How the amino acid series of a protein determines its 3-dimensional constitution is an enormous challenge in biology and chemistry. major specialists within the fields of NMR spectroscopy, X-ray crystallography, protein engineering and molecular modeling supply provocative insights into present perspectives at the protein folding challenge and numerous facets for destiny growth.
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Additional info for Ciba Foundation Symposium 161 - Protein Conformation
However, we include only the repulsion terms of the non-bonded contacts. This approach is attractive in the way it can use information from force fields, NMR restraints and other experimental methods. Kollman: Figure 3 suggested that a buried serine is rarely substituted by threonine, or almost anything else. Why is that? Blundell: We compare the substitution patterns of serine and threonine in several structural environments. If there is a buried threonine or serine residue, with hydrogen bonds from the side chain oxygen to a main chain CO and NH function, the position of the hydroxyl is fixed.
Adenine is shown in spoke form and the Ca2+ ion as a shaded ball. The domains may each be divided into two subdomains (labelled 1, 2, 3 and 4). Domains 1 and 3 have the same topology. Both the N- and C-termini are in subdomain 1 . The points of cross-over from subdomains 1 to 3 are close to each other in the lower part of the middle of the diagram. Thus, although there is little similarity in sequence, many important functions are retained. Nature, it seems to me, is very clever. It’s not clear to me, Professor Blundell, how your approach can find such relationships.
J . Smith et a1 1991), we were struck by the fact that although in the interior of the protein the large majority of side chains appeared to be well described by a single rotameric state, this was not the case for many surface residues. Active sites are usually, almost by definition, on the surfaces of proteins. If, for example, small changes in conformation are seen in a crystal structure can we be sure that they are really significant? Could they not simply reflect differences in the selection of particular species from sets of interconverting conformers having similar energies?
Ciba Foundation Symposium 161 - Protein Conformation