We explore the dynamical large deviations of a lattice heteropolymer model of a protein by means of path sampling of trajectories. We uncover the existence of nonequilibrium dynamical phase transitions in ensembles of trajectories between active and inactive dynamical phases, whose nature depends on the properties of the interaction potential. We consider three potentials: two heterogeneous int...

We characterize the "sequence landscapes" in several simple, heteropolymer models of proteins by examining their mutation properties. Using an efficient flat-histogram Monte Carlo search method, our approach involves determining the distribution in energy of all sequences of a given length when threaded through a common backbone. These calculations are performed for a number of Protein Data Ban...

A quantitative structure-property relationship (QSPR) was used to design model protein sequences that fold repeatedly and relatively rapidly to stable target structures. The specific model was a 125-residue heteropolymer chain subject to Monte Carlo dynamics on a simple cubic lattice. The QSPR was derived from an analysis of a database of 200 sequences by a statistical method that uses a geneti...

The clathrin triskelion, which is a three-legged pinwheel-shaped heteropolymer, is a major component in the protein coats of certain post-Golgi and endocytic vesicles. At low pH, or at physiological pH in the presence of assembly proteins, triskelia will self-assemble to form a closed clathrin cage, or "basket". Recent static light scattering and dynamic light scattering studies of triskelia in...

The synthesis of RNA by chromatin-bound RNA polymerase (E.C. 2.7.7.6.) from white potato tubers proceeds at a low rate, which is enhanced after slicing the tissue, however. Concomitantly DNA template availability as measured with saturating amounts of Escherichia coli polymerase is diminished drastically. Nearest neighbor frequency analysis proved that the RNA synthesized on chromatin of intact...

AIMS This study aims to identify a high level exopolysaccharide (EPS) producer thermophile that in turn could be used as a model organism to study the biological mechanisms and whole genome organization of EPS-producing thermophilic bacteria. METHODS AND RESULTS Thermophilic isolates were screened, and then growth and EPS production of the best producer Brevibacillus thermoruber strain 423 we...

The DNA molecule is the support of the genetic information. It is a right-handed double helix, 22 angstrom in diameter, and 50 nm in the persistence length. The two strands of the helix are complementary in their nucleotide sequence with about 10 nucleotide pairs per helical turn. DNA is a long and strongly charged heteropolymer. It bears on average one elementary negative charge per each 0.17 ...

In this paper we extend the Gaussian self–consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are transformed to a form containing only the mean squared distances between pairs of monomers. These equations are further expressed in terms of instantaneous gra...

Introduction The iron storage protein ferritin is a heteropolymer composed of H and L subunits (1). The H subunit contains a ferroxidase site, whereas the L chain provides the nucleation centers for deposition of the ferrihydrite core (1). The subunit ratio H:L varies across different tissues and cell types (2). Recent reports used the paramagnetic ferritin core as a probeless MRI reporter (3, ...

Nervous system tissues from a number of patients with idiopathic neurological disorders were examined for biochemical evidence of RNA tumor virus infection. RNase-sensitive DNA polymerase activity was found in a cytoplasmic particulate fraction from two patients with Guamanian amyotrophic lateral sclerosis (ALS) but not in brains from two normal U.S. individuals. The buoyant density of the en...