@article {2019|2121,
	title = {OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field},
	journal = {Journal of Chemical Theory and Computation},
	volume = {15},
	year = {2019},
	pages = {3875-3888},
	doi = {10.1021/acs.jctc.9b00202},
	url = {https://doi.org/10.1021/acs.jctc.9b00202},
	author = {Barroso da Silva, Fernando Luis and Sterpone, Fabio and Philippe Derreumaux}
}
@article {2017|2041,
	title = {Fast coarse-grained model for RNA titration.},
	journal = {J Chem Phys},
	volume = {146},
	year = {2017},
	month = {2017 Jan 21},
	pages = {035101},
	abstract = {<p>A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-H{\"u}ckel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKshifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.</p>
},
	keywords = {Azotobacter vinelandii, Introns, Models, Chemical, Molecular Dynamics Simulation, Monte Carlo Method, Protein Structure, Secondary, Protons, RNA, RNA, Catalytic, Titrimetry},
	issn = {1089-7690},
	doi = {10.1063/1.4972986},
	author = {Barroso da Silva, Fernando Luis and Philippe Derreumaux and Pasquali, Samuela}
}
@article {2017|2038,
	title = {Protein-RNA complexation driven by the charge regulation mechanism.},
	journal = {Biochem Biophys Res Commun},
	year = {2017},
	month = {2017 Jul 12},
	abstract = {<p>Electrostatic interactions play a pivotal role in many (bio)molecular association processes. The molecular organization and function in biological systems are largely determined by these interactions from pure Coulombic contributions to more peculiar mesoscopic forces due to ion-ion correlation and proton fluctuations. The latter is a general electrostatic mechanism that gives attraction particularly at low electrolyte concentrations. This charge regulation mechanism due to titrating amino acid and nucleotides residues is discussed here in a purely electrostatic framework. By means of constant-pH Monte Carlo simulations based on a fast coarse-grained titration proton scheme, a new computer molecular model was devised to study protein-RNA interactions. The complexation between the RNA silencing suppressor p19 viral protein and the 19-bp small interfering RNA was investigated at different solution pH and salt conditions. The outcomes illustrate the importance of the charge regulation mechanism that enhances the association between these macromolecules in a similar way as observed for other protein-polyelectrolyte systems typically found in colloidal science. Due to the highly negative charge of RNA, the effect is more pronounced in this system as predicted by the Kirkwood-Shumaker theory. Our results contribute to the general physico-chemical understanding of macromolecular complexation and shed light on the extensive role of RNA in the cell\&$\#$39;s life.</p>
},
	issn = {1090-2104},
	doi = {10.1016/j.bbrc.2017.07.027},
	author = {Barroso da Silva, Fernando Luis and Philippe Derreumaux and Pasquali, Samuela}
}
@article {2016|1765,
	title = {Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin},
	journal = {Soft Matter},
	volume = {12},
	number = {25},
	year = {2016},
	pages = {5600{\textendash}5612},
	abstract = {Spider silk is a fascinating material combining mechanical properties such as maximum strength and high toughness comparable or better than man-made materials, with biocompatible degradability characteristics. Experimental measurements have shown that pH triggers the dimer formation of the N-terminal domain (NTD) of the major ampullate spidroin 1 (MaSp 1). A coarse-grained model accounting for electrostatics, van der Waals and pH-dependent charge-fluctuation interactions, by means of Monte Carlo simulations, gave us a more comprehensive view of the NTD dimerization process. A detailed analysis of the electrostatic properties and free energy derivatives for the NTD homoassociation was carried out at different pH values and salt concentrations for the protein wild type and for several mutants. We observed an enhancement of dipole-dipole interactions at pH 6 due to the ionization of key amino acids, a process identified as the main driving force for dimerization. Analytical estimates based on the DVLO theory framework corroborate our findings. Molecular dynamics simulations using the OPEP coarse-grained force field for proteins show that the mutant E17Q is subject to larger structural fluctuations when compared to the wild type. Estimates of the association rate constants for this mutant were evaluated by the Debye-Smoluchowski theory and are in agreement with the experimental data when thermally relaxed structures are used instead of the crystallographic data. Our results can contribute to the design of new mutants with specific association properties.},
	issn = {1744-683X},
	doi = {10.1039/c6sm00860g},
	author = {Barroso da Silva, Fernando Luis and Pasquali, Samuela and Philippe Derreumaux and Dias, Luis Gustavo}
}
