An example of pi-pi stacking of the guanidinium groups, can be seen on a structure which I worked on; pdb-code: 2x2u. Look at the interactions between Arg 77 and its symmetry mate, with Arg 144 (and symmetry copy) flanking, giving rise to a stack of 4 Arginine guanidinium groups, with a sulphate ion neutralising the environment.
Such pi-pi stacking is also commonly seen with Tyrosine and Phenylalanine, with cation-pi interactions also common (e.g. Lys NZ to the planar side of Phe). Resonance is not really a correct description of these delocalised pi-orbitals; as there are no single and double bonds, but all the bonds are an average of both types. Additionally, remember that the Arginine(s) may not actually be charged, as the local environment of ionic sidechains can move the pKa value(s) a long way from the expected value for an isolated sidechain, with the pH of the crystallisation condition also potentially affecting what is charged. Andrew Purkiss. On Tue, 2013-10-08 at 18:34 +0200, Nadir T. Mrabet wrote: > Yes, indeed Andrey. > And this results from resonance (tautomerization) of the guanidinium group. > > Regards, > > Nadir Mrabet > > Pr. Nadir T. Mrabet > Structural & Molecular Biochemistry > N-gere - INSERM U-954 > University of Lorraine, Nancy > School of Sciences and Technologies > & School of Medicine > 9, Avenue de la Foret de Haye, BP 184 > 54505 Vandoeuvre-les-Nancy Cedex > France > Phone: +33 (0)3.83.68.32.73 > Fax: +33 (0)3.83.68.32.79 > E-mail: Nadir.Mrabet <at> univ-lorraine.fr > > On 08/10/2013 18:01, Andrey Feklistov wrote: > > Hi Jan, > > > > please note, Arg-Arg proximity is not always repulsive: guanidinium groups > > can associate bridged by H-bonds and interactions with water molecules or > > neighboring amino acids. There are many examples of these unusual Arg > > formations, see for reference: > > > > Neves, Yeager and Abagyan (2012) "Unusual Arginine Formations in Protein > > Function and Assembly: Rings, Strings and Stacks", J. Phys. Chem. B 116, > > 7006−7013 > > > > Hope this is helpful, > > > > Andrey > > -- Andrew Purkiss X-ray Laboratory London Research Institute Cancer Research UK
