Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis

Abstract

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

Neutron scattering in the biological sciences: progress and prospects

“…The pK a of any ionizable group can be significantly influenced by the local electrostatic field generated at the site by the protein. When X-ray crystallographic data are available to ultrahigh resolution, some H atoms may be visible or their positions may be inferred from precise geometrical parameter analyses (Neumann & Tittmann, 2014), and the combination of atomicresolution X-ray crystallographic data with quantum-chemical or charge-density analysis can then provide a further level of detail on the chemical profile of the enzyme (Jelsch et al, 2000;Liebschner et al, 2009;Zarychta et al, 2015). However, even when such ultrahigh-resolution data can be obtained, a significant fraction (typically >50%) of more mobile or labile H atoms remain difficult to discern, leaving specific questions concerning catalytic mechanisms unanswered.…”

The electrostatic potential of dynamic charge densities

“…One method of analysis comprises the consideration of the ESP on a surface enveloping the molecule. In applications to small and large molecules up to proteins, the ESP has thus been used to identify electrophilic and nucleophilic sides, to characterize hydrogen bonds, and to analyse intermolecular interactions ( Dauter, 2016;Niranjana Devi et al, 2017;Sirohiwal et al, 2017;Zarychta et al, 2015;Zhurova et al, 2016).…”

On the Charge Density Refinement of Odd-Order Multipoles Invariant under Crystal Point Group Symmetry

“…Charge density studies based on ultra high-resolution X-ray diffraction data from crystals of biological macromolecules yield experimentally determined physico-chemical properties of proteins and nucleic acids [1], molecular systems often too large for simulations and quantum-mechanical calculations to be feasible or accurate [2][3][4][5]. X-ray scattering at ultra high-resolution carries information about bonding and non-bonding atomic valence electron density that departs from spherical symmetry around the nucleus, and therefore these charge density studies are based on multipolar expansions of atomic densities [6,7].…”