Techniques in Protein Chemistry

Foreword

Preface

Acknowledgments

Section I Mass Spectrometry of Peptides and Proteins

Identification of 2-D Gel Proteins at the Femtomole Level by Molecular Mass Searching of Peptide Fragments in a Protein Sequence Database

Characterization by Mass Spectrometry of Conjugates Between Proteins and Low Molecular Weight Chemicals

Protein Ladder Sequencing: Towards Automation

Mass Spectrometric Protocol for the Analysis of UV-Crosslinked Protein- Nucleic Acid Complexes

β-Lactamases: Probing the Mechanism of Action by Electrospray Ionisation Mass Spectrometry (ESI MS)

Electrospray Mass Spectral Analysis of the (AT)-Arylazido-β-alanyl NAD+ Modified Bovine Heart Mitochondrial NADH Dehydrogenase

Protease Digestions on PVDF Membranes for Matrix-Assisted Laser Desorption Mass Spectrometry

Section II Analysis of Posttranslational Processing Events

Structural Characterization of a Novel Tetrasaccharide Attached to Ser-61 of Human Factor IX by Mass Spectrometry and Ή NMR Spectroscopy

Primary Structure of Gallinacin-1, an Antimicrobial β-Defensin from Chicken Leukocytes

Site-Specific Glycosylation of Recombinant Stem Cell Factor

Strategies for the Characterizaton of Carbohydrates from Glycoproteins by Mass Spectrometry

Distinction between Phosphorylated and Sulfated Peptides by Matrix Assisted Laser Desorption Ionization Reflector Mass Spectrometry at the Sub Picomole Level

Characterization of the Natural and Radiation Induced Modification of Histones

Selective Detection of Thr-, Ser-, and Tyr-Phosphopeptides in Complex Digests by Electrospray LC-MS

Section III Protein Sequencing and Amino Acid Analysis

A Synthetic Peptide for Evaluating Protein Sequencing Capabilities: Design of ABRF-93SEQ and Results

Combined Edman-Chemical and Laser-Desorption Mass Spectrometric Approaches to Micro Peptide Sequencing: Optimization and Applications

Selective Sequencing of Peptides with N-Terminal Ser or Thr in Mixtures

Characterization of Phosphorylation Sites in Bovine Rhodopsin Using Modified Gas Phase Sequencing Programs

Strategies for Increasing the Sensitivity of N-Terminal Sequence Analysis

Alkylation of Cysteine Residues with 3-Bromopropylamine: Identification by Protein Sequencing and Quantitation by Amino Acid Analysis

Instability of Cysteine Labeling with 4-(Aminosulfonyl)-7-fluoro-2,l,3- benzoxadiazole (ABD-F)

Elution of Proteins from Polyacrylamide Gels onto the Hewlett-Packard Sequencing Column

High Sensitivity Peptide Sequence Analysis Using in Situ Proteolysis on High Retention PVDF Membranes and a Biphasic Reaction Column Sequencer

A One-Step Enzymatic Digestion Procedure for PVDF-Bound Proteins That Does Not Require PVP-40

Tryptic in Situ Digestion in the Presence of Dimethylsulfoxide

Amino Acid Analysis of Phospho-Peptides: ABRF-93AAA

Section IV Peptide and Protein Separations and Other Methods

Protein and Peptide Recovery from Polyacrylamide Gels

High-Resolution Large-Scale Isoelectric Focusing of Proteins in a Chemically Defined Buffer System

Applications of Tandem Capillary HPLC in the Isolation of Proteins for Characterization Using Microsequencing and Mass Spectrometry

Analytical Ultracentrifugation Analysis of the Self-Association of κ-Bungarotoxin

A Facile Method for the Release, Labeling, and CE Analysis of Glycoprotein Oligosaccharides

The Resonant Mirror: A Versatile Tool for the Study of Biomolecular Interactions

Post-run Analysis of Proteins Purified by Capillary Electrophoresis with Membrane Fraction Collection

Section V Protein Design and Functional Domain Analysis

In Vitro Expression of Serpins

Altering Substrate Specificity and Detecting Processivity in Nucleases

Mutagenesis of n2-Site Metal-Binding Glutamate Residues in E. coli Glutamine Synthetase

Reconstitution in Vitro of the Interleukin-6/Interleukin-6 Receptor Interaction: Direct Monitoring Using a Biosensor Employing Surface Plasmon Resonance Detection

Functional Zone Identification by Biophysics Techniques: The Interaction of Calmodulin with Regulatory Peptides

Characterization of the Reactive Cysteine Residues of the β-Galactosidase α-Acceptor Deletion Mutant EA22

Characterization of a 32-Residue Peptide from Rat DNA Polymerase β with Single-Stranded DNA-Binding Affinity

Mapping the Retinoid-Binding Domain of Cellular Retinaldehyde-Binding Protein

Section VI Protein Conformation, Folding, and Modeling

Probing the Structure of a Human Interleukin-6 Mutant by Limited Proteolysis

Extraction and Characterization of Molecular Surface Knobs and Holes for the Study of Complex Formation

Design of an Auto-Associative Neural Network with Hidden Layer Activations That Were Used to Reclassify Local Protein Structures

The Effects of Local Environments on the Pattern of Amino-Acid Substitution in Homologous Protein Structures: The Role of Side-Chain to Main-Chain van der Waals Interactions

Modeling Human Chorionic Gonadotropin Using Distance Geometry and Immunological Constraints

Section VII NMR Analysis of Peptide and Protein Solution Structures

NMR Methods Used to Derive Solution Conformations in Peptides

Measuring Global and Local Structural Free Energy Changes in Staphylococcal Nuclease by NMR-Observed Hydrogen Exchange

Mapping of Specific Protein-Protein Interactions by NMR

Protein Folding Intermediates Characterized by Pulsed Hydrogen Exchange

Application of Equilibrium and Stopped-Flow 19F NMR Spectroscopy to Protein Folding: Studies of E. coli Dihydrofolate Reductase

Protein Hyperfine Resonance Assignments in Glycera dibranchiata Monomer Hemoglobin Component IV

Section VIII Peptide Synthesis and Peptide Libraries

FMOC Solid Phase Synthesis of PhosphopeptidesSynthesis of Uniform Peptide Libraries and Methods for Physico-Chemical Analysis

A General Strategy for the Synthesis of Eosin Fluorescein Energy Transfer Substrates for High Sensitivity Screening of Protease Inhibitors

Variable Success of Peptide-Resin Cleavage and Deprotection Following Solid- Phase Synthesis

Membrane Protecting Sequences and New Antimicrobial Peptides Identified through the Screening of Synthetic Peptide Combinatorial Libraries

Phage Display of Random Peptides on a Protein Scaffold

New Methodologies in the Preparation of Peptide Libraries

Using Peptoid Libraries [Oligo N-Substituted Glycines] for Drug Discovery

Construction and Screening of Libraries of Peptide and Non-Peptide Structures

Index