1
$\begingroup$

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

$\endgroup$
4
  • $\begingroup$ 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

1 Answer 1

0
$\begingroup$

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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.