Molecular dynamics simulations of HPr under hydrostatic pressure

Biopolymers
Muriel CanaliaHans Robert Kalbitzer

Abstract

The histidine-containing protein (HPr) plays an important role in the phosphotransferase system (PTS). The deformations induced on the protein structure at high hydrostatic pressure values (4, 50, 100, 150, and 200 MPa) were previously (H. Kalbitzer, A. Görler, H. Li, P. Dubovskii, A. Hengstenberg, C. Kowolik, H. Yamada, and K. Akasaka, Protein Science 2000, Vol. 9, pp. 693-703) analyzed by NMR experiments: the nonlinear variations of the amide chemical shifts at high pressure values were supposed to arise from induced shifts in the protein conformational equilibrium. Molecular dynamics (MD) simulations are here performed, to analyze the protein internal mobility at 0.1 MPa, and to relate the nonlinear variations of chemical shifts observed at high pressure, to variations in conformational equilibrium. The global features of the protein structure are only slightly modified along the pressure. Nevertheless, the values of the Voronoi residues volumes show that the residues of alpha-helices are more compressed that those belonging to the beta-sheet. The alpha-helices are also displaying the largest internal mobility and deformation in the simulations. The nonlinearity of the 1H chemical shifts, computed from the MD simulation snap...Continue Reading

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Citations

May 7, 2009·Annual Review of Biophysics·Roger FourmeIsabella Ascone
Jan 1, 2010·Advances and Applications in Bioinformatics and Chemistry : AABC·Benjamin BardiauxThérèse E Malliavin
Aug 19, 2006·Proteins·Daniel TrzesniakWilfred F van Gunsteren

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