Investigating energy‐based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1

Abstract

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates.

Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State

“…Previous studies have shown that presenting an ensemble of molecular conformations, which adhere to certain experimental constraints, provides a means to characterize the inherent flexibility of biomolecules that cannot be achieved by simply examining the conformation for a single structure. , Especially for RNA aptamers in the absence of ligand, it has been shown that, although the stem structures are generally stable, the single-stranded bulges and loop regions, including ligand binding sites, exist as an ensemble of conformations lacking defined structures . Thus, the determination of an ensemble of conformations for the apo state, rather than a single structure, is a promising approach to characterize the structure of an apo aptamer.…”