Dear Thomas
i'm not very expert in intrinsically disordered proteinsMD but i think
that run MD simulation of an intrinsically disordered peptide using CS
restraint could be a risk.
Actually, the softwares for CS predictions (based on empirical
observations) such as SPARTA, CamShift and (personal opinion) also
SHIFTS could fail in the prediction of the CS of intrinsically
disordered proteins or peptides, because usually based with empirical
relation with folded protein structures.
So, running a MD simulation of a completely unfolded peptide with
chemical shift restraints, you could put a random bias in your
simulation.
My opinion is that the best solution is: run a quite long MD, make
cluster analysis of the different conformations and calculate the CS.
Then you can evaluate the correlation between the calculated and the
experimental CS, in my personal experience this is more meaningful
than other parameters. Some interesting works about NMR shifts and
disordered structures have been done by the Blackledge and Vendruscolo
groups.
Moreover you can see these papers about Chemical Shift and MD:
Accurate Random Coil Chemical Shifts from an Analysis of Loop Regions
in Native States of Proteins De Simone et al. JACS 2009.
Defining Conformational Ensembles of Intrinsically Disordered and
Partially Folded Proteins Directly from Chemical Shifts
Malene Ringkjøbing Jensen, Loc Salmon, Gabrielle Nodet and Martin Blackledge
Journal of the American Chemical Society
2010 132 (4), 1270-1272
D.W. Li and R. Brüschweiler, Certification of Molecular Dynamics
Trajectories with NMR Chemical Shifts , J. Phys. Chem. Letters 1,
246-248 (2010)
Jacopo
2011/6/23 Thomas Evangelidis <tevang3.gmail.com>:
> Dear Amber users,
>
> I want to simulate the dynamics of an *intrinsically disordered *peptide (40
> aa) at 298 K and 1 bar, with ff9SB-ILDN or ff99SBnmr1. I have 13CO, 13Ca,
> and 13Cb NMR chemical shift values for a homologous peptide (82% sequence
> identity, 90% sequence similarity) which all lie within the random coil
> area. Do you reckon it is worth applying chemical shift restraints taken
> from the homologue to my target peptide , or just leave the ff do its job
> and then see if the calculated chemical shifts correlate with the
> experimental? I would greatly appreciate any comments about this case.
>
> thanks in advance,
> Thomas
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tevang.bioacademy.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 23 2011 - 05:00:03 PDT
