Tertiary structure, proteins and

Different arrangements of the data from these experiments have allowed the study of several aspects linked to protein folding, namely (a) changes in the protein secondary structure, (b) changes in the protein tertiary structure, and (c) global mechanistic and structural description of the protein-folding process. The results obtained are briefly presented in the following subsections. 

Globular Proteins Tertiary Structure and Functional Diversity... 

QuiochOk F. A., Carbohydrate-binding Proteins Tertiary Structures and Protein-Sugar Interactions , Ann. Rev. Biochem. 55 (1986) 287-315. 

Quiocho, F.A. Carbohydrate-binding proteins Tertiary structures and protein-sugar interactions. Ann. Rev. Biochein. 1986. 55. 287-315. 

Brookhaven National Laboratory, Upton, NY 11973 Contains atom positional coordinates for some protein tertiary structures and associated data (references, symmetry, inhibitors, cofactors, and the like)... 

S. Sun, Reduced representation approach to protein tertiary structure prediction statistical potential and simulated annealing, J. Theor. Biol. 172 (1995), 13-32. 

Protein tertiary structure is also influenced by the environment In water a globu lar protein usually adopts a shape that places its hydrophobic groups toward the interior with Its polar groups on the surface where they are solvated by water molecules About 65% of the mass of most cells is water and the proteins present m cells are said to be m their native state—the tertiary structure m which they express their biological activ ity When the tertiary structure of a protein is disrupted by adding substances that cause the protein chain to unfold the protein becomes denatured and loses most if not all of Its activity Evidence that supports the view that the tertiary structure is dictated by the primary structure includes experiments m which proteins are denatured and allowed to stand whereupon they are observed to spontaneously readopt their native state confer matron with full recovery of biological activity... 

All peptidases within a family will have a similar tertiary structure, and it is not uncommon for peptidases in one family to have a similar structure to peptidases in another family, even though there is no significant sequence similarity. Families of peptidases with similar structures and the same order of active site residues are included in the same clan. A clan name consists of two letters, the first representing the catalytic type as before, but with the extra letter P , and the second assigned sequentially. Unlike families, a clan may contain peptidases of more than one catalytic type. So far this has only been seen for peptidases with protein nucleophiles, and these clans are named with an initial P . Only three such clans are known. Clan PA includes peptidases with a chymotrypsin-like fold, which besides serine peptidases such as chymotrypsin... 

Proteins derive their powerful and diverse capacity for molecular recognition and catalysis from their ability to fold into defined secondary and tertiary structures and display specific functional groups at precise locations in space. Functional protein domains are typically 50-200 residues in length and utilize a specific sequence of side chains to encode folded structures that have a compact hydrophobic core and a hydrophilic surface. Mimicry of protein structure and function by non-natural ohgomers such as peptoids wiU not only require the synthesis of >50mers with a variety of side chains, but wiU also require these non-natural sequences to adopt, in water, tertiary structures that are rich in secondary structure. 

Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997 268 209-25. 

Cross-links, which impose strong conformational constraints on the intervening segment of the chain, generally are not classified as elements of secondary or tertiary structure. Disulfide cross-links in protein may certainly stabilize both secondary and tertiary structure, and such cross-links have the... 

In summary, formalin-treated does not significantly perturb the native structure of RNase A at room temperature. It also serves to stabilize the protein against the denaturing effects of heating as revealed by the increase in the denaturation temperature of the protein. However, formalin-treatment does not stabilize RNase A sufficiently to prevent the thermal denaturation of the protein at temperatures used in heat-induced AR methods as shown by both DSC and CD spectropolarimetry. This denaturation likely arrises from the heat-induced reversal of formaldehyde cross-links and adducts, as shown in Figure 15.4 of Section 15.4. Further, cooling formalin-treated RNase A that had been heated to 95°C for 10 min does not result in the restoration of the native structure of the protein, particularly in regard to protein tertiary structure. 

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