Kazi Amirul Hossain, Mariana Valério, Pedro Medina, et al.
All-atom umbrella sampling window (labelled 1.4) for the free energy of HER2 siRNA translocation from the LNP through the LNP-endosomal membrane stalk. The reaction coordinate is the Y distance between the LNP lipids near the RNA and the RNA phosphates. Data related to the manuscript 'When lipids embrace RNA: pH-driven dynamics and mechanisms of LNP-mediated siRNA delivery' (Fig. 4).
Kazi Amirul Hossain, Mariana Valério, Pedro Medina, et al.
All-atom umbrella sampling window (labelled 0.9) for the free energy of HER2 siRNA translocation from the LNP through the LNP-endosomal membrane stalk. The reaction coordinate is the Y distance between the LNP lipids near the RNA and the RNA phosphates. Data related to the manuscript 'When lipids embrace RNA: pH-driven dynamics and mechanisms of LNP-mediated siRNA delivery' (Fig. 4).
Kazi Amirul Hossain, Mariana Valério, Pedro Medina, et al.
Calibration run for the constant pH MD parametrization of the ionizable lipid DLin-MC3-DMA (MC3), following the phbuilder workflow: a single MC3 molecule in water with ions and a buffer particle, position-restrained, with lambda fixed at 0.00 (buffer 1.00), 1 ns, used to fit the dV/dlambda correction (Fig. S19 of 'When lipids embrace RNA: pH-driven dynamics and mechanisms of LNP-mediated siRNA delivery').
Kazi Amirul Hossain, Mariana Valério, Pedro Medina, et al.
All-atom (CHARMM36) simulation of the small HER2-siRNA LNP in contact with an endosomal membrane vesicle after stalk formation, backmapped from Martini 3 with CG2AT, in which 50% of the protonated ionizable lipids (MC3H) were converted to neutral MC3. Part of the study of pH-driven mechanisms of LNP-mediated siRNA endosomal escape.
Classical MD simulations of pre-embedded dimeric horizontal SoD complex in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-unrestrained and NBFIX conditions (replica 1).
Classical MD simulations of pre-embedded horizontal SoD in large POPC:cholesterol (2:1) bilayers (150 Å x 150 Å) , simulated at +100 mV with COM-restraints and NBFIX conditions (replica 6).
Classical MD simulations of pre-embedded horizontal SoD in large POPC:cholesterol (2:1) bilayers (150 Å x 150 Å) , simulated at +100 mV with COM-unrestrained and NBFIX conditions (replica 5).
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-unrestrained and prosECCo75 applied to FE2P only (replica 2).
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-restraints and prosECCo75 applied to FE2P only (replica 6).
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-unrestrained and prosECCo75 applied to all charged residues (replica 3).
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-restraints and NBFIX conditions (replica 6).
Classical MD simulations of pre-embedded horizontal SoD in POPC:cholesterol (2:1) bilayers, simulated at +100 mV with COM-restraints and NBFIX conditions (replica 4).