Protein crystallization nomenclature

Fig. 7.14 Nomenclature for characteristic regions of peptide c >,t /-space taken from Karplus (1996). The frequencies of observed peptide conformations in protein crystal structures decrease from areas enclosed by a heavy solid line to regions enclosed by a plain solid line, to dashed outlines. Areas outside the dashed lines are disallowed in peptide conformational space. The lines are an approximate rendering of the exact contours given by Karplus (1996).

A later calculation disputed these results in that anti-anti was computed to be the most stable conformer . This work, however, was limited to the SCF level, using a 6-31 -I- -l-G basis set. (If consulting the original paper, it is important to note that this set of workers reversed the standard nomenclature for syn and anti.) Anti-syn was computed to be somewhat less stable, followed by syn-anti and syn-syn. These results were compared to a statistical survey of such interactions in proteins where a marked propensity was observed for the syn-syn structure, the least stable in the gas phase. In contrast, the anti-anti configuration, most stable in the gas phase, is observed rarely in proteins. The authors attributed these discrepancies to crystal packing forces. There also seems to be a preference in the crystals for centrosymmetric (or nearly so) Fl-bonds between carboxyl and carboxy-late, although noncentrosymmetric H-bonds are also present in large numbers. Centrosym-... 

Metabolic pathways of microorganisms Portal to ProTherm (protein thermodynamics), ProNit (protein-nucleic acid interactions), biomolecule structures Crystal data and crystallization conditions for proteins, nucleic acids, and complexes Enzyme nomenclature and properties See B.5... 

J., and Dean, D.H. 1998. Revision of the nomenclature for the Bacillus thur-ingiensis pesticidal crystal proteins. Microbiol. Mol. Biol. Ren, 62, 807. 

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