While studies of secondary structure interactions have focused on local interacting features, there is a need for a more global characterization of packing-induced aligned packing of secondary structures. This study presents an analysis of the distribution of globally sampled secondary structures within selected subunits of a selected set of multimeric proteins. Comparisons are made between the...

The packing structures of transmembrane helices are traditionally attributed to patterns in residues along the contact surface. In this view, besides keeping the helices confined in the membrane, the bilayer has only a minor effect on the helices structure. Here, we use two different approaches to show that the lipid environment has a crucial effect in determining the cross-angle distribution o...

MOTIVATION In many proteins, helix-helix interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining associations between protein units. However, the determination of a set of rules that guide helix-helix interaction has been elusive. In order to gain further insight into the helix-helix interface, we have developed a comprehensive package of...

The slow-wave dispersive properties of a traveling-wave tube (TWT) changes considerably when either the helix is supported by a dielectric or the waveguide is filled with plasma. The dispersive properties of the dielectric-supported helix waveguide have been examined for different geometric parameters of the helix waveguide. The dispersion relation of the helix mode is found to be upshifted by ...

The geometry of helix-helix packing in globular proteins is comprehensively analysed within the model of the superposition of two helix lattices which result from unrolling the helix cylinders onto a plane containing points representing each residue. The requirements for the helix geometry (the radius R, the twist angle omega and the rise per residue delta) under perfect match of the lattices a...

The aim of this study is to generate initial candidate models for bundles of transmembrane helices. Such models may then be further refined by eg. molecular dynamics simulations. Each helix is treated as a rigid body represented by a direction vector and the coordinates of its centre of mass. Constituent residues are mapped onto the helix axis in order to maintain the amino acid sequence depend...

A three dimensional model of the basic Helix-Loop-Helix motif and its sequence specific recognition of DNA is described. The basic-helix I is modeled as a continuous ?-helix because no ?-helix breaking residue is found between the basic region and the first helix. When the basic region of the two peptide monomers are aligned in the successive major groove of the cognate DNA, the hydrophobi...

In this paper we present methods for approximating a helix segment by quintic Bézier curves or quintic rational Bézier curves based on the geometric Hermite interpolation technique in space. The fitting curve interpolates the curvatures as well as the Frenet frames of the original helix at both ends. We achieve a high accuracy of the approximation by giving a proper parametrization of the curve...

Helical gears are commonly used in industry as they have advantages of higher power density, quieter operation etc., compared to spur gears. Conventional gear design is based on various design criteria, including durability and bending strength load rating. In recent times, fracture failure modes are gaining importance in addition to conventional failure modes. Stresses due to operating fatigue...