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.

No abstract uploaded!

No abstract uploaded!

No abstract uploaded!

We analyze the transport properties of a set of symmetry-breaking extensions of the ChirikovTaylor Map. The spatial and temporal asymmetries result in the loss of periodicity in momentum direction in the phase space dynamics, enabling the asymmetric diffusion which is the origin of the unidirectional motion. The simplicity of the model makes the calculation of the global dynamical properties of the system feasible both in phase space and in controlling-parameter space. We present the results of numerical experiments which show the intricate dependence of the asymmetric diffusion to the controlling parameters.