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I'm attempting to model the mechanosensitive channels of large conductance (MscL) in E. coli for finite element analysis purposes. I have a number of papers where this has been done, and one shows the modelling with van der Waals forces (as seems logical), but is it known how/where these forces exist?

For references, two papers I'm using have videos and pictures:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183822#sec013 (see the movies S1 & S2)

https://www.cell.com/action/showFullTextImages?pii=S0006-3495%2806%2971838-0

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  • $\begingroup$ What do you mean by "how/where these forces exist?" $\endgroup$
    – user37894
    May 26, 2018 at 18:48
  • $\begingroup$ Well, the N-terminus is connected to the TM1, which is connected to the TM2, which is connected to the C-terminus... how are they connected? $\endgroup$
    – Asinine
    May 30, 2018 at 16:03
  • $\begingroup$ There are two types of interactions: bonded and non-bonded. There are two types of non-bonded interactions: electrostatic and non-electrostatic. Electrostatic (also known as 'polar') interactions are usually modeled using Coulombic potential energy equation; non-electrostatic (also known as 'non-polar' or 'van der Waals') interactions are usually modeled using Lennard-Jones potential energy equation. $\endgroup$
    – user37894
    May 31, 2018 at 6:37
  • $\begingroup$ Thank you @MartinKlvana, if you put that as an answer I'll vote it. It's exactly what I was looking for. $\endgroup$
    – Asinine
    Jun 4, 2018 at 21:31

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It is the combination of intra- and inter-molecular interactions that determines the conformation of the protein.

There are two types of interactions: bonded and non-bonded. There are two types of non-bonded interactions: electrostatic and non-electrostatic. Electrostatic (also known as 'polar') interactions are usually modeled using Coulombic potential energy equation; non-electrostatic (also known as 'non-polar' or 'van der Waals') interactions are usually modeled using Lennard-Jones potential energy equation.

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