A fourier fingerprint-based method for protein surface representation

A crucial enabling technology for structural genomics is the development of algorithms that can predict the putative function of novel protein structures: the proposed functions can subsequently be experimentally tested by functional studies. Testable assignments of function can be made if it is possible to attribute a putative, or indeed probable, function on the basis of the shapes of the binding sites on the surface of a protein structure. However the comparison of the surfaces of 3D protein structures is a computationally demanding task. Here we present four surface representations that can be used locally to describe the global shape of specifically bounded local region models. The most successful of these representations is obtained by a Fourier analysis of the distribution of surface curvature on concentric spheres around a surface point and summarizes a 24 A diameter spherically clipped region of protein surface by a fingerprint of 18 Fourier amplitude values. Searching experiments using these fingerprints on a set of 366 proteins demonstrate that this provides an effective and an efficient technique for the matching of protein surfaces.     

Modular syntheses of isoxazoloazepinones and pyrazoloazepinones

Herein we described an optimised synthesis of isoxazoloazepinone and novel heterocycle pyrazoloazepinone. These syntheses are modular in nature and fast to execute. The title compounds were obtained pure without the intervention of chromatography.     

The isotropy subalgebra of the canonical 3-form of a semisimple Lie algebra

The isotropy subalgebra of the canonical 3-form of a semisimple Lie algebra over a field of characteristic zero is computed. Its isotropy subgroup is also studied.     

A classical trajectory study of the photodissociation of T1 acetaldehyde: the transition from impulsive to statistical dynamics

Previous experimental and theoretical studies of the radical dissociation channel of T(1) acetaldehyde show conflicting behavior in the HCO and CH(3) product distributions. To resolve these conflicts, a full-dimensional potential-energy surface for the dissociation of CH(3)CHO into HCO and CH(3) fragments over the barrier on the T(1) surface is developed based on RO-CCSD(T)/cc-pVTZ(DZ) ab initio calculations. 20,000 classical trajectories are calculated on this surface at each of five initial excess energies, spanning the excitation energies used in previous experimental studies, and translational, vibrational, and rotational distributions of the radical products are determined. For excess energies near the dissociation threshold, both the HCO and CH(3) products are vibrationally cold; there is a small amount of HCO rotational excitation and little CH(3) rotational excitation, and the reaction energy is partitioned dominantly (>90% at threshold) into relative translational motion. Close to threshold the HCO and CH(3) rotational distributions are symmetrically shaped, resembling a Gaussian function, in agreement with observed experimental HCO rotational distributions. As the excess energy increases the calculated HCO and CH(3) rotational distributions are observed to change from a Gaussian shape at threshold to one more resembling a Boltzmann distribution, a behavior also seen by various experimental groups. Thus the distribution of energy in these rotational degrees of freedom is observed to change from nonstatistical to apparently statistical, as excess energy increases. As the energy above threshold increases all the internal and external degrees of freedom are observed to gain population at a similar rate, broadly consistent with equipartitioning of the available energy at the transition state. These observations generally support the practice of separating the reaction dynamics into two reservoirs: an impulsive reservoir, fed by the exit channel dynamics, and a statistical reservoir, supported by the random distribution of excess energy above the barrier. The HCO rotation, however, is favored by approximately a factor of 3 over the statistical prediction. Thus, at sufficiently high excess energies, although the HCO rotational distribution may be considered statistical, the partitioning of energy into HCO rotation is not.     

Structural DNA profiles: single sequence queries

Structural DNA profiles use the structural properties of the constituent octamers either to observe any characteristics of a single sequence that are unusual (a single sequence query) or to visualize a pattern common to a set of sequences (a multiple sequence query). They are an aid in understanding structural reasons for functional DNA activity. Profiles that answer single sequence queries are introduced and Profile Manager (a software application developed to automate profile generation) is presented. Two sequences that are similar by their nucleotide composition but are known to be very different by structure are analyzed, resulting in useful illustrations that agree with the experimental nuclear magnetic resonance structures.     

Genomic data analysis using DNA structure: an analysis of conserved nongenic sequences and ultraconserved elements

Recent comparative studies of the human and mouse genomes have revealed sets of conserved nongenic sequences (CNGs) and sets of ultraconserved elements (UCEs). Both sets of sequences, which exhibit extremely high levels of conservation, extend over hundreds of bases and have no known function. Since there is no detectable sequence homology between paralogous CNGs or UCEs in either of the species, an alignment-free technique is needed for their analysis. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers, including information on stability, the minimum energy conformation, and flexibility. We have used Fourier techniques to analyze the UCEs and CNGs in terms of their octamer structural properties, to reveal structural correlations which may indicate possible functions for some of these sequences.     

Graphitic encapsulation of catalyst particles in carbon nanotube production

A new model is proposed for the encapsulation of catalyst metal particles by graphite layers that are obtained, for example, in low-temperature chemical vapor deposition production of carbon nanotubes (CNTs). In this model graphite layers are primarily formed from the dissolved carbon atoms in the metal-carbide particle when the particle cools. This mechanism is in good agreement with molecular dynamics simulations (which show that precipitated carbon atoms preferentially form graphite sheets instead of CNTs at low temperatures) and experimental results (e.g., encapsulated metal particles are found in low-temperature zones and CNTs in high-temperature regions of production apparatus, very small catalyst particles are generally not encapsulated, and the ratio of the number of graphitic layers to the diameter of the catalyst particle is typically 0.25 nm(-1)).     

The main involutions of the metaplectic group

We determine the set of automorphisms of a metaplectic group which lift the main involution of the general linear group over an infinite field. Some basic properties of these automorphisms are also established.