Conformational analysis protein crystallography

The primary structure of P. is elucidated by the standard methods of sequence analysis (see Proteins). The conformation of P. is an important determinant of their biological activity. It is stabilized by peptide and disulfide bonds In P. containing unusual bonds and/or constituents other factors also stabilize the conformation. Although X-ray crystallography (see) was used in the elucidation of the three-dimensional structures of insulin and gramicidin S, the conformational analysis of P. is now by preference carried out in solution, using the spectroscopic methods ORD, CD, IR, NMR and ESR. 

An application of the ROCS program has been reported recently (82). New scaffolds for small molecule inhibitors of the ZipA-FtsZ protein-protein interaction have been found. The shape comparisons are made relative to the bioactive conformation of a HTS hit, determined by X-ray crystallography. A followup X-ray crystallographic analysis also showed that ROCS accurately predicted the binding mode of the inhibitor. This result offers the first experimental evidence that validates the use of ROCS for scaffold hopping purposes. 

G-Protein-coupled receptors do not lend themselves to analysis by either NMR or x-ray crystallography due to their structural dependence on an intact cell membrane. In our laboratories we pursued this valuable structural information by utilizing a combination of structural homology modeling, molecular dynamics, systematic conformational searching methods, and mutagenesis experiments. The combination of these techniques led to a proposed model of bradykinin bound to the agonist site on its receptor [41]. 

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