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S Rackovsky

Publications and source records attributed to S Rackovsky.

25 records · Page 2Linked to original sources
PubMed1988

Protein comparison and classification: a differential geometric approach.

A method is proposed for rapidly, quantitatively comparing protein structures of arbitrary sizes, based on the differential geometric representation. The method is applied to a group of 22 protein x-ray structures, and the resulting network of closest relationships is delineated. Several well-known fold types are automatically detected as groupings of related structures, even when the constituent proteins are of different lengths. A complete gradation of types is shown to be detected, ranging from all-helical to all-beta-structure proteins. A relationship among functionally similar proteins is shown in several cases, even where their three-dimensional structures differ. It is suggested that the positions of proteins within the network of relationships correspond with their folding mechanisms.

Protein Conformation↗
PubMed1985

Substitutions of proline 76 in yeast iso-1-cytochrome c. Analysis of residues compatible and incompatible with folding requirements.

Fine-structure genetic mapping previously revealed numerous nonfunctional cyc1 mutations having alterations at or near the site corresponding to amino acid position 76 of iso-1-cytochrome c from the yeast Saccharomyces cerevisiae. DNA sequencing of the alterations in four of these cyc1 mutations indicated that the normal Pro-76 was replaced by Leu-76. Revertants containing at least partially functional iso-1-cytochromes c were isolated, and the alterations were analyzed by DNA sequencing and protein analysis. Specific activities of the altered iso-1-cytochromes c were estimated in vivo by growth of the strains in lactate medium; compared to normal iso-1-cytochrome c with Pro-76, the following activities were associated with the following replacements: approximately 90% for Val-76, approximately 60% for Thr-76, approximately 30% for Ser-76, approximately 20% for Ile-76, and 0% for Leu-76. In order to develop an understanding of the factors that determine whether or not an altered iso-1-cytochrome c will function, we undertook a theoretical analysis which led to the conclusion that the activity of the proteins was dependent on both short- and long-range interactions. Short-range interactions were estimated from studies on known protein structures which gave the likelihood that various amino acids would be found in a local backbone configuration similar to the native protein; long-range interactions with the rest of the molecule were analyzed by considering the size of the side chain. We believe this approach can be used to analyze a wide variety of mutant proteins.

Amino Acid Sequence↗
PubMed1984

On the redox conformational change in cytochrome c.

The relationship between the crystal structures of oxidized and reduced tuna cytochrome c has been reexamined by a superposition method motivated by recent studies of the cytochrome c-cytochrome c peroxidase complex. It is shown that the observed structural changes precisely reflect the binding face suggested by chemical modification studies. It is further suggested that the large observed motion of lysine-27 and a smaller overall motion of the two binding edges constitute a redox binding-affinity switch and that the driving force for the conformational change of the protein is provided by the internal conformational change and charge redistribution of the heme, which cause it to tilt, under the influence of covalent and nonbonded interactions, within its protein envelope. A picture is presented of the molecule as an electron storage/transfer machine with three elements--a binding module, an electron storage module, and a conformational energy-storage module.

Animals↗
PubMed1977

Hydrophobicity, hydrophilicity, and the radial and orientational distributions of residues in native proteins.

The radial distributions of the Calpha and side-chain atoms in a sample of 13 native proteins have been examined. It is found that there are substantial differences in behavior between different atoms of the same amino acid. In particular, the Calpha atoms of polar residues show no particular preference for being far from the center of mass. In light of these results, a new criterion for hydrophobicity and hydrophilicity is proposed--namely, the orientational preference of the side chain. The distribution of this property is shown, and it is suggested that this provides a basis for incorporating hydrophobic interactions into a protein folding algorithm.

Amino Acids↗
PubMedDate not supplied

Influence of ordered backbone structure on protein folding. A study of some simple models.

Four series of model molecules, each of which contains a coil section and one or two sections of fixed ordered backbone structure, have been examined to locate their low-energy conformations in water. The four series are: helix-coil, helix-coil-helix, extended-coil, and extended-coil-extended. In each series, the length of the coil is allowed to vary from four to ten residues, while the nuclei (ordered backbone structures) are held fixed at six residues. By comparing these molecules, it is observed that the low-energy conformations of those containing two nuclei can be regarded as being derived from low-energy conformations of molecules containing one nucleus. This suggests that folding of proteins containing preformed nuclei proceeds through interactions between the nuclei and adjacent non-regular sections of the chain rather than between nuclei. It is also observed that helices are better promoters of globularity than extended strands. These results are compared with those from recent studies of various aspects of protein folding.

Models, Molecular↗