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Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations

Eric J. Sorin ^*, Young Min Rhee ^*, Bradley J. Nakatani ^* and Vijay S. Pande ^*   

Departments of ^* Chemistry, Biophysics, and Structural Biology, and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California

Correspondence: Address reprint requests to Vijay S. Pande, Asst. Professor, Dept. of Chemistry, Dept. of Structural Biology, and the SSRL85, Stanford University, Stanford, CA 94305-3080. Tel.: 650-723-3660; Fax: 650-725-0259; E-mail: pande{at}stanford.edu.

The helical hairpin is one of the most ubiquitous and elementary secondary structural motifs in nucleic acids, capable of serving functional roles and participating in long-range tertiary contacts. Yet the self-assembly of these structures has not been well-characterized at the atomic level. With this in mind, the dynamics of nucleic acid hairpin formation and disruption have been studied using a novel computational tool: large-scale, parallel, atomistic molecular dynamics simulation employing an inhomogeneous distributed computer consisting of more than 40,000 processors. Using multiple methodologies, over 500 µs of atomistic simulation time has been collected for a large ensemble of hairpins (sequence 5'-GGGC[GCAA]GCCU-3'), allowing characterization of rare events not previously observable in simulation. From uncoupled ensemble dynamics simulations in unperturbed folding conditions, we report on 1), competing pathways between the folded and unfolded regions of the conformational space; 2), observed nonnative stacking and basepairing traps; and 3), a helix unwinding-rewinding mode that is differentiated from the unfolding and folding dynamics. A heterogeneous transition state ensemble is characterized structurally through calculations of conformer-specific folding probabilities and a multiplexed replica exchange stochastic dynamics algorithm is used to derive an approximate folding landscape. A comparison between the observed folding mechanism and that of a peptide ß-hairpin analog suggests that although native topology defines the character of the folding landscape, the statistical weighting of potential folding pathways is determined by the chemical nature of the polymer.

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