Prion may change from its norm form to a pathogenesis state causing the Mad Cow Diseases.

With Peter Vedell

Proteins fold into unique and stable 3D structures. At times, they misfold into irregular forms which can, in some cases, cause diseases. The conventional molecular dynamics simulation method is an appealing approach to the study of protein folding, but is limited to small time-scales due to the required small time-steps (1e-15sec) in the solution of the initial-value problem. The approach of using a boundary-value problem promises a greater potential for long time simulation and especially for simulation of transition of protein conformation. We have developed a class of multiple shooting algorithms for the solution of the boundary-value problems for protein dynamics simulation and applied to several test cases including a six-atom argon cluster and a 29-atom alanine dipeptide.

 

conformational transformation

A single shoot algorithm is used to find a set of conditions at the initial point so that the solution curve for the corresponding initial-value problem can also satisfy the conditions at the end point (on the target).

 

A multiple shooting algorithm is used to find a set of conditions at a selected set of intermediate points so that a series of single shootings can be carried out in between adjacent intermediate points, to produce a set of solution curves that can be pieced together into a smooth solution curve for the original boundary-value problem.

 

The shooting methods can be applied effectively to obtain the solution of boundary value problems for the transition of molecular conformation. The required computation for the solution of such problems for large systems can be enormous. However, the methods are more favorable for parallel computing than other conventional approaches

Phone: 515-294-8165

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E-mail: zhijun@iastate.edu

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Energy:

-22.6kcal

 

Energy:

-20.4kcal