Biomedical subjects

David C Richardson

Publications and source records attributed to David C Richardson.

5 recordsLinked to original sources

PubMed2003

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).

Amino Acids↗

PubMed2003

Tropheryma whippelii as a cause of afebrile culture-negative endocarditis: the evolving spectrum of Whipple's disease.

With the advent of molecular diagnostics culture-negative endocarditis caused by the organism Tropheryma whippelii is an increasingly described entity. We describe two patients with afebrile, culture-negative endocarditis caused by T. whippelii who had neither the gastrointestinal nor arthritic manifestations of Whipple's disease. Whipple's disease is a systemic illness caused by the organism Tropheryma whippelii and is typically characterized by diarrhea, weight loss, and arthropathy [Clin. Microbiol. Rev. 2001;14:561-583; Medicine (Baltimore) 1997;76:170-184]. Whipple's endocarditis is relatively common in autopsy studies [Can. J. Cardiol. 1996;12:831-834] but has rarely been diagnosed before death. With the advent of molecular diagnostic tools such as the polymerase chain reaction (PCR), Tropheryma whippelii as a cause of culture-negative endocarditis has become increasingly recognized [Clin. Infect. Dis. 2001;33:1309-1316; Ann. Intern. Med. 1999;131:112-116; Infection 2001;29:44-47; Ann. Intern. Med. 2000;132:595]. With this increased recognition has come the realization that Whipple's endocarditis can occur without other common manifestations of Whipple's disease [Ann. Intern. Med. 1999;131:112-116; Infection 2001;29:44-47; Ann. Intern. Med. 2000;132:595]. We report here two cases of Whipple's endocarditis without discrete febrile illness, gastrointestinal manifestations, or arthritic manifestations, diagnosed by PCR of resected valvular material.

Aged↗

PubMed2003

Evaluation of a rapid PCR assay for diagnosis of meningococcal meningitis.

We compared the results of Gram staining and culture of cerebrospinal fluid to results obtained with a rapid PCR assay for the diagnosis of meningococcal meningitis in 281 cases of suspected bacterial meningitis. PCR had a sensitivity of 97% compared to a sensitivity of 55% for culture, and the PCR specificity was 99.6%. PCR results were available within 2 h of the start of the assay.

Base Sequence↗

PubMed2002

Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation.

The fact that natural beta-sheet proteins are usually soluble but that fragments or designs of beta structure usually aggregate suggests that natural beta proteins must somehow be designed to avoid this problem. Regular beta-sheet edges are dangerous, because they are already in the right conformation to interact with any other beta strand they encounter. We surveyed edge strands in a large sample of all-beta proteins to tabulate features that could protect against further beta-sheet interactions. beta-barrels, of course, avoid edges altogether by continuous H-bonding around the barrel cylinder. Parallel beta-helix proteins protect their beta-sheet ends by covering them with loops of other structure. beta-propeller and single-sheet proteins use a combination of beta-bulges, prolines, strategically placed charges, very short edge strands, and loop coverage. beta-sandwich proteins favor placing an inward-pointing charged side chain on one of the edge strands where it would be buried by dimerization; they also use bulges, prolines, and other mechanisms. One recent beta-hairpin design has a constrained twist too great for accommodation into a larger beta-sheet, whereas some beta-sheet edges are protected by the bend and reverse twist produced by an Lbeta glycine. All free edge strands were seen to be protected, usually by several redundant mechanisms. In contrast, edge strands that natively form beta H-bonded dimers or rings have long, regular stretches without such protection. These results are relevant to understanding how proteins may assemble into beta-sheet amyloid fibers, and they are especially applicable to the de novo design of beta structure. Many edge-protection strategies used by natural proteins are beyond our current abilities to constrain by design, but one possibility stands out as especially useful: a single charged side chain near the middle of what would ordinarily be the hydrophobic side of the edge beta strand. This minimal negative-design strategy changes only one residue, requires no backbone distortion, and is easy to design. The accompanying paper [Wang, W. & Hecht, M. H. (2002) Proc. Natl. Acad. Sci. USA 99, 2760-2765] makes use of the inward-pointing charge strategy with great success, turning highly aggregated beta-sandwich designs into soluble monomers.

Amino Acid Sequence↗

PubMed2002

Evaluation of the Makromed dipstick assay versus PCR for diagnosis of Plasmodium falciparum malaria in returned travelers.

Microscopy has been the traditional reference standard for malaria diagnosis. However, difficulty in maintaining the required technical skills, particularly in areas where malaria is not endemic, has prompted the development of rapid nonmicroscopic diagnostic assays based on the detection of malaria parasite antigen in whole blood. In this study, we evaluated the performance of one such device, the Makromed dipstick test, blindly compared to PCR and microscopy for the diagnosis of Plasmodium falciparum malaria in 200 febrile returned travelers. The Makromed assay detects the presence of P. falciparum-specific histidine-rich protein II with an antigen capture immunochromatographic strip format. Compared to PCR as the reference standard, the dipstick assay had a sensitivity of 97.0% and a specificity of 96.0%. The positive and negative predictive values were 81.2% and 99.5%, respectively. Rapid malaria diagnostic devices may provide a useful diagnostic adjunct in a clinical setting.

Adolescent↗