Thursday, March 31, 2011

Discussion of the Mulholland Paper

This is the discussion page for the Mulholland paper titled:

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the
Acylation of Wild Type and K73A Mutant TEM-1 Class A beta-Lactamase

General notes on the paper

  • The study is an ongoing project at the Mulholland group. Initial QM/MM calculations was done using AM1/CHARMM22[2] on the very same structure, later gas phase QM corrections were calculated at the B3LYP/6-31+G(d)//AM1/CHARMM22 level of theory[3]. The presented paper, discuss the application of MP2 and SCS-MP2 in the QM region in the field of the MM charges.

  • The structure used in this study is generated by using a mutated (E166N) beta-Lactamase structure (PDB: 1FQG) because of its resolution. The structure preparation was discussed in the 2005 paper by the same group [3]. To obtain the wild type, a single mutation was made based on a lower resolution structure. Hydrogens were added and the whole thing was solvated using a huge sphere (26 Å in radius) of pre-equilibrated water (see discussion below). Once a satisfactory initial structure was obtained, minimization of water, then crystal structure was carried out. Finally, a total of 3284 atoms was obtained (56 QM atoms and 3228 MM atoms) centered around the hydroxylic oxygen on Ser70.

  • As a result, a potential energy barrier is generated based on two reaction coordinates (again, see discussion below). The authors do note, that entropy, thermal and zero-point vibration corrections are for direct comparison to experiment.

Topics of (intense) discussion:

  • Reaction Coordinates: Of the two reaction coordinates used in this study, one of them, Ryz, involved three distances. This could lead to multiple geometries having the same distance parameter. There is no mention in the paper about how this is circumvented albeit the figures looks like everything went fine.
  • To be fixed, or not to be: There is no clear information about how much water and structure is fixed beyond the 18 Å radius during the minimization of the water and/or protein structure. In the 2005 paper, the generation of the structure is explained as "... truncated, by deleting every water molecule and residue, which did not have a heavy atom within 18 Å of the reaction center", where as the later 2009 paper, the statement is "Every atom further than 18 Å away was held fixed". The implications of this, is either a thin shell at a distance 18 Å away or an 8 Å thick water shell around the entire complex.
  • You cannot trust the barrier: As the authors mention themselves, one should add vibrational corrections as well as entropy effects. At least, to confirm the results, another snapshot of the geometry should be made (including all the steps as was done to prepare the structure).

[1] Hermann et al, J. Phys. Chem. A, 2009, 113, 11984
[2] Hermann et al, J. Am. Chem. Soc. 2003, 125, 9590
[3] Hermann et al, J. Am. Chem. Soc. 2005, 127, 4454
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