Thermal Motions of the E. coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations

Abstract

The E. coli glucose-galactose chemosensory receptor is a 309 residue, 32 kDa protein consisting of two distinct structural domains. We used two computational methods to examine 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. We primarily 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 all-atom molecular dynamics (MD) simulation. Both LBMC and MD simulations were performed using both the apo and glucose-bound form of the protein, with LBMC exhibiting significantly larger fluctuations. The LBMC simulations are in general agreement with the disulfide trapping experiments of Careaga & Falke (J. Mol. Biol., 1992, Vol. 226, 1219-35), 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 experimental rate constants. Nevertheless, we believe that our semi-atomistic approach could be used to study fluctuations in other proteins, perhaps for ensemble docking or other analyses of protein flexibility in virtual screening studies.

Carbohydrate Affinity for the Glucose–Galactose Binding Protein Is Regulated by Allosteric Domain Motions

“…Collective motions would have to occur with correlation times between 10 –4 s and 10 –8 s since the molecular alignment tensor (derived from RDC data) differs significantly from the rotational diffusion tensor (derived from NMR relaxation data) while order parameters S 2 are not significantly reduced. This is consistent with recent semiatomistic molecular simulations . Upon glucose binding, a general decrease in S 2 is observed that proves such hinge motions persist in holo GGBP, however, on a faster nanosecond time scale (≤12 ns).…”

“…This is consistent with recent semiatomistic molecular simulations. 56 Upon glucose binding, a general decrease in S 2 is observed that proves such hinge motions persist in holoGGBP, however, on a faster nanosecond time scale (≤12 ns). The neat entropic contribution found reflects an increase in dynamics that shall be attributed to coupled motions between the two domains.…”

Tunable, Mixed-Resolution Modeling Using Library-Based Monte Carlo and Graphics Processing Units

“…Thus, all protein atomic positions are tracked in the present LBMC implementation, unlike in our previous LBMC protein simulations. 34,36 …”

“…Library approaches can offer tremendous efficiency for small, implicitly solvated peptides, 35,38–40 and also great flexibility in constructing and sampling protein models. 34,36,37 Memory can also be exploited in molecular simulations by tabulating interactions among molecules or fragments, which can speed up calculations and smooth interactions. 41 …”

“…Library approaches can offer tremendous efficiency for small, implicitly solvated peptides 35,38−40 sampling protein models. 34,36,37 Memory can also be exploited in molecular simulations by tabulating interactions among molecules or fragments, which can speed up calculations and smooth interactions. 41 Here, we report the application of memory-intensive librarybased computing to construct mixed-resolution models of proteins.…”