Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks

Abstract

Protein-protein interfaces are often stabilized by a small number of dominant contacts, exemplified by the overrepresentation of arginine residues at oligomerization interfaces. Positively charged arginines are most commonly involved in ion pairs of opposite charge; however, previous work of Scheraga and coworkers described the stable, close range interaction between guanidinium pairs in a solvated environment. To extend this work, we searched over 70 thousand protein structures and complexes for unusual formations of arginine residues supported by the electron density. Symmetry transformations were used to generate full assemblies. Clusters of four to eight arginine residues with Cζ-Cζ distances < 5 Å, organized as rings with 4 to 8 members, stacks of two arginines, and strings of stacked arginines, are commonly located at the interfaces of oligomeric proteins. The positive charge is properly balanced by negatively charged counter ions in about 90% of the cases. We also observed planar stacking of guanidinium groups, bridged by hydrogen bonds and interactions with water molecules. The guanidinium groups are commonly involved in 5 hydrogen bonds with water molecules and acceptor groups from surrounding amino acids. Water molecules have a bridging effect on the arginine pairs, but in some cases small molecular weight chemicals in the crystallization buffer may be misinterpreted as water molecules. In summary, despite electrostatic repulsion, arginines do form various clusters that are exposed to interact with and potentially be controlled or switched by charged metabolites, membrane lipids, nucleic acids or side chains of other proteins. Control of the stability of arginine clusters may play an important role in protein-protein oligomerization, molecular recognition and ligand binding.

Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors

“…Instead, R1948 of the mutant kinase reorients toward the ATP binding site, forming an unusual ion-pair with R2032 that restricts P-loop flexibility. This interaction, although uncommon, has also been observed in other proteins as a stabilizing factor (26)(27)(28).…”

The Mitochondrial Fission Receptor MiD51 Requires ADP as a Cofactor

“…The interface is largely composed of electrostatic interactions between charged residues from a loop, and the interface has a buried surface area of 1,184.1 Å 2 (Figure 3B). Additionally, the guanidinium groups from a pair of Arg169 residues from α-helix number 2 adopt a planar stacking conformation (Neves et al, 2012), and their interaction is bridged through hydrogen bonds with a sulfate group. The interaction surface of MiD51 is distinct from that of other NTase family members known to dimerize.…”

Application of GPCR Structures for Modelling of Free Fatty Acid Receptors

“…Although this is the first arginine pairing observed in GPCRs, arginine-arginine short-range interactions are found in many other proteins, where these residues are involved in binding of nucleotides, organic acids and other negatively charged bioactive molecules. From analysis of 67,520 crystal structures containing clusters of positively charged arginines, Neves and colleagues (Neves et al 2012) demonstrated that guanidium groups tend to sit in polar pockets or are exposed to solvent. In a much earlier study, computer simulations of Magalhaes and colleagues (Magalhaes et al 1994) have predicted the importance of solvent environment for arginine pairing.…”