Main description:

Even though they are present in nature, non-proteinogenic amino acids are usually defined as unnatural or non-natural. Beside their structural diversity, interest in these compounds is due to their occurrence in nature, their biological properties, the analytical aspects, their use as probes, and their incorporation into peptides and proteins, among other reasons. Divided into five convenient sections, Unnatural Amino Acids: Methods and Protocols deals with enzymatic methods used to produce non-natural amino acids, aspects concerning the presence of unnatural amino acids in peptides with antimicrobial properties, genetic incorporation of unnatural amino acids into proteins (yeast and mammalian cells), and detection and quantification of D-amino acids and related enzymes. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and accessible, Unnatural Amino Acids: Methods and Protocols serves as an ideal guide for scientists and contributes to directing the attention of researchers to the many fields of growing scientific interest in non-natural amino acids.

Contents:

Part I. Synthesis of Unnatural Amino Acids

1. Preparation of Unnatural Amino Acids with Ammonia-lyases and 2,3-aminomutases

Laszlo Poppe, Csaba Paizs, Klaudia Kovacs, Florin-Dan Irimie, and Beata Vertessy

2. Multistep Enzyme Catalyzed Reactions for Unnatural Amino Acids

Paola D'Arrigo and Davide Tessaro

3. Enzymatic Production of Enantiopure Amino Acids from Mono-substituted Hydantoin Substrates

Gwynneth F. Matcher, Rosemary A. Dorrington, and Stephanie G. Burton

4. Preparation of Glutamate Analogues by Enzymatic Transamination

Thierry Gefflaut, Zeinab Assaf, and Martine Sancelme

5. Carbon-Carbon Bond Forming Enzymes for the Synthesis of Non-natural Amino Acids

Pere Clapes, Jesus Joglar, and Mariana Gutierrez

6. Engineering Cyclic Amidases for Non-natural Amino Acid Synthesis

Francisco Javier Las Heras-Vazquez, Josefa Maria Clemente-Jimenez, Sergio Martinez-Rodriguez, and Felipe Rodriguez-Vico

Part II. Application of Unnatural Amino Acids

7. NMR Analysis of Unnatural Amino Acids in Natural Antibiotics

Franca Castiglione

8. Site-specific Incorporation of Unnatural Amino Acids as Probes for Protein Conformational Changes

Jennifer C. Peeler and Ryan A. Mehl

9. Application of Unnatural Amino Acids to the De novo Design of Selective Antibiotic Peptides

Rickey P. Hicks and Amanda L. Russell

10. Use of Unnatural Amino Acids to Probe Structure-activity Relationships and Mode-of-action of Antimicrobial Peptides

Alessandro Tossi, Marco Scocchi, Sotir Zahariev, and Renato Gennaro

Part III. Use of Unnatural Amino Acids in Protein Synthesis

11. Experimental Methods for Scanning Unnatural Amino Acid Mutagenesis

Jia Liu and Ashton T. Cropp

12. Genetic Incorporation of Unnatural Amino Acids into Proteins in Yeast

Qian Wang and Lei Wang

13. Site-specific Incorporation of Unnatural Amino Acids into Proteins in Mammalian Cells

Nobumasa Hino, Kensaku Sakamoto, and Shigeyuki Yokoyama

14. Incorporation of Unnatural Non-a-amino Acids into the N-terminus of Proteins in a Cell-free Translation System

Takahiro Hohsaka

15. Site Specific Modification of Proteins by the Staudinger-phosphite Reaction

Paul Majkut, Verena Boehrsch, Remigiusz Serwa, Michael Gerrits, and Christian P. R. Hackenberger

Part IV. D-amino Acids: Analysis and Applications

16. HPLC Methods for Determination of D-aspartate and N-methyl-D-aspartate

George H. Fisher and Mara Tsesarskaia

17. Estimation of Chronological Age from the Racemization Rate of L- and D-aspartic Acid: How to Completely Separate Enantiomers from Dentin

Toshiharu Yamamoto and Susumu Ohtani

18. Enzymatic Detection of D-amino Acids

Gianluca Molla, Luciano Piubelli, Federica Volonte, and Mirella S. Pilone

19. An Enzymatic-HPLC Assay to Monitor Endogenous D-serine Release from Neuronal Cultures

Inna Radzishevsky and Herman Wolosker

20. Electrophysiological Analysis of the Modulation of NMDA-receptors Function by d-serine and Glycine in the Central Nervous System

Fabrice Turpin, Glenn Dallerac, and Jean-Pierre Mothet

21. Biosensors for D-amino Acid Detection

Silvia Sacchi, Elena Rosini, Laura Caldinelli, and Loredano Pollegioni

22. Analysis of D- -aspartyl Isomers at Specific Sites in Proteins

Noriko Fujii and Norihiko Fujii

23. Nutritional Value of D-amino Acids, D-peptides and Amino Acid Derivatives in Mice

Mendel Friedman and Carol E. Levin

Part V. Enzymes Active on D-amino Acids

24. Preparation and Assay of Recombinant Serine Racemase

Florian Baumgart, Clara Aicart-Ramos, and Ignacio Rodriguez-Crespo

25. Assay of Amino Acid Racemases

Masumi Katane, Masae Sekine, and Hiroshi Homma

26. Assays of D-amino Acid Oxidases

Gabriella Tedeschi, Loredano Pollegioni, and Armando Negri

27. Enzymes Acting on D-amino Acid Containing Peptides

Yasuhisa Asano