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W Kabsch

Publications and source records attributed to W Kabsch.

49 records · Page 3Linked to original sources
PubMed1984

On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.

The search for amino acid sequence homologies can be a powerful tool for predicting protein structure. Discovered sequence homologies are currently used in predicting the function of oncogene proteins. To sharpen this tool, we investigated the structural significance of short sequence homologies by searching proteins of known three-dimensional structure for subsequence identities. In 62 proteins with 10,000 residues, we found that the longest isolated homologies between unrelated proteins are five residues long. In 6 (out of 25) cases we saw surprising structural adaptability: the same five residues are part of an alpha-helix in one protein and part of a beta-strand in another protein. These examples show quantitatively that pentapeptide structure within a protein is strongly dependent on sequence context, a fact essentially ignored in most protein structure prediction methods: just considering the local sequence of five residues is not sufficient to predict correctly the local conformation (secondary structure). Cooperativity of length six or longer must be taken into account. Also, we are warned that in the growing practice of comparing a new protein sequence with a data base of known sequences, finding an identical pentapeptide sequence between two proteins is not a significant indication of structural similarity or of evolutionary kinship.

Amino Acid Sequence↗
PubMed1983

How good are predictions of protein secondary structure?

The three most widely used methods for the prediction of protein secondary structure from the amino acid sequence are tested on 62 proteins of known structure using a program package and data collection not previously available. None of these methods predicts better than 56% of the residues correctly, for a three state model (helix, sheet and loop). The algorithms of Robson et al. [J. Mol. Biol. (1978) 120, 97-120] and Lim [J. Mol. Biol. (1974) 88, 873-894] are the best of those tested. New methods, now under development, can be tested against this benchmark.

Amino Acid Sequence↗
PubMed1982

The ten helical twist angles of B-DNA.

On the assumption that the twist angles between adjacent base-pairs in the DNA molecule are additive a linear system of 40 equations was derived from experimental measurements of the total twist angles for different pieces of DNA of known sequences. This system of equations is found to be statistically consistent providing a solution for all ten possible twist angles of B-DNA by a least squares fitting procedure. Four of the calculated twist angles were not known before (tau AC, tau AG, tau CA, tau TA). The other six twist angles calculated are very close to the experimentally measured ones (tau AA, tau AT, tau CC, tau OG, tau GA, tau GC). The data used were obtained by the electrophoretic band-shift method (1-3), crystallography (4) and nuclease digestion of DNA adsorbed to mica or Ca-phosphate surface (5,6). The validity of the principle of additivity of the twist angles implies that the angle between any particular two base-pairs is a function of only these base-pairs, independent of nearest neighbours.

DNA↗
PubMed1981

Three-dimensional structure of the complex of skeletal muscle actin and bovine pancreatic DNAse I at 6-A resolution.

The structure of rabbit skeletal muscle actin complexed with bovine pancreatic DNase I has been determined by x-ray crystallographic methods at 6-A resolution. The analysis was based on a new orthorhombic crystal form, space group P212121, with one complex in the asymmetric unit. Six isomorphous heavy-atom derivatives yielding an overall figure of merit of 0.72 have been used to calculate the electron-density map. Molecular models for actin and DNase I derived from this map have dimensions 67 X 40 X 37 A and 50 X 50 X 40 A, respectively. The actin molecule is elongated and consists of a larger and a smaller domain, each containing density regions resembling a central beta-pleated sheet surrounded by alpha-helices. The highest electron-density peak is found in the cleft between the two domains, perhaps indicating the bound ATP. Observed crystal contacts between actin molecules and a model for the F-actin filament are discussed. Two high-affinity Ca2+-binding sites which also bind Ba2+ have been located at the surface of the DNase I molecule.

Actins↗