R C van Schaik | PubMed Health

PubMed1992

Conformational search by potential energy annealing: algorithm and application to cyclosporin A.

A major problem in modelling (biological) macromolecules is the search for low-energy conformations. The complexity of a conformational search problem increases exponentially with the number of degrees of freedom which means that a systematic search can only be performed for very small structures. Here we introduce a new method (PEACS) which has a far better performance than conventional search methods. To show the advantages of PEACS we applied it to the refinement of Cyclosporin A and compared the results with normal molecular dynamics (MD) refinement. The structures obtained with PEACS were lower in energy and agreed with the NMR parameters much better than those obtained with MD. From the results it is further clear that PEACS samples a much larger part of the available conformational space than MD does.

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PubMed1991

On deriving spatial protein structure from NMR or X-ray diffraction data.

During the last decade it has become possible to derive the spatial structure of small proteins in solution using multidimensional NMR spectroscopy measurements and interpreting the data in terms of a chemical atomic model. The NMR experiments generate a set of interproton distance constraints, which is subsequently used to generate spatial structures that satisfy the experimental data. Correspondingly, crystallographic least-squares and molecular dynamics refinement is routinely applied to obtain a protein structure that is compatible with the observed structure factor amplitudes. The quality of the structure obtained will depend on the number and quality of the experimental data and on the searching power of the refinement method and protocol. The potential energy annealing conformational search (PEACS) algorithm is shown to be an improvement over standard molecular dynamics search methods. The use of time-dependent distance or structure factor restraints in molecular dynamics refinement yields a much better representation of experimental information than the fixed, static restraints which have generally been used until now. Conventional structure refinement methods lead to a too static and rigid picture of a protein in solution or in the crystalline state.

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