6 research outputs found
Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method
The challenge in protein structure prediction using homology
modeling
is the lack of reliable methods to refine the low resolution homology
models. Unconstrained all-atom molecular dynamics (MD) does not serve
well for structure refinement due to its limited conformational search.
We have developed and tested the constrained MD method, based on the
generalized NewtonâEuler inverse mass operator (GNEIMO) algorithm
for protein structure refinement. In this method, the high-frequency
degrees of freedom are replaced with hard holonomic constraints and
a protein is modeled as a collection of rigid body clusters connected
by flexible torsional hinges. This allows larger integration time
steps and enhances the conformational search space. In this work,
we have demonstrated the use of torsional GNEIMO method without using
any experimental data as constraints, for protein structure refinement
starting from low-resolution decoy sets derived from homology methods.
In the eight proteins with three decoys for each, we observed an improvement
of âŒ2 Ă
in the rmsd in coordinates to the known experimental
structures of these proteins. The GNEIMO trajectories also showed
enrichment in the population density of native-like conformations.
In addition, we demonstrated structural refinement using a âfreeze
and thawâ clustering scheme with the GNEIMO framework as a
viable tool for enhancing localized conformational search. We have
derived a robust protocol based on the GNEIMO replica exchange method
for protein structure refinement that can be readily extended to other
proteins and possibly applicable for high throughput protein structure
refinement
Chimeric Cyanovirin-MPER Recombinantly Engineered Proteins Cause Cell-Free Virolysis of HIV-1
All-Atom Models of the Membrane-Spanning Domain of HIV-1 gp41 from Metadynamics
The 27-residue membrane-spanning domain (MSD) of the HIV-1 glycoprotein gp41 bears conserved sequence elements crucial to the biological function of the virus, in particular a conserved GXXXG motif and a midspan arginine. However, structure-based explanations for the roles of these and other MSD features remain unclear. Using molecular dynamics and metadynamics calculations of an all-atom, explicit solvent, and membrane-anchored model, we study the conformational variability of the HIV-1 gp41 MSD. We find that the MSD peptide assumes a stable tilted α-helical conformation in the membrane. However, when the side chain of the midspan Arg 694 âsnorkelsâ to the outer leaflet of the viral membrane, the MSD assumes a metastable conformation where the highly-conserved N-terminal core (between Lys681 and Arg694 and containing the GXXXG motif) unfolds. In contrast, when the Arg694 side chain snorkels to the inner leaflet, the MSD peptide assumes a metastable conformation consistent with experimental observations where the peptide kinks at Phe697 to facilitate Arg694 snorkeling. Both of these models suggest specific ways that gp41 may destabilize viral membrane, priming the virus for fusion with a target cell