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Advanced Methods in Protein Sequence Determination

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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.
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