[gmx-users] Simulating Peptides

Mateusz Marianski marianski at fhi-berlin.mpg.de
Wed Jul 8 16:11:17 CEST 2015

Hi Suniba,

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:
> Hello
> 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.
> Regards
> Suniba
> Sent from my iPhone

Mateusz Marianski, PhD
email:          marianski at fhi-berlin.mpg.de
phone:                     +49-30-8413-4849
der Max-Planck-Gesellschaft
Faradayweg 4-6
14195 Berlin, Germany

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