[AMBER] simulations of proteins with 2 domains connected by a linker

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Thu, 12 Mar 2020 10:57:47 +0100

Dear all,

We are doing some explicit solvent simulations (ff14SB, SPC water model,
PBC, 250 ns till now) of different modular proteins that have 2 domains
connected by a flexible linker of 17 to 31 aminoacids. We are interested
in the structural ensemble adopted by the linker region in the presence
of the 2 domains and how it influences the relative motion of the domains.

However, in all simulations the domains colapse on each other quite fast
and get stuck, not much inter domain motion happening after the colapse.

Does any of you have experience with such systems and if yes, could you
share this experience ? Is this behavior we observe expected ? Is it
dependent on the force field , water model or other parameters ?

Thanks for any advice

Best wishes

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Thu Mar 12 2020 - 03:00:01 PDT
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