scholarly journals Transmembrane Potential of Physiologically Relevant Model Membranes: Effects of Membrane Asymmetry

Author(s):  
Xubo Lin ◽  
Alemayehu A. Gorfe

<div><div>Transmembrane potential difference (𝑉௠) plays important roles in regulating various biological</div><div>processes. At the macro level, 𝑉௠ can be experimentally measured or calculated using the Nernst</div><div>or Goldman-Hodgkin-Katz equation. However, the atomic details responsible for its generation</div><div>and impact on protein and lipid dynamics still need to be further elucidated. In this work, we</div><div>performed a series of all-atom molecular dynamics simulations of symmetric model membranes of</div><div>various lipid compositions and cation contents to evaluate the relationship between membrane</div><div>asymmetry and 𝑉௠. Specifically, we studied the impact of the asymmetric distribution of POPS (1-</div><div>palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine), PIP2 (phosphatidylinositol 4,5-bisphosphate),</div><div>𝑁𝑎ା, 𝐾ା and 𝐶𝑎ଶା on 𝑉௠ using atomically detailed molecular dynamics simulations of symmetric</div><div>model membranes. The results suggest that, for an asymmetric POPC-POPC/POPS bilayer in the</div><div>presence of NaCl, enrichment of the monovalent anionic lipid POPS in the inner leaflet polarizes</div><div>the membrane (∆𝑉௠ < 0). Intriguingly, replacing a third of the POPS lipids by the polyvalent</div><div>anionic signaling lipid PIP2 counteracts this effect, resulting in a smaller negative membrane</div><div>potential. We also found that replacing 𝑁𝑎ା ions in the inner region by 𝐾ା depolarizes the</div><div>membrane (∆𝑉௠ > 0), whereas replacing by 𝐶𝑎ଶା polarizes the membrane. These divergent effects</div><div>arise from variations in the strength of cation-lipid interactions and are correlated with changes in</div><div>lipid chain order and head group orientation. </div></div>

2020 ◽  
Author(s):  
Xubo Lin ◽  
Alemayehu A. Gorfe

<div><div>Transmembrane potential difference (𝑉௠) plays important roles in regulating various biological</div><div>processes. At the macro level, 𝑉௠ can be experimentally measured or calculated using the Nernst</div><div>or Goldman-Hodgkin-Katz equation. However, the atomic details responsible for its generation</div><div>and impact on protein and lipid dynamics still need to be further elucidated. In this work, we</div><div>performed a series of all-atom molecular dynamics simulations of symmetric model membranes of</div><div>various lipid compositions and cation contents to evaluate the relationship between membrane</div><div>asymmetry and 𝑉௠. Specifically, we studied the impact of the asymmetric distribution of POPS (1-</div><div>palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine), PIP2 (phosphatidylinositol 4,5-bisphosphate),</div><div>𝑁𝑎ା, 𝐾ା and 𝐶𝑎ଶା on 𝑉௠ using atomically detailed molecular dynamics simulations of symmetric</div><div>model membranes. The results suggest that, for an asymmetric POPC-POPC/POPS bilayer in the</div><div>presence of NaCl, enrichment of the monovalent anionic lipid POPS in the inner leaflet polarizes</div><div>the membrane (∆𝑉௠ < 0). Intriguingly, replacing a third of the POPS lipids by the polyvalent</div><div>anionic signaling lipid PIP2 counteracts this effect, resulting in a smaller negative membrane</div><div>potential. We also found that replacing 𝑁𝑎ା ions in the inner region by 𝐾ା depolarizes the</div><div>membrane (∆𝑉௠ > 0), whereas replacing by 𝐶𝑎ଶା polarizes the membrane. These divergent effects</div><div>arise from variations in the strength of cation-lipid interactions and are correlated with changes in</div><div>lipid chain order and head group orientation. </div></div>


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Renu Wadhwa ◽  
Neetu Singh Yadav ◽  
Shashank P. Katiyar ◽  
Tomoko Yaguchi ◽  
Chohee Lee ◽  
...  

AbstractPoor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs—withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.


2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.


2014 ◽  
Vol 118 (19) ◽  
pp. 5119-5129 ◽  
Author(s):  
Sara K. Hansen ◽  
Mikkel Vestergaard ◽  
Lea Thøgersen ◽  
Birgit Schiøtt ◽  
Niels Chr. Nielsen ◽  
...  

2018 ◽  
Vol 20 (23) ◽  
pp. 15841-15851 ◽  
Author(s):  
Xubo Lin ◽  
Vinay Nair ◽  
Yong Zhou ◽  
Alemayehu A. Gorfe

Transmembrane potential modulates the structure and dynamics of lipid head-groups and acyl chains.


2019 ◽  
Vol 7 (45) ◽  
pp. 14198-14204
Author(s):  
Lu Ning ◽  
Guangchao Han ◽  
Yuanping Yi

The impact of the branching positions of alkyl chains on temperature dependent aggregation is rationalized by atomistic molecular dynamics simulations.


Soft Matter ◽  
2017 ◽  
Vol 13 (41) ◽  
pp. 7665-7676 ◽  
Author(s):  
Upayan Baul ◽  
Satyavani Vemparala

Using atomistic molecular dynamics simulations, the role of lipid composition in the interactions of multiple methacrylate antimicrobial polymer agents with model membranes, and the consequent response of the membranes is studied.


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