Biomolecules

In this study, the genes involved in the initial attack on fluorene by Sphingomonas sp. LB126 were investigated. The ? and ? subunits of a dioxygenase complex (FlnA1A2), showing 63% and 51% sequence identity respectively, with the subunits…

2-Ethyhexyl nitrate (2-EHN) is a major additive of fuel which is used to comply with the cetane number of diesel. Because of its wide use and possible accidental release, 2-EHN is a potential pollutant of the environment. In this study,…

Initial reactions involved in the bacterial degradation of polycyclic aromatic hydrocarbons (PAHs) include a ring-dihydroxylation catalyzed by a dioxygenase and a subsequent oxidation of the dihydrodiol products by a dehydrogenase. In this…

In Sphingomonas CHY-1, a single ring-hydroxylating dioxygenase is responsible for the initial attack of a range of polycyclic aromatic hydrocarbons (PAHs) composed of up to five rings. The components of this enzyme were separately purified…

Mathew-Fenn et al. (Science (2008) 322, 446-9) measured end-to-end distances of short DNA and concluded that stretching fluctuations in several consecutive turns of the double helix should be strongly correlated. I argue that this…

Experiments show that for many two state folders the free energy of the native state DG_ND([C]) changes linearly as the denaturant concentration [C] is varied. The slope, m = d DG_ND([C])/d[C], is nearly constant. The m-value is associated…

Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various…

We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…

It is presented that the positions of amino acids within Genetic Code Table follow from strict their physical and chemical properties as well as from a pure formal determination by the Golden mean.

This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their…

We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…

The AGBNP2 implicit solvent model, an evolution of the Analytical Generalized Born plus Non-Polar (AGBNP) model we have previously reported, is presented with the aim of modeling hydration effects beyond those described by conventional…

Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…

We consider a charged Brownian particle in an asymmetric bistable electrostatic potential biased by an externally applied or induced time periodic electric field. While the amplitude of the applied field is independent of frequency, that of…

Synthesis of the biological "energy currency molecule" adenosine triphosphate ATP is accomplished by FoF1-ATP synthase. In the plasma membrane of Escherichia coli, proton-driven rotation of a ring of 10 c subunits in the Fo motor powers…

In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…

An $k$-noncrossing RNA structure can be identified with an $k$-noncrossing diagram over $[n]$, which in turn corresponds to a vacillating tableaux having at most $(k-1)$ rows. In this paper we derive the limit distribution of irreducible…

We present a numerical study of the effect of knotting on the ejection of flexible and semiflexible polymers from a spherical, virus-like capsid. The polymer ejection rate is primarily controlled by the knot, which moves to the hole in the…

The importance of mutator clones in the adaptive evolution of asexual populations is not fully understood. Here we address this problem by using an ab initio microscopic model of living cells, whose fitness is derived directly from their…

Molecular dynamics studies within a coarse-grained structure based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects in the native structure of a knot. The first protein, N-acetylornithine…