Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.
In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.
Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
Maura
M
Malinska
Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
Zbigniew
Z
Dauter
D000818:Animals; D002417:Cattle; D018360:Crystallography, X-Ray / Q000379:methods*; D043542:DNA, Z-Form / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D055672:Static Electricity; D014357:Trypsin / Q000737:chemistry*; D014965:X-Rays
D043542:DNA, Z-Form; D009842:Oligopeptides; D014357:Trypsin
electrostatic potential; high-resolution X-ray crystal structures; interaction energy; spherical atom model; transferable aspherical atom model