Combinatorial Peptide Library Protocols

During the course of evolution, an imbalance was created between the rate of vertebrate genetic adaptation and that of the lower forms of living organisms, such as bacteria and viruses. This imbalance has given the latter the advantage of generating, relatively quickly, molecules with unexpected structures and features that carry a threat to vertebrates. To compensate for their weakness, vertebrates have accelerated their own evolutionary processes, not at the level of whole organism, but in specialized cells containing the genes that code for antibody molecules or for T-cell receptors. That is, when an immediate requirement for molecules capable of specific interactions arose, nature has preferred to speed up the mode of Darwinian evolution in pref- ence to any other approach (such as the use of X-ray diffraction studies and computergraphic analysis). Recently, Darwinian rules have been adapted for test tube research, and the concept of selecting molecules having particular characteristics from r- dom pools has been realized in the form of various chemical and biological combinatorial libraries. While working with these libraries, we noticed the interesting fact that when combinatorial libraries of oligopeptides were allowed to interact with different selector proteins, only the actual binding sites of these proteins showed binding properties, whereas the rest of the p- tein surface seemed "inert. " This seemingly common feature of protein- having no extra potential binding sites--was probably selected during evolution in order to minimize nonspecific interactions with the surrounding milieu.

Klappentext

A valuable collection of new and unique techniques for the construction and use of peptide libraries. These powerful methods include protocols for the chemical synthesis of peptide libraries, for constructing peptide libraries that are displayed on the surface of filamentous phage or bacteria, and for the rapid screening of these libraries for molecules with biospecific properties. Additional methods permit identifying specific enzyme substrates, investigating the recognition spectra of various binding proteins, epitope mapping, and identifying mimotopes. State-of-the-art techniques, combined with clear step-by-step instructions, make this book an essential tool in the selection of peptides suitable for drug development.

Zusammenfassung
While working with these libraries, we noticed the interesting fact that when combinatorial libraries of oligopeptides were allowed to interact with different selector proteins, only the actual binding sites of these proteins showed binding properties, whereas the rest of the p- tein surface seemed "inert.

Inhalt
Synthesis of a One-Bead One-Compound Combinatorial Peptide Library.- Enzyme-Linked Calorimetric Screening of a One-Bead One-Compound Combinatorial Library.- Synthesis and Screening of Positional Scanning Combinatorial Libraries.- Synthesis and Screening of Peptide Libraries on Continuous Cellulose Membrane Supports.- Peralkylation.- to Combinatorial Solid-Phase Assays for Enzyme Activity and Inhibition.- Preparation of Biocompatible Resins for Library Syntheses.- Intramolecular Fluorescence-Quenched Substrate Libraries.- The Solid-Phase Enzyme Inhibitor Library Assay.- Determination of Peptide Substrate Motifs for Protein Kinases Using a One-Bead One-Compound Combinatorial Library Approach.- The Use of Peptide Library for the Determination of Kinase Peptide Substrates.- Analysis of Protein Kinase Substrate Specificity by the Use of Peptide Libraries on Cellulose Paper (SPOT-Method).- Generation of Multiuse Peptide Libraries for Functional Screenings.- Functional Screening of Multiuse Peptide Libraries Using Melanophore Bioassay.- The Basic Structure of Filamentous Phage and Its Use in the Display of Combinatorial Peptide Libraries.- Construction and Use of a 20-mer Phage Display Epitope Library.- Construction of Disulfide-Constrained Random Peptide Libraries Displayed on Phage Coat Protein VIII.- Conformational Mimicry Through Random Constraints Plus Affinity Selection.- The Use of Combinatorial Libraries to Identify Ligands That Interact with Surface Receptors in Living Cells.- Screening Phage Display Peptide Libraries on Nitrocellulose Membranes.- Identification of Disease-Specific Epitopes.- Identification of Peptide Ligands for the Antigen Binding Receptor Expressed on Human B-Cell Lymphomas.- Major Histocompatibility Complex Allele-Specific Peptide Librariesand Identification of T-Cell Mimotopes.- Phage Display of Peptide Libraries on Protein Scaffolds.- Displaying Libraries of Conformationally Constrained Peptides on the Surface of Escherichia coli as Flagellin Fusions.- Combinatorial Peptide Library as an Immunogen.