Showing papers by "Chris Sander published in 1983"

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

Abstract: For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.

A yeast gene encoding a protein homologous to the human c-has/bas proto-oncogene product.

Abstract: Organisms amenable to easy genetic analysis should prove helpful in assessing the function of at least those proto-oncogene products which are highly conserved in different eukaryotic cells. One obvious possibility is to pursue the matter in Drosophila melanogaster DNA, which has sequences homologous to several vertebrate oncogenes1–3. Another is to turn to the yeast Saccharomyces cerevisiae, if it contains proto-oncogene sequences. Here we report the identification of a gene in S. cerevisiae which codes for a 206 amino acid protein (YP2) that exhibits striking homology to the p21 products of the human c-has/bas proto-oncogenes4,5 and the transforming p21 proteins of the Harvey (v-rasH)6 and Kirsten (v-rasK)7 murine sarcoma viral oncogenes. The YP2 gene is located between the actin8,9 and the tubulin gene10 on chromosome VI11 and is expressed in growing cells. The protein it encodes might share the nucleotide-binding capacity of p21 proteins22–24.