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 also 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 kinetic and thermodynamic properties of RNA-like heteropolymers, and physical reasons for this phenomenon.


RESULTS
It is shown that increasing the strength of long-range contacts can accelerate the finding of the native secondary structure for RNA-like heteropolymers. Decreasing the strength of long-range contacts results in deceleration of this process. The physical reason for this phenomenon is the increase in the average energy of non-native structures and, as a consequence, the increase (in absolute value) of the relative value of native energy from strengthening long-range contacts under constant energy of the native state. Statistical analysis of natural RNAs has shown that the mean stability of helices formed by the pairing of regions that are remote along the chain prevails over the mean stability of helices formed by regions that are close along the chain.


CONCLUSIONS
The kinetics simulations suggest that the folding of the RNA secondary structure depends on the structural factors of the native state. One of these factors accelerating large RNA folding is the existence of strong long-range helices in the native secondary structure.
Galzitskaya
O V
OV
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. ogalzit@sun.ipr.serpukhov.su
D000818:Animals; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D007700:Kinetics; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000737:chemistry; D013816:Thermodynamics
D001704:Biopolymers; D016337:RNA, Catalytic; D012336:RNA, Ribosomal, 16S; D012313:RNA