University of Alberta

About: University of Alberta is a education organization based out in Edmonton, Alberta, Canada. It is known for research contribution in the topics: Population & Health care. The organization has 65403 authors who have published 154847 publications receiving 5358338 citations. The organization is also known as: Ualberta & UAlberta.

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.

Abstract: A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts – RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of ∼20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (< 1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Hα), 0.980 (13Cα), 0.996 (13Cβ), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http://redpoll.pharmacy.ualberta.ca.

Evidence in Favor of a Broad Framework for Pronunciation Instruction

Abstract: We had native English-speaking (NS) listeners evaluate the effects of 3types of instruction (segmental accuracy; general speaking habits and prosodic factors; and nospecific pronunciation instruction) on the speech of 3 groups of English as a second language(ESL) learners. We recorded their sentences and extemporaneously produced narratives at thebeginning and end of a 12-week course of instruction. In a blind rating task, 48 native Englishlisteners judged randomized sentences for accentedness and comprehensibility. Six experiencedESL teachers evaluated narratives for accent, comprehensibility, and fluency. Although bothgroups instructed in pronunciation showed significant improvement in comprehensibility andaccentedness on the sentences, only the global group showed improvement in comprehensibilityand fluency in the narratives. We argue that the focus of instruction and the attentional demandson speakers and listeners account for these findings.