Advanced Methods in Protein Sequence Determination: (25 Molecular Biology, Biochemistry and Biophysics / Molekularbiologie, Biochemie und Biophysik)

Confusion now hath made his masterpiece Macbeth II iii 72 Whence and what are those execrable shape? Paradise Lost Ib 1 681 Confusion worse confounded Paradise Lost Ib 1 995 When the manuscript for the first part of this book was proposed, it was anticipated that the discussion of the entire field of protein se- quencing could be covered in a single volume - from purification and characterization of the protein through fragmentation by chemical or enzymic means and, finally, to reassembly of the identified individual peptides into the reconstructed total sequence. It soon became evident that this would not be possible. While the intent was to restrict the expose of procedures only to that information concerned with "hands on" wet chemistry, it became apparent that a thorough presentation would require, in addition, a discussion of certain instrumental and more theoretical approaches not included in the first volume. Furthermore, the entire understanding of the field of protein sequencing has advanced appreciably since the inception of this book. The purpose of the first volume was to provide practical information in sufficient detail to permit the researcher to undertake the actual sequencing procedures in his own laboratory.

Table of Contents:
1 Step-wise Degradation of Peptides Attached to Solid Supports.- I. Introduction.- II. Choice of Solid Support.- A. Polystyrene Beads.- B. Glass Beads.- III. Attachment of Peptides to Supports.- A. Carboxyl Activation Methods.- B. Amino Group Coupling.- IV. Step-wise Degradation Procedures.- A. Isothiocyanate Methods.- B. Thioacetylation Method.- V. Automation of Solid Phase Degradation.- A. Semi-Automated Operation.- B. An Inexpensive Automated Apparatus.- VI. Concluding Remarks.- 2 Coupling Methods and Strategies in Solid-Phase Sequencing.- I. Introduction.- II. Coupling Procedures.- A. Attachment by Activation of Carboxyl Groups.- B. Attachment of Amino Side Chains Using p-Phenylene Diisothiocyanate.- C. Combined Methods of Attachment.- D. Sequencing Resins.- E. Summary of Attachment Procedures.- III. Sequencing Strategies.- 3 Sequencing Peptides and Proteins Lacking Free ?-Amino Groups.- I. Introduction.- II. Isolation and Detection of Peptides Lacking Free ?-Amino Groups.- III. PCA-Terminating Peptides and Proteins.- A. Chemical Approaches.- B. Enzymatic Removal of PCA Residues.- IV. Acylated Peptides and Proteins.- A. Chemical Identification Procedures.- B. Enzymatic Removal of Acetylated Amino-Terminal Residues.- V. Concluding Remarks.- 4 Use of Antibody in the Study of Protein Structure.- I. Introduction.- II. Measurement of the Ag-Ab Reaction.- III. The Effect of Conformational Changes on the Antigenicity of Proteins.- IV. Detection of Sequence Changes in Proteins with Antibodies.- V. Use of Antibody in the Study of Protein Evolution.- 5 Polarization of Light and Protein Structure.- I. Introduction.- II. Plane Polarized Light.- III. Circularly Polarized Light.- IV. Circular Dichroism.- V. Drude Equation.- VI. Optical Properties of Amino Acids.- VII. Optical Properties of Peptides.- VIII. Conclusion.- 6 The X-ray Crystallography Technique in Protein Sequencing.- I. Introduction.- II. Outline of the Protein Crystallographic Method.- III. Some Important Concepts in X-ray Diffraction Analysis of Protein Crystals.- IV. Building up the Electron Density Map.- V. Interpretation of the Electron Density Map.- A. Molecular Boundary.- B. Main Chain.- C. Model Building.- D. The Side Chains.- E. Refinement of the Protein Structure.- VI. Correlation of the Chemical Sequence with the Electron Density Maps.- A. Structure Interpretation with Chemical Sequence.- B. Structure Interpretation with Partial Sequence.- VII. Conclusion.- 7 Amino Acid Sequence Determination by Mass Spectrometry.- I. Introduction.- II. Instrumentation and Techniques.- A. Ionization.- B. Analysis.- C. Resolution.- D. Sample Introduction.- III. Mass Spectrometry of Peptides.- A. Derivatization of Peptides.- B. Determination of Amino Acid Sequence from the Mass Spectrum.- C. Analysis of Peptide Mixtures.- IV. Concluding Remarks.- A. Recent Developments in Instrumentation.- B. Relationship of Mass Spectrometry to Conventional Methods for Sequence Analysis.- 8 Peptide Sequence Analysis by Nuclear Magnetic Resonance Spectroscopy.- I. Introduction.- II. NMR Principles.- III. Amino Acid Composition and Residue Identification.- A. Analysis of High Resolution 1H Spectra.- B. Analysis of High Resolution 13C Spectra.- C. Use of Paramagnetic Shift and Relaxation Enhancement (Broadening) Probes.- D. Sample Preparation.- IV. Conclusions.- References.