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Author Nilges, Michael ♦ Briinger, Axel T.
Source CiteSeerX
Content type Text
File Format PDF
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Description A novel approach for the modeling of coiled coils through molecular dynamics is described and applied to the dimeriza-tion region of the yeast transcriptional activator GCN4. Initially, a model is created consisting of C ° atoms only, representing an idealized coiled coil with infinite pitch. Human bias in the placing of the other atoms is reduced by an automatic building procedure using simulated annealing with simple geometric restraints. The resulting all-atom model is then allowed to relax during a short molecular dynamics run using an empirical energy function and weak restraints which reflect the coiled coil assumption. These models are then further refined using unrestrained molecular dynamics in water. In this report we test the model-building procedure on the known dimerization region of catabolyte gene activator protein (CAP), part of which forms a coiled coil, and we predict the structure of the coiled coil dimerization region (the 'leucine zipper ' domain) of GCN4. Several models are built, starting from different arrangements of the C ° atoms in the initial structures. The final structures show similar crossing angles of the coiled coil, although this was not used as a restraint in the calculation. The leucines adopt a ladder-like conformation around the 2-fold axis of the coiled coil. A number of electrostatic interactions could be identified which may contribute to the stability of the helical structure of the monomers and of the dimer. Key words: coiled coil/GCN4/leucine zipper/model building/ molecular dynamics
Educational Role Student ♦ Teacher
Age Range above 22 year
Educational Use Research
Education Level UG and PG ♦ Career/Technical Study
Learning Resource Type Article
Publisher Date 1991-01-01
Publisher Institution Protein Eng