On `globbicity' of low-resolution protein structures

Abstract

Using Harker's [Harker (1953). Acta Cryst. 6, 731±736] idea of spherically averaged polyatomic groups or`globs' as the units of structure suitable for analyzing low-resolution diffraction data from protein crystals,`globbic' scattering factors have been calculated for main-chain peptide units and amino-acid side-chain groups to 3 A Ê resolution via Debye's [Debye (1915). Ann. Phys. (Leipzig), 46, 809±823] scattering formula. It is shown that the scattering factors are insensitive to intra-globbic conformational variation and can be approximated fairly well by a single-Gaussian formula, i.e. f g (s) = Z g exp(À1.7Z g s 2 ), where s = (sin)/! and Z g is the total electron count for the atoms of the glob. Phase errors due to the globbic approximation and their effect on electrondensity maps at 3.5 A Ê resolution have been assessed via calculations for the crambin structure; this analysis indicates that the globbic scattering factors will be useful in efforts to develop procedures for direct-methods phasing of diffraction data to $3.5 A Ê resolution from protein crystals.

Hierarchical description of protein structure fragments obtained from analyses of promolecular electron density distributions

“…At the particular value of t = 1.5 bohr 2 , fragments are similar to the groups of atoms used by Guo et al [5] in their globbic description of a protein structure. An interest of such decomposition results lies in the possible link with ED map interpretation programs based on the use of protein fragments databases.…”

“…MoPro implements spherical and multipolar atomic models, and combines methods usually applied both in biological macromolecules and in small compounds crystallography fields. We will also present some applications of these methods to several macromolecular systems, including 0.66Å resolution Human Aldose Reductase [3,4] and 0.62Å resolution RD1 Antifreeze protein [5]. A theoretical method applied to describe protein structures in terms of hierarchically related substructures is presented [1].…”

Topological Analysis of Proteins as Derived from Medium and High‐resolution Electron Density: Applications to Electrostatic Properties

“…For the lower-resolution structures the density maxima often do not correspond to atomic positions but should rather be associated with atomic groups. For example, at @3-Å resolution, we and others have shown that for protein crystallography there is a correspondence between ED peaks and the backbone or side-chain atoms of the amino acid residues [1][2][3]. For example, Guo et al [2] showed that 3-Å resolution ED distributions could be reconstructed from structure factors generated by residue centers.…”

Symbolic Addition in Protein Electron Crystallography – a Method for Finding Projected Helices

“…The scale of this phasing procedure can vary greatly, from simulation of the overall protein mass distribution (Andersson & Hovm611er, 1996) to generalized scattering factors for amino acid segments (Guo et al, 1995). In electron crystallography, it has been observed that the projection of a helical column might also be treated as a pseudoatomic glob (Dorset, 1997a).…”