Crystallography Research Today is a free monthly online journal that collates and summarizes the latest research about Crystallography, including details on x-ray crystals, techniques, analyses, structures.

Rapid chain tracing of polypeptide backbones in electron-density maps.

Terwilliger TC

Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate C(alpha) positions at spacings of approximately 0.6 A along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C(alpha) positions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the process. The method was applied to 42 density-modified electron-density maps at resolutions from 1.5 to 3.8 A. A total of 21 428 residues in these maps were traced in 24 CPU min with an overall r.m.s.d. of 1.61 A for C(alpha) atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.

Published 24 February 2010 in Acta Crystallogr D Biol Crystallogr, 66: 285-94.
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Articles on Crystallography published 24 February 2010:

Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV.   Acta Crystallogr D Biol Crystallogr, 66: 304-8.

The structure of a 14 kDa structural protein from Acidianus two-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0 A wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structure, one chloride ion turned out to be essential to achieve phasing. The minimal data requirements and the relative contributions of the Cl and S atoms to phasing are discussed. This work supports the ... [Abstract] [Full-text]

Rapid model building of beta-sheets in electron-density maps.   Acta Crystallogr D Biol Crystallogr, 66: 276-84.

A method for rapidly building beta-sheets into electron-density maps is presented. beta-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C(beta) atoms along the strand averaged over all repeats present in the strand. The beta-strands obtained are then assembled into a single atomic model of the beta-sheet regions. The ... [Abstract] [Full-text]

Rapid model building of alpha-helices in electron-density maps.   Acta Crystallogr D Biol Crystallogr, 66: 268-75.

A method for the identification of alpha-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where alpha-helices appear as tubes of density. The positioning and direction of the alpha-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ... [Abstract] [Full-text]

Articles on Crystallography published 23 February 2010:

X-ray structures of the peridinin-chlorophyll-protein reconstituted with different chlorophylls.   FEBS Lett, 584(5): 973-8.

The peridinin-chlorophyll a-protein (PCP) from dinoflagellates is a soluble light harvesting antenna which gathers incoming photons mainly by the carotenoid peridinin. In PCPs reconstituted with different chlorophylls, the peridinin to chlorophyll energy transfer rates are well predicted by a Förster-like theory, but only if the pigment arrangements are identical in all PCPs. We have determined the X-ray structures of PCPs reconstituted with Chlorophyll-b (Chl-b), Chlorophyll-d (Chl-d) and ... [Abstract] [Full-text]

Biophysical and X-ray crystallographic analysis of Mps1 kinase inhibitor complexes.   Biochemistry, 49(8): 1689-701.

The dual-specificity protein kinase monopolar spindle 1 (Mps1) is a central component of the mitotic spindle assembly checkpoint (SAC), a sensing mechanism that prevents anaphase until all chromosomes are bioriented on the metaphase plate. Partial depletion of Mps1 protein levels sensitizes transformed, but not untransformed, human cells to therapeutic doses of the anticancer agent Taxol, making it an attractive novel therapeutic cancer target. We have previously determined the X-ray structure ... [Abstract] [Full-text]

Articles on Crystallography published 3 February 2010:

Clindamycin hydrochloride monohydrate and its ethanol solvate.   Acta Crystallogr C, 66: o97-100.

Clindamycin hydrochloride, an antibiotic of the lincomycin family, was crystallized as the monohydrate, namely (2S,4R)-2-(N-{(1S,2S)-2-chloro-1-[(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylsulfanyl)perhydropyran-2-yl]propyl}aminocarbonyl)-4-propylpyrrolidinium chloride monohydrate, C(18)H(34)ClN(2)O(5)S(+).Cl(-).H(2)O, (I), and as the monohydrate ethanol solvate, C(18)H(34)ClN(2)O(5)S(+).Cl(-).H(2)O.C(2)H(6)O, (II). The conformation of the clindamycin molecule in both crystal structures is the same ... [Abstract] [Full-text]

Seven 3-methylidene-1H-indol-2(3H)-ones related to the multiple-receptor tyrosine kinase inhibitor sunitinib.   Acta Crystallogr C, 66: o71-8.

The solid-state structures of a series of seven substituted 3-methylidene-1H-indol-2(3H)-one derivatives have been determined by single-crystal X-ray diffraction and are compared in detail. Six of the structures {(3Z)-3-(1H-pyrrol-2-ylmethylidene)-1H-indol-2(3H)-one, C(13)H(10)N(2)O, (2a); (3Z)-3-(2-thienylmethylidene)-1H-indol-2(3H)-one, C(13)H(9)NOS, (2b); (3E)-3-(2-furylmethylidene)-1H-indol-2(3H)-one monohydrate, C(13)H(9)NO(2).H(2)O, (3a); 3-(1-methylethylidene)-1H-indol-2(3H)-one, ... [Abstract] [Full-text]

Methyl 4-O-beta-D-galactopyranosyl alpha-D-mannopyranoside methanol 0.375-solvate.   Acta Crystallogr C, 66: o67-70.

Methyl beta-D-galactopyranosyl-(1-->4)-alpha-D-mannopyranoside methanol 0.375-solvate, C(13)H(24)O(11).0.375CH(3)OH, (I), was crystallized from a methanol-ethanol solvent system in a glycosidic linkage conformation, with varphi' (O5(Gal)-C1(Gal)-O1(Gal)-C4(Man)) = -68.2 (3) degrees and psi' (C1(Gal)-O1(Gal)-C4(Man)-C5(Man)) = -123.9 (2) degrees , where the ring is defined by atoms O5/C1-C5 (monosaccharide numbering); C1 denotes the anomeric C atom and C6 the exocyclic hydroxymethyl C atom in ... [Abstract] [Full-text]

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