Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics

J Comput Aided Mol Des. 2005 May;19(5):329-40. doi: 10.1007/s10822-005-7003-0.

Abstract

The dynamical aspects of the fully hydrated TEM-1 beta-lactamase have been determined by a 5 ns 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 anchors the omega-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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Computer Simulation
  • Crystallography, X-Ray
  • Enzyme Stability
  • Hydrogen Bonding
  • Models, Molecular
  • Protein Conformation
  • Protein Structure, Tertiary
  • Protons
  • Thermodynamics
  • Water / chemistry
  • beta-Lactamases / chemistry*

Substances

  • Protons
  • Water
  • beta-Lactamases
  • beta-lactamase TEM-1