[gmx-users] Simulating Peptides
marianski at fhi-berlin.mpg.de
Wed Jul 8 16:11:17 CEST 2015
You touch here very complicated system that requires lot of literature
research first. Few hints:
1. Amyloid-Beta (AB) is intrinsically disordered protein. The PDB you
point to is a nmr structure measured in some helix-inducing solvent and
it does not maintain the structure in water (physiological) solution.
Thus I would be reluctant to study its "unfolding" because it might
bring little of relevance to the water solution. If You want to look at
the AB free-energy landscape in water, I would suggest looking at
Pande's paper first: doi:10.1016/j.bpj.2011.12.002
2. Following from the paper, in water You face all sort of sampling
problems, thus You need to reach really long time scales to obtain any
meaningful result. Otherwise You might be biased toward some metastable
states which stability are just artifacts of poor sampling/short timescales.
3. There's no full AB plaques structure (as far as I am aware), just its
hydrophobic part (vide PDB 2beg (mono), 2lmn (di) and 2lmp (tri)). You
will probably find some refs in under this pdb's.
On 07/08/2015 03:35 PM, su wrote:
> I am going to simulate the Unfolding process of Amyloid beta peptide (PDB ID 1IYT) and the fibrillar structure as well, Alone and with ligands. Can anyone suggest a good tutorial or reference article for the same? For the papers that i studies, none has explained the MD process.
> Sent from my iPhone
Mateusz Marianski, PhD
email: marianski at fhi-berlin.mpg.de
14195 Berlin, Germany
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