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**Unformatted text preview: **Bioinformatics 2 -- lecture 10 Ramachandran angles Sidechain chi angles Rotamers Dead End Elimination Theorem Backbone angles phi and psi In 1968, G.N.Ramachandran built a model like this, ala-ala-ala, to explore the relationship between interatomic distnces and the two freely rotatable packbone angles phi and psi. Atom-atom distances that were too close were not permissible. What angles were permissible? Ramachandran Plot Best Allowed The regions labeled alpha and beta represent valleys of stability, surrounded by a high energy plateau. Values of phi are limited primarily to the range between -60 degrees and -150 degrees. For psi, the range is limited to regions centered about -60 degrees and +120 degrees Use SEQ:Measure-->Ramachandran Plot to view all residues in your protein plotted phi versus psi. This plot is for all amino acids except Pro and Gly. Backbone angle statistics Colors represent the frequency (in bins of 10x10) of phi/psi angles. E,B and H are most common. L, l and x are found most often in Gly. Allowed regions are islands . Are bonds really "freely rotatable"? Sidechain angle space -- rotamers A random sampling of Phenylalanine sidechains, when superimposed, fall into three classes: rotamers . This simpliFes the problem of sidechain modeling. All we have to do is select the right rotamers and we're close to the right answer. Sidechain modeling Given a backbone conformation and the sequence, can we predict the sidechain conformations? Energy calculations are sensitive to small changes . So the wrong sidechain conformation will give the wrong energy. Goal of sidechain modeling Desmet et al, Nature v.356, pp339-342 (1992) Given the sequence and only the backbone atom coordinates, accurately model the positions of the sidechains . fne lines = true structure think lines = sidechain predictions using the method of Desmet et al. Steric interactions determine allowed rotamers CG H H H O = C N CA CB C G H H H O = C N CA CB C G H H H O = C N CA CB...

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