Folded structures, accessible surface

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. 

Lee and Richards (1971) defined the solvent-accessible surface as that described by the center of a solvent molecule rolled about the surface of a solute molecule. This concept and its offspring are the basis of various computations of the contribution of hydration to the thermodynamics of protein folding and the thermodynamics of protein interactions. Ed-sall and McKenzie (1983) reviewed the literature on the thermodynamics of transfer processes used to model hydration and correlated this information with protein structure results analyzed according to the Lee and Richards formalism. Other notable reviews are those by Richards (1977), Nemethy et al. (1981), and Nemethy (1986). 

In the case of large complex and folded molecular structures, a part of the van der Waals surface is buried in the, interior and is thus inaccessible to solvent interactions which mainly govern the chemical behaviour of molecules in solution. Therefore, in order to obtain the best representation of the outer surface and overall shape of the molecule the solvent-accessible molecular surface was proposed. It was originally defined [Lee and Richards, 1971] as the surface across which the centre of a spherical approximation of the solvent is passed when the solvent sphere is rolled over the van der Waals surface of the molecule. The radius (1.5 A) of the solvent sphere is usually chosen to approximate the contact surface formed when a water molecule interacts with the considered molecule. If there are several grooves or minor cavities on the van der Waals surface where the rolling sphere cannot enter, then the solvent-accessible surface will be significantly different from the van der Waals siuface. 

The crystal structure of galactose oxidase from the fungus Dactylium dendroides has been determined. Accordingly, galactose oxidase (639 amino acid residues) consists of three domains predominantly formed from /3-structures (Figure 14). The first domain (residues 1-155) has a /3-sandwich structure. The catalytic domain (residues 156-532) comprises a seven-fold /3-propeller based on the kelch structural motif The copper lies on the solvent-accessible surface of this domain close to the pseudo seven-fold axis. The third domain (residues 533-639) is comprised of seven /3-strands. The copper site on the second domain lies in a region extremely rich... 

Proteins are highly complex, folded polypeptide chains consisting of at least 20 different amino acids that are strung together in unique sequences, which relate to structure and function. Particular amino acids in proteins may be further modified post-translationally to contain a wide variety of covalent modifications normally found in native proteins. The way in which a peptide chain is wrapped and folded governs each amino acid s relative exposure to the outside environment, but post-translational modifications also can obscure the protein surface from easy access to the solvent environment. 

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