@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|2096,
	title = {String method solution of the gating pathways for a pentameric ligand-gated ion channel.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {114},
	year = {2017},
	month = {2017 05 23},
	pages = {E4158-E4167},
	abstract = {<p>Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.</p>
},
	keywords = {Computer Simulation, Ligand-Gated Ion Channels, Models, Biological, Models, Chemical},
	issn = {1091-6490},
	doi = {10.1073/pnas.1617567114},
	author = {Lev, Bogdan and Murail, Samuel and Poitevin, Fr{\'e}d{\'e}ric and Cromer, Brett A and Marc Baaden and Delarue, Marc and Allen, Toby W}
}
