Current Research in Protein Chemistry

Current Research in Protein Chemistry: Techniques, Structure, and Function focuses on the techniques and methods used for determining the structure and function of proteins. Topics covered range from protein folding and stability to catalysis by chimeric proteins, amino acid and peptide analysis, applications of mass spectrometry to peptide and protein analysis, and protein sequencing. This book is divided into six sections encompassing 55 chapters. The first chapter describes a novel method for protein hydrolysis by means of microwave irradiation that uses Teflon-Pyrex tubes. This is followed by a discussion of the application of high performance capillary electrophoresis to the analysis of amino acids. The sections that follow focus on mass spectrometric methods, protein sequencing, and capillary electrophoresis as well as protein stability, chimeric proteins and enzyme modifications, and protein structure prediction. The crystal structure of human interleukin-1alpha, the acid-denatured states of proteins, solubility of recombinant proteins expressed in Escherichia coli, and catalysis by chimeric proteins are considered. The reader is also introduced to peptide mapping and internal sequencing of proteins from acrylamide gels, new approaches to covalent sequence analysis, alkaline denaturation of hemoglobin, and measurements of disulfide bond stabilities in protein folding intermediates. Students and researchers interested in protein chemistry will find this book extremely helpful.

Foreword

Preface

Dedication to Emil T. Kaiser and Irving S. Sigal

Acknowledgments

Section I Techniques: Amino Acid Analysis; Peptides and Proteins

1. A Rapid and Novel Means of Protein Hydrolysis by Microwave Irradiation Using Teflon-Pyrex Tubes

2. Analysis of Amino Acids by High Performance Capillary Electrophoresis

3. An Evaluation of Microwave Heating for the Vapor Phase Hydrolysis of Proteins: I. Comparison to Vaper Phase Hydrolysis for 24 Hours

4. Performance Evaluation: Automatic Hydrolysis and PTC Amino Acid Analysis

5. A Collaborative Amino Acid Analysis Study from the Association of Biomolecular Resource Facilities

6. Recent Developments in Solid Phase Peptide Synthesis Using the 9-Fluorenylmethyloxycarbonyl (FMOC) Protecting Group Strategy

7. Relationships of Paramecium and Endocrine Secretory Proteins

8. Quantitative Electrotransfer of Proteins from Polyacrylamide Gels onto PVDF Membranes

9. Selective Isolation of Disulfide-Containing Peptides from Trypsin Digests Using Strong Cation Exchange HPLC

Section II Techniques: Mass Spectrometric Methods; Protein Sequencing; Capillary Electrophoresis

10. Analysis of Peptides and Proteins by Tandem Quadrupole Mass Spectrometry

11. Protein and Oligopeptide Sequence Analysis on the TSQ-70 Triple Quadrupole Mass Spectrometer

12. Sequence Analysis of Peptides by Plasma Desorption Mass Spectrometry

13. Study of the Primary Structure of Recombinant Proteins with a Benchtop Gas Chromatograph-Mass Spectrometer-Computer Data Syste

14. Synthesis and Mass Spectrometry of Phosphotyrosine-Containing Peptides

15. Design, Characterization, and Results of ABRF-89SEQ: A Test Sample for Evaluating Protein Sequencer Performance in Protein Microchemistry Core Facilities

16. Extended N-Terminal Protein Sequencing of Clostridium botulinum Neurotoxin Type A Fragments: Continuous Sequence to Seventy Residues Both from Glass-Fiber Filter Using the Gas Phase and Polyvinylidene Difluoride Using the Pulsed Liquid Phase Sequence

17. Peptide Mapping and Internal Sequencing of Proteins from Acrylamide Gels

18. New Approaches to Covalent Sequence Analysis

19. Analysis of Brain Constituents by Capillary Electrophoresis

20. Capillary Electrophoresis Analysis of Species Variations in the Tryptic Maps of Cytochrome C

21. Ultrafast Protein Analysis: A Powerful Technique for Recombinant Protein Process Monitoring

22. Separation and Characterization of Proteins in the Range of 1 to 200 kDa with HPEC™

23. Protein Detection during Poly aery lamide Gel Electrophoresis Using High Resolution Dynamic Imaging

Section III Protein Folding

24. Design, Computer Derived Structure and Biological Activity of Three Bicyclic Gonadotropin Releasing Hormone (GnRH) Antagonists

25. The H-Helix of Myoglobin as a Potential Independent Protein Folding Domain

26. Probing the Role of Position 49 in the Folding of the Alpha Subunit of Tryptophan Synthase from Escherichia coli

27. Tests of Isolated ß-Sheet Formation in a Cyclic Peptide from BPTI

28. Spectroscopic and Chromatographic Studies of Native and Denatured States of T4 Lysozymes

29. Studies of the Alkaline Denaturation of Hemoglobin in an NMR Optical Stopped-Flow Apparatus

30. Conformational Studies of Peptides Corresponding to the LDL Receptor Cytoplasmic Tail and Transmembrane Domain

31. Biochemical and Biophysical Comparison of Bacterial DnaK and Mammalian hsc73, Two Members of an Ancient Stress Protein Family

Section IV Protein Structure/Stability

32. The Crystal Structure of Human Interleukin-1α

33. Crystal Structure of a Protein-Toxin Solved from a Predicted Model

34. Segmental Accommodation: A Novel Conformational Change Induced upon Ligand Binding by Thymidylate Synthase

35. Subunit Interactions and the Function of Tumor Necrosis Factor

36. Structure Prediction Methods for Membrane Proteins: Comparison with the X-Ray Structure of the R. viridis Photosynthetic Reaction Centre

37. The Sequence Attributes Method for Determining Correlations Between Amino Acid Sequence and Protein Secondary Structure

38. Acid-Denatured States of Proteins

39. Estimation of Protein Stability: Comparison of Calorimetric and Denaturant Studies

40. Engineering of Multiple Disulfide Bonds Dramatically Stabilizes T4 Lysozyme

41. E. coli Thioredoxin Stability is Greatly Enhanced by Substitution of Aspartic Acid 26 by Alanine

42. Measurements of Disulfide Bond Stabilities in Protein Folding Intermediates

43. Solubility of Recombinant Proteins Expressed in Escherichia coli

Section V Chimeric Proteins and Enzyme Modifications

44. Multiple Determinants for Substrate Specificities in Cytochrome P450 Isozymes

45. Catalysis by Chimeric Proteins: Conversion of a ß-Lactamase to a D,D-Carboxypeptidase

46. Molecular Mapping of Immunogenic Determinants of Human CD4 Using Chimeric Interspecies Molecules and Anti-CD4 Antibodies

47. Ecballium elaterium Trypsin Inhibitor II (EETI II) as a Vehicle for New Functions

48. Comparison of the Dimerization, Stability and Inhibitor Binding Between HIV-1 Protease Wild Type and Active Site Mutant

49. Structure/Function Analysis of IL-2 Toxin: Fragment B Requirements for the Translocation of Fragment A into the Cytosol of Target Cells

50. Alteration of the Site of Adenylylation of Glutamine Synthetase by Site-Directed Mutagenesis

Section VI Structure Prediction Workshop

51. Three-Dimensional Protein Structure Prediction Workshop: Overview and Summary

52. Protein Structure Prediction

53. Knowledge-Based Protein Modelling: Human Plasma Kallikrein and Human Neutrophil Defensin

54. Application of a Knowledge-Based Strategy to the Prediction of Protein Tertiary Structure

55. Structure Determination of Haloalkane Dehalogenase

Index