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This study introduces an algorithm for video denoising based on improved dual‐domain filtering and 3D block matching. The wavelet thresholding based on 3D block matching is introduced to make full use of the correlation of video sequence in order to apply dual‐domain filtering to the video. A layered approach is used that attempts denoising in both a base layer and a detail layer. The result of wavelet thresholding based on 3D block matching is used as a guide image to make the base layer smoother. Shrinkage of short‐time Fourier transform coefficients further decreases the noise in the detail layer. Experimental results show that the authors' algorithm generates a better base layer and detail layer than the traditional dual‐domain filtering algorithms. The subjective and objective comparisons of different algorithms also prove that the proposed algorithm performs better for video denoising. [ABSTRACT FROM AUTHOR]

Abstract: Nitronate monooxygenase (NMO) is an FMN‐dependent enzyme that oxidizes the neurotoxin propionate 3‐nitronate (P3N) and represents the best‐known system for P3N detoxification in different organisms. The crystal structure of the first eukaryotic Class I NMO from Cyberlindnera saturnus (CsNMO) has been solved at 1.65 Å resolution and refined to an R‐factor of 14.0%. The three‐dimensional structures of yeast CsNMO and bacterial PaNMO are highly conserved with the exception of three additional loops on the surface in the CsNMO enzyme and differences in four active sites residues. A PEG molecule was identified in the structure and formed extensive interactions with CsNMO, suggesting a specific binding site; however, 8% PEG showed no significant effect on the enzyme activity. This new crystal structure of a eukaryotic NMO provides insight into the function of this class of enzymes. [ABSTRACT FROM AUTHOR]

Clinical inhibitor amprenavir (APV) is less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). We solved the crystal structure of PR2 with APV at 1.5 Å resolution to identify structural changes associated with the lowered inhibition. Furthermore, we analyzed the PR1 mutant (PR1M) with substitutions V32I, I47V, and V82I that mimic the inhibitor binding site of PR2. PR1M more closely resembled PR2 than PR1 in catalytic efficiency on four substrate peptides and inhibition by APV, whereas few differences were seen for two other substrates and inhibition by saquinavir (SQV) and darunavir (DRV). High resolution crystal structures of PR1M with APV, DRV, and SQV were compared with available PR1 and PR2 complexes. Val/Ile32 and Ile/Val47 showed compensating interactions with SQV in PR1M and PR1, however, Ile82 interacted with a second SQV bound in an extension of the active site cavity of PR1M. Residues 32 and 82 maintained similar interactions with DRV and APV in all the enzymes, whereas Val47 and Ile47 had opposing effects in the two subunits. Significantly diminished interactions were seen for the aniline of APV bound in PR1M and PR2 relative to the strong hydrogen bonds observed in PR1, consistent with 15- and 19-fold weaker inhibition, respectively. Overall, PR1M partially replicates the specificity of PR2 and gives insight into drug resistant mutations at residues 32, 47, and 82. Moreover, this analysis provides a structural explanation for the weaker antiviral effects of APV on HIV-2. [ABSTRACT FROM AUTHOR]

Saquinavir (SQV), the first antiviral HIV-1 protease (PR) inhibitor approved for AIDS therapy, has been studied in complexes with PR and the variants PRI84V and PRV82A containing the single mutations I84V and V82A that provide resistance to all the clinical inhibitors. Atomic resolution crystal structures (0.97-1.25 Å) of the SQV complexes were analyzed in comparison to the protease complexes with darunavir, a new drug that targets resistant HIV, in order to understand the molecular basis of drug resistance. PRI84V and PRV82A complexes were obtained in both the space groups P21212 and P212121, which provided experimental limits for the conformational flexibility. The SQV interactions with PR were very similar in the mutant complexes, consistent with the similar inhibition constants. The mutation from bigger to smaller amino acids allows more space to accommodate the large group at P1′ of SQV, unlike the reduced interactions observed in darunavir complexes. The residues 79-82 have adjusted to accommodate the large hydrophobic groups of SQV, suggesting that these residues are intrinsically flexible and their conformation depends more on the nature of the inhibitor than on the mutations in this region. This analysis will assist with development of more effective antiviral inhibitors. Proteins 2007. © 2007 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Video endoscopy, a modality of minimally invasive surgery, has proven to be significantly less invasive to the patient. However, by relying on a video interface to observe the surgical scene, several nonintuitive effects need to be contended with. One of these is the reduction or removal of the discrepancy in view position and orientation between the surgeon and the endoscope. Eliminating artifacts in the visual feedback is important for the improvement of the effectiveness of the surgical procedures. This article presents a novel rendering technique to produce the scene from a “surgeon-centric” viewpoint to create greater transparency for optimizing the visual precision of the endoscopic procedures. © 2005 Wiley Periodicals, Inc. Int J Imaging Syst Technol 14, 181–185, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.20022 [ABSTRACT FROM AUTHOR]

Choline oxidase from Arthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose-methanol-choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand-enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250-255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.

Calcium ions, which are important signaling molecules, can be detected in the endoplasmic reticulum by an engineered mutant of green fluorescent protein (GFP) designated CatchER with a fast off-rate. High resolution (1.78-1.20 Å) crystal structures were analyzed for CatchER in the apo form and in complexes with calcium or gadolinium to probe the binding site for metal ions. While CatchER exhibits a 1:1 binding stoichiometry in solution, two positions were observed for each of the metal ions bound within the hand-like site formed by the carboxylate side chains of the mutated residues S147E, S202D, Q204E, F223E and T225E that may be responsible for its fast kinetic properties. Comparison of the structures of CatchER, wild-type GFP and enhanced GFP confirmed that different conformations of Thr203 and Glu222 are associated with the two forms of Tyr66 of the chromophore which are responsible for the absorbance wavelengths of the different proteins. Calcium binding to CatchER may shift the equilibrium for conformational population of the Glu222 side chain and lead to further changes in its optical properties.

Crystals have been grown of the carboxylesterase Est30 from Bacillus stearothermophilus by hanging-drop vapor diffusion using ammonium sulfate as precipitant. The crystals diffracted to better than 2.0 A resolution. X-ray diffraction data were reduced in space group C222(1), with unit-cell parameters a = 55.83, b = 58.15, c = 179.65 A. R(merge) was 0.038 for 17 449 independent reflections with a completeness of 85.1%. V(M) was calculated to be 2.43 A(3) Da(-1), which suggested that there was one molecule of Est30 in the asymmetric unit. These crystals are suitable for structure determination.