Peter,<br><br>firstly- thanks for the so detailed discussion.<br><br>The negative aspects of water-vacum-water sandwich system wich you provided indeed keep me from the modelling of such system.<br><br>Indeed I found some information about influence of the specific lipids on the stability of the protein by the regulation of tight packing contacts. I think that specific cholesterol binding sites in the receptor are very good example of such regulation due to heigh regidy of the dual apolar rings of that lipid.<br>
<br>How do you think is there any way to simulate such membrane packing forces by introducing of the lipid-like layer ? What are the most appropriate might be in that case? E.g I've found in the Justin's tutorial cyclohexan layer as the membrane-like solvent but I suppose that ussage of the smaller apolar mollecule might be more similar to acyl-like interior.<br>
<br>James<br><br><div class="gmail_quote">2012/2/2 Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 2012-02-02 11:57:22AM +0300, James Starlight wrote:<br>
> Peter,<br>
><br>
> Yes the main reason is the CPU economy for such experiment. My current<br>
> experiment consist of investigation of the tight paking forces (primarily<br>
> vdv effect) in the membrane receptor by inclusion of some point mutations.<br>
><br>
><br>
> Actyally I think that simple biphastic system ( like in the Justin tutorial<br>
> but with vacum layer instead of cyclohexane) is exactly that I need. How I<br>
> could make such layers system where water dont move into the middle layer?<br>
><br>
><br>
> James<br>
<br>
</div>The main issue is that vacuum is not a phase. Vacuum is simply empty space.<br>
A particle's interaciton with vacuum is null, by definition so a<br>
"biphasic" system with one of the "phases" being nothing is literally not<br>
comparable to a true biphasic system. You have to realize this from a<br>
physical point of view... Moreover, how do you know for certain that the<br>
hydrophobic interaction between TM and lipid does not contribute to the<br>
TM bundle packing and the interactions you are trying to study? Remember,<br>
it has been shown that TMs "may flex to satisfy hydrophobic mismatch".<br>
(Yeagle, et al Biochim Biophys Acta. 2007 Mar;1768(3):530-7)<br>
<br>
Is using united-atom bilayer (Berger lipids, from Justin's KALP-15/DPPC<br>
tutorial) still computationally unacceptable for you? (Tieleman et al 2006<br>
J. Phys.: Condens. Matter 18 S1221). I did mention earlier also adding some<br>
coupling parameters to use a coarse-grained bilayer with all-atom protein<br>
too.<br>
<br>
Anyway, if you are really adamant about not using explicit bilayer,<br>
I thought about this a little. Maybe try using explicit waters in the non-<br>
membrane portions of the system, then use implicit solvent (GBSA) with<br>
the correct dielectric to mimic a hydrophobic phase....<br>
I have no methodology for this approach.<br>
<br>
If I were to take your request of "How do I use explicit water but vacuum"<br>
literally: An all-atom system that preserves the vacuum in the membrane region<br>
of the system would involve making a 2 walls of immobile waters:<br>
You select a monolayer of waters at each end that you want to act as the<br>
wall. Rename them to a different residue name in your .gro file. Reorder<br>
the .gro file so that all the wall-water atoms are in their own contiguous<br>
section. Copy the .itp you use for the mobile waters to another .itp, edit<br>
and change the moleculetype to your wall residue name. Add the new .itp<br>
to your .top. Either use freeze_grps or position restraints on the wall<br>
oxygens to prevent them from moving. This approach has many many problems<br>
associated with it, not least that of: "what do you do with the waters<br>
in the solvent accessible space" and the fact that since there is vaccum<br>
surrounding the outside of the TM bundle and waters inside the TM bundle,<br>
your protein may explode from the lateral motion of the waters inside the<br>
solvent accessible spaces pushing against the TMs...<br>
<div class="HOEnZb"><div class="h5"><br>
><br>
><br>
><br>
><br>
><br>
> 2012/1/30 Peter C. Lai <<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>><br>
><br>
> > I am not sure of the actual interpretive value of such a methodology.<br>
> > Are you just trying to save computational time by not having to simulate<br>
> > an all atom bilayer? The solvent layer is going to contribute to the<br>
> > majority of the computation cost in the first place. As an example, the<br>
> > bilayer we are using for GPCR work consisting of 238 POPC molecules adds<br>
> > 30552 atoms out of a total of 99547 atoms, In any case, people have been<br>
> > conducting all-atom simulations of opsins since at least 2005 because<br>
> > of the availability of computational resources. See: Lemaitre V., Yeagle,<br>
> > P.,<br>
> > Watts, A. Biochemistry 2005, 44, 12667-12680 . So it is unlikely that<br>
> > any reviewers today will accept an opsin system simulated in anything but.<br>
> ><br>
> > Perhaps a biphasic implicit solvent model would work better for you (unsure<br>
> > if gromacs can support an "exterior" dielectric and an interior<br>
> > dielectric).<br>
> > There may also be some people using a coarse-grained bilayer with an<br>
> > all-atom<br>
> > protein, but again, unless you have carefully determined the coupling<br>
> > parameters between a MARTINI bilayer and an all-atom protein, there will<br>
> > be doubts about the usefulness of such a system.<br>
> ><br>
> > If you really must do without the bilayer, you might be able to get away<br>
> > with using strong i,i+4 distance constraints within your TMs to preserve<br>
> > helical stability while the entire protein is solvated.<br>
> ><br>
> ><br>
> > On 2012-01-30 10:50:35AM +0400, James Starlight wrote:<br>
> > > David, Justin<br>
> > ><br>
> > > Thanks again for help!<br>
> > ><br>
> > ><br>
> > > I have just few questions about in vacum sumulation of membrane proteins.<br>
> > ><br>
> > ><br>
> > > I want to simulate GPCR receptor wich have big transmembrane ( helix)<br>
> > > domain and some connecting loop regions wich are exposed to the solvent.<br>
> > ><br>
> > > As I understood in classical vacum simulation all charges must be redused<br>
> > > to avoid its collapse.<br>
> > ><br>
> > > I want to build biphastic system water-vacum-water where loops would be<br>
> > in<br>
> > > water and TM helixes in vacum region.<br>
> > ><br>
> > > Something like this I've read in old publications about simulation of<br>
> > > bacteriorhodopsin <a href="http://ukpmc.ac.uk/abstract/MED/10412722" target="_blank">http://ukpmc.ac.uk/abstract/MED/10412722</a><br>
> > ><br>
> > ><br>
> > > 1- Could you tell me where I could found possible algorithm about builing<br>
> > > of such water-vacum-water system?<br>
> > ><br>
> > > 2- Also I'd like to specify what should I do with the charges residues.<br>
> > I'd<br>
> > > like to use AMBER-like or OPLS ff for such simulation As I understood I<br>
> > > must neitralize only charges in TM helices and keep residues in LOOP<br>
> > > intact. Might this aproache be correct?<br>
> > ><br>
> > ><br>
> > > James<br>
> > ><br>
> > > 2012/1/29 David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
> > ><br>
> > > > On 2012-01-29 17:09, James Starlight wrote:<br>
> > > ><br>
> > > >> Hi, Justin.<br>
> > > >><br>
> > > >> Yes. The GFP chromophore is a part of backbone. It's formed from Ser<br>
> > Tyr<br>
> > > >> Gly by cyclisation of the Ser with Gly and subsequent dehydrotation.<br>
> > As<br>
> > > >> the consequence the mature chromophore has cyclised structure wich<br>
> > named<br>
> > > >> as the CRO residue in PDB structure.<br>
> > > >><br>
> > > >> I've made for this CRO residue topology via PRODG server for GROMOS<br>
> > ff.<br>
> > > >><br>
> > > >> Than I've imported that new chromophore.top into the topology.top of<br>
> > my<br>
> > > >> structure in accordance to your tutorial.<br>
> > > >><br>
> > > >> Finally I've merged CRO.gro and protein.gro ( I've cut CRO from the<br>
> > pdb<br>
> > > >> for creation of the topoogy for my protein via pdb2gmx)<br>
> > > >><br>
> > > >> Than I've done minimisation and chromophore have been diffused from my<br>
> > > >> protein :) It seems that I must add covalent bond between CRO and<br>
> > > >> protein into the topology. But how I could do it for my multi topology<br>
> > > >> file ?<br>
> > > >><br>
> > > ><br>
> > > > You need to add the bonds angles etc. The easiest way would be to make<br>
> > a<br>
> > > > special bond (specbond.dat file). You need an rtp entry for your cro<br>
> > group<br>
> > > > as well. Then pdb2gmx makes the necessary bonds.<br>
> > > ><br>
> > > > Of course you can make all the bonds, angles, diehdrals and pairs<br>
> > manually<br>
> > > > as well, but that is tedious and error prone.<br>
> > > ><br>
> > > >><br>
> > > >> James<br>
> > > >><br>
> > > >> 2012/1/29 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>
> > > >><br>
> > > >><br>
> > > >><br>
> > > >><br>
> > > >> James Starlight wrote:<br>
> > > >><br>
> > > >> Hi David!<br>
> > > >><br>
> > > >> Thanks for reference I'll study it carefully.<br>
> > > >><br>
> > > >><br>
> > > >> I have some general question about the vacuum simulation<br>
> > > >><br>
> > > >> 1- I've found that common GROMOS fields are not suitable for<br>
> > the<br>
> > > >> vacuum simulation because of its implementation for condensed<br>
> > > >> phase .<br>
> > > >> But In some referencces I've found that people use 53.6 ff for<br>
> > > >> the in<br>
> > > >> vacuum simulation. In addition Ive done minimisation and<br>
> > > >> equilibration<br>
> > > >> in that ff in vacuum and my system have not been collapse :) Is<br>
> > > >> there<br>
> > > >> any wy to adopt this ff for the in vacum ?<br>
> > > >><br>
> > > >> 2- I have uncommon onject for simulation. It's GFP protein<br>
> > where<br>
> > > >> chromophore group ( like ligand) is covalent bonded to the<br>
> > > >> backbone of<br>
> > > >> this protein. As I've understood in Justins tutorial there are<br>
> > > >> no any<br>
> > > >> covalent bonds between protein and ligand. But how I could make<br>
> > > >> this<br>
> > > >> bond if I operate with TWO topology files ( one for<br>
> > chromophore and<br>
> > > >> another for protein itself) ? I've done all steps in<br>
> > accordance to<br>
> > > >> Justins tutorial but on the minimisation step my chromphore<br>
> > dissuse<br>
> > > >> out of the protein interior because of absent of backbone<br>
> > group.<br>
> > > >><br>
> > > >><br>
> > > >> The GFP chromophore is part of the backbone of the protein, is it<br>
> > not?<br>
> > > >><br>
> > > >> The tutorial I have for a protein-ligand complex should not be<br>
> > taken<br>
> > > >> to mean that all non-protein entities are physically separate<br>
> > > >> entities. Plenty of cofactors, chromophores, and the like are<br>
> > > >> covalently attached to the protein.<br>
> > > >><br>
> > > >> -Justin<br>
> > > >><br>
> > > >> --<br>
> > > >> ==============================**__==========<br>
> > > >><br>
> > > >><br>
> > > >> Justin A. Lemkul<br>
> > > >> Ph.D. Candidate<br>
> > > >> ICTAS Doctoral Scholar<br>
> > > >> MILES-IGERT Trainee<br>
> > > >> Department of Biochemistry<br>
> > > >> Virginia Tech<br>
> > > >> Blacksburg, VA<br>
> > > >> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
> > > >> <a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>__**<a href="http://vt.edu/Pages/Personal/justin" target="_blank">vt.edu/Pages/Personal/justin</a><<br>
> > <a href="http://vt.edu/Pages/Personal/justin" target="_blank">http://vt.edu/Pages/Personal/justin</a>><br>
> > > >> <<a href="http://www.bevanlab.biochem." target="_blank">http://www.bevanlab.biochem.</a>**<a href="http://vt.edu/Pages/Personal/justin" target="_blank">vt.edu/Pages/Personal/justin</a><<br>
> > <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>><br>
> > > >> ><br>
> > > >><br>
> > > >> ==============================**__==========<br>
> > > >><br>
> > > >><br>
> > > >> --<br>
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> > > >><br>
> > > ><br>
> > > > --<br>
> > > > David van der Spoel, Ph.D., Professor of Biology<br>
> > > > Dept. of Cell & Molec. Biol., Uppsala University.<br>
> > > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
> > > > <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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> > Peter C. Lai | University of Alabama-Birmingham<br>
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