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lecture10 - Bioinformatics 2 lecture 10 Ramachandran angles...

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Bioinformatics 2 -- lecture 10 Ramachandran angles Sidechain chi angles Rotamers Dead End Elimination Theorem
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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?
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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.
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Backbone angle statistics Colors represent the frequency (in bins of 10°x10°) 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"?
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Sidechain angle space -- rotamers A random sampling of Phenylalanine sidechains, when superimposed, fall into three classes: rotamers . This simplifies the problem of sidechain modeling. All we have to do is select the right rotamers and we're close to the right answer.
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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.
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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 . fine lines = true structure think lines = sidechain predictions using the method of Desmet et al.
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Steric interactions determine allowed rotamers CG H H H O = C N CA CB CG H H H O = C N CA CB CG H H H O = C N CA CB "m" "p" "t" -60° gauche 180° anti/trans +60° gauche
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