039798-1 gnd |
| topic_facet | Enzymes Enzymes Synthesis Enzym Enzymkatalyse Modell |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018002067&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018002067&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT kirbyanthonyjohn fromenzymemodelstomodelenzymes AT hollfelderflorian fromenzymemodelstomodelenzymes |