It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and i...

Two proteins of 53,000 and 56,000 mol wt have been found to be associated with coated vesicles (CV) purified from bovine brain and chicken liver. These proteins share molecular weights, isoelectric points, and antigenic determinants with alpha- and beta-tubulins purified from bovine brain. Based on SDS PAGE and electron microscopic analysis of controlled pore glass bead exclusion column fractio...

Two-component systems are frequently involved in the adaptation of bacteria to changing environmental conditions at the level of transcriptional regulation. Here we report the characterization of members of the two-component systems of the gastric pathogen Helicobacter pylori deduced from the genome sequence of strain 26695. We demonstrate that the response regulators HP166, HP1043, and HP1021 ...

C3 exhibits two common allotypic variants that may be separated by gel electrophoresis and are called C3 fast (C3 F) and C3 slow (C3 S). C3 F, the less common variant, occurs at appreciable frequencies only in Caucasoid populations (gene frequency = 0.20). An increased prevalence of the C3 F allele has been reported in patients with partial lipodystrophy, IgA nephropathy, and Indian childhood h...

Authors contributed equally to this work.

Two-component systems constitute prevalent signaling pathways in bacteria and mediate a large variety of adaptative cellular responses. Signaling proceeds through His-Asp phosphorelay cascades that involve two central partners, the histidine protein kinase and the response regulator protein. Structural studies have provided insights into some design principles and activation mechanisms of these...

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, sev...

Adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes large-scale motions of its Lid and AMP-binding domains when its open form closes over its substrates, AMP and Mg2+-ATP. The third domain, the Core, is relatively stable during closing. The resulting trajectory is analyzed with a principal component analysis method that decomposes the atom motions into modes or...

While molecular visualization software has advanced over the years, today, most tools still operate on individual molecular structures with little facility to manipulate large multi-component complexes, or depict molecular flexibility. We extend and accelerate 3D image-based rendering via programmable graphics units to provide an order of magnitude speedup over traditional triangle-based render...

C ritical limb ischemia is associated with significant morbidity and mortality. Revascularization is not always feasible or successful. Consequently, in a worryingly high percentage of patients, amputation is the only option. It is hoped that a wider understanding of the molecular mechanisms underpinning limb ischemia can help develop new and truly revolutionary therapeutic strategies. In this ...