Folded structures, accessible

The A20 antibody did not bind significantly to native SR vesicles, but solubilization of the membrane with C Eg or permeabilization of the vesicles by EGTA exposed its epitope and increased the binding more than 20-fold [139], By contrast, the A52 antibody reacted freely with the native sarcoplasmic reticulum, while the A25 antibody did not react either in the native or in the C Eg solubilized or permeabilized preparations, and required denaturation of Ca " -ATPase for reaction, Clarke et al, [139] concluded that the epitope for A52 is freely exposed on the cytoplasmic surface, while the epitope for A20 was assigned to the luminal surface, where it became accessible to cytoplasmic antibodies only after solubilization or permeabilization of the membrane. The epitope for A25 is assumed to be on the cytoplasmic surface in a folded structure and becomes accessible only after denaturation. 

Component selection may be driven by internal rather than external factors. Thus, access to a stable folded structure may drive the selection, within a diverse set of... 

There are many ways to assess the structure of a folded protein. Many of them are spectroscopic, such as circular dichroism (CD), fluorescence, infrared, and Raman. These methods can be combined with the use of stress to measure the stability of the folded structure by perturbing it with heat or chemicals (Figure 8). High resolution structural information (determined in atomic detail) is often obtained by X-ray crystallography or nuclear magnetic resonance (NMR). These data are routinely deposited in the RSCB (Research Collaboratory for Structural Bioinformatics) protein database for public access. ... 

RB Russell, GJ Barton. Structural features can be unconserved m proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. J Mol Biol 244 332-350, 1994. 

JU Bowie, ND Clarke, CO Paho, RT Sauer. Identification of protein folds Matching hydro-phohicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins Struct Func Genet 7 257-264, 1990. 

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