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about secondary structure query
- nareshthota
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9 years 6 months ago #4151
by nareshthota
about secondary structure query was created by nareshthota
Hi
i have used martini force field in some of my simulations. I have used random coil confirmation for the peptide molecules in my simulations during start up. Will it remain as random coil till the end of simulation system. If not how to measure which type of structure is there during simulation run?.
Thanks
Naresh
i have used martini force field in some of my simulations. I have used random coil confirmation for the peptide molecules in my simulations during start up. Will it remain as random coil till the end of simulation system. If not how to measure which type of structure is there during simulation run?.
Thanks
Naresh
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- Clement
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9 years 6 months ago #4152
by Clement
Replied by Clement on topic about secondary structure query
You simply can't. Martini in its current published form doesn't allow change of secondary structure (fixed from the start).
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9 years 6 months ago - 9 years 6 months ago #4154
by nareshthota
Replied by nareshthota on topic about secondary structure query
Dear Clement,
Thanks. Does It mean the peptides will be in the same random coil secondary configuration till the end of the simulation even when there is an aggregation for form certain morphologies like micelles and tubes.
Naresh
Thanks. Does It mean the peptides will be in the same random coil secondary configuration till the end of the simulation even when there is an aggregation for form certain morphologies like micelles and tubes.
Naresh
Last edit: 9 years 6 months ago by nareshthota.
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9 years 6 months ago #4155
by Clement
Replied by Clement on topic about secondary structure query
Precisely. It means that you won't see helix or sheet formation for/inside *one* peptide. But secondary structure (helix, coil or whatnot, fixed by the topology - "bonded parameters" - of your peptide) is different than quaternary structure (association of these peptides, following the rules defined by the non-bonded parameters), and that you can check with Martini.
But we might need more information on what you really want to do...
But we might need more information on what you really want to do...
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9 years 6 months ago - 9 years 6 months ago #4156
by nareshthota
Replied by nareshthota on topic about secondary structure query
Dear Clement,
Let us assume that i used some n number of peptides with random coil confirmation for each of them at start up. By the end of the simulation if they merge and aggregate to form spherical structure(let's say micelle). Then how to measure that agrregated micelles for their secondary or quaternary structures using martini?.
Thanks,
Naresh
Let us assume that i used some n number of peptides with random coil confirmation for each of them at start up. By the end of the simulation if they merge and aggregate to form spherical structure(let's say micelle). Then how to measure that agrregated micelles for their secondary or quaternary structures using martini?.
Thanks,
Naresh
Last edit: 9 years 6 months ago by nareshthota.
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9 years 6 months ago #4157
by Clement
Replied by Clement on topic about secondary structure query
We are not talking about change of intrinsic structure now... Peptides will associate indeed, dynamically hopefully, associate and dissociate. Probably form aggregates, a micelle or a matrix, depending on the residues composing the peptides.
But I still don't know what do you want to measure. What does "to measure that aggregated micelles for their secondary or quaternary structures" mean?
But I still don't know what do you want to measure. What does "to measure that aggregated micelles for their secondary or quaternary structures" mean?
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9 years 6 months ago #4158
by nareshthota
Replied by nareshthota on topic about secondary structure query
Dear Clement,
What i mean, if they form aggregated structure, is there any secondary structure like beta sheet or alpha helix formed between those peptides with in the aggregated structure?.
Thanks and Regards,
Naresh Thota
What i mean, if they form aggregated structure, is there any secondary structure like beta sheet or alpha helix formed between those peptides with in the aggregated structure?.
Thanks and Regards,
Naresh Thota
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9 years 5 months ago #4161
by Clement
Replied by Clement on topic about secondary structure query
This is what I said earlier: we're talking here about quaternary structure, interaction between different peptides, in which sheet or helices are not strictly defined (beta sheets or alpha helix are describing secondary structure for ONE peptide). Martini has limitations for secondary structure change only (not allowed by the current model); what happens when two or three peptides associates is completely different.
Short answer: yes you can potentially see this.
Short answer: yes you can potentially see this.
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9 years 5 months ago #4163
by nareshthota
Replied by nareshthota on topic about secondary structure query
Dear Clement,
Then how to measure Quaternary structure quantitatively. Is it only possible by visual means?.
Thanks,
Naresh
Then how to measure Quaternary structure quantitatively. Is it only possible by visual means?.
Thanks,
Naresh
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9 years 5 months ago - 9 years 5 months ago #4164
by Clement
Replied by Clement on topic about secondary structure query
I guess you can study that quantitatively. But honestly I never gave it any thought. I'm going to ask around...
If you're decided to use secondary structure markers to define quaternary structure, you can probably use a tweaked version of existing analysis tools. But most of them are for AA conformations, and you might have to backmap/shortly equilibrate your CG to define such structural properties. Would be a good idea to do this anyway!
Another idea, not requiring to backmap things, is to use contact maps. Since in CG you can't really define clearly helices or sheets...
Sorry, on on that one you're on your own. I'm going to show this post to others and hopefully you'll get more answers. Good luck.
If you're decided to use secondary structure markers to define quaternary structure, you can probably use a tweaked version of existing analysis tools. But most of them are for AA conformations, and you might have to backmap/shortly equilibrate your CG to define such structural properties. Would be a good idea to do this anyway!
Another idea, not requiring to backmap things, is to use contact maps. Since in CG you can't really define clearly helices or sheets...
Sorry, on on that one you're on your own. I'm going to show this post to others and hopefully you'll get more answers. Good luck.
Last edit: 9 years 5 months ago by Clement.
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9 years 5 months ago #4165
by xavier
Replied by xavier on topic about secondary structure query
If I understand correctly you are looking for a way to identify secondary structure elements with a simulation of a protein sequence that was defined in Martini as coil. Two things:
1- in Martini the level of description of a protein does not allow the model to choose by its self which secondary structure element (SSE) to form. The potential used is simply too minimal, so the protein does not have the possibility to discriminate. It is not even given the possibility to discriminate.
The Martini protein topology includes the information on the secondary structure. It is either an helix, and extended structure (sheet-like) or a coil. Helices and sheets are relatively easy to define using angles and dihedrals, but coil is more tricky and we choose to give it a complete flexibility and no proper test has been done to evaluate the reliability of coil "structures" in Martini. It is just something flexible to mimic loops in proteins when necessary.
2- This said your "coil" has probably collapsed because that what the model would do … not clear if this is realistic. You should be judge of this. To determine the existence of structure at the atomistic level you'd be using phi/psi angles of each residue to give it a SSE. In Martini these angles do not exist so you CAN NOT do it. Instead you could determine the formation of structure that would resemble an helix of a extended structure using the values of angles and dihedrals of consecutive backbone beads. You could use the range of values that we use to define their structure in the topology, see Monticelli-et.al-JCTC-2008. Note however that in sheets H-bonds participate to the stabilisation of adjacent sheets … in Martini you do not have this …
A final note to warn you about using Martini for unfolded (coil) proteins. There have been no test whatsoever to evaluate its reliability. Please be very careful with the interpretation you'll make of what you find. You may full yourself and others.
Good luck.
1- in Martini the level of description of a protein does not allow the model to choose by its self which secondary structure element (SSE) to form. The potential used is simply too minimal, so the protein does not have the possibility to discriminate. It is not even given the possibility to discriminate.
The Martini protein topology includes the information on the secondary structure. It is either an helix, and extended structure (sheet-like) or a coil. Helices and sheets are relatively easy to define using angles and dihedrals, but coil is more tricky and we choose to give it a complete flexibility and no proper test has been done to evaluate the reliability of coil "structures" in Martini. It is just something flexible to mimic loops in proteins when necessary.
2- This said your "coil" has probably collapsed because that what the model would do … not clear if this is realistic. You should be judge of this. To determine the existence of structure at the atomistic level you'd be using phi/psi angles of each residue to give it a SSE. In Martini these angles do not exist so you CAN NOT do it. Instead you could determine the formation of structure that would resemble an helix of a extended structure using the values of angles and dihedrals of consecutive backbone beads. You could use the range of values that we use to define their structure in the topology, see Monticelli-et.al-JCTC-2008. Note however that in sheets H-bonds participate to the stabilisation of adjacent sheets … in Martini you do not have this …
A final note to warn you about using Martini for unfolded (coil) proteins. There have been no test whatsoever to evaluate its reliability. Please be very careful with the interpretation you'll make of what you find. You may full yourself and others.
Good luck.
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