CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

A proximal femoral implant preserves physiological bone deformation: a biomechanical investigation in cadaveric bones

The aim of this study was to compare the perturbances in bone deformation patterns of the proximal femur due to a conventional cemented femoral stem and a novel uncemented implant designed on the principles of osseointegration. Five matched pairs of fresh frozen human femora were mechanically tested. Bone deformation patterns, measured with a video digitizing system under 1.5 kN joint force, showed that the cemented Spectron femoral implant caused significant alterations to the proximal femoral deformation pattern, whereas the Gothenburg osseointegrated titanium femoral implant did not significantly alter the bone behaviour (p < 0.05). Vertical micromotions measured under 1 kN after 1000 cycles were within the threshold of movement tolerable for bone ingrowth (21 microm for the Gothenburg system and 26 microm for the cemented implant).Published versio

Engineering of Cyclodextrin Product Specificity and pH Optima of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1

The product specificity and pH optimum of the thermostable cyclodextrin glycosyltransferase (CGTase) from Thermoanaerobacterium thermosulfurigenes EM1 was engineered using a combination of x-ray crystallography and site-directed mutagenesis. Previously, a crystal soaking experiment with the Bacillus circulans strain 251 β-CGTase had revealed a maltononaose inhibitor bound to the enzyme in an extended conformation. An identical experiment with the CGTase from T. thermosulfurigenes EM1 resulted in a 2.6-Å resolution x-ray structure of a complex with a maltohexaose inhibitor, bound in a different conformation. We hypothesize that the new maltohexaose conformation is related to the enhanced α-cyclodextrin production of the CGTase. The detailed structural information subsequently allowed engineering of the cyclodextrin product specificity of the CGTase from T. thermosulfurigenes EM1 by site-directed mutagenesis. Mutation D371R was aimed at hindering the maltohexaose conformation and resulted in enhanced production of larger size cyclodextrins (β- and γ-CD). Mutation D197H was aimed at stabilization of the new maltohexaose conformation and resulted in increased production of α-CD. Glu258 is involved in catalysis in CGTases as well as α-amylases, and is the proton donor in the first step of the cyclization reaction. Amino acids close to Glu258 in the CGTase from T. thermosulfurigenes EM1 were changed. Phe284 was replaced by Lys and Asn327 by Asp. The mutants showed changes in both the high and low pH slopes of the optimum curve for cyclization and hydrolysis when compared with the wild-type enzyme. This suggests that the pH optimum curve of CGTase is determined only by residue Glu258.

Appearance of breast cysts in planar geometry photoacoustic mammography using 1064-nm excitation

In the search for improved imaging modalities for detection and diagnosis of breast cancer, a high negative prediction value is also important. Photoacoustic (optoacoustic) imaging is a relatively new technique that has high potential for visualizing breast malignancies, but little is known about the photoacoustic appearance of benign lesions. In this work, we investigate the visibility of benign breast cysts in forward-mode photoacoustic mammography using 1064-nm light, as currently applied in the Twente photoacoustic mammoscope. Results from (Monte Carlo and k-wave) simulations and phantom measurements were used to interpret results from patient measurements. There was a strong agreement among the results from simulations, phantom, and patient measurements. Depending on the absorption contrast between cyst and breast tissue, cysts were visible as either one or two confined high-contrast areas representing the front and the back of the cyst, respectively. This edge enhancement is most likely the consequence of the local sudden change in the absorbed energy density and Grüneisen coefficients. Although the current forward-mode single-wavelength photoacoustic mammoscope cannot always unambiguously discriminate cysts from malignancies, this study reveals specific features of cysts compared to malignancies, which can be exploited for discrimination of the two abnormalities in future modifications of the image

Structural and functional characterization of Pseudomonas aeruginosa CupB chaperones

Pseudomonas aeruginosa, an important human pathogen, is estimated to be responsible for,10% of nosocomial infections worldwide. The pathogenesis of P. aeruginosa starts from its colonization in the damaged tissue or medical devices (e. g. catheters, prothesis and implanted heart valve etc.) facilitated by several extracellular adhesive factors including fimbrial pili. Several clusters containing fimbrial genes have been previously identified on the P. aeruginosa chromosome and named cup [1]. The assembly of the CupB pili is thought to be coordinated by two chaperones, CupB2 and CupB4. However, due to the lack of structural and biochemical data, their chaperone activities remain speculative. In this study, we report the 2.5 A crystal structure of P. aeruginosa CupB2. Based on the structure, we further tested the binding specificity of CupB2 and CupB4 towards CupB1 (the presumed major pilus subunit) and CupB6 (the putative adhesin) using limited trypsin digestion and strep-tactin pull-down assay. The structural and biochemical data suggest that CupB2 and CupB4 might play different, but not redundant, roles in CupB secretion. CupB2 is likely to be the chaperone of CupB1, and CupB4 could be the chaperone of CupB4:CupB5:CupB6, in which the interaction of CupB4 and CupB6 might be mediated via CupB5

Search for CP violation in D0 and D+ decays

A high statistics sample of photoproduced charm particles from the FOCUS (E831) experiment at Fermilab has been used to search for CP violation in the Cabibbo suppressed decay modes D+ to K-K+pi+, D0 to K-K+ and D0 to pi-pi+. We have measured the following CP asymmetry parameters: A_CP(K-K+pi+) = +0.006 +/- 0.011 +/- 0.005, A_CP(K-K+) = -0.001 +/- 0.022 +/- 0.015 and A_CP(pi-pi+) = +0.048 +/- 0.039 +/- 0.025 where the first error is statistical and the second error is systematic. These asymmetries are consistent with zero with smaller errors than previous measurements.Comment: 12 pages, 4 figure

Search for CP violation in D0 and D+ decays

A high statistics sample of photoproduced charm particles from the FOCUS (E831) experiment at Fermilab has been used to search for CP violation in the Cabibbo suppressed decay modes D+ to K-K+pi+, D0 to K-K+ and D0 to pi-pi+. We have measured the following CP asymmetry parameters: A_CP(K-K+pi+) = +0.006 +/- 0.011 +/- 0.005, A_CP(K-K+) = -0.001 +/- 0.022 +/- 0.015 and A_CP(pi-pi+) = +0.048 +/- 0.039 +/- 0.025 where the first error is statistical and the second error is systematic. These asymmetries are consistent with zero with smaller errors than previous measurements.Comment: 12 pages, 4 figure

New FOCUS results on charm mixing and CP violation

We present a summary of recent results on CP violation and mixing in the charm quark sector based on a high statistics sample collected by photoproduction experiment FOCUS (E831 at Fermilab). We have measured the difference in lifetimes for the $D^0$ decays: $D^0 \to K^-\pi^+$ and $D^0 \to K^-K^+$. This translates into a measurement of the $y_{CP}$ mixing parameter in the \d0d0 system, under the assumptions that $K^-K^+$ is an equal mixture of CP odd and CP even eigenstates, and CP violation is negligible in the neutral charm meson system. We verified the latter assumption by searching for a CP violating asymmetry in the Cabibbo suppressed decay modes $D^+ \to K^-K^+\pi^+$, $D^0 \to K^-K^+$ and $D^0 \to \pi^-\pi^+$. We show preliminary results on a measurement of the branching ratio $\Gamma(D^{*+}\to \pi^+ (K^+\pi^-))/\Gamma(D^{*+}\to \pi^+ (K^-\pi^+))$.Comment: 9 pages, 6 figures, requires espcrc2.sty. Presented by S.Bianco at CPConf2000, September 2000, Ferrara (Italy). In this revision, fixed several stylistic flaws, add two significant references, fixed a typo in Tab.

A Measurement of the Ds+ Lifetime

A high statistics measurement of the Ds+ lifetime from the Fermilab fixed-target FOCUS photoproduction experiment is presented. We describe the analysis of the two decay modes, Ds+ -> phi(1020)pi+ and Ds+ -> \bar{K}*(892)0K+, used for the measurement. The measured lifetime is 507.4 +/- 5.5 (stat.) +/- 5.1 (syst.) fs using 8961 +/- 105 Ds+ -> phi(1020)pi+ and 4680 +/- 90 Ds+ -> \bar{K}*(892)0K+ decays. This is a significant improvement over the present world average.Comment: 5 pages, 3 figures, 2 tables, submitted to PR