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Analysis of protein-protein interaction sites without natively folded protein samples: fi ction or fact?

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Hernandez-Alvarez,  B       
Conservation of Protein Structure and Function Group, Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

Malesevic, M., Pöhlmann, A., Lücke, C., Träger, M., Jahreis, G., Hernandez-Alvarez, B., et al. (2008). Analysis of protein-protein interaction sites without natively folded protein samples: fi ction or fact?. Poster presented at 30th European Peptide Symposium (30EPS), Helsinki, Finland.


Cite as: https://hdl.handle.net/21.11116/0000-000B-C9D2-5
Abstract
Protein-protein and protein-ligand interactions are among the few essential cell processes whose understanding provide us insights into fundamental events of the life cycle. Aside from in silico methods, natively folded proteins are an absolute prerequisite in all current biotechnological tools used for the study of these interactions. However, the recently developed IANUS peptide array has a potential to evolve in to a protein-free method for detection of protein-protein interaction sites. Using this assay, protein-protein interactions could be represented by and investigated as peptide-peptide interactions using peptide pairs immobilized on a solid support.(1) .Two main obstacles had to be overcome for successful implementation of this array: (i) the library size and (ii) identifi cation of interacting peptide pairs. If, for example, interactions between two small proteins of only approx. 100 amino acids each should be analyzed, a library of ca. 2500 peptide pairs would be needed to cover all possible combinations of overlapping peptides derived from these proteins. Although libraries of several thousand peptides were already successfully synthesized, the library size could be reduced drastically if the binding pocket of one protein is already known or if the protein-ligand interactions are studied. Up to date, two methods for the identifi cation of interacting peptides in a library have been developed in our group. Both methods will be demonstrated in studies of protein-protein and protein-ligand interactions.