Regensburg 2019 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 1: Protein structure and dynamics

BP 1.9: Vortrag

Montag, 1. April 2019, 12:15–12:30, H4

MD Simulation Studies of Protein Dynamics in Molecule-Shaped Confinement — •Timothy Wohlfromm and Michael Vogel — TU Darmstadt, Institut für Festkörperphysik, Hochschulstr. 6, 64289, Darmstadt, Germany

We report on findings regarding dynamics of the elastin-like poly-peptide (VPGVG)₅₀ and its surrounding hydration shell in confinement. An understanding of confinement effects on protein dynamics is of utmost importance to improve our still limited knowledge about protein functions in the crowded interior of cells. To isolate pure geometrical effects of the confinement on protein dynamics, we generated the pores consisting of the same type of molecules as the solvent, in our case water, but restrained in position by harmonic potentials of varying restoring forces to simulate confining surfaces with differing rigidity. Moreover, we use a pore shape which is consistent with the protein shape such that the thickness of the hydration layer is well defined. Varying the thickness of hydration layers we find that the minimal hydration level for the confined protein to show bulk behaviour is 1 g/g, defined as ratio of water mass to protein mass. We observe in spatially resolved analyses that the correlation times of water vary by more than one order of magnitude across the confinement depending on the rigidity of the pore wall. We find a correlation between the slowdown of water molecules in vicinity of the protein surface and the protein dynamics. This effect is not caused by the reduced center of mass motion of the protein in confinement, but related to internal flexibility. These results shed new light on protein-solvent couplings.