Insights into interfacial activation from an open structure of Candida rugosa lipase.

The structure of the Candida rugosa lipase determined at 2.06-A resolution reveals a conformation with a solvent-accessible active site. Comparison with the crystal structure of the homologous lipase from Geotrichum candidum, in which the active site is covered by surface loops and is inaccessible from the solvent, shows that the largest structural differences occur in the vicinity of the active site. Three loops in this region differ significantly in conformation, and the interfacial activation of these lipases is likely to be associated with conformational rearrangements of these loops. The "open" structure provides a new image of the substrate binding region and active site access, which is different from that inferred from the structure of the "closed" form of the G. candidum lipase

Harmonization of multi-site functional MRI data with dual-projection based ICA model

Modern neuroimaging studies frequently merge magnetic resonance imaging (MRI) data from multiple sites. A larger and more diverse group of participants can increase the statistical power, enhance the reliability and reproducibility of neuroimaging research, and obtain findings more representative of the general population. However, measurement biases caused by site differences in scanners represent a barrier when pooling data collected from different sites. The existence of site effects can mask biological effects and lead to spurious findings. We recently proposed a powerful denoising strategy that implements dual-projection (DP) theory based on ICA to remove site-related effects from pooled data, demonstrating the method for simulated and in vivo structural MRI data. This study investigates the use of our DP-based ICA denoising method for harmonizing functional MRI (fMRI) data collected from the Autism Brain Imaging Data Exchange II. After frequency-domain and regional homogeneity analyses, two modalities, including amplitude of low frequency fluctuation (ALFF) and regional homogeneity (ReHo), were used to validate our method. The results indicate that DP-based ICA denoising method removes unwanted site effects for both two fMRI modalities, with increases in the significance of the associations between non-imaging variables (age, sex, etc.) and fMRI measures. In conclusion, our DP method can be applied to fMRI data in multi-site studies, enabling more accurate and reliable neuroimaging research findings

Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme

The MnmE-MnmG complex is involved in tRNA modification. We have determined the crystal structure of Escherichia coli MnmG at 2.4-A resolution, mutated highly conserved residues with putative roles in flavin adenine dinucleotide (FAD) or tRNA binding and MnmE interaction, and analyzed the effects of these mutations in vivo and in vitro. Limited trypsinolysis of MnmG suggests significant conformational changes upon FAD binding.This work was supported by grant GSP-48370 from the Canadian Institutes of Health Research (to M.C. and A.M.) and grant BFU2007-66509 from the Ministerio de Ciencia e Innovación (to M.-E.A.).Peer reviewe

Koszulity and Koszul modules of dual extension algebras

Let A and B be algebras, and let T be the dual extension algebra of A and B. We provide a different method to prove that T is Koszul if and only if both A and B are Koszul. Furthermore, we prove that an algebra is Koszul if and only if one of its iterated dual extension algebras is Koszul, if and only if all its iterated dual extension algebras are Koszul. Finally, we give a necessary and sufficient condition for a dual extension algebra to have the property that all linearly presented modules are Koszul modules, which provides an effective way to construct algebras with such a property

Crystallization and preliminary X-ray analysis of heparinase II from Pedobacter heparinus

Heparinase II from Pedobacter heparinus (formerly Flavobacterium heparinum), which acts on both heparin and heparan sulfate, is one of several glycosaminoglycan-degrading enzymes produced by this organism. This enzyme, with a molecular weight of 84 kDa, utilizes a lytic mechanism to cleave the alpha(1-4) glycosidic bond between hexosamine (D-glucosamine) and L-iduronic or D-glucuronic acid, resulting in a product with an unsaturated sugar ring at the non-reducing end. The enzyme was crystallized by the hanging-drop vapour -diffusion method. The crystals belong to orthorhombic space group P2(1)2(1)2(1) and diffract to 2 A resolution. There are two molecules in the asymmetric unit, consistent with the finding that recombinant heparinase II functions as a dimer in solutionEnglish15333943NRC publication: Ye

Hochschild cohomology rings of Temperley-Lieb algebras

The authors first construct an explicit minimal projective bimodule resolution (ℙ, δ) of the Temperley-Lieb algebra A, and then apply it to calculate the Hochschild cohomology groups and the cup product of the Hochschild cohomology ring of A based on a comultiplicative map Δ: ℙ → ℙ ⊗A ℙ. As a consequence, the authors determine the multiplicative structure of Hochschild cohomology rings of both Temperley-Lieb algebras and representation-finite q-Schur algebras under the cup product by giving an explicit presentation by generators and relations

Crystallization and preliminary X-ray analysis of chondroitinase B from Flavobacterium heparinum

UI - 99234359NRC publication: Ye