Hidden Conformation Events in DNA Base Extrusions: A Generalized-Ensemble Path Optimization and Equilibrium Simulation Study

Abstract

DNA base extrusion is a crucial component of many biomolecular processes. Elucidating how bases are selectively extruded from the interiors of double-strand DNAs is pivotal to accurately understanding and efficiently sampling this general type of conformational transitions. In this work, the on-the-path random walk (OTPRW) method, which is the first generalized ensemble sampling scheme designed for finite-temperature-string path optimizations, was improved and applied to obtain the minimum free energy path (MFEP) and the free energy profile of a classical B-DNA major-groove base extrusion pathway. Along the MFEP, an intermediate state and the corresponding transition state were located and characterized. The MFEP result suggests that a base-plane-elongation event rather than the commonly focused base-flipping event is dominant in the transition state formation portion of the pathway; and the energetic penalty at the transition state is mainly introduced by the stretching of the Watson-Crick base pair. Moreover to facilitate the essential base-plane-elongation dynamics, the surrounding environment of the flipped base needs to be intimately involved. Further taking the advantage of the extended-dynamics nature of the OTPRW Hamiltonian, an equilibrium generalized ensemble simulation was performed along the optimized path; and based on the collected samples, several base-flipping (opening) angle collective variables were evaluated. In consistence with the MFEP result, the collective variable analysis result reveals that none of these commonly employed flipping (opening) angles alone can adequately represent the base extrusion pathway, especially in the pre-transition-state portion. As further revealed by the collective variable analysis, the base-pairing partner of the extrusion target undergoes a series of in-plane rotations to facilitate the base-plane-elongation dynamics. A base-plane rotation angle is identified to be a possible reaction coordinate to represent these in-plane rotations. Notably, these in-plane rotation motions may play a pivotal role in determining the base extrusion selectivity.

Recent developments in methods for identifying reaction coordinates

“…[93–98] Some recent extensions have also been used in studies of reactive dynamics using CHIT. [46,47] For more details of these methods, we refer readers to recent reviews. [89,99]…”

Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

“…Regarding the original string method, two sampling issues are worth noting: (a) because images are independently explored, the on-the-path continuity of the environmental degrees of freedom cannot be guaranteed; (b) the CV degrees of freedom are restricted from regular MD sampling and thus it is challenging for a being-optimized path that represents an unfavorable mechanism to be switched into the correct reaction channel. To overcome these issues, we developed a generalized ensemble sampling based string path optimization method: the on-the-path random walk (OTPRW) algorithm 24,27 . In OTPRW, the CV-space pathway is represented by a set of λ -dependent functions Z ( λ ) = ( z 1 ( λ ),…, z m ( λ )), in which Z (0) = Z A and Z (1) = Z B , where the progressing parameter λ is set equal to the percentage of the on-the-path distance of the corresponding state from the starting point Z A .…”

“…Through the biasing function f m ( λ ), which can be adaptively obtained via either the metadynamics 24 or the ABF method 27 , the target system, instead of being constrained on non-communicating images, can randomly walk along the instantaneous path to collect samples for the following path optimization. Thereby, the structural continuity of the environmental degrees of freedom can be naturally ensured; notably at a joint image state between two pathways, the system can switch from an unfavorable pathway to a better reaction channel (Figure 3).…”

“…The OTPRW method has been successfully applied to the studies of the transformation between Chorismate and Prephenate 24 , where eight CVs were used, and the DNA base extrusion process 27 , where ten CVs were employed. In these studies, single-trajectory OTPRW simulations led to nicely converged MFEPs, which could be convincingly validated via the committor analysis.…”

“…In this review, we focus our discussion on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. Our review is largely based on our earlier and recent studies; these studies respectively represent early applications of the metadynamics free energy sampling method 26 and the on-the-path random walk path sampling method 24,27 on enzyme reaction systems. We hope that our presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study.…”