AMBER Archive (2003)

Subject: Re: Domain/Helix movement/MD

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Fri Jan 31 2003 - 10:52:59 CST

Dear Jian,
there's a paper on multi-nanosecond solvated MD on HIV protease in which
both the ~20-residue flaps opened. That might interest you.

Scott, Schiffer (2000): Structure 8, 1259.

All the best,

 Martin
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Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem

> Dear All,
>
> I am seeking some adivce on simulating the large domain (or Helix)
> movement on ligand binding. I tried the MD simulations with GB model for a
> few ns but the large conformational change indicated by biochemical data
> still can not be detected by the simulations. Except for the explicit
> water simulations and the high temperature MD, are there other better
> strategies?
>
> If you successfully detected the large conformational change by MD, would
> you point me to some references and share your experience?
>
> Regards,
>
> Jian Hui