A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular1H−1H proximities in solution

DISGEO is a new implementation of a distance geometry algorithm which has been specialized for the calculation of macromolecular conformation from distance measurements obtained by two-dimensional nuclear Overhauser enhancement spectroscopy. The improvements include (1) a decomposition of the complete embedding process into two successive, more tractable calculations by the use of “substructures”, (2) a compact data structure for storing incomplete distance information on a structure, (3) a more efficient shortest-path algorithm for computing the triangle inequality limits on all distances from this information, (4) a new algorithm for selecting random metric spaces from within these limits, (5) the use of chirality constraints to obtain good covalent geometry without the use ofad hoc weights or excessive optimization. The utility of the resultant program with nuclear magnetic resonance data is demonstrated by embedding complete spatial structures for the protein basic pancreatic trypsin inhibitor vs all 508 intramolecular, interresidue proton-proton contacts shorter than 4.0 Å that were present in its crystal structure. The crystal structure could be reproduced from this data set to within 1.3 Å minimum root mean square coordinate difference between the backbone atoms. We conclude that the information potentially available from nuclear magnetic resonance experiments in solution is sufficient to define the spatial structure of small proteins.     

The nature of the trifluoperazine binding sites on calmodulin and troponin-C

We have employed 1H-nuclear magnetic resonance spectroscopy to study the interaction of the drug trifluoperazine with calmodulin and troponin-C. Distinct trifluoperazine-binding sites exist in the N- and C-terminal halves of both proteins. Each site consists of a group of hydrophobic side-chains brought into proximity by the Ca2+-dependent juxtaposition of two alpha-helical segments of the protein, each, in turn, belonging to a different Ca2+-binding site in the protein half. The trifluoperazine-induced inhibition of the biological activating ability of calmodulin appears to result from conformational restrictions conferred upon the protein by the bound drug.     

The muscle layer of the canine gallbladder and cystic duct

The muscle layer of the canine gallbladder wall and cystic duct was found to be a three-dimensional meshwork of smooth muscle bundles which appear loosely and irregularly arranged on the mucosal aspect and consolidate to form a homogeneous plate-like layer on the serosal aspect. The muscle bundles are tightly woven around interspersed pockets of loose connective tissue in the gallbladder wall and gradually become loosely arranged with more prominent amounts of intervening connective tissue in the cystic duct. The muscle layer is thickest in the gallbladder wall and becomes progressively thinner out into the cystic duct. No anatomic sphincter was observed. Ultrastructural organization revealed individual muscle fibers to be of irregular profile, often branching, widely spaced with intervening collagen fibers, and having few cell-to-cell contacts.     

Role of Chlamydia trachomatis and HLA-B27 in sexually acquired reactive arthritis.

Inflammatory arthritis, tendinitis, and fasciitis after non-specific urethritis ("sexually acquired reactive arthritis" (SARA)) was studied prospectively in 531 men with non-specific urethritis, with particular reference to the frequency of isolation of Chlamydia trachomatis and the presence of HLA-B27. Satisfactory cultures were obtained from the urethral swabs from 384 patients; and HLA typing was performed on 482, of whom 30 (6%) were HLA-B27-positive. Arthritis developed in 16 patients, and five of the 14 (36%) with satisfactory cultures were positive for C trachomatis; 135 of the patients without arthritis were also positive for C trachomatis, an identical proportion. Seven of the 15 patients (40%) with arthritis who were HLA-typed were HLA-B27-positive. Six of the 30 patients with HLA-B27 developed peripheral arthritis in contrast to only nine of the 452 patients lacking the antigen, suggesting a tenfold increase susceptibility. C trachomatis, however, was no more prevalent in cultures from HLA-B27-positive men than from the others. Thus carriage of C trachomatis is unlikely to be influenced by HLA-B27. C trachomatis may be an important pathogen in some cases of SARA but does not appear to be an exclusive trigger factor for this condition.     

Analysis of glycopeptides as borate complexes by polyacrylamide gel electrophoresis

A new method using polyacrylamide gel electrophoresis in a Tris-borate buffer to analyze Pronase-derived glycopeptides is described. Examination of immunoglobulin, Sindbis virus, and ovalbumin-radiolabeled glycopeptides by this system demonstrates a pattern similar to that seen after Bio-Gel-P-6 chromatography and, in addition, exposes a heterogeneity in the immunoglobulin and Sindbis virus glycopeptides not apparent after gel filtration. The resolution of glycopeptides by gel electrophoresis depends on the inclusion of borate ions in the sample, the gel, and the electrophoresis buffer. The borate ions react with neutral sugars, converting them to charged complexes which migrate during electrophoresis. The number of borate ions bound to a glycopeptide is a function of the composition, sequence, and linkages of the carbohydrates. Gel electrophoresis of glycopeptides in a borate buffer has several advantages: (1) The method requires no new equipment or special skills beyond those necessary for conventional polyacrylamide gel electrophoresis; (2) when performed on a slab gel, up to 24 samples can be analyzed simultaneously; and (3) since detection is by radio-autography, small amounts of radiolabeled glycopeptides can be visualized by prolonging the exposure time. These characteristics are advantageous for studies of glycopeptides based on digestion products resulting from incubations with specific exo- and endo-glycosidases. Untreated glycopeptides have been compared on the same gel with glycopeptides sequentially treated with different glycosidases to gain structural information.     

Changes in Wheat Leaf Polysomal Messenger RNA Populations during the Early Stages of Rust Infection: EFFECTS OF CHLORAMPHENICOL AND LINCOMYCIN ON CELL-FREE TRANSLATION BY POLYSOMES FROM HEALTHY AND INFECTED LEAVES

Polysomes isolated from a susceptible variety of wheat leaves (cultivar W2691) and those inoculated with the wheat stem rust fungus (f. sp. tritici, race 126-ANZ-6, 7) were incubated in a cell-free protein-synthesizing system. Under these conditions, different size classes of polypeptides, ranging in molecular weight from 10,000 to 80,000, are radiolabeled. Using double-isotope labeling technique, we show that some discrete size classes of polypeptides are synthesized in significantly greater quantitites by polysomes from inoculated leaves compared to the corresponding size classes synthesized by polysomes from healthy leaves. These results confirm our previous observation that there are significant changes in the wheat leaf polysomal messenger RNA populations at 3 days after inoculation with the rust fungus.The effects of the organelle-specific inhibitors of protein synthesis, chloramphenicol and lincomycin, on in vitro polysomal messenger RNA translation were investigated. The polypeptides synthesized by polysomes from healthy and inoculated leaves in the presence of chloramphenicol were compared. The results show that, even in the presence of this antibiotic, the polysomes from inoculated leaves synthesize greater quantities of some size classes of polypeptides. These data indicate that changes in polysomal messenger RNA populations involve, at least in part, cytoplasmic messenger RNA.     

Inhibition of cyclopropane fatty acid synthase by sinefungin and A9145C

Sinefungin and A9145C, antifungal antibiotic analogs of S-adeno-sylmethionine isolated from $\text{Streptomyces}\text{,}\text{griseolus}$, have been found to be very effective $\text{in}\text{,}\text{vitro}$ inhibitors of cyclopropane fatty acid synthase from $\text{Lactobacillus}\text{,}\text{plantarum}$. Both compounds exhibit linear competitive inhibition with a K_i for Sinefungin of 220 nM and a K_i for A9145C of 11 nM.