Dear All,
I'm running explicit solvent simulations of a globular protein with a long linker connected to a helical peptide. The linker is a long CYX-bound non-peptide with a PEG-amide type of structure. I use ff19SB with OPC water model, add ions to ~0.15 mM level and to neutralize the system.
The equilibration runs fine but then I see an overall drift of the connected peptide to the carrier protein. It's basically trying to fold into the protein.
As a control, I ran 1qm9 (solution NMR structure), which has two loosely associated subdomains connected with a peptide linker. After 200 ns, the subdomains came much closer to each other and the linker remained solvated. In other words, there is tighter association than experimentally observed.
Not sure how much the non-peptide nature of my linker is impacting this.
I'm wondering how much of it is real and how much is due to underestimated solvation. Does anyone have experience modeling these types of solvent-exposed structures? Do you think I've hit the limits of the force field or am I missing something?
Thank you in advance!
Sasha
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Oleksandr "Sasha" Buzko
Computational Biology
ImmunityBio
9922 Jefferson Blvd
Culver City, CA 90230
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Received on Wed Mar 13 2024 - 08:00:02 PDT
