Abstract
Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been shown that the geometry in refined structures can differ significantly from that present in libraries; for example, it was recently reported that the guanidinium moiety in arginine is not symmetric. In this work, the asymmetry of the Nϵ-Cζ-Nη1 and Nϵ-Cζ-Nη2 valence angles in the guanidinium moiety is confirmed. In addition, it was found that the Cδ atom can deviate significantly (more than 20°) from the guanidinium plane. This requires the relaxation of the planar restraint for the Cδ atom, as it otherwise causes the other atoms in the group to compensate by distorting the guanidinium core plane. A new set of restraints for the arginine side chain have therefore been formulated, and are available in the software package Phenix, that take into account the asymmetry of the group and the planar deviation of the Cδ atom. This is an example of the need to regularly revisit the geometric restraint libraries used in macromolecular refinement so that they reflect the best knowledge of the structural chemistry of their components available at the time.
Highlights
With 12 side-chain atoms and a molecular weight of about 174 Da, arginine is one of the largest standard amino acids
As the process of manually examining the extrema and removing unreliable entries from the result list is not tractable, a statistically robust outlier-rejection method using the interquartile range, Tukey’s fences (Beyer, 1981), was applied to the torsion angles C—N"—C—N1 (T1), C—N"—C—N2 (T2) and T1 À T2
To analyse the planarity of the guanidinium group, we examined the torsion angles T1 (C—N"—C—N1) and T2 (C—N"—C—N2)
Summary
With 12 side-chain atoms and a molecular weight of about 174 Da, arginine is one of the largest standard amino acids. As the guanidinium group is hydrophilic, arginine residues are often located on the surface of the protein, so that the side chain can point towards solvent and form hydrogen bonds. Arginine is very flexible: it has four angles (C –C , C –C , C –C and C–N") that yield 60 allowed rotameric configurations (Hintze et al, 2016). This inherent flexibility and the fact that arginine is frequently located on the surface, where it is not sterically confined by neighbouring residues, often causes the density in crystallographic Fourier maps to be partly or completely missing for many atoms of the side chain. As a result of the typically low observation-to-parameter ratio and the lack of high-resolution data in macromolecular crystallography, stereochemical restraints are required to maintain the correct geometry of arginine residues during crystallographic refinement
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