[chimerax-users] polymer modeling and conjugation

[Victor Ejigah]

Dear Elaine,
                Great to hear from you. Your response is quite helpful.
Thank you.


Victor

On Thu, Nov 11, 2021 at 12:57 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Victor!
> This answer discusses both Chimera and ChimeraX...although there is a
> separate chimera-users at cgl.ucsf.edu address for Chimera questions, you
> don't need to re-send; I will try to answer your questions here for both.
>
> (1 & 2) For biopolymers, Chimera can build peptides of any length, or
> helical  DNA, RNA, DNA/RNA.  It does not predict the conformation, though
> -- you have to tell it what  peptide backbone angles you want.  It is not
> really intended for building other types of organic polymers, although you
> can do it "manually" with lots of steps, by gradually adding atoms/bonds.
> You can "conjugate" by joining models, which just means adding a bond
> between two molecules that were previously separate.  See Chimera "Build
> Structure" tool, with parts including Start Structure, Modify Structure,
> Join Models, etc.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html
> >
>
> ChimeraX also has a Build Structure tool but it doesn't have all the parts
> of the Chimera one yet.  It doesn't have Join Models section, for example.
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>
>
> Organic polymer building may be somewhat tedious and inefficient in
> Chimera.  If there were some other tool good for building organic polymers
> you might use that instead, and then import it (e.g. PDB file) into Chimera
> for joining to the antibody  structure.
>
> I haven't modeled organic polymers in general (other than proteins and
> nucleic acids) so I'm not familiar with what other programs one would use
> to build them, sorry.  Probably there are many relevant programs and maybe
> even webservers to do that.
>
> (3) Seems like Chimera is more likely to be able to build it than ChimeraX
> currently, so there is no export issue.  However, I don't see how you could
> use MD ensemble since there would just be one structure, not an ensemble.
> Maybe you meant Chimera's molecular dynamics simulation tool?  Just be
> aware that that tool was developed for small molecule simulations and has
> many limitations. See the boxed warning on its help page:
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
>
> Also it may have problems assigning simulation parameters to the polymer
> moiety and  to the bond between it and the protein.
>
>  For thorough analysis of complex macromolecular structures and medium- to
> longer-length simulations, you may need to use some other package like
> AMBER or GROMACS instead of Chimera.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 11, 2021, at 8:00 AM, Victor Ejigah via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi Elaine,
> >               I am using chimeraX for protein analysis and simulations
> and recently, we have a question we want to explore by first simulating
> before going to the wet lab. We want to conjugate a polymer of different
> molecular weight to an antibody and thereafter determine the impact of the
> MW of each polymer on the binding affinity of the mAB to its ligand.
> Therefore, we want to know
> > 1) Can we create polymers of different sizes with chimera? If not, can
> you recommend alternatives?
> > 2) What tool can we use for conjugation( assuming chimera can be of
> help)?
> > 3) Can such conjugates be exported to Chimera1.5 for MD ensemble since
> Chimera X does not have this feature?
> > I will be most glad to hear from you soon.
> > Kind regards,
> > Victor (PhD student @Howard University)
>
>
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