[chimerax-users] MLP value of the ASP and GLU carboxylate

[Zhijie Li]

Hi Elaine,

Thanks for the explanation. I understand the complications.  However this function directly affects a button in the GUI that a lot of user probably will press.  In Chimera it also controls a preset scenario?  For membrane proteins it might not be a problem but for soluble proteins the outcome might be quite misleading. I think if the underlying parameters are highly questionable it is probably better not to make it so accessible to the users. Or maybe add a caveat note in the documents?  Just my opinions.

Regards,

Zhijie

> On Jul 12, 2019, at 11:46 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Zhijie,
> We’ve also noticed the same issues with these atomic potentials.  However, so far we have only implemented the MLP method based on pyMLP with these original values (developed by others), not wanting to get into the parametrization business ourselves.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html>
> <https://github.com/plantigrade/pyMLP>
> 
> There may be different atomic potential sets for use with MLP that were already developed by others, but they would take time to add, so we haven’t thoroughly researched the issue.  If you have opinions or suggestions, let us know.
> 
> As an alternative, I’ve provided a ChimeraX command script to color protein surfaces by the Kyte-Doolittle hydropathy values of amino acids (like the preset that is available in Chimera).  
> <http://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc>
> 
> However, those Kyte-Doolittle values are simply a constant for each amino acid type, rather than a potential that varies in 3D space.  Still I find that the two approaches (Kyte-Doolittle values vs. MLP) often give a very similar picture of a transmembrane protein.
> 
> You can add it as a custom preset in ChimeraX using the instructions here:
> <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
> 
> It could be easily modified to any amino acid hydrophobicity scales, or you could have multiple presets for the different scales.  Several scales are shown in this table from the Chimera User Guide:
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jul 11, 2019, at 9:48 PM, Zhijie Li <zhijie.li at utoronto.ca> wrote:
>> 
>> Hello,
>> 
>> I noticed that the lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py: 
>> 
>> 'ASP': {'C': -0.54,
>>         'CA': 0.02,
>>         'CB': 0.45,
>>         'CG': 0.54,
>>         'N': -0.44,
>>         'O': -0.68,
>>         'OD1': -0.68,
>>         'OD2': 0.53}
>> 'GLU': {'C': -0.54,
>>         'CA': 0.02,
>>         'CB': 0.45,
>>         'CD': -0.54,
>>         'CG': 0.45,
>>         'N': -0.44,
>>         'O': -0.68,
>>         'OE1': -0.68,
>>         'OE2': 0.53},
>> 
>> As as result the hydrophobic surface representation always show hydrophobic patchs on the carboxylates, which look quite odd to me.   Is there a justification for this setting?  In addition, aren't the two oxygens in the carboxylate equal considerting that they are in resonance?
>> 
>> Zhijie
>