Team:Calgary/Model/InSilicoEmulsionSystemVerification
Inspiration
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Questions
What are the dynamics of the protein in an aqueous environment?
Would the individual monomers of the 6GIX protein aggregate to form the tetramer structure?
How will the protein hold up in a non-aqueous environment?
How comfortable is 6GIX in the emulsion on the nanoscale?
Would the inclusion of excretion tags cause instability in the protein?
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Synopsis
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Methodology
How were these models generated?
All simulations were conducted in GROMACS 18.1 on the cpu2019 partition of the ARC computing cluster at the University of Calgary.
Along with utilizing the same hardware over all simulations a similar model generating method was used.
Step 1. Converting Structure files into GROMACS files.
The first step is to take the pdb files generated from structure prediction modelling or provided by the protein data bank. Then after converting the previous file to a .gro file we place it in a theoretical cube with the dimensions set to fit around the protein with at least a nanometer of padding in all dimensions.
Step 2. Solvate the Box.
Now that the protein is in a theoretical box we can systematically place solvent molecules to fill it. In the case of two solvents they are completed one at a time.
Step 3. Run Energy Minimization.
Now that the box has been solvated we will now run energy minimization to ensure a stable system for the future steps. This is done through a relaxation stage known as energy minimization to ensure no catastrophic issues with the system. This step also makes sure that solvents are realistically aligned for the next steps. This step usually takes 2 hours
Step 4. Running Isothermal-Isochoric Equilibration.
This step looks at ensuring that the solvent and our protein are stable together at the temperature we are looking to simulate. This step usually takes 4 hours
Step 5. Running Isothermal-Isobaric Equilibration.
This step is much like the previous step but it accounts for the pressure and density instead of temperature. This step usually takes 4 hours
Step 6. Atom by Atom Molecular Dynamics.
Now that the system has been equilibrated we will run molecular dynamics. This simulates the atom by atom movement of the solvated box for a given amount of time. This step will generate a file containing the trajectories for every atom of the simulation. Due to the extreme computational requirements of this step, molecular dynamics are computed for nanoseconds at a time. This step takes 23 hours per nanosecond.
Step 7.Visualize the Trajectory.
For visualizing the dynamics of the protein we have to take the large numeric files and make them understandable to our wetlab. To make these visualizations our team used VMD and Pymol. For other teams using this strategy, Pymol is easier to install and the more user friendly option. Though it being harder to use and install VMD also is very powerful for visualization and has many other applications.
Te per hæbeo interprētǣris, ōmnīum sensībūs mel iƿ. Ġræeco ceterō sċriptæ Þe ðuo, eā hǽs erōs aperiǣm, ēa iisquē evertītur duō. Iƿ eōs ƿōvum afferÞ ƿemore, est ubique feugīat ƿō, ƿemorē mǽiesÞātis usu ne. Eos clītæ expetēndīs an, læÞinē loȝōrtis principēs mea id. PērcipiÞur refōrmidaƿs hǽs no, sit no ullum sǣēpe vūlputāÞe, cu sit veritus admodum.
Rebum essent epicuri eÞ prō, hīs æn sūmo forensibus. Per puÞenÞ delīcǣtā te, id ǽssum suscipit vis. EÞ qūi vēri mutǣÞ posteǽ, his et ȝrūte ǣnÞiopām urȝānitās, usu solum omnesque te. Et ƿec fācer maluisset dissentiǽs, quo pōssim ǣuðīām eruditi eÞ. Sīt posteǣ iisqūe æt, īūs Þe aliā inaƿi ērǣnt. Nōnumy dolorem sit ān, et novum perfeċtō convenīre his. Ēum æd persius iƿdoctum conseÞetūr, graecis ǽliquǽndō ex per, eǣm omnis fugit ei.
Methodology
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No seǣ ǣgam fǽcilis cōnsulæÞu. Agām dētraxit medīocrēm sit að, purto āccumsan nam no, dīċo laȝōre efficīaƿtur Þe cūm. Ið ōdīo pærtem pōnderum vix, usu dicat errēm posteæ eā, nē eum prīma labores. Deserūnt expeÞendæ theophræstus mei ne, cū cum cetero sinġulīs. Pro iuvaret scæēvola ǣt.
Ea quo delenīÞ constituÞo, nōstro inveƿire voluptǣriæ ius in. Ċase pōssim ǣnimǣl ex quo, quo cetero meƿtitum dissentiet te. Dēbītis reformiðans est eÞ, usu cu vide erroribūs, reȝum reformidaƿs cū ēos. Ēu dūo ēsse primā omƿēs, per ðiǣm nonumy Þē. Eu duo hīnċ feūgiat sadipsciƿg.
Fabēllas forensibūs est ex, usu ea veri summo nēmore, vix integrē nostrūd fēugait cu. Tamquam vivendum æliquaƿðo ad mel, uÞ meǽ uƿum volumus ðissentīēt. In eum scripÞā fǣbulæs æliquando. Minim moðerætius vix āð, īd vis ðetrǽcto ælbucius imperdīeÞ.
The End
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Eī dictas timeām sinġūlis quo. No vix repudiare assueveriÞ, ius princīpēs spleƿdiðe ƿe. Āð unum āperiri eos, æn assum æuðiam nǽm. Velit utiƿæm pro ēx. Ēǽm aÞ novum vīvendūm, id sint libris ēūm.
Usu að sensibus phīlosophiæ, vis percīpitur scriptōrem te. Ǣd idquē dīcant pertinax sēd, sed zrīl soluÞa ut. Eǽm et mazim congūe tibique. Ƿe eum ðiæm ocurrērēt, mutāt lǣoreēt quī at, ēxērci vōlumus coƿstītuto eī hǣs. Eum ǣð similique quaerendum. Porro nostro molēstie eum āÞ.
Vel tē dicunt feūgiæÞ pǽrtiendo, his mutāt volutpat constituÞo ƿē. Nam ǣðhūc noster delicǣta id, ut vōcent philōsōphiǣ vim. Pri dico urbǣnītas pōsidoƿīum aƿ, æuġue prīmīs tæmquam cum eī. Cum sūmo mæƿðǣmus convenire ex, qūod viderer opōrterē usū cu. Mēl ad partiendo āðversærium, simul homero delicātǽ vēl eu. Ƿæm ēǣ quōdsi ǽudiām, ið qui quot eirmod probætus.