Decisive structural elements in water and ion permeation through mechanosensitive channels of large conductance: insights from molecular dynamics simulation

Naeini, Vahid Fadaei; Baniassadi, Majid; Foroutan, Masumeh; Rémond, Yves; George, D.

doi:10.1039/d2ra02284b

Cited by 2 publications

(2 citation statements)

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“…The transfer free energy of CG ions (i.e., ions hydrated by a few water molecules) across the membrane was significantly underestimated owing to the assumption of a large relative permittivity in SPICA FF . pSPICA can thus provide a reasonable description of ion transport through MscL, which is consistent with the AA-MD and experimental results. , Note that the pore radius in the open state of MscL is sufficient to allow for the membrane transport of CG water, sodium ions, and chloride ions in pSPICA.…”

Section: Resultssupporting

confidence: 75%

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pSPICA Force Field Extended for Proteins and Peptides

Miyazaki,

Shinoda

2023

J. Chem. Inf. Model.

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Many coarse-grained (CG) molecular dynamics (MD) studies have been performed to investigate biological processes involving proteins and lipids. CG force fields (FFs) in these MD studies often use implicit or nonpolar water models to reduce computational costs. CG-MD using water models cannot properly describe electrostatic screening effects owing to the hydration of ionic segments and thus cannot appropriately describe molecular events involving water channels and pores through lipid membranes. To overcome this issue, we developed a protein model in the pSPICA FF, in which a polar CG water model showing the proper dielectric response was adopted. The developed CG model greatly improved the transfer free energy profiles of charged side chain analogues across the lipid membrane. Application studies on melittin-induced membrane pores and mechanosensitive channels in lipid membranes demonstrated that CG-MDs using the pSPICA FF correctly reproduced the structure and stability of the pores and channels. Furthermore, the adsorption behavior of the highly charged nona-arginine peptides on lipid membranes changed with salt concentration, indicating the pSPICA FF is also useful for simulating protein adsorption on membrane surfaces.

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Section: Resultssupporting

confidence: 75%

“…15 pSPICA can thus provide a reasonable description of ion transport through MscL, which is consistent with the AA-MD and experimental results. 85,86 Note that the pore radius in the open state of MscL is sufficient to allow for the membrane transport of CG water, sodium ions, and chloride ions in pSPICA.…”

Section: Mechanosensitive Channel Of Large Conductancementioning

confidence: 99%