Synthetic Conformations
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Synthetic Conformations

Empirical Energy Functions

During the docking of two proteins conformational changes can be observed ( induced fit ). Especially in the active site of a protein amino acid sidechains change their conformation. In this research work molecular mechanics force fields (like AMBER) are used to score these conformational changes.

plot of three conformations of arginine 154 in protein 1ACB histogramm of energy minima for each angle of arginine histogramm of energy minima for each angle of arginine
In a first step synthetic conformations are build by rotating the amino acid sidechain torsion angles (CHI angles). For each conformation the potential energy is calculated using the AMBER force field. Then a search of the energetic best conformations has been performed. We recieved a distribution of the torsion angles for each aminoacid type. At the moment only one torsion angle is modified at a time. We plan to develop a model to perform conformational changes on the whole sidechain at once.

This project is supported by the DFG graduate program Bioinformatics.

sneumann@TechFak.Uni-Bielefeld.DE Last Update: 18 Dec 02