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The RNA folding problem: a variational problem within an adiabatic approximation
A Fernández1, B Niel, T Burastero
1Instituto de Matemática, Universidad Nacional del Sur, Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina. inmabb@criba.edu.ar
Biophysical Chemistry
|October 7, 1998
Summary
Biopolymer folding, particularly for RNA, is a rapid process. Our study reveals a least-effort principle guiding folding pathways to achieve functional conformations on biologically relevant timescales.
Area of Science:
- Biophysics
- Computational Biology
- Molecular Biology
Background:
- Biopolymer folding is rapid and robust, suggesting a coarse-grained conformational space.
- Understanding RNA folding dynamics is crucial for deciphering biological function.
Purpose of the Study:
- To develop a theoretical framework for rapid biopolymer folding.
- To identify principles governing efficient RNA folding pathways.
Main Methods:
- Derivation of a variational principle using adiabatic approximation.
- Integration of fast-relaxing molecular motions.
- Stochastic process for generating folding pathways based on a least effort principle.
Main Results:
- A least effort principle emerges, minimizing conformational entropy and maximizing base pairing.
- Base-pairing contact patterns (BPPs) treated adiabatically.
- The least-time pathway (brachistochrone) maximizes the probability distribution of folding timespans for functional RNAs.
Conclusions:
- The derived pathway explains conserved structural features of active RNA conformations.
- Folding pathways are optimized for speed and efficiency on biologically relevant timescales.
- The model provides insights into the kinetic control of biopolymer folding.