Automating the identification and analysis of protein {beta}-barrels

ßBarrels are widespread and well-studied featuresof a great many protein structures. In this paper an unsuper-visedmethod for the detection of P-barrels is developed based ontechniques from graph theory. The hydrogen bonded connectivityof ß-sheets is derived using standard pattern recognitiontechniques and expressed as a graph. Barrels correspond to topologicalrings in these connectivity graphs and can thus be identifiedusing ring perception algorithms. Following from this, the characteristictopological structure of a barrel can be expressed using a novelform of reduced nomenclature that counts sequence separationsbetween successive members of the ring set These techniquesare tested by applying them to the detection of barrels in anon-redundant subset of the Brookhaven database. Results indicatethat topological rings do seem to correspond uniquely to ß-barrelsand that the technique, as implemented, finds the majority ofbarrels present in the dataset.     

FOLD: integrated analysis and display of protein secondary structure

FOLD, a computer program for the definition and analysis of protein secondary structure, is described. Algorithms implemented in the software are reviewed. These include methods for the identification of simple features such as hydrogen bonds, alpha helices, beta strands, beta bulges, and beta and psi turns. Techniques are also described for the definition and analysis of higher-order structures, such as beta hairpins, beta sheets and their topology, and beta barrels. In addition to considerable textual output the program supports visualization of protein secondary structure in either an atom-based display style or one reproducing the characteristics of a so-called ribbon drawing.     

Martensitic transformations in Ti-Mo alloys

A detailed investigation has been made of the structure of alloys of the Ti-Mo system containing up to 10wt% Mo, water-quenched from the-phase region. With increase in molybdenum content, the martensite structure changes from hexagonal () to orthorhombic () at 4 wt% Mo, and at 10 wt% Mo, the structure is completely retained . For alloy compositions <4 wt% Mo, there is a diffusional component in the transformation of the -phase at the quench rates employed. There is a transition, with increase in molybdenum content, in morphology (from massive to acicular) and in substructure (from dislocations to twins). However, the transitions in crystallography, morphology and sub-structure are not directly related to one another except for an abrupt loss of dislocation substructure at the/ transition. The to crystallographic transition has the characteristics of a second order transformation, and evidence has been obtained of the existence of a spinodal within the metastable orthorhombic system. The orthorhombic martensites of Ti-6 and 8 wt% Mo decompose during quenching producing a fine modulated structure within the martensite plates, consistent with a proposed spinodal mode of decomposition.     

Studies on insect fibrous proteins: the structural protein of the ootheca in the praying mantis, Sphodromatis centralis Rehn

Histological studies have been made on the left colleterial gland which secretes the α-type structural protein in the ootheca of Sphodromantis centralis. Three distinct types of secretory cell are present in the gland wall, and each has a complex apical ‘end-apparatus’ composed of closely packed canalicules radiating from a central cavity. Structural protein is synthesized in the cytoplasm, passed through the canalicules into the cavity of the end-apparatus, and extruded into the lumen as strongly birefringent, apparently membrane-free globules. At this stage the globules consist of numerous concentric layers of long, parallel fibrils, 0·05–0·1 μm in diameter. In each successive layer the fibril direction is rotated through an angle of about 18° about an axis perpendicular to the layers, in the manner of cholesteric phase systems. When sectioned, the globules reveal a regular ‘lamellated’ structure similar to that apparent in sections of some insect and crustacean cuticles. A three-dimensional model has been constructed to illustrate this phenomenon. During ootheca formation fibrils become transformed into thin ‘crystalline’ ribbons, about 15 μm long, 1–2 μm wide and 200–300 Å thick. Very regular diamond-shaped ribbons may be obtained in vitro by mixing structural protein globules from dissected left glands with optimum concentrations (0·005–·025 m ) of calcium chloride in unbuffered solution. Experiments suggest that calcium ions play an important part in the natural process of ribbon formation.     

The semantics of augmented constraint diagrams

Constraint diagrams are a diagrammatic notation which may be used to express logical constraints. They generalize Venn diagrams and Euler circles, and include syntax for quantification and navigation of relations. The notation was designed to complement the Unified Modelling Language in the development of software systems.Since symbols representing quantification in a diagrammatic language can be naturally ordered in multiple ways, some constraint diagrams have more than one intuitive meaning in first-order predicate logic. Any equally expressive notation which is based on Euler diagrams and conveys logical statements using explicit quantification will have to address this problem.We explicitly augment constraint diagrams with reading trees, which provides a partial ordering for the quantifiers (determining their scope as well as their relative ordering). Alternative approaches using spatial arrangements of components, or alphabetical ordering of symbols, for example, can be seen as implicit representations of a reading tree.Whether the reading tree accompanies the diagram explicitly (optimizing expressiveness) or implicitly (simplifying diagram syntax), we show how to construct unambiguous semantics for the augmented constraint diagram.     

Rotational superposition: a review of methods

Rotational superposition is one of the most commonly used algorithms in molecular modelling. Many different methods of solving superposition have been suggested. Of these, methods based on the quaternion parameterization of rotation are fast, accurate, and robust. Quaternion parameterization-based methods cannot result in rotation inversion and do not have special cases such as co-linearity or co-planarity of points. Thus, quaternion parameterization-based methods are the best choice for rotational superposition applications.     

In situ oxidation of Ni30 wt%Cr and TDNiCr in the high voltage electron microscope

In situ oxidation of Ni-30Cr and TDNiCr (Ni20wt %Cr2 vol. %ThO₂) in the high voltage electron microscope has been used to examine the early stages of oxidation over the temperature range ～ 450–700°C in 15 Torr O₂. Companion studies on thin foils and bulk specimens oxidized out of the microscope gave results similar to the in situ studies, indicating that the in situ results reveal true oxidation behavior. A notable feature was the observation that oxide nucleation and growth occurred on a variety of interfaces, such as grain boundaries, large inclusions, and slip bands. The growth of grain boundary oxides was studied, and a mechanism is proposed to account for the kinetics.     

Thermodynamic analysis in the design of process networks

Thermodynamic analyses based on the concepts of irreversible entropy increases or exergy losses have frequently been suggested as pointers to sources on inefficiency in chemical processes. For instance, by evaluating the entropy gain in distillation systems, an incentive might be identified for research into thermodynamically more effient separation technology.

However, a process engineer seeking to design a practical flowsheet with present day technology is much less certain about the value of thermodynamic analysis. In his environment of technical constraints, the interpretation of thermodynamic criteria is by no means straightforward and may even lead to incorrect conclusions unless some care is taken.

The present paper describes an approach overcoming this problem. Examples are quoted from the studies of two industrial processes (Sulphuric acid and nitric acid). Further, a generalised discussion is given and results are quoted from the successful application of the approach in fourteen ICI design projects.