Solid-State NMR Validation of OPLS4: Structure of PC-Lipid Bilayers and Its Modulation by Dehydration.

Atomistic molecular dynamics (MD) simulations are a much-used tool for investigating the structure and dynamics of biomembranes with atomic resolution. The validity of the representations obtained is determined by the accuracy and realism of the MD model (force field). Here, we evaluated the proprietary OPLS4 force field of Schrödinger, Inc.

Targeting ocular tissues with intravenously administered aptamers selected by SELEX.

Ocular diseases create a significant economic burden and decrease in quality of life worldwide. Drugs and carrier molecules that penetrate ocular tissues after intravenous administration are needed for more efficient and patient-friendly treatment of ocular diseases. Here, ocular barrier-penetrating aptamers were selected through the utilization of SELEX and intravenous injection in rats.

RNA-protein complexes and force field polarizability.

Molecular dynamic (MD) simulations offer a way to study biomolecular interactions and their dynamics at the atomistic level. There are only a few studies of RNA-protein complexes in MD simulations, and here we wanted to study how force fields differ when simulating RNA-protein complexes: 1) argonaute 2 with bound guide RNA and a target RNA, 2) CasPhi-2 bound to CRISPR RNA and 3) Retinoic acid-inducible gene I C268F variant in complex with double-stranded RNA. We tested three non-polarizable force fields: Amber protein force fields ff14SB and ff19SB with RNA force field OL3, and the all-atom OPLS4 force field.

Structure of POPC Lipid Bilayers in OPLS3e Force Field.

It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon-hydrogen order parameters of POPC (1-palmitoyl-2-oleoylphosphatidylcholine) lipid bilayers at varying hydration conditions and ion concentrations. The results show that OPLS3e behaves similarly to the CHARMM36 force field and relatively accurately follows the experimentally measured for the lipid headgroup, the glycerol backbone, and the acyl tails.