Dear all, I'm trying to determine the binding energy of a membrane protein to the membrane. Ultimately I need to compare the binding energy of the same protein to two similar types of lipid, the hypothesis being that there should be a slight difference.
I considered two options: alchemical transformations and umbrella sampling. Alchemical transformations leave a very large vacuum in the membrane so are nigh on impossible. Justin Lemkul recommended I do this via pull/umbrella-sampling as he did in his paper (http://dx.doi.org/10.1021/jp202217f). He was simulating a single-helix protein, but one of the proteins I need to do this for is a 7-Transmembrane-helix structure, so pulling it out of the membrane would leave a massive hole in the middle of the membrane, which is filled with water and not lipids. I find it hard to believe this would work and give a reliable result, so I turn to you to ask for opinions/alternatives! Thanks in advance. Victor On 24 February 2014 14:13, sojovictor <sojovic...@gmail.com> wrote: > Thanks so much, Justin! > > Your comments and paper are very helpful indeed. With "by eye" I meant I > just need to know whether one is bigger than the other, but you're complete > right: no need to speak in qualitative terms when I can quantitatively > determine DeltaDeltaG. > > Thanks again! > > > Victor Sojo > > > > > On 23 February 2014 17:37, Justin Lemkul [via GROMACS] < > ml-node+s5086n5014747...@n6.nabble.com> wrote: > > > > > > > On 2/23/14, 11:54 AM, sojovictor wrote: > > > > > Thanks, Justin! That's really helpful indeed. > > > > > > You are correct, I want to know what's the energy change in replacing > > one > > > lipid with the other, hypothesising that going to the "wrong" lipid > will > > > imply an energetic cost. > > > > > > Via umbrella sampling, I would thus: > > > > > > 1) Set up a full system with protein, lipids, solvent, and ions. > > > 2) Pull the protein perpendicularly out of the membrane and into the > > solvent > > > (which means I'd need a lot of solvent in the direction of the pull, > > such > > > that there's always enough space to fit the protein and still avoid > > boundary > > > interactions, as you explain in you tutorial, thanks!). > > > 3) Do the exact same thing with the other system, independently. > > > 4) See just by eye what the difference is and hope it matches my > > prediction. > > > > > > > I don't understand what "by eye" means here. You'll get a free energy > > difference between the embedded and solvated states, i.e. the > > binding/insertion > > energy. There's nothing qualitative about that. That's deltaG for a > > particular > > lipid type, and the deltadeltaG is simply the difference between the two. > > > > > Now, my question about using umbrella sampling for this purpose: is it > > > reasonable to use the whole membrane (say, the group of lipids) as my > > > immobile reference? In your tutorial you use a chain, in which all > > members > > > are covalently bound to each other, so I didn't know whether you could > > use a > > > group of independent molecules instead. I assume it will be fine, then. > > > > > > > Don't assume from the tutorial that you need an immobile reference. The > > fact > > is, you don't. You need to define a sensible reaction coordinate that > > describes > > embedded and water-solvated states. Neither of those intrinsically > > requires any > > sort of position restraint. > > > > What I had was a very specific case, and if you read my paper from which > > the > > tutorial was derived, you will find that the restraints there are used > for > > a > > special purpose to mimic fibril stability. That's not the case in most > > umbrella > > sampling runs. During the generation of configurations, you may need > some > > restraints to prevent perturbation of the bilayer structure, but that > > depends on > > how you generate those configurations. A more pertinent example would be > > http://dx.doi.org/10.1021/jp202217f. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > [hidden email] <http://user/SendEmail.jtp?type=node&node=5014747&i=0> | > (410) > > 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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