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PubMed1999

Energy-level statistics in the fine conformational resolution of RNA folding dynamics.

This work is aimed at determining the energy-level statistics of the fine resolution of soft-mode dynamics warranting an adiabatically simplified structural relaxation of a folding biopolymer chain. The parameters defining the intrabasin structure relaxation are specified for RNA, so that each Watson-Crick base-pairing pattern may be treated as a quasiequilibrium ensemble of substates or torsional isomers within relevant folding time scales. The temperature-dependent threshold for energy dispersion associated with the fine structure of each superbasin is determined so as to warrant the adiabatic entrainment of the torsional dynamics.

Base Pairing↗

PubMed1998

The RNA folding problem: a variational problem within an adiabatic approximation.

Biopolymer folding is an expeditious process taking place within timescales incommensurably shorter than ergodic times. Furthermore, its robustness suggests that the process must depend on a relatively coarse level of resolution of conformation space. To account for these features while focusing on the RNA context, we derive a variational principle formulated within an adiabatic approximation obtained by integrating out fast-relaxing molecular motions. Folding pathways are generated by means of a stochastic process which begets a least effort principle reflecting a stepwise minimization of the conformational entropy cost for each folding event with concurrent maximization of the base pairing. This economy of the process is found to have kinetic consequences if we treat base-pairing contact patterns (BPPs) adiabatically, that is, as quasi-equilibrium states: the probability distribution of overall folding timespans associated to the process resolved at the BPP level is maximized at the brachistochrone or overall least-time pathway for functionally-competent RNAs. In turn, this pathway is shown to yield all the phylogenetically-conserved structural features of the active conformation within biologically-relevant timescales.

Base Sequence↗