Peptide Characterization and Application Protocols (Methods in Molecular Biology, 386)

✍ Scribed by Gregg B. Fields (editor)

• Publisher: Humana
• Year: 2007
• Tongue: English
• Leaves: 344
• Category: Library

✦ Synopsis

Peptide Characterization and Application Protocols is dedicated entirely to the characterization of peptides and their applications for the study of biochemical systems and the contributing authors are all leaders in the field of peptide research. Part I, Characterization, presents the most recent advances in select analytical techniques, including high-performance liquid chromatography (HPLC) for purification and evaluation of peptides and mass spectrometry (MS) for the analysis of standard and modified peptides. Innovative methods of synthesis and characterization of membrane peptides are also presented. Part II, Application, presents a variety of specific applications for synthetic peptides. The collected protocols demonstrate the systematic manner in which peptides can be constructed, analyzed, and applied to attack contemporary problems in biochemistry, and this book will be an indispensable aid in the pursuit of new directions in peptide research.

✦ Table of Contents

1-59745-430-3_BookFrontMatter_OnlinePDF.pdf
Peptide Characterization and Application Protocols
Preface
Contents
Contributors
1-59745-430-3_1_OnlinePDF.pdf
PartI: Characterization
HPLC Analysis and Purification of Peptides
Colin T. Mant, Yuxin Chen, Zhe Yan, Traian V. Popa, James M. Kovacs, Janine B. Mills, Brian P. Tripet, and Robert S. Hodges
Introduction
Scope of Chapter
Properties of Peptides and Proteins and Practical Implications
HPLC Modes Used in Peptide Separations
Capillary Electrophoresis
Materials
Chemical and Solvents
Columns and Capillaries
Instrumentation
Methods
Size-Exclusion HPLC
Ion-Exchange HPLC
Reversed-Phase HPLC
HILIC/CEX
Capillary Electrophoresis
Preparative HPLC of Synthetic Peptides and Recombinant Proteins
Notes
1-59745-430-3_2_OnlinePDF.pdf
Identification of Proteins Based on MS/MS Spectra and Location of Posttranslational Modifications
Kathryn L. Stone, Myron Crawford, Walter McMurray, Nancy Williams, and Kenneth R. Williams
Introduction
Materials
LC/MS/MS
Alkaline Phosphatase Digestion
Comparative Peptide Mapping
Radiosequencing
Methods
MS/MS Analysis
De Novo MS/MS Interpretation
Location of Sites of Phosphorylation
Alkaline Phosphatase Digestion/MALDI-MS Approach to Locating Sites of Protein Phosphorylation
Location of Other Sites of Protein Posttranslational Modification
Notes
1-59745-430-3_3_OnlinePDF.pdf
Determination of Phosphorylated and O-Glycosylated Sites by Chemical Targeting (CTID) at Ambient Temperature
Gary M. Hathaway, phd
Introduction
Materials
-Elimination and Michael Addition
Phosphopeptides and Glycosylated Peptide
MALDI-TOF Mass Spectrometry
Casein Phosphopeptides
Methods
Preparation of Ba(OH)2
-Elimination and Michael Addition
Digestion by Lysine Endopeptidase
Analysis by MALDI-TOF Mass Spectrometry
Preparation of Casein Phosphopeptides
Notes
1-59745-430-3_4_OnlinePDF.pdf
Synthesis, Biosynthesis, and Characterization of Transmembrane Domains of a G Protein--Coupled Receptor
Fred Naider
Introduction
G Protein---Coupled Receptors
Synthesis of Membrane Peptides (30--60 Residues): Peptide Design and Synthesis
Materials
Synthesis of Membrane Peptides
Biosynthesis of Membrane Peptides
Methods
Synthesis of Membrane Peptides
Biosynthesis of Membrane Peptides
SDS-PAGE and Western Blot Procedures
Purification of Fusion Protein
Cyanogen Bromide Release of Target Membrane Peptide
HPLC Purification of Target Membrane Peptide
Circular Dichroism Spectroscopy of Membrane Peptides
Notes
1-59745-430-3_5_OnlinePDF.pdf
PartII: Applications
Application of Topologically Constrained Mini-Proteins as Ligands, Substrates, and Inhibitors
Janelle L. Lauer-Fields, Dmitriy Minond, Keith Brew, and Gregg B. Fields
Topology and Templates
Template-Assembled Synthetic Proteins
Disulfide-Stabilized Structures
Peptide-Amphiphiles
Materials
Methods
Template-Assembled Synthetic Protein Methods and Applications
Disulfide-Stabilized Structures: Methods and Applications
Peptide-Amphiphile Methods and Applications
Notes
1-59745-430-3_6_OnlinePDF.pdf
Proteolytic Profiling of the Extracellular Matrix Degradome
Diane Baronas-Lowell, Janelle L. Lauer-Fields, Mohammad Al-Ghoul, and Gregg B. Fields
Introduction
Proteolytic Profiling Technologies
Collagen in Cancer Progression
MMPs and Melanoma Metastasis
Profiling MMP Activities Using Fluorogenic Triple-Helical Substrates
MMPs and Cell Signaling Pathways in Melanoma
Melanoma Interactions with Neighboring Cell Types During Metastasis
Materials
Equipment
Cells, Media and Reagents
Methods
Preparation of Peptide-Amphiphiles: Synthesis, Purification, Analytical and Structural Characterization.
Induction of Melanoma Cells
Semi-Quantitative RT-PCR
Quantitative RT-PCR
Cell-Specific Protein Expression
Cellular MMP Assays
Protein Electrophoresis
Gelatin Zymography
1-59745-430-3_7_OnlinePDF.pdf
-Amyloid Protein Aggregation
Marcus A. Etienne, Nadia J. Edwin, Jed P. Aucoin, Paul S. Russo, Robin L. McCarley, and Robert P. Hammer
Introduction
Materials
Inhibitor Peptide Synthesis, Purification, and Characterization
A1-40 Peptide Aggregation
Circular Dichroism Measurements
Scanning Force Microscopy
Transmission Electron Microscopy
Fluorescence Measurements
Cell Viability Assay
Methods
Peptide Synthesis
Peptide Cleavage
Peptide Purification and Characterization
A1-40 Peptide Aggregation (Monomeric Starting Material)(see Notes 2 and 3)
A1-40 Peptide Aggregation (Protofibril/Fibril Formation)
Circular Dichroism Spectroscopy Measurements
Scanning Force Microscopy
Transmission Electron Microscopy (see Fig. 3)
Fluorescence Measurements
Cell Viability Assay
Dynamic Light Scattering Measurements
Fluorescence Photobleaching Recovery Measurements
Notes
1-59745-430-3_8_OnlinePDF.pdf
Radiometal-Labeled Somatostatin Analogs for Applications in Cancer Imaging and Therapy
Jason S. Lewis and Carolyn J. Anderson
Introduction
Materials
Chelator-Peptide Synthesis
Radiolabeling of Peptides
In Vitro Receptor-Binding Assays
Methods
Preparation of Chelator-Peptide Conjugates
Radiolabeling Methods
In Vitro Receptor-Binding Assays
In vivo Evaluation of Radiolabeled Peptides
Notes
1-59745-430-3_9_OnlinePDF.pdf
Cell-Penetrating Proline-Rich Peptidomimetics
Josep Farrera-Sinfreu, Ernest Giralt, Miriam Royo, and Fernando Albericio1
Introduction
-Amino-1L-Proline-Derived Peptides
Synthesis of Poly(proline) Dendrimers
Materials
Solid-Phase Synthesis
Enzymatic Stability, Cell Culture, and Lysis
Methods
General Solid-Phase Synthesis Procedures
Solid-Phase -Peptide Syntheses
Solid-Phase Synthesis of Dendrimers
Purification and Characterization of Peptides and Dendrimers
Enzymatic Stability Studies
Treatment of Cell Cultures With CF-Labeled Peptides or Dendrimers
Notes
1-59745-430-3_10_OnlinePDF.pdf
Peptide-Mediated Targeting of Liposomesto Tumor Cells
Evonne M. Rezler, David R. Khan, Raymond Tu, Matthew Tirrell, and Gregg B. Fields
Introduction
Materials
Methods
Synthesis and Purification of PAs
Structural Characterization of PAs
Liposome Preparation
LUV and SUV Characterization
Incorporation of PAs into the LUVs
PA-Targeted LUV Stability
PA Targeting of LUVs to Cells
Cell Culture
Fluorescence Microscopy
Notes
1-59745-430-3_11_OnlinePDF.pdf
Peptide-Mediated Delivery of Nucleic Acids into Mammalian Cells
Sébastien Deshayes, Federica Simeoni, May C. Morris, Gilles Divita, and Frédéric Heitz
Introduction
Materials
Cell Cultures
Oligonucleotide and Transfection Reagents
Peptide-Carrier MPG
Methods
Preparation of MPG/Oligonucleotide Complexes
Example of Application: An MPG-mediated siRNA Delivery
Lipid-Based Formulation for Oligonucleotide Delivery
Notes
1-59745-430-3_12_OnlinePDF.pdf
Broth Microdilution Antibacterial Assay of Peptides
Laszlo Otvos and Mare Cudic
Introduction
Working With Bacteria
Most Frequently Used Terms
Special Considerations for Peptide Antibiotics
Resistance Induction
Materials
Equipment
Medium and Reagents
Preparation of Media and Agar for Bacterial Grow
Prepare Peptide/Antibiotic Solutions
Methods
Antibacterial Assay
Resistance Induction
Notes
1-59745-430-3_13_OnlinePDF.pdf
Depsipeptide Synthesis
Maciej Stawikowski and Predrag Cudic
Introduction
Materials
Methods
Carbodiimide/4-Dimethylaminopyridine Coupling Method
Ester Bond Formation Using the Boc-Amino Acid N-Hydroxysuccinimide Ester Method
Mitsunobu Esterification
Yamaguchi Esterification
Protection of Hydroxyl Groups During Solid-Phase Depsipeptide Synthesis
Solid-Phase Reaction Monitoring
Notes
1-59745-430-3_BookBackMatter_OnlinePDF.pdf
Index