22 research outputs found
Steady-state simulations using weighted ensemble path sampling
We extend the weighted ensemble (WE) path sampling method to perform rigorous
statistical sampling for systems at steady state. The straightforward
steady-state implementation of WE is directly practical for simple landscapes,
but not when significant metastable intermediates states are present. We
therefore develop an enhanced WE scheme, building on existing ideas, which
accelerates attainment of steady state in complex systems. We apply both WE
approaches to several model systems confirming their correctness and efficiency
by comparison with brute-force results. The enhanced version is significantly
faster than the brute force and straightforward WE for systems with WE bins
that accurately reflect the reaction coordinate(s). The new WE methods can also
be applied to equilibrium sampling, since equilibrium is a steady state
Thermal Motions of the E. Coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations
The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa
protein consisting of two distinct structural domains. In this computational
study, we studied the protein's thermal fluctuations, including both the large
scale interdomain movements that contribute to the receptor's mechanism of
action, as well as smaller scale motions, using two different computational
methods. We employ extremely fast, "semi-atomistic" Library-Based Monte Carlo
(LBMC) simulations, which include all backbone atoms but "implicit" side
chains. Our results were compared with previous experiments and an all-atom
Langevin dynamics simulation. Both LBMC and Langevin dynamics simulations were
performed using both the apo and glucose-bound form of the protein, with LBMC
exhibiting significantly larger fluctuations. The LBMC simulations are also in
general agreement with the disulfide trapping experiments of Careaga & Falke
(JMB, 1992; Biophys. J., 1992), which indicate that distant residues in the
crystal structure (i.e. beta carbons separated by 10 to 20 angstroms) form
spontaneous transient contacts in solution. Our simulations illustrate several
possible "mechanisms" (configurational pathways) for these fluctuations. We
also observe several discrepancies between our calculations and experiment.
Nevertheless, we believe that our semi-atomistic approach could be used to
study the fluctuations in other proteins, perhaps for ensemble docking, or
other analyses of protein flexibility in virtual screening studies.Comment: 23 pages, 4 figures, 2 table
Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1
AbstractSodium coupled cotransporters of the five-helix inverted repeat (5HIR) superfamily use an alternating access mechanism to transport a myriad of small molecules across the cell membrane. One of the primary steps in this mechanism is the conformational transition from a state poised to bind extracellular substrates to a state that is competent to deliver substrate to the cytoplasm. Here, we construct a coarse-grained model of the 5HIR benzylhydantoin transporter Mhp1 that incorporates experimental structures of the outward- and inward-open states to investigate the mechanism of this conformational change. Using the weighted ensemble path-sampling method, we rigorously sample the outward- to inward-facing transition path ensemble. The transition path ensemble reveals a heterogeneous set of pathways connecting the two states and identifies two modes of transport: one consistent with a strict alternating access mechanism and another where decoupling of the inner and outer gates causes the transient formation of a continuous permeation pathway through the transporter. We also show that the conformational switch between the outward- and inward-open states results from rigid body motions of the hash motif relative to the substrate bundle, supporting the rocking bundle hypothesis. Finally, our methodology provides the groundwork for more chemically detailed investigations of the alternating mechanism