Dear Adrian, Dear Vinicius,
Thank you very much for your answer. These results are very interesting and
are in complete agreement with what I found running pH-REMD, that is the
effect of explicit NaCl has a minimal effect on pKa.
It is also very interesting the see the effect of the changes in GB salt
concentration.
Eric
On 7 February 2017 at 13:28, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Dear Eric
>
> I am sorry for the delay answering your query.
>
> My student, Vinicius Cruzeiro, gave a draft of a response to you and I sat
> on it too long. I copied it below, and point that that it was all his work,
> while I agree with his conclusions.
>
>
> Adrian
>
> --------------------------
>
> Dear Eric Lang,
>
>
>
> Thanks for bringing this interesting question up. In order to better
> address your question, I have ran the explicit CpHMD simulations again but
> longer, for 50 ns. In my simulations I place the ACE-CYS-NME system
> inside a 1680 water molecules box, of volume 59052.89 A^3. I have done the
> simulations randomly adding no ions, 1 Na+ Cl- pair, or 4 Na+ Cl- pairs.
> From the explicit solvent point of view, this correspond to the following
> ionic strengths: 0 M, 0.028 M, and 0.112 M. I’ve also ran the
> simulations for two different GB salt concentrations: 0.1 M or 0.4 M. These
> are the results:
>
>
>
> GB Salt Concentration
>
> No ions
>
> 1 Na+ Cl- pair
>
> 4 Na+ Cl- pairs
>
> 0.1 M
>
> f=0.51152
>
> pKa=8.520
>
> f=0.50201
>
> pKa=8.503
>
> f=0.53882
>
> pKa=8.568
>
> 0.4 M
>
> f=0.47026
>
> pKa=8.448
>
> f=0.46207
>
> pKa=8.434
>
> f=0.46302
>
> pKa=8.436
>
>
>
> There are two points I would like to discuss here:
>
>
>
> 1) Although the MD is done with Explicit Solvent, the MC steps are done
> based on GB calculations. Although the explicit ions are not directly
> included in the GB calculations, they might affect the conformational
> distribution of the ACE-CYS-NME system, mainly if there a closer
> interaction. What the results show is that this effect is minimum on the
> pKa., as you can see the results are basically the same by adding explicit
> ions or not.
>
>
>
> 2) We see the GB Salt Concentration change from 0.1 to 0.4 M affects the
> pKa a little bit. This effect is expected by the construction of GB (you
> would be able to predict this behavior from the GB equations).
> Experimentally speaking, there is also a generally small ionic strength
> dependence of the pKa, see: http://onlinelibrary.wiley.
> com/doi/10.1016/0307-4412(90)90017-I/abstract
>
>
>
> The reference Free Energy necessary for AMBER’s CpHMD methodology needs to
> be computed reproducing as close as possible the environment in which the
> experimental pKa reference value was obtained. Once this value is obtained,
> it should be good to be used to make predictions even on other GB salt
> concentrations. The table above shows that, for the system studied, adding
> ions explicitly makes no significant difference in the pKa results (thus no
> significant difference too on the reference Free Energy calculation). I
> believe this conclusion most hold true for other systems unless there is a
> fix and close interaction between the explicit ion ions and the system.
>
>
>
> Best regards,
> ------------------------------
>
>
> On 2/7/17 8:22 AM, Eric Lang wrote:
>
> Hello,
>
> This post is partly a reply to my previous post but also extends on it.
>
> I decided to test more carefully the effect of having explicit Na+ and Cl-
> ions at a concentration of 0.1 M with the model compounds for Lys, His, Glu
> and Cys (shamelessly the titrable residues I am currently interested in).
>
> To do this, I prepared the systems ACE-X-NNE (where X is the titrable
> residue) and solvated them in a 20 A TIP3P solvent buffer and added 7 or 6
> explicit Na+ and Cl- ions (depending on the number of water molecules added
> to solvate the residues of interest). After minimisation, heating and
> equilibration, I ran a 10 ns CpHMD simulation at pH=pKa and then pH-REMD at
> pH = pKa ± 0.1 pKa ± 0.2 pKa ± 1.2 (as in the Jason’s paper on explicit
> solvent pH-REMD) for 20 ns. Results between CpHMD and pH-REMD are
> consistent and here I will just show the pH-REMD results.
>
> Basically, I do not see significant differences in the calculated pKa
> whether I add explicit ions or not (_salt here means in the presence of 0.1
> M of explicit NaCl):
>
> Lys Lys_salt Cys Cys_salt Glu Glu_salt His
> His_salt
> pKa 10.35 10.38 8.35 8.34 4.82 4.82 6.31 6.31
> n 1.01 1.00 1.02 1.01 0.96 0.97 1.01
> 1.01
>
> I do find it a bit surprising as, after all, I would have expected that the
> presence of ions interacting with the titrable residues would make some
> differences as my early results suggested, nonetheless these much more
> thorough simulations suggest the effect is negligible.
>
> Please note that I did not include error bars by either dividing the
> pH-REMD trajectories into small chunks or by running multiple simulations.
> However, the good agreement between the predicted pKa values obtained from
> pH-REMD and from CpHMD (the values agree at a maximum of ± 0.03 pK units)
> suggests that dividing the pH-REMD into chunks would lead to similar
> variations.
>
> However, I am now a bit concerned by the shift between calculated and
> theoretical pKa, especially in the case of Glu (4.8 calculated instead of
> the 4.4 it has been parametrised for), and to a lesser extend His (6.3 vs.
> 6.5). Are those kinds of deviations within the accuracy of the method? I
> would have expected deviations of no more than ± 0.1 pK units.
>
> I thought this could be due to the force field, as I am using ff14SB (see
> this post for more details: http://archive.ambermd.org/201611/0108.html),
> so I repeated the simulations with the original ff10 force field
>
> Lys_ff10 Cys_ff10 Glu_ff10 His_ff10
> pKa 10.39 8.52 4.90 6.39
> n 1.01 1.01 0.97 1.02
>
> In the case of Lys, Glu and His, the results are similar between the two
> force fileds, suggesting that ff14SB can be used for constant pH MD.
> However, the pKa of Cys is slightly higher with ff10 than with ff14SB,
> could it be somehow because the unprotonated Cys is not defined in the
> standard ff14SB?
>
> Nonetheless the pKa of Glu is still quite high compared with the
> theoretical one. Could it be a problem with the parametrisation of GL4 in
> amber 16?
>
> I would really appreciate if you could share your opinion on either or not
> these differences should be considered problematics and if some fine tuning
> of the parameters / reparametrisation would be useful.
>
> I am happy to share my input/output files if needed.
>
> Many thanks in advance,
>
> Eric
>
>
> On 30 January 2017 at 12:33, Eric Lang <eric.lang.bristol.ac.uk> <eric.lang.bristol.ac.uk> wrote:
>
>
> Hello,
>
>
>
> I have noticed in the original paper on CpHMD in explicit solvent (http://pubs.acs.org/doi/abs/10.1021/ct401042b) that the pKa of the model
> compounds were calculated with the model compounds solvated in explicit
> water but in the absence of explicit ions. However, when switching to the
> GB potential in the explicit solvent CpHMD workflow, an ionic concentration
> of 0.1 M is used. Therefore, the reference energies are calculated assuming
> a 0.1 M ionic concentration but the dynamics of the model compounds are
> performed without ions.
>
> In contrast, in the hen egg white lysozyme example of the paper, Na+ and
> Cl- ions are added to neutralise the system and have a 0.1 M concentration
> of NaCl. This is also done in Jason’s tutorial on Explicit solvent MD.
>
>
>
> I was therefore wondering if there was a reason for not adding ions to the
> water box when calculating the pKa of the model compounds as it would make
> sense to do it to remain consistent with the GB calculations.
>
>
>
> I ran a quick 1 ns CpHMD test of the Cys model compound (ACE-CYS-NME)
> following the same protocol as reported in the paper.
>
> If I do not add any explicit ions, as per the paper, I end up after at pH
> =8.5 with the expected pKa/protonated fraction:
>
>
> Solvent pH is 8.500
>
> CYS 2 : Offset 0.007 Pred 8.507 Frac Prot 0.504 Transitions 3403
>
> Average total molecular protonation: 0.504
>
>
>
> However, if I add 1 Na+ and 1 Cl- to approximate a 0.1 M NaCl
> concentration and run the same CpHMD, then I obtain the following:
>
>
>
> Solvent pH is 8.500
>
> CYS 2 : Offset -0.187 Pred 8.313 Frac Prot 0.394 Transitions 3923
>
> Average total molecular protonation: 0.394
>
>
>
> If I increase the simulation time to 3 ns this result is confirmed:
>
> Solvent pH is 8.500
>
> CYS 2 : Offset -0.171 Pred 8.329 Frac Prot 0.403 Transitions 11383
>
> Average total molecular protonation: 0.403
>
>
>
> When I look at the trajectory, the Na+ ion interacts with the S- of Cys,
> so it is not due (or only due) to a change in dynamics due to the presence
> of the ions but because of electrostatic interactions between the
> deprotonated Cys state and the sodium ion.
>
> I understand that this is a simple test and more work would be required to
> indeed acuratly capture the effect of adding explicit ions to the model
> compounds simulations, having for example a larger solvent box would enable
> to better approximate the 0.1 M NaCl concentration, and running pH-replica
> exchange would give more accurate results. In addition, I didn’t try any
> other titrable residues at this stage either.
>
>
>
> Nonetheless, I am a bit worried about these results and the effect of not
> having explicit ions when the reference energies where calculated. Overall
> is this not going to lead to a small error in the calculated pKa due to the
> fact that the model compounds were simulated in the absence of explicit
> ions? When running the simulations of a protein of interest with explicit
> ions, the same ions-charged residues interaction will occur. But perhaps
> I am missing something important there, so I would be grateful to have your
> opinion on this matter.
>
>
>
> Many thanks in advance,
>
>
>
> Eric
>
> --
>
> Eric Lang
>
> BrisSynBio Postdoctoral Research Associate Modelling
> Centre for Computational Chemistry
> School of Chemistry - University of Bristol
> Bristol BS8 1TS - United Kingdom
>
>
>
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor.
> Department of Chemistry
> University of Floridaroitberg.ufl.edu352-392-6972 <(352)%20392-6972>
>
>
--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Wed Feb 08 2017 - 04:30:03 PST
