Hi all, I am simulating a membrane protein embedded in a detegent micelle (didodecyl maltoside DDM micelle). I am using total 167 number of DDM monomers and 17 cholesterol hemisuccinate (CHS) molecules for mimicking experimental conditions under which it has been attempted to be crystallized. Thus the protein I have is not a crystal structure its a homology model based on a close analog. The experimental aggregation number of DDM forming a micelle is ~145 and I am taking 167 for building my initial micelle followed by replacing some of them randomly with CHS molecules. I did 50 ns of NPT equilibration using gradual release of position restraints on all the components of the system. My production run is 300 ns long. I am using gromos54a7 force field and the united-atom formalism. I am observing that the protein is detached from the micellar core and comes near the periphery of the preformed micelle after 300 ns. The protein is exposed to solvent. Now I dont have any doubt about my equilibration but am I getting something weird? I dont know if my initial DDM model was erroneous. Have someone else come across such thing? The model has been used frequently in our research group( pubs.acs.org/doi/abs/10.1021/jacs.6b08742) and for crystal structures have been shown located near the core of the micelle. The other part of the story is the protein I am studying is experimentally known to be prone to aggregation. So I dont know whether I should be happy or sad about the results. One possible thing may be an inadequate number of DDM monomers to begin with but then how for a well- resolved crystal structure the protein-detergent complex (PDC) with the identical initial DDM construct is very stable? Is the protein going outside since due to its inherent tendency to aggregate or this is an artifact of my simulation which was wrong to begin with. In that case, I have to alter to monomers to construct the pre-formed micelle.
I looked up literature and could not see anything similar. It seems like the PDC is quite stable over time as suggested by some of references from Prof Mark Sansom's eminent research group. I will be obliged if someone guides me a little bit in this regard. Any literature or material which include such observation will be really helpful in understanding whats going on. Thanks in advance Soumadwip Ghosh Post Doctoral Research Associate Prof. Vaidehi Nagarajan's Research Group City of Hope Cancer Research Center Duarte, CA United States -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.