Resonance was to be understood exactly as meaning all the bonds are
averaged between both types (single and double bonds).
Furthermore, fluctuations in the immediate environment will affect
electron distribution with time, as proteins exist in a dynamic state.
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 19:27, Andrew Purkiss wrote:
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
