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Forming large vesicles/liposomes
- Junb
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3 years 11 months ago #8532
by Junb
Forming large vesicles/liposomes was created by Junb
Dear Friends,
I am working on forming large vesicles/liposomes (~50nm diameter) using Martini FF to investigate forming mechanism with drug loaded system based on different conditions, such as co-solvents, temperatures. However, I am having trouble to form blank/empty vesicles with large size around ~50nm diameter. I was trying to form using simple DPPC and water system, and I tried to follow several publications using Martini FF, and still cannot form the target size.
Could I please have some of your ideas or suggestions or reference paper, in order to guide me to form large vesicles? Thank you very much in advance.
Jun
I am working on forming large vesicles/liposomes (~50nm diameter) using Martini FF to investigate forming mechanism with drug loaded system based on different conditions, such as co-solvents, temperatures. However, I am having trouble to form blank/empty vesicles with large size around ~50nm diameter. I was trying to form using simple DPPC and water system, and I tried to follow several publications using Martini FF, and still cannot form the target size.
Could I please have some of your ideas or suggestions or reference paper, in order to guide me to form large vesicles? Thank you very much in advance.
Jun
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- siewert
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3 years 11 months ago #8538
by siewert
Replied by siewert on topic Forming large vesicles/liposomes
There are generally three ways to make vesicles:
1) Self-assembly. This works in principle, but the system might easily get trapped in metastable states and thus might take a long time. Self-assembly, however, can be guided by means of templating potentials, such as described in H.J. Risselada, A.E. Mark, S.J. Marrink. The application of mean field boundary potentials in simulations of lipid vesicles. JPC-B, 112:7438-7447, 2008.
2) From a bicelle. If you start from a bicelle, you will find that it will undergo a transition to a vesicle, driven by the minimization of the line tension at the rim of the bicelle.
3) Pre-assembled, using e.g. the Charmm-GUI, see: Y. Qi, H.I. Ingólfsson, X. Cheng, J. Lee, S.J. Marrink, W. Im. CHARMM-GUI Martini Maker for coarse-grained simulations with the Martini force field. JCTC, 11:4486–4494, 2015.
In all cases, also note that after formation of the vesicle, equilibration of the amount of lipids between the inner and outer leaflets is still required, see: H.J. Risselada, S.J. Marrink. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Phys. Chem. Chem. Phys., 11:2056-2067, 2009.
Which option did you take ? And where did you get stuck ?
1) Self-assembly. This works in principle, but the system might easily get trapped in metastable states and thus might take a long time. Self-assembly, however, can be guided by means of templating potentials, such as described in H.J. Risselada, A.E. Mark, S.J. Marrink. The application of mean field boundary potentials in simulations of lipid vesicles. JPC-B, 112:7438-7447, 2008.
2) From a bicelle. If you start from a bicelle, you will find that it will undergo a transition to a vesicle, driven by the minimization of the line tension at the rim of the bicelle.
3) Pre-assembled, using e.g. the Charmm-GUI, see: Y. Qi, H.I. Ingólfsson, X. Cheng, J. Lee, S.J. Marrink, W. Im. CHARMM-GUI Martini Maker for coarse-grained simulations with the Martini force field. JCTC, 11:4486–4494, 2015.
In all cases, also note that after formation of the vesicle, equilibration of the amount of lipids between the inner and outer leaflets is still required, see: H.J. Risselada, S.J. Marrink. Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations. Phys. Chem. Chem. Phys., 11:2056-2067, 2009.
Which option did you take ? And where did you get stuck ?
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- bart
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3 years 11 months ago - 3 years 11 months ago #8539
by bart
Replied by bart on topic Forming large vesicles/liposomes
Heya,
I was working on a similar problem a while ago and a collegue and I made a pretty dirty script to quickly build large vesicles. It makes use of a grid on a sphere. I uploaded it to a git repository and added some documentation. Hopefully this can get the job done for you, or at least help you on your way.
Cheers,
Bart
I was working on a similar problem a while ago and a collegue and I made a pretty dirty script to quickly build large vesicles. It makes use of a grid on a sphere. I uploaded it to a git repository and added some documentation. Hopefully this can get the job done for you, or at least help you on your way.
Cheers,
Bart
Last edit: 3 years 11 months ago by bart.
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- Junb
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3 years 11 months ago #8540
by Junb
Replied by Junb on topic Forming large vesicles/liposomes
Hi Siewert,
Thank you so much for your reply and helpful information.
case 1) as you mentioned is more fit for my research goal since self-assemble process is what I am interested in. From the paper you shared with me, I noticed that MFFA will replace part of explicit solvent (inner and external water shell) which certainly will help with calculation time to form large vesicles.
But my concerns are,
(1) if later I want to have drug molecules to be simulated with lipids to form vesicles, will this approach can proper model drug encapsulation process into vesicles since inner explicit water will be replaced by MFFA?
(2) later if I want to model the shear stress (deform the box shape) impact to the size difference of vesicles, will this can be proper studied since not all solvent molecules really exist in the system?
I apologize for my dummy questions since I am still studying CG simulations. And I would really appreciate your thoughts and help.
Thank you so much for your reply and helpful information.
case 1) as you mentioned is more fit for my research goal since self-assemble process is what I am interested in. From the paper you shared with me, I noticed that MFFA will replace part of explicit solvent (inner and external water shell) which certainly will help with calculation time to form large vesicles.
But my concerns are,
(1) if later I want to have drug molecules to be simulated with lipids to form vesicles, will this approach can proper model drug encapsulation process into vesicles since inner explicit water will be replaced by MFFA?
(2) later if I want to model the shear stress (deform the box shape) impact to the size difference of vesicles, will this can be proper studied since not all solvent molecules really exist in the system?
I apologize for my dummy questions since I am still studying CG simulations. And I would really appreciate your thoughts and help.
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- Junb
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3 years 11 months ago #8541
by Junb
Replied by Junb on topic Forming large vesicles/liposomes
Hi Bart,
Thank you so much for your reply and helpful information.
I apologize I did not state clearly about my questions. Actually I am interested in the self-assemble process to form large vesicles , so pre-assembled vesicles will be not fit for my study. Thanks again.
Thank you so much for your reply and helpful information.
I apologize I did not state clearly about my questions. Actually I am interested in the self-assemble process to form large vesicles , so pre-assembled vesicles will be not fit for my study. Thanks again.
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