Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 Å resolution as a first test case

Abstract

The number of protein structures re®ned at a resolution higher than 1.0 A Ê is continuously increasing. Subatomic structures may deserve a more sophisticated model than the spherical atomic electron density. In very high resolution structural studies (d < 0.5 A Ê ) of small peptides, a multipolar atom model is used to describe the valence electron density. This allows a much more accurate determination of the anisotropic thermal displacement parameters and the estimate of atomic charges. This information is of paramount importance in the understanding of biological processes involving enzymes and metalloproteins. The structure of the scorpion Androctonus australis Hector toxin II has been re®ned at 0.96 A Ê resolution using synchrotron diffraction data collected at room temperature. Re®nement with a multipolar electron-density model in which the multipole populations are transferred from previous peptide studies led to the observation of valence electrons on covalent bonds of the most ordered residues. The re®ned net charges of the peptide-bond atoms were of the correct sign but were underestimated. Such protein-structure re®nements against higher resolution data collected at cryogenic temperature will enable the calculation of experimental atomic charges and properties such as electrostatic potentials.

Aspherical-atom scattering factors from molecular wave functions. 1. Transferability and conformation dependence of atomic electron densities of peptides within the multipole formalism

“…Efforts have been made toward aspherical-atom re®nement using the limited model. The study on the scorpion Androctonus australis Hector toxin II (room-temperature data of 0.96 A Ê resolution) also revealed bonding effects, but led to an underestimation of the net charges on the peptide-bond atoms (Housset et al, 2000). In the case of the protein crambin (0.54 A Ê resolution, low-temperature data), the re®nement resulted in multipole parameters within 25% of those from the transferable database but lower bonding features than predicted by the database (Ferna  ndez-Serra et al, 2000).…”

The active site of hen egg-white lysozyme: flexibility and chemical bonding

“…Electron densities based on multipole models of proteins have previously been considered for crambin Schmidt et al, 2011), human aldose reductase (Guillot et al, 2008) and trypsin (Schmidt et al, 2003). Multipole parameters have been refined in these cases, whereas for scorpion toxin (Housset et al, 2000) a multipole model was developed with multipole parameters fixed to database values. A similar approach was used for a series of neuraminidase-inhibitor complexes (Dominiak et al, 2009).…”

The Crystal Structure of a Novel, Inactive, Lysine 49 PLA2 from Agkistrodon acutus Venom

“…Recently, however, it has been demonstrated that charge density refinement for biological macromolecules can also be carried out if the diffraction resolution is high enough and if the atomic thermal motion is sufficiently low. For example, the application of charge density refinement to the structure of a scorpion protein at 0.96-Å resolution showed visible bonding density between some main-chain atoms (21). The best example of charge density analysis applied to biological macromolecules, however, is provided by exhaustive refinement, at the ultrahigh resolution of 0.54 Å, of the valence electron distribution in crambin, a small protein with 46 residues (22).…”