bound water and genome of bacteriophages

Author: Tsotne Dvali
Keywords: bacteriophages, bounded water, biophysics, DNA, ds-DNA, DNA-water-protein
Annotation:

The importance of water for the functioning of macromolecules and biosystems, in general, has long been known. Determining the role of water according to structural and functional hierarchy is quite difficult in the activity of specific molecules and in conformational or transformation( conversion ) cycles. In order to take into account the fundamental processes and the defining all effects of the system, it is necessary to create the map that represents biophysical processes in a single model, summarizing the structural and functional purpose of each component, their characteristics inside and outside ( in separation ) the system. The interaction of water molecules with the genome (ds-DNA) determines its shape/structure, which is somewhat induced by the composition of the environment. The seminar includes a few combined theories and analysis of overviewed studies and models, for the interpretation of the structural-functional hierarchy of the system. Overview of different sources and conclusions based on few models. In particular, the purpose/role of the structural differences generated by the hydration effects of two complementary DNA nucleotide pairs for the system itself is illustrated in several different forms. The enthalpic-entropic relationships revealed by the thermodynamic analysis of the biosystem, as well as the increase in local heat capacity during dissociation/formation processes, are associated with changes in the environment (conversion phases | The increase in heat capacity in DNA and proteins is significantly different - per gram - (0.15 kJ/K mol-ft) 0.18 J/K gram. Which in itself is much lower than 0.5 -0.7 J/K gram for glob. protein's heat capacity increment) ). It is important to connect the hierarchy of mechanisms inducing various processes to the structural characteristics of the system; The role of water in the formation of different units, and in the energy conversion. Analysis of bacteriophage DNA packaging mechanisms and models of DNA structure itself combining several studies. The analysis of the well-known duplex anvil/spool model, is a critique of conclusions from several simplified simulations and models created on the basis of cryo-microscopic studies of this topic. All for combining energetics of packaging machinery and inductive processes into the simplified model. Analysis of the effects and processes determined by the characteristics of water molecules. In particular observations on the individual interactions of protein and DNA with water, in a defined framework of dimensional and thermodynamical characteristics of the system, allows conclusions to be drawn about the specific functions of structured/bounded water.