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. 2020 Dec 1;76(Pt 12):1159-1166.
doi: 10.1107/S2059798320013534. Epub 2020 Nov 24.

Arginine off-kilter: guanidinium is not as planar as restraints denote

Nigel W Moriarty  1 , Dorothee Liebschner  1 , Dale E Tronrud  2 , Paul D Adams  1
Affiliations

Arginine off-kilter: guanidinium is not as planar as restraints denote

Nigel W Moriarty et al. Acta Crystallogr D Struct Biol. .

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.

Keywords: arginine; chemical restraints; guanidine; macromolecular refinement; planarity.

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Figures

Figure 1
Figure 1
Diagram of the guanidinium moiety that terminates the side chain of arginine, including a schematic representation of the T1 and T2 torsion angles.
Figure 2
Figure 2
The Cδ atom can deviate significantly from the guanidinium plane in arginine. Three views of arginine (Arg242) in PDB entry 2xfr (0.97 Å resolution). Light blue, 2mF obs − DF model map at 1 r.m.s. contour. Orange, 2mF obs − DF model map at 5 r.m.s. contour. The locations of the Cα and Cβ atoms are shown with lines.
Figure 3
Figure 3
Bond-length and angle r.m.s.d. values averaged in 0.1 Å resolution bins. Refinements with standard arginine restraints are plotted using green lines and flexible restraints are shown in orange. The r.m.s.d. values for the whole model are shown as dashed lines, while the arginine-only r.m.s.d. values are shown as solid lines. The inset shows the number of refinements in each resolution bin.
Figure 4
Figure 4
Values of the Cδ—N∊—Cζ—Nη1 torsion angle for the standard restraints (green) and flexible restraints (orange) in 0.1 Å resolution bins.
Figure 5
Figure 5
Planar r.m.s.d. (a, c) and r.m.s.Z (b, d) values for Cδ and N∊ atoms in the guanidinium moiety averaged in 0.1 Å resolution bins. Refinements using the standard restraints are shown as green lines, while orange lines denote the flexible restraints. Atom Cδ is shown in (a) and (b) and atom N∊ is shown in (c) and (d). The e.s.d. for Cδ is shown for the standard (0.020 Å) and flexible (0.095 Å) restraints for reference. The lower row is on the same scale as the upper graphs.
Figure 6
Figure 6
Planar r.m.s.d. (a, c) and r.m.s.Z (b, d) values for Nη1 and Nη2 atoms in the guanidinium moiety averaged in 0.1 Å resolution bins. Refinements using the standard restraints are shown as green lines, while orange lines denote the flexible restraints. Atom Nη1 is shown in (a) and (b) and atom Nη2 is shown in (c) and (d). The lower row is on the same scale as the upper graphs.
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References

    1. Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352–367. - PMC - PubMed
    1. Berkholz, D. S., Krenesky, P. B., Davidson, J. R. & Karplus, P. A. (2010). Nucleic Acids Res. 38, D320–D325. - PMC - PubMed
    1. Beyer, H. (1981). Biom. J. 23, 413–414.
    1. Brünger, A. T. (1992). X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. New Haven: Yale University Press.
    1. Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389–397. - PubMed