Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

The synthesis of (−)-varitriol and (−)-3′-epi-varitriol via a Ramberg-Bäcklund route

A concise route to the anti-tumour natural product (−)-varitriol, together with its novel isomer (−)-3′-epi-varitriol, is described using a Horner-Wadsworth-Emmons (HWE)/conjugate addition/Ramberg-Bäcklund sequence as the cornerstone. The flexibility of the synthetic route has been demonstrated by the preparation of novel varitriol analogues.     

DETECTION OF DNA-PSORALEN PHOTOADDUCTS in situ

Abstract— An immunological method, with the use of specific immune serum, has been developed for detection of 8-methoxypsoralen (8-MOP) photoadducts to DNA, formed in situ in cell nuclei, after combined treatment with 8MOP and UV-A irradiation (Zarçbska et al. , 1978). Lymphocytes fixed on slides or in suspension, and cryostat sections of different mammalian tissues, served as antigenic substrate, after treatment with 8-MOP and UV-A in vitro. Specific fluorescence in these substrates was detected in the nuclei after treatment with 30 ˜ 140 kJ/m² UV-A in the presence of 0.1-0.3 μg/cm² 8-MOP. PHA-stimulated-lymphocytes appeared to be the most sensitive substrate.
However, hairless mice treated with high doses of UV-A in vivo , 70 ˜ 360 kJ/m² did not reveal a specific fluorescence of epidermal nuclei, unless a high local concentration of 8-MOP was attained.
The apparent discrepancy in the level of photoadduct detection between the in vitro and in vivo treated specimens was explained by the low number of DNA-8-MOP-photoadducts formed in vivo under these experimental conditions. The relevance of these findings to the role of DNA-8-MOP-photoadducts formed during PUVA photochemotherapy is discussed.     

A density functional theory study of sulfur poisoning

Density functional theory calculations have been used to investigate the chemisorption of H, S, SH, and H(2)S as well as the hydrogenation reactions S+H and SH+H on a Rh surface with steps, Rh(211), aiming to explain sulfur poisoning effect. In the S hydrogenation from S to H(2)S, the transition state of the first step S+H-->SH is reached when the S moves to the step-bridge and H is on the off-top site. In the second step, SH+H-->H(2)S, the transition state is reached when SH moves to the top site and H is close to another top site nearby. Our results show that it is difficult to hydrogenate S and they poison defects such as steps. In order to address why S is poisoning, hydrogenation of C, N, and O on Rh(211) has also been calculated and has been found that the reverse and forward reactions possess similar barriers in contrast to the S hydrogenation. The physical origin of these differences has been analyzed and discussed.     

Identification of Error Types in Preservice Teachers' Attempts to Create Fraction Story Problems for Specified Operations

The purpose of this research was to determine if recognizable error types exist in the work of preservice teachers required to create story problems for specific fraction operations. Students were given a particular single‐operation fraction expression and asked to do the calculation and then create a story problem that would require the use of both the expression and calculation to answer the story problem. Distinct error types, determined by mathematical and grammatical characteristics, were identified by the researchers. These error types were then used to analyze an additional set of work samples to determine frequency rates of error types. Future research will involve evaluating the efficacy of specific instructional methods with the goal of reducing the frequency of certain error types.     

On the optimum design of piston rings

We study a family of control problems that arise in the design of dynamically loaded bearings which have a minimum power loss; in particular, we study the design of piston rings with minimum parasitic power loss.This research was partially supported by NSF Grant No. MCS-77-05624.     

The input impedance of the dielectric resonator antenna

Dielectric cylinders of very high permittivity have been used in the past as resonant cavities, but since the structure is not enclosed by metallic walls, electromagnetic fields do exist beyond the geometrical boundaries of the structure and part of the power is radiated. Through the proper choice of geometry and permittivity this radiation can become the dominant feature of the structure and become an efficient antenna for use at millimeter wave frequencies. Both experimental and theoretical investigations of a variety of these dielectric resonator antennas have been undertaken. In particular, the input impedance of a probe-fed cylindrical structure was examined in detail and a comparison of theoretical and experimental results was made.     

Two-dimensional packing of short DNA with nonpairing overhangs in cationic liposome-DNA complexes: from Onsager nematics to columnar nematics with finite-length columns

We report the formation of liquid crystalline (LC) phases of short double-stranded DNA with nonpairing (nonsticky) overhangs, confined between two-dimensional (2D) lipid bilayers of cationic liposome-DNA complexes. In a landmark study (Science2007, 318, 1276), Nakata et al. reported on the discovery of strong end-to-end stacking interactions between short DNAs (sDNAs) with blunt ends, leading to the formation of 3D nematic (N) and columnar LC phases. Employing synchrotron small-angle X-ray scattering, we have studied the interplay between shape anisotropy-induced and DNA end-to-end interaction-induced N ordering for 11, 24, and 48 bp sDNA rods with single-stranded oligo-thymine (T) overhangs modulating the end-to-end interactions. For suppressed stacking interactions with 10-T overhangs, the volume fraction of sDNA at which the 2D isotropic (I)-to-N transition occurs for 24 and 48 bp sDNA rods depended on their length-to-width (L/D) shape anisotropy, qualitatively consistent with Onsager's theory for the entropic alignment of rigid rods. As the overhang length is reduced from 10 to 5 and 2 T for 24 and 48 bp sDNA, the N-to-I transition occurs at lower volume fractions, indicating the onset of some degree of end-to-end stacking interactions. The 11 bp sDNA rods with 5- and 10-T overhangs remain in the I phase, consistent with their small shape anisotropy (L/D ≈ 1.9) below the limit for Onsager LC ordering. Unexpectedly, in contrast to the behavior of 24 and 48 bp sDNA, the end-to-end interactions between 11 bp sDNA rods with 2-T overhangs set in dramatically, and a novel 2D columnar N phase (N(C)) with finite-length columns formed. The building blocks of this phase are comprised of 1D stacks of (on average) four 11 bp DNA-2T rods with an effective L(stacked)/D ≈ 8.2. Our findings have implications for the DNA-directed assembly of nanoparticles on 2D platforms via end-to-end interactions and in designing optimally packed LC phases of short anisotropic biomolecules (such as peptides and short-interfering RNAs) on nanoparticle membranes, which are used in gene silencing and chemical delivery.     

A compact piecewise-linear voronoi diagram for convex sites in the plane

In the plane the post-office problem, which asks for the closest site to a query site, and retraction motion planning, which asks for a one-dimensional retract of the free space of a robot, are both classically solved by computing a Voronoi diagram. When the sites arek disjoint convex sets we give a compact representation of the Voronoi diagram, usingO (k) line segments, that is sufficient for logarithmic time post-office location queries and motion planning. If these sets are polygons withn total vertices given in standard representations, we compute this diagram optimally in Θ (k logn) deterministic time for the Euclidean metric and inO (k logn logm) deterministic time for the convex distance function defined by a convexm-gon. This work was supported by NSERC in the form of a Graduate Scholarship and two Research Grants.     

Optimum design of one-dimensional journal bearings

When two surfaces in relative motion are separated by a thin layer of viscous fluid, they are kept apart by the pressure generated in the fluid film due to viscous forces. The magnitude of the resultant of this pressure is the load capacity of the bearing. We find the shape of a one-dimensional journal bearing which supports the greatest load.