GEOMETRICAL FACTOR AND PHYSICAL REASONS FOR ITS INFLUENCE ON THE KINETIC AND THERMODYNAMIC PROPERTIES OF RNA-LIKE HETEROPOLYMERS

Background: It has been shown that not only the primary sequence but a lso the geometry of the native conformation influences the kinetic and thermodynamic properties of a protein-like model, The purpose of this paper is to elucidate the geometrical factor, which affects the kinet ic and thermodynamic properties of RNA-like heteropolymers, and physic al reasons for this phenomenon. Results: It is shown that increasing t he strength of long-range contacts can accelerate the finding of the n ative secondary structure for RNA-like heteropolymers. Decreasing the strength of long-range contacts results in deceleration of this proces s, The physical reason for this phenomenon is the increase in the aver age energy of non-native structures and, as a consequence, the increas e (in absolute value) of the relative value of native energy from stre ngthening long-range contacts under constant energy of the native stat e, Statistical analysis of natural RNAs has shown that the mean stabil ity of helices formed by the pairing of regions that are remote along the chain prevails over the mean stability of helices formed by region s that are close along the chain. Conclusions: The kinetics simulation s suggest that the folding of the RNA secondary structure depends on t he structural factors of the native state. One of these factors accele rating large RNA folding is the existence of strong long-range helices in the native secondary structure.