Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

Crystal form transition during heating of solvent-induced crystalline syndiotactic polystyrene

The phase transition of two kinds of solvent-induced crystalline syndiotactic polystyrene (sPS). gamma-sPS and delta(c)-sPS, has been studied via WAXD and DSC. gamma-sPS transform to a-sPS at 195-225 degrees C before melt during heating, whereas delta(e)-sPS transform to first gamma-sPS and then a-sPS at 100-200 degrees C and 200-215 degrees C, respectively. The transition of delta(e)-gamma and gamma-a occurs for below melting point of sPS indicates they are all solid-solid transition.

Low-temperature oxidation of methane to form formaldehyde: role of Fe and Mo on Fe-Mo/SiO2 catalysts, and their synergistic effects

The partial oxidation of methane with molecular oxygen was performed on Fe-Mo/SiO2 catalysts. Iron was loaded on the Mo/SiO2 catalyst by chemical vapor deposition of Fe-3(CO)(12). The catalyst showed good low-temperature activities at 723-823 K. Formaldehyde was a major condensable liquid product on the prepared catalyst. There were synergistic effects between iron and molybdenum in Fe-Mo/SiO2 catalysts for the production of formaldehyde from the methane partial oxidation. The activation energy of Mo/SiO2 decreased with the addition of iron and approached that of the Fe/SiO2. The concentration of isolated molybdenum species (the peak at 1148 K in TPR experiments) decreased as the ion concentration increased and had a linear relationship with the selectivity of methane to formaldehyde. The role of Fe and Mo in the Fe-Mo/SiO2 catalyst was proposed: Fe is the center for the C-H activation to generate reaction intermediates, and Mo is the one for the transformation of intermediates into formaldehyde. Those phenomena were predominant below 775 K.

Closed form solutions of T-stress in plane elasticity crack problems

The T-stress is considered as an important parameter in linear elastic fracture mechanics. In this paper, several closed form solutions of T-stress in plane elasticity crack problems in an infinite plate are investigated using the complex potential theory. In the line crack case, if the applied loading is the remote stress or the concentrated forces, the T-stress can be derived from the basic field. Here, the basic field is defined as the field caused by the applied loading in the infinite plate without the crack. For the circular are crack, the T-stress can be abstracted from a known solution. For the cusp crack problems, the T-stress can be separated from the obtained stress solution for which the conformal mapping technique is used.

Twinning partial multiplication at grain boundary in nanocrystalline fcc metals

Most deformation twins in nanocrystalline face-centered cubic fcc metals have been observed to form from grain boundaries. The growth of such twins requires the emission of Shockley partials from the grain boundary on successive slip planes. However, it is statistically improbable for a partial to exist on every slip plane. Here we propose a dislocation reaction and cross-slip mechanism on the grain boundary that would supply a partial on every successive slip plane for twin growth.This mechanism can also produce a twin with macrostrain smaller than that caused by a conventional twin.

Growth of deformation twins in room-temperature rolled nanocrystalline nickel

Deformation twinning has been observed in room-temperature rolled nanocrystalline Ni. The growth of the deformation twins via the emission of partial dislocations from a grain boundary has been examined in detail. Partial dislocations on neighboring slip planes may migrate for different distances and then remain in the grain interior, leading to the formation of a steplike twin boundary TB . With continued twin growth, the TBs become gradually distorted and lose their coherent character due to accumulated high stresses. Moreover, we propose that microtwins may form near such TBs due to the emission of partial dislocations from the TB.

Precipitation of nanocrystals in glasses by electron irradiation: An alternative path to form glass ceramics?

This letter demonstrates an alternative method to form gallium silicate glass ceramics using high-energy electron irradiation. Compared with glass ceramics obtained from the conventional thermal treatment method, the distribution and crystal sizes of the precipitated Ga2O3 nanoparticles are the same. An advantage of this method is that the spatial distribution of the precipitated nanoparticles can be easily controlled. However, optically active dopants Ni2+ ions do not participate in the precipitation during electron irradiation. (c) 2007 American Institute of Physics.

Form Birefringence in thin films with oblique columnar structures

Effective medium theory is useful for designing optical elements with form birefringent subwavelength structures. Thin films fabricated by oblique deposition are similar to the two-dimensional surface relief subwavelength gratings. We use the effective medium theory to calculate the anisotropic optical properties of the thin films with oblique columnar structures. The effective refractive indices and the directions are calculated from effective medium theory. It is shown that optical thin films with predetermined refractive indices and birefringence may be engineered.

Recent origin of a hominoid-specific splice form of neuropsin, a gene involved in learning and memory

Neuropsin is a secreted-type serine protease involved in learning and memory. The type II splice form of neuropsin is abundantly expressed in the human brain but not in the mouse brain. We sequenced the type II-spliced region of neuropsin gene in humans and representative nonhuman primate species. Our comparative sequence analysis showed that only the hominoid species (humans and apes) have the intact open reading frame of the type II splice form, indicating that the type II neuropsin originated recently in the primate lineage about 18 MYA. Expression analysis using RT-PCR detected abundant expression of the type II form in the frontal lobe of the adult human brain, but no expression was detected in the brains of lesser apes and Old World monkeys, indicating that the type II form of neuropsin only became functional in recent time, and it might contribute to the progressive change of cognitive abilities during primate evolution.

A human-specific mutation leads to the origin of a novel splice form of neuropsin (KLK8), a gene involved in learning and memory

Neuropsin (kallikrein 8, ELKS) is a secreted-type serine protease preferentially expressed in the central nervous system and involved in learning and memory. Its splicing pattern is different in human and mouse, with the longer form (type II) only express

Functional characterization of the human-specific (type II) form of kallikrein 8, a gene involved in learning and memory

Kallikrein 8 (KLK8) is a serine protease functioning in the central nervous system, and essential in many aspects of neuronal activities. Sequence comparison and gene expression analysis among diverse primate species identified a human-specific splice for