From: Brian Radak (brian.radak_at_gmail.com)
Date: Sun Apr 04 2021 - 14:56:14 CDT

It's true that constant-pH MD is a costly approach here. When possible,
enumeration is a higher certainty, especially if you do not expect
correlation between residues. However, if you are _just_ curious about
histidines, you could run with a reduced move set and get better
performance (ie assume ASP and GLU are deprotonated).

Another question is whether you are interested in the protonation states
for a specific structure or not. That could greatly reduces the length of
simulation needed and also increase the utility of constant-pH MD finding
multiple well-populated states.

Cheers,
BKR

On Sun, Apr 4, 2021, 3:09 PM Gumbart, JC <gumbart_at_physics.gatech.edu> wrote:

> It’s not that we thought constant pH wouldn’t work, but just that we are
> not especially familiar with the method. Here’s an example of a study on a
> related enzyme in which they used it successfully:
> https://urldefense.com/v3/__https://aip.scitation.org/doi/full/10.1063/5.0020458__;!!DZ3fjg!qHIah8a00r2V7vAYDaebHGOIU4-yZufSUc1k6QyPF_SJhdZU0kcUGZIL883k8oyP7w$
> <https://urldefense.com/v3/__https://aip.scitation.org/doi/full/10.1063/5.0020458__;!!DZ3fjg!qiAD3f7mt7lc30MuT_0aXrx3MwRRPaAlonE0FSFEs9I85WynxYQ-mzOPINsueH5f3g$>
>
> I’m also not sure that constant pH would be shorter than the individual
> simulations we ran, given that I think (but could be wrong) that it’s
> slower, plus we would have had to run longer than 20 ns to get anything
> converged. Not to mention the time it would have taken us to become
> familiar with the approach and how to use it * well*.
>
> You have a range of methods to choose from with varying levels of
> complexity, including just guessing based on the local environment (what we
> often do!), semi-empirical methods (Schrodinger’s protein preparation
> wizard may be able to handle nucleic acids? but it’s not free), running
> multiple simulations to test to different combinations of assignments (you
> don’t have to be exhaustive - many can be disregarded at the outset), and
> then constant pH. None of them are necessarily right or wrong and
> selecting one just depends on the time/accuracy trade-off you want to make.
>
> Best,
> JC
>
> On Apr 4, 2021, at 9:53 AM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
> I never used constant pH MD, although I was aware of NAMD implementation
> of it.
> The reason to investigate HIS protonation was twofold: the overwhelmingly
> presence of nucleosides and the two recent papers mentioned on previous
> posts in this thread, where constant HIS protonation was used and the
> various possible states explored by MD. Why they did not take the shorter
> route of constant pH MD? The authority of the authors let me think that
> constant pH MD is no panacea.
>
> francesco
>
> On Sun, Apr 4, 2021 at 2:28 AM Miro Astore <miro.astore_at_gmail.com> wrote:
>
>> You might consider constant ph simulations? They're supported in namd.
>>
>> On Sat., 3 Apr. 2021, 6:43 pm Francesco Pietra, <chiendarret_at_gmail.com>
>> wrote:
>>
>>> Hi Josh and James
>>> I had already seen another checking the MD stability for the various
>>> protonation states of HIS:
>>>
>>> Histidine protonation and the activation of viral fusion proteins,
>>> Daniela S. Mueller, Thorsten Kampmann, Ragothaman Yennamalli, Paul R.
>>> Young, Bostjan Kobe
>>> and Alan E. Mark, Biochemical Society Transactions (2008) Volume 36,
>>> part 1
>>>
>>> With so many HISs as in my case, the combinations scale tremendously up
>>> and one fears to miss the most important overall state.
>>> There is a need of new software to assign the protonation states of HIS.
>>> Also, if there is a fine tuning of HSE vs HSD, changeable during MD in
>>> response to the interaction with the strongly negative electrostatics of
>>> the nucleosides, things become complicated indeed.
>>>
>>> But I'll read James' paper and I'll try the suggested Propka and
>>> DelphiPKa, if not else to see the output.
>>>
>>> What about the famous ROSETTA? Perhaps, however, it just uses Propka or
>>> Delphi PKa.
>>>
>>> thanks
>>> francesco
>>>
>>> On Sat, Apr 3, 2021 at 1:35 AM Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>>>
>>>> Admittedly, it has been a while since I looked at propka output in
>>>> detail, but when I run regular proteins through pdb2pqr (
>>>> https://urldefense.com/v3/__https://server.poissonboltzmann.org/__;!!DZ3fjg!qHIah8a00r2V7vAYDaebHGOIU4-yZufSUc1k6QyPF_SJhdZU0kcUGZIL882qNv272Q$
>>>> <https://urldefense.com/v3/__https://server.poissonboltzmann.org/__;!!DZ3fjg!tsqIFHVKijNxX_B1fbFz9jygI2pMsbnGZC8el-7pPOZ9fT3WcvW5y8s__expakzqDA$>),
>>>> it claims to use PropKa to assign charges, and the pqr files that come out
>>>> definitely seem to have a made an attempt to choose between HSD and HSE, so
>>>> I assume there is something in the PropKa output that it is using to
>>>> determine histidine protonation. For the applications I was using it for,
>>>> this level of detail has been fine, but JC is right, you can also just try
>>>> all protonation state combinations and see what makes sense.
>>>>
>>>>
>>>>
>>>> -Josh
>>>>
>>>>
>>>>
>>>> *From: *"Gumbart, JC" <gumbart_at_physics.gatech.edu>
>>>> *Date: *Friday, April 2, 2021 at 4:43 PM
>>>> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>
>>>> *Cc: *Francesco Pietra <chiendarret_at_gmail.com>, VMD Mailing List <
>>>> vmd-l_at_ks.uiuc.edu>, "henin_at_ibpc.fr" <henin_at_ibpc.fr>, "zhu13_at_llnl.gov" <
>>>> zhu13_at_llnl.gov>
>>>> *Subject: *Re: vmd-l: histidine protonation
>>>>
>>>>
>>>>
>>>> I’m not sure about DelphiPka, but Propka doesn’t tell you which
>>>> nitrogen to put the proton on. We found running simulations of different
>>>> states and checking their stability to be the most reliable (albeit more
>>>> time-consuming) way to assign protons to histidines:
>>>> https://urldefense.com/v3/__https://pubs.rsc.org/en/content/articlelanding/2021/sc/d0sc04942e__;!!DZ3fjg!qHIah8a00r2V7vAYDaebHGOIU4-yZufSUc1k6QyPF_SJhdZU0kcUGZIL883xwhX9gA$
>>>> <https://urldefense.com/v3/__https:/pubs.rsc.org/en/content/articlelanding/2021/sc/d0sc04942e__;!!HXCxUKc!gvFYR3OpPr1fjuH1jJQ1NtrWmWfgzesHlw-bJ5W_WnlWlHNPuvfRXD9_XBJvm84$>
>>>>
>>>>
>>>>
>>>> We ran for 20 ns x 3, but you can often see a disruption sooner.
>>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>> JC
>>>>
>>>>
>>>>
>>>> On Apr 2, 2021, at 2:26 PM, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>>>>
>>>>
>>>>
>>>> Hi Francesco,
>>>>
>>>>
>>>>
>>>> Propka (https://urldefense.com/v3/__https://github.com/jensengroup/propka__;!!DZ3fjg!qHIah8a00r2V7vAYDaebHGOIU4-yZufSUc1k6QyPF_SJhdZU0kcUGZIL881IHkishg$
>>>> <https://urldefense.com/v3/__https:/github.com/jensengroup/propka__;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFDRl_oZJA$>)
>>>> or DelphiPka (https://urldefense.com/v3/__https://github.com/delphi001/DelphiPka__;!!DZ3fjg!qHIah8a00r2V7vAYDaebHGOIU4-yZufSUc1k6QyPF_SJhdZU0kcUGZIL881Q3B0qpQ$
>>>> <https://urldefense.com/v3/__https:/github.com/delphi001/DelphiPka__;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFCAQcr_zA$>)
>>>> in principle should be able to handle non-protein ionizable groups.
>>>>
>>>>
>>>>
>>>> -Josh
>>>>
>>>>
>>>>
>>>> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Francesco Pietra <
>>>> chiendarret_at_gmail.com>
>>>> *Date: *Friday, April 2, 2021 at 1:36 PM
>>>> *To: *VMD Mailing List <vmd-l_at_ks.uiuc.edu>, "henin_at_ibpc.fr" <
>>>> henin_at_ibpc.fr>, "zhu13_at_llnl.gov" <zhu13_at_llnl.gov>
>>>> *Subject: *vmd-l: histidine protonation
>>>>
>>>>
>>>>
>>>> Hi
>>>>
>>>> I am faced with the problem of establishing the protonation status of
>>>> many histidine residues present in a nucleic acid-protein ensemble, both
>>>> inside and on the periphery. All that in the framework of CHARMM36 for NAMD
>>>> MD.
>>>>
>>>>
>>>>
>>>> Servers for direct assignment, like H++, are useless because of the
>>>> presence of nucleic acids.
>>>>
>>>>
>>>>
>>>> I came across two interesting old posts by Zhu and Henin to this
>>>> concern and wonder whether there is anything additionally useful for the
>>>> above ensemble
>>>>
>>>> *From:* Fangqiang Zhu (*fzhu_at_ks.uiuc.edu*
>>>> <fzhu_at_ks.uiuc.edu?Subject=Re:%20%20how%20can%20I%20know%20which%20type%20HIS%20belong%20to?(HSD,HSE,HSP)>
>>>> )
>>>> *Date:* Sat Nov 29 2003 - 00:22:03 CST
>>>>
>>>> *From:* Jérôme Hénin (*jerome.henin_at_uhp-nancy.fr*
>>>> <jerome.henin_at_uhp-nancy.fr?Subject=Re:%20%20how%20can%20I%20know%20which%20type%20HIS%20belong%20to?(HSD,HSE,HSP)>
>>>> )
>>>> *Date:* Sat Nov 29 2003 - 04:37:30 CST
>>>>
>>>> Thanks for advice
>>>>
>>>> francesco pietra
>>>>
>>>>
>>>>
>>>
>