The dynamical aspects of the fully hydrated TEM-1 β-lactamase have been determined by a 5ns Molecular Dynamics simulation. Starting from the crystallographic coordinates, the protein shows a relaxation in water with an overall root mean square deviation from the crystal structure increasing up to 0.17 nm, within the first nanosecond. Then a plateau is reached and the molecule fluctuates around an equilibrium conformation. The results obtained in the first nanosecond are in agreement with those of a previous simulation (Diaz et al., J. Am. Chem. Soc., (2003) 125, 672-684). The successive equilibrium conformation in solution shows an increased mobility characterized by the following aspects. A flap-like translational motion anchores the Ω-loop to the body of the enzyme. A relevant part of the backbone dynamics implies a rotational motion of one domain relative to the other. The water molecules in the active site can exchange with different residence times. The H-bonding networks formed by the catalytic residues are frequently interrupted by water molecules that could favour proton transfer reactions. An additional simulation, where the aspartyl dyad D214-D233 was considered fully deprotonated, shows that the active site is destabilized. © Springer 2005.
|Titolo:||Dynamical aspects of TEM-1 β-Lactamase probed by molecular dynamics|
|Autori interni:||ASCHI, MASSIMILIANO|
|Data di pubblicazione:||2005|
|Rivista:||JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN|
|Appare nelle tipologie:||1.1 Articolo in rivista|