Force Field development

The first two publications below entail corrections (NBFIX) of the CHARMM Van der Waals interactions between K+, Na+, Ca2+ and carboxylate groups of the protein. These are based on osmotic pressure and binding affinity calculations that are used to tune the parameters according to the associated experimental data. The derived K+ and Ca2+ parameters are now part of the official CHARMM force field.

The last two publications entail the derivation of charges and Van der Waals interactions of Ectoine and surfactant molecules based on quantum calculations and the antechamber package of AMBER.

Corresponding author: *

Joint first author: #

Liao J, MARINELLI F#, Lee C, Huang Y, Faraldo-Gómez JD, Jiang Y (2016). Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger. NAT STRUCT MOL BIOL. doi:10.1038/nsmb.3230. Link.
MARINELLI F, Almagor L, Hiller R, Giladi M, Khananshvili D, Faraldo-Gómez JD (2014). Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation. PROC NATL ACAD SCI USA. doi:10.1073/pnas.1415751111, PDF, Link
MARINELLI F*, Sorrenti A, Corvaglia V, Leone V, Mancini G (2012). Molecular description of the propagation of chirality from molecules to complex systems: different mechanisms controlled by hydrophobic interactions. CHEM-EUR J, vol. 18; p. 14680-14688, ISSN: 0947-6539, doi: 10.1002/chem.201202342, Link
MARINELLI F, Kuhlmann SI, Grell E, Kunte HJ, Ziegler C, Faraldo-Gomez JD (2011). Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins. PROC NATL ACAD SCI USA, vol. 108; p. E1285-E1292, ISSN: 0027-8424, doi: 10.1073/pnas.1112534108, PDF, Link

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