[AMBER] NMR chemical shift restraints for an intrinsically disordered peptide

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Thu, 23 Jun 2011 12:32:06 +0300

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 Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece
email: tevang.bioacademy.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Jun 23 2011 - 03:00:03 PDT
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