RE: Umbrella sampling of a protein through a membrane

From: Villalain Boullon, Jose (
Date: Fri Apr 12 2019 - 01:49:24 CDT

Dear JC,

Thank you very much for your response.

For the SMD simulation the protein, folded, is inserted in the centre of the membrane. Then it is applied a relatively small force to the alpha carbons in both the z- and z+ directions, together with a small restraint to the lipids to maintain the membrane integrity. The protein, passing through the membrane, unfolds and then it folds again when in the solvent. So it is not an effect of the applied force. That structural change, related to the lipid interaction, is what I would like to study.

Do you suggest to repeat again the SMD ?. Using another force might be ?. As I have said, the force is small enough so that the protein unfolds and folds again under the same parameters.

Even if I repeat the SMD, the problem with the window range remains ;-) .

Thanks a lot,

De: Gumbart, JC <>
Enviado el: viernes, 12 de abril de 2019 5:59
Para:; Villalain Boullon, Jose <>
Asunto: Re: namd-l: Umbrella sampling of a protein through a membrane

Before even deciding the specifics, you need to think more about the protein changing its structure. This is, in essence, another degree of freedom of your system which will likely be challenging to sample well. For example, if it starts to unfold as it enters the membrane, does it always unfold in the exact same way? If you repeat the SMD, do you get the same behavior? Presumably not, in which case a 1D PMF will not converge because the protein will keep sampling new and random conformations.

So is the structural change expected? Or is it a product of pulling too fast? Maybe you want to restrain the conformation, assuming you can justify it biologically.


On Apr 11, 2019, at 3:00 AM, Villalain Boullon, Jose <<>> wrote:

Dear all,

I have been through the NAMD tutorial “Methods for calculating Potentials of Mean Force” and now I would like to obtain the PMF of a peptide through a membrane trying to applied what I think I have learned. I have already minimized and equilibrated the system (protein in the centre of the membrane) and have run SMD on the system through the z direction. So far so good.

I want to obtain now the PMF using ABF but I am standing without really knowing what to do. The coordinate I should use is the z direction and have to select different windows (equally spaced) that cover the entire previous simulation.

The protein changes its structure in a significant way while it passes through the membrane and its centre of mass, relative to the centre of the bilayer, changes significantly through the simulation. I suppose the minimum range of the windows I have to work with should be that one that encompass the entire protein. Am I right ?. But in similar works I have read, the range of the windows is rather small (2 A). Which is really the range I should use ?. Independent of the protein size and/or its centre of mass?.

Thanks a lot for your help.

Prof. José Villalaín
Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE)
Edificio Torregaitán, Ala Este - D2.01
Universidad "Miguel Hernández" - Campus de Elche
E-03202 Elche-Alicante (España-Spain)

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