A comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large molecules

Abstract

The differences between two databases describing the polypeptide main chain in terms of charge-density parameters, directly usable in protein structure refinements, are discussed. These databases contain averaged multipole populations of peptide pseudo-atoms obtained from refinement against theoretical simulated data and against high-resolution experimental data on small peptide or amino acid molecules. The main discrepancy becomes apparent when electrostatic properties are calculated.

A Theoretical Databank of Transferable Aspherical Atoms and Its Application to Electrostatic Interaction Energy Calculations of Macromolecules

“…2 Its merits relative to the experimental databank pioneered by Pichon-Pesme et al 3 have been the subject of a previous discussion. 4,5 In a more recent article, the databank has been used to evaluate the electrostatic component of the interaction between fragments of the antibiotic vancomycin and substrate molecules, with the nonelectrostatic contribution evaluated with perturbationtheory-based pairwise atom-atom potentials. 6 The databank may be compared with the invariom approach, pursued by Dittrich and co-workers, in which aspherical atoms are defined by one atom in an as close as possible bonding environment.…”

Response to the paperA comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large molecules, by Pichon-Pesme, Jelsch, Guillot & Lecomte (2004)

“…However, the performance of the theoretical databank has been veri®ed by the thorough comparison with extensive density functional calculations. On the other hand, while the original PJGL databank dates back as far as 1995 and (as stated) is now complete, to our knowledge, no such studies using the experimental databank have been published yet, with the exception of some deformation density maps (Pichon-Pesme et al, 1995;Jelsch et al, 2000) and several two-dimensional maps of the electrostatic potential (Muzet et al, 2003;Pichon-Pesme et al, 2004). In practice, the latter can be reasonably well predicted even by the point-charge model (Williams, 1988;Breneman & Wilberg, 1990).…”

“…A paper was recently published in Acta Crystallographica Section A by Pichon-Pesme et al (2004), called PJGL in the following, that deals with the comparison of the experimental databank of aspherical pseudoatom parameters developed by those authors with the relatively new theoretical approach reported recently by us (Koritsanszky et al, 2002).…”

High-resolution crystallography and drug design

“…software MOPRO Pichon-Pesme et al, 2004). He described applications to aldose reductase, showed how the electrostatic potential derived from the multipolar model fits theoretical calculations using quantum mechanics, and explained the characteristics of ligand binding.…”