Protein partially denatures during pulling

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sun Feb 11 2007 - 01:01:40 CST

First of all, I wanted to thank everybody for the nice discussion about
SMD and ensembles. Now I have a question about how to set some parameters
for constant velocity pulling.

I am pulling two proteins of a complex away from each other at constant
velocity. I have set the speed to 5 A/ns and the spring constant to 14
pN/A. After 12 ns the force has ramped to a maximum of 670 pN and some
hydrogen bonds have broken. Unfortunately, after another 2 ns one of the
proteins partially denatures. Probably, this happens because I am pulling
too rough. How can I avoid denaturation of the proteins? Shall I reduce
the speed or the spring constant or both?

I have tried to increase the spring constant to 140 pN/A and at the same
time decrease the speed to 1 A/ns. I observe large oscillations of the
force. After 11 ns the force has ramped to 270 pN (running average) but I
still do not observe any unbinding, i.e., no hydrogen bond has broken (the
simulation is still running). I also have one simulation with the same
speed as the first one (5 A/ns) but a stiffer spring (140 pN/A). After 5
ns the force has ramped to 1200 pN but still no unbinding observed. In
these two simulations the proteins remained structured.

What could be an optimal combination of speed + stiffness in order not to
denature the complex but still observe unbinding in a reasonable amount of
time?

The first two simulations were peformed in NVE, the third one in CPT. The
time step is 2 fs (SHAKE). Before pulling the complex was equilibrated for
10 ns at 300 K with CPT using Langevin.

Thank you very much for any help.

Gianluca

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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