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#31 · Structural bio & protein design

Protonation and ion handling shape membrane transport and penetration in MD simulations

2 preprints · 1 published
Items per day, last 8 weekstoday: 3

The dominant thread is explicit molecular dynamics of membrane-associated systems, in which protonation state and ion handling are treated as resolved variables rather than fixed assumptions. Long-timescale simulations of the asymmetric dual-pore Fluc channel identify two distinct fluoride conduction mechanisms, with a dynamic role for the central region and a transporting role for sodium. All-atom simulations of Colistin A with a Pseudomonas aeruginosa outer membrane model show that the +2 protonation state penetrates deeper than other forms. The Brucella melitensis type IV secretion system preprint provides static structural characterization for virtual screening and does not share this dynamic thread. What is new relative to static structural description is the tracking of protonation-dependent and environment-dependent states across these systems.

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Preprints

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