Foldamers: structure, properties and applications (Weinheim, 2007). - ОГЛАВЛЕНИЕ / CONTENTS
Навигация

Архив выставки новых поступлений | Отечественные поступления | Иностранные поступления | Сиглы
ОбложкаFoldamers: structure, properties and applications / ed. by S.Hecht, I.Huc. - Weinheim: Wiley-VCH, 2007. - xxii, 434 p.: ill. - Incl. bibl. ref. - Ind.: p.427-434. - Пер. заг.: Фолдамеры: структура, свойства и применение. - ISBN 978-3-527-31563-5
 

Место хранения: 02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents
 
     Foreword ................................................... V
     Preface ................................................... XV
     List of Contributors ..................................... XIX

Part 1  Structure: Foldamer Design Concepts ..................... 1

1    Foldamers Based on Local Conformational Preferences ........ 3
     Ivan Hue and Louis Cuccia
1.1  Introduction ............................................... 3
1.2  Rigidly Locked Molecules ................................... 4
1.3  Predictable Foldamers ...................................... 5
     1.3.1  Local Conformational Control ........................ 6
     1.3.2  Folded Conformations of π-conjugated Systems ........ 9
     1.3.3  Partially π-conjugated Oligomers ................... 16
1.4  Semi-rigid Backbones ...................................... 17
     1.4.1  Tertiary Aromatic Amides, Imides and Ureas ......... 18
     1.4.2  Tertiary Aliphatic Amides: Polyprolines and
            Peptoids ........................................... 20
     1.4.3  Hindered Polymer and Oligomer Backbones ............ 23
1.5  Conformational Transitions ................................ 25
1.6  Conclusion and Perspectives ............................... 27
     References ................................................ 28

2    Foldamers Based on Remote Intrastrand Interactions ........ 35
     Philippe Le Crel and Cities Guichard
2.1  Introduction .............................................. 35
2.2  What can be Learned from Strategies used to Control
     Conformations of α-Polypeptides? .......................... 36
2.3  Helices from Homogeneous Oligomeric Backbones with
     Periodicity at the Monomer Level: ω-Peptides and their
     Analogs ................................................... 37
     2.3.1  Compact Helices with Large (>10 atoms) H-bonded
            Rings .............................................. 37
     2.3.2  Extended Helices with Small H-bonded Rings
            Centered at a Single Residue ....................... 45
2.4  Oligoamide Mixed Helices .................................. 51
     2.4.1  The α-Oligopeptide Precedent: from Antibiotic
            Gramicidin A to Poly-Gin Aggregates in
            Huntington's Disease ............................... 52
     2.4.2  Introducing Periodicity at the Level of a Dimer
            Unit in β-Peptides leads to a Remarkably Stable
            Mixed Helical Fold ................................. 53
     2.4.3  Extending the Concept of Mixed Helices ............. 56
2.5  Nonperiodic Structures: Open Chain β-Turn-like Motifs
     and Hairpins in Designed Homo-oligomers ................... 58
     2.5.1  Sheet-forming ω-peptides ........................... 58
     2.5.2  Turn Segment for Hairpin Formation ................. 59
2.6  Expanding Structural Diversity with Heterogeneous
     Backbones ................................................. 61
     2.6.1  From Discrete γ-Amino Acid Guests in α-Helices
            to Helical α, ω- and β,γ-Peptide Hybrids ........... 61
     2.6.2  Hairpins from α, ω-Peptide Hybrids ................. 65
     2.6.3  Sculpting New Shapes by Integrating H-Bonding,
            Aromatic Interactions and Multiple Levels of
            Pre-organization ................................... 66
2.7  Conclusion and Outlook .................................... 67
     References ................................................ 68

3    Foldamers Based on Solvophobic Effects .................... 75
     Yan Zhao and Jeffrey S. Moore
3.1  Introduction .............................................. 75
3.2  Learning from Solvophobically Driven Assemblies -
     Intermolecular Solvophobic Interactions ................... 77
3.3  Learning from Synthetic and Biological Polymers ........... 81
3.4  Recent Advances in Foldamers Based on Solvophobic
     Effects ................................................... 84
     3.4.1  Foldamers Stabilized by Adjacent, Identical
            Aromatic Units ..................................... 85
     3.4.2  Foldamers Stabilized by Adjacent Donor-acceptor
            Aromatic Units ..................................... 87
     3.4.3  Foldamers Stabilized by Nonadjacent Aromatic
            Units .............................................. 92
     3.4.4  Foldamers Stabilized by Aliphatic Units ........... 100
3.5  Conclusions and Outlook .................................. 103
     References ............................................... 104

4    Foldamer Hybrids: Defined Supramolecular Structures
     from Flexible Molecules .................................. 109
     Carsten Schmuck and Thomas Rehm
4.1  Introduction ............................................. 109
4.2  Hybridization of Oligomers with Well-defined Structures .. 112
     4.2.1  Coiled Coils and Helix Bundles .................... 112
     4.2.2  Intertwined Strands ............................... 116
     4.2.3  Stacks of Helical Strands and Macrocycles ......... 117
     4.2.4  Tapes and Hydrogen-bonded Sheets .................. 120
4.3  Hybridization-induced Folding of Unstructured Molecules .. 122
     4.3.1  Hydrogen-bonded Tapes ............................. 122
     4.3.2  Helices Based on Metal-ligand Interactions and
            Salt Bridges ...................................... 127
     4.3.3  Double-stranded Hybrids Based on Aryl-aryl
            Interactions and Hydrophobic Contacts ............. 130
     4.3.4  Hybrids Based on DNA-base-pairing Recognition ..... 132
4.4  Formation of Large Polymeric Aggregates via
     Self-assembly ............................................ 136
4.5  Applications of Foldamer Hybridization ................... 139
4.6  Conclusion ............................................... 143
     References ............................................... 143

5    Control of Polypeptide Chain Folding and Assembly ........ 147
     Rajkishor Rai and Padmanabhan Balaram
5.1  Introduction ............................................. 147
5.2  Helix Promotion by Backbone Substitution ................. 150
     5.2.1  α-Aminoisobutyric Acid (Aib) and Related Dialkyl
            Amino Acids ....................................... 150
     5.2.2  Diproline Segments ................................ 152
5.3  Hairpin Design using Obligatory Turn Segments ............ 155
     5.3.1  DPro-Xxx Turns .................................... 155
     5.3.2  Aib-DXxx Turns .................................... 357
     5.3.3  Asn-Gly Turns ..................................... 159
     5.3.4  Expanded Loop Segments ............................ 161
     5.3.5  Choice of Strand Residues ......................... 161
5.4  Helix-Helix Motifs ....................................... 162
5.5  Multi-stranded β-Sheets .................................. 164
5.6  Mixed Helix-Sheet (α/β) Structures ....................... 165
5.7  Conclusions .............................................. 367
     References ............................................... 168

6    Simulation of Folding Equilibria ......................... 173
     Wilfred F. van Cunsteren and Zrinka Cattin
6.1  Introduction ............................................. 173
6.2  Dynamical Simulation of Folding Equilibria under
     Different Thermodynamic and Kinetic Conditions ........... 175
6.3  Variation of the Composition of the Polypeptide Analogs
     and the Solvent .......................................... 178
6.4  Convergence of the Simulated Folding Equilibrium ......... 181
6.5  Sensitivity of the Folding Equilibrium to the Force
     Field Used ............................................... 184
6.6  Comparison of Simulated with Experimentally Measured
     Observables .............................................. 185
6.7  Characterization of the Unfolded State and the Folding
     Process .................................................. 186
6.8  Conclusion ............................................... 190
     References ............................................... 190

Part 2  Function: From Properties to Applications ............. 193

7    Foldamer-based Molecular Recognition ..................... 195
     Jorge Becerril, Johanna M. Rodriguez, Ishu Saraogi and
     Andrew D. Hamilton
7.1  Introduction ............................................. 195
7.2  Small Molecule Recognition Using Foldamers ............... 396
     7.2.1  Receptors for Water Molecules ..................... 396
     7.2.2  Receptors for Ammonium Cations .................... 198
     7.2.3  Receptors for Hydrophobic Small Molecules ......... 201
     7.2.4  Receptors for Saccharides ......................... 204
     7.2.5  Receptors of Other Organic Molecules .............. 207
7.3  Protein Recognition ...................................... 230
     7.3.1  Abiotic Synthetic Foldamers ....................... 233
     7.3.2  Peptidomimetic Foldamers .......................... 232
7.4  Mimicry of Biomineralization: Recognition of Crystal
     Surfaces Using Foldamers ................................. 217
     7.4.1  Introduction to Biomineralization ................. 237
     7.4.2  Biomimetic Synthesis of Calcite Using Foldamers ... 220
     7.4.3  Biomimetic Synthesis of CdS Using Foldamers ....... 224
7.5  Conclusion ............................................... 224
     References ............................................... 225

8    Biological Applications of Foldamers ..................... 229
     Marc Koyack and Richard Cheng
8.1  Introduction ............................................. 229
     8.1.1  β-Peptides ........................................ 230
     8.1.2  Peptoids .......................................... 231
     8.1.3  Peptide Nucleic Acids (PNA) ....................... 233
     8.1.4  DNA-Binding Oligoamides ........................... 232
     8.1.5  Aryl Amides and Aryl Ureas ........................ 234
     8.1.6  meta-Phenylene Ethynylenes (mPE) .................. 235
     8.1.7  Terphenyls ........................................ 235
8.2  Design Strategies ........................................ 236
     8.2.1  Direct Sequence Conversion ........................ 237
     8.2.2  Distribution of Physicochemical Properties ........ 240
     8.2.3  Modular Assembly .................................. 248
     8.2.4  Grafting Bioactive Functionalities onto
            Scaffolds ......................................... 253
8.3  Outlook and Future Directions ............................ 257
     References ............................................... 257

9    Protein Design ........................................... 267
     Jean-Luc Jestin and Frédéric Pecorari
9.1  Introduction ............................................. 267
9.2  Design of Proteins from Natural Scaffolds ................ 269
     9.2.1  Design of Enzymes ................................. 270
     9.2.2  Design of Binding Proteins ........................ 272
9.3  Design of Proteins from Building Blocks .................. 275
     9.3.1  Design of Proteins from Structural Domains ........ 275
     9.3.2  Design of Proteins from Secondary Structures ...... 277
9.4  Design of Proteins using Altered Alphabets ............... 280
     9.4.1  Design of Proteins using Reduced Alphabets ........ 280
     9.4.2  Design of Proteins using Extended Alphabets ....... 281
9.5  Design of Proteins de novo ............................... 284
     9.5.1  Computational Design of New Folds and
            Experimental Proofs ............................... 284
     9.5.2  Combinatorial and Experimental Design ............. 284
9.6  Conclusion ............................................... 286
     References ............................................... 287

10   Nucleic Acid Foldamers: Design, Engineering and
     Selection of Programmable Biomaterials with
     Recognition, Catalytic and Self-assembly Properties ...... 291
     Arkadiusz Chworos and Luc Jaeger
10.1 Introduction ............................................. 291
10.2 Principles of Nucleic Acid Foldamers ..................... 292
     10.2.1 Structural Principles: Hierarchical Organization
            and Modularity .................................... 292
10.3 Synthesis of Nucleic Acid Foldamers and Analogs .......... 303
10.4 Combinatorial Approaches for Isolating Functional
     Nucleic Acid Foldamers ................................... 306
10.5 DNA Architectonics ....................................... 307
     10.5.1 Rational Design of DNA Tiles ...................... 308
     10.5.2 Principle of Tensegrity and Mode of Assembly ...... 309
10.6 RNA Architectonics ....................................... 310
     10.6.1 General Approach .................................. 310
     10.6.2 Examples of RNA Nano-architectures ................ 313
10.7 Self-assembly Strategies for Building Complex Nucleic
     Acid Nanostractures ...................................... 315
     10.7.1 Programmable Self-assembly ........................ 315
10.8 Ornamentation and Functionalization of Nucleic Acid
     Architectures ............................................ 319
     10.8.1 General Principles ................................ 319
     10.8.2 Nucleic Acid Foldamers for Sensors, Medicine and
            Nano-electronics .................................. 319
10.9 Conclusions .............................................. 321
     References ............................................... 323

11   Helically Folding Polymers ............................... 331
     Eiji Yashima and Katsuhiro Maeda
11.1 Introduction ............................................. 331
11.2 Helical Polymers with High Helix Inversion Barriers
     (Static Helical Polymers) ................................ 332
     11.2.1 Poly(triarylmethyl methacrylate)s ................. 333
     11.2.2 Polychloral ....................................... 334
     11.2.3 Polyisocyanides ................................... 336
     11.2.4 Polyguanidines .................................... 337
11.3 Helical Polymers with Low Helix Inversion Barriers
     (Dynamic Helical Polymers) ............................... 338
     11.3.1 Dynamic Helical Polymers Assisted by Covalent
            Bonding ........................................... 339
     11.3.2 Dynamic Helical Polymers Assisted by Noncovalent
            Bonding ........................................... 344
     11.3.3 Memory of Induced Helical Chirality ............... 351
11.4 Inversion of Macromolecular Helicity ..................... 355
11.5 Applications of Helical Polymers ......................... 359
11.6 Conclusion ............................................... 362
     References ............................................... 363

12   Polyisocyanides: Stiffened Foldamers ..................... 367
     Matthijs B.J. Otten, Ceroid A. Metselaar, Jeroen
     J.L.M. Cornelissen, Alan E. Rowan and Roeland
     J.M. Nolte
12.1 Introduction ............................................. 367
12.2 Preparation .............................................. 368
12.3 Conformation ............................................. 370
12.4 Stiffening the Helix ..................................... 377
12.5 Functionalized Polyisocyanides ........................... 387
12.6 Conclusions .............................................. 398
     References ............................................... 398

13   Foldamers at Interfaces .................................. 403
     Jan van Esch, Hennie Valkenier, Sebastian Hartwig, and
     Stefan Hecht
13.1 Introduction ............................................. 403
13.2 Folding in Solution and at Interfaces .................... 405
     13.2.1 Types of Interactions ............................. 406
     13.2.2 Thermodynamics .................................... 406
     13.2.3 Design Considerations ............................. 408
     13.2.4 Scope ............................................. 409
13.3 Helical Structures ....................................... 410
     13.3.1 Adsorption of Helical Structures at Interfaces .... 410
     13.3.2 Loss of Helicity upon Adsorption .................. 412
     13.3.3 Helical Structures Formed upon Adsorption ......... 414
13.4 Sheet Structures ......................................... 415
     13.4.1 Adsorbed Sheet Structures at Interfaces ........... 415
     13.4.2 Enhanced Sheet Formation upon Adsorption .......... 417
     13.4.3 Change in Sheet Structure upon Adsorption ......... 420
13.5 Turn Elements and Hairpins ............................... 421
13.6 Outlook .................................................. 423
     References ............................................... 424

     Index .................................................... 427


Архив выставки новых поступлений | Отечественные поступления | Иностранные поступления | Сиглы
 

[О библиотеке | Академгородок | Новости | Выставки | Ресурсы | Библиография | Партнеры | ИнфоЛоция | Поиск | English]
  Пожелания и письма: branchl@gpntbsib.ru
© 1997-2020 Отделение ГПНТБ СО РАН (Новосибирск)
Статистика доступов: архив | текущая статистика
 

Документ изменен: Wed Feb 27 14:26:42 2019. Размер: 21,135 bytes.
Посещение N 1208 c 12.08.2014