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
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
Yes, the two arginines are from two different models. One has the antibody and
the other one the ligand. But if you imagine that both are bound to the
receptor, asp still can't be entrapped between the arginines.
And if the asp was entrapped between the two arginine it would also mean that
the
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 io
Jan,
Ionic interaction does reduce the charges born by the partners in isolation.
This is why charged residues found in the protein core are always paired.
Furthermore, concerning arg, beyond the fact that they are found to
autointeract as Andrey pointed out, the charge they bear is spread over
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
Thanks for your responses,
Andrey, I had no idea about these arginine associations. In this case
the arginines are facing each other guanidinium to guanidinium. I
guess they wouldn't attract. Nadir, the asp is not entrapped between
the two arginines. But Hermann is probably right by saying that th
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) "U
a significant drop in
affinity which may explain the effect of the antibody.
Best,
Herman
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jan
van Agthoven
Gesendet: Montag, 7. Oktober 2013 22:47
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb]
endet: Montag, 7. Oktober 2013 22:47
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] repulsive effects of arginine
>
> Hi everyone,
> I'm working on structure of an antibody that inhibits a receptor. The
> antibody doesn't induce any conformational change in the receptor an
@JISCMAIL.AC.UK] Im Auftrag von Jan van
Agthoven
Gesendet: Montag, 7. Oktober 2013 22:47
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] repulsive effects of arginine
Hi everyone,
I'm working on structure of an antibody that inhibits a receptor. The antibody
doesn't induce any conformational
Hi everyone,
I'm working on structure of an antibody that inhibits a receptor. The
antibody doesn't induce any conformational change in the receptor and
doesn't bind the ligand binding site. If we superimpose the receptor
with antibody and ligand the only hindrance we find is a electrostatic
repuls
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