Computer Graphics in the Solution of the Chain Deformation Problem

Stellman, Steven D.

Go and Scheraga have given a general solution for determining the possible conformations of a section of a flexible polymeric chain between two fixed bonds (if the bonds coincide, the problem is equivalent to ring closure). Often, the fixed bonds are related by symmetry, such as that imposed by helicity or folding of antiparallel chains. A technique is shown for obtaining solutions using interactive computer graphics, whereby a plausible chain conformation or fold is approximated manually and completed by mathematical minimization. The procedure allows rapid, repetitive exploration of multiple solutions, and has many options for changing constraints. As an example, the backbone conformation of GpC, a dinucleoside phosphate, is used as a starting model, and gives upon minimization a set of backbone angles in the range of 11-fold helical RNA.


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American Chemical Society Publications
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April 4, 2014