Comparison between self-guided langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

This article presents a comparative analysis of two replica-exchange simulation methods for the structure refinement of protein loop conformations, starting from low-resolution predictions. The methods are self-guided Langevin dynamics (SGLD) and molecular dynamics (MD) with a Nosé-Hoover thermostat. We investigated a small dataset of 8- and 12-residue loops, with the shorter loops placed initially from a coarse-grained lattice model and the longer loops from an enumeration assembly method (the Loopy program). The CHARMM22 + CMAP force field with a generalized Born implicit solvent model (molecular-surface parameterized GBSW2) was used to explore conformational space. We also assessed two empirical scoring methods to detect nativelike conformations from decoys: the all-atom distance-scaled ideal-gas reference state (DFIRE-AA) statistical potential and the Rosetta energy function. Among the eight-residue loop targets, SGLD out performed MD in all cases, with a median of 0.48 Å reduction in global root-mean-square deviation (RMSD) of the loop backbone coordinates from the native structure. Among the more challenging 12-residue loop targets, SGLD improved the prediction accuracy over MD by a median of 1.31 Å, representing a substantial improvement. The overall median RMSD for SGLD simulations of 12-residue loops was 0.91 Å, yielding refinement of a median 2.70 Å from initial loop placement. Results from DFIRE-AA and the Rosetta model applied to rescoring conformations failed to improve the overall detection calculated from the CHARMM force field. We illustrate the advantage of SGLD over the MD simulation model by presenting potential-energy landscapes for several loop predictions. Our results demonstrate that SGLD significantly outperforms traditional MD in the generation and populating of nativelike loop conformations and that the CHARMM force field performs comparably to other empirical force fields in identifying these conformations from the resulting ensembles.