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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.

SUBMITTER: Cashman DJ

PROVIDER: S-EPMC3021764 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

Cashman D J DJ Mamonov A B AB Bhatt D D Zuckerman D M DM

Current topics in medicinal chemistry 20110101 2

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 ...[more]

PMID: 20939787

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Project description:Ingested galactose can enhance postexercise liver glycogen repletion when combined with glucose but effects on muscle glycogen synthesis are unknown. In this double-blind randomized study participants [7 men and 2 women; V̇o2max: 51.1 (8.7) mL·kg-1·min-1] completed three trials of exhaustive cycling exercise followed by a 4-h recovery period, during which carbohydrates were ingested at the rate of 1.2 g·kg-1·h-1 comprising glucose (GLU), galactose (GAL) or galactose + glucose (GAL + GLU; 1:2 ratio). The increase in vastus lateralis skeletal-muscle glycogen concentration during recovery was higher with GLU relative to GAL + GLU [contrast: +50 mmol·(kg DM)-1; 95%CL 10, 89; P = 0.021] and GAL [+46 mmol·(kg DM)-1; 95%CL 8, 84; P = 0.024] with no difference between GAL + GLU and GAL [-3 mmol·(kg DM)-1; 95%CL -44, 37; P = 0.843]. Plasma glucose concentration in GLU was not significantly different vs. GAL + GLU (+ 0.41 mmol·L-1; 95%CL 0.13, 0.94) but was significantly lower than GAL (-0.75 mmol·L-1; 95%CL -1.34, -0.17) and also lower in GAL vs. GAL + GLU (-1.16 mmol·-1; 95%CL -1.80, -0.53). Plasma insulin was higher in GLU + GAL and GLU compared with GAL but not different between GLU + GAL and GLU. Plasma galactose concentration was higher in GAL compared with GLU (3.35 mmol·L-1; 95%CL 3.07, 3.63) and GAL + GLU (3.22 mmol·L-1; 95%CL 3.54, 2.90) with no difference between GLU + GAL (0.13 mmol·L-1; 95%CL -0.11, 0.37) and GLU. Compared with galactose or a galactose + glucose blend, glucose feeding was more effective in postexercise muscle glycogen synthesis. Comparable muscle glycogen synthesis was observed with galactose-glucose coingestion and exclusive galactose-only ingestion.NEW & NOTEWORTHY Postexercise galactose-glucose coingestion or exclusive galactose-only ingestion resulted in a lower rate of skeletal-muscle glycogen replenishment compared with exclusive glucose-only ingestion. Comparable muscle glycogen synthesis was observed with galactose-glucose coingestion and exclusive galactose-only ingestion.

Dataset Information

Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

Publications

Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

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