In 3U9C we observed even 6 arginines (residues A278, A280 and A306
plus symmetry mates of chain B) mediating a crystalline contact by
pi/pi stacking. We called this motif an "arginine zipper"
(see Fig. 5 in dx.doi.org/10.1107/S0907444912016587).
Karsten Niefind
> 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
>
--------------------------------
Karsten Niefind, PhD
University of Cologne
Department of Chemistry
Institute of Biochemisty
Otto-Fischer-Str. 12-14
D-50674 Cologne
Tel.: +49 (0)221 4706444
Fax: +49 (0)221 4703244
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