Re: Protein partially denatures during pulling

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Mon Feb 12 2007 - 18:29:00 CST

Hi Gianluca,

I do not have a lot of experience on protein unbinding, but my guess
would be that a smaller velocity is the best way to get a more realistic
trajectory. You may also want to try pulling the center of mass of a
group of residues (instead of single atoms), unless you are already doing
so.

Regards,
Marcos

On Sat, 10 Feb 2007, Gianluca Interlandi wrote:

> 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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