@article {2018|2138,
	title = {Three Weaknesses for Three Perturbations: Comparing Protein Unfolding Under Shear, Force, and Thermal Stresses},
	journal = {J Phys Chem B},
	volume = {122},
	year = {2018},
	month = {Dec},
	pages = {11922-11930},
	abstract = {<p>The perturbation of a protein conformation by a physiological fluid flow is crucial in various biological processes including blood clotting and bacterial adhesion to human tissues. Investigating such mechanisms by computer simulations is thus of great interest, but it requires development of ad hoc strategies to mimic the complex hydrodynamic interactions acting on the protein from the surrounding flow. In this study, we apply the Lattice Boltzmann Molecular Dynamics (LBMD) technique built on the implicit solvent coarse-grained model for protein Optimized Potential for Efficient peptide structure Prediction (OPEP) and a mesoscopic representation of the fluid solvent, to simulate the unfolding of a small globular cold-shock protein in shear flow and to compare it to the unfolding mechanisms caused either by mechanical or thermal perturbations. We show that each perturbation probes a specific weakness of the protein and causes the disruption of the native fold along different unfolding pathways. Notably, the shear flow and the thermal unfolding exhibit very similar pathways, while because of the directionality of the perturbation, the unfolding under force is quite different. For force and thermal disruption of the native state, the coarse-grained simulations are compared to all-atom simulations in explicit solvent, showing an excellent agreement in the explored unfolding mechanisms. These findings encourage the use of LBMD based on the OPEP model to investigate how a flow can affect the function of larger proteins, for example, in catch-bond systems.</p>
},
	doi = {10.1021/acs.jpcb.8b08711},
	author = {Languin-Catto{\"e}n, Olivier and Melchionna, Simone and Philippe Derreumaux and Guillaume Stirnemann and Sterpone, Fabio}
}
@article {2016|1764,
	title = {Thermal activation of {\textquoteleft}allosteric-like{\textquoteright} large-scale motions in a eukaryotic Lactate Dehydrogenase.},
	journal = {Sci. Reports},
	volume = {7},
	year = {2016},
	pages = {41092},
	author = {M. Katava and M. Maccarini and G. Villain and A. Paciaroni and M. Sztucki and O. Ivanova and D. Madern and Fabio Sterpone}
}
@conference {2016|1608,
	title = {Toward Microscopic Simulations of Proteins in Cell-Like Environments},
	booktitle = {Biophys. J.},
	volume = {110},
	number = {3, 1},
	year = {2016},
	note = {60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, FEB 27-MAR 02, 2016},
	month = {feb},
	pages = {386A},
	publisher = {Biophys Soc},
	organization = {Biophys Soc},
	issn = {0006-3495},
	author = {Fabio Sterpone and Philippe Derreumaux and Melchionna, Simone}
}
@article {2012|1795,
	title = {Thermophilic proteins: insight and perspective from in silico experiments},
	journal = {Chem. Soc. Rev.},
	volume = {41},
	year = {2012},
	pages = {1665{\textendash}1676},
	publisher = {The Royal Society of Chemistry},
	abstract = {Proteins from thermophilic and hyperthermophilic organisms are stable and function at high temperatures (50-100 [degree]C). The importance of understanding the microscopic mechanisms underlying this thermal resistance is twofold: it is key for acquiring general clues on how proteins maintain their fold stable and for targeting those medical and industrial applications that aim at designing enzymes that can work under harsh conditions. In this tutorial review we first provide the general background of protein thermostability by specifically focusing on the structural and thermodynamic peculiarities; next{,} we discuss how computational studies based on Molecular Dynamics simulations can broaden and refine our knowledge on such special class of proteins.},
	author = {Sterpone, Fabio and Melchionna, Simone}
}
@article {2004|1718,
	title = {Temperature dehydration of C12E6 micelle},
	journal = {Langmuir},
	volume = {20},
	year = {2004},
	pages = {4311{\textendash}4314},
	author = {Fabio Sterpone and C. Pierleoni and G. Briganti and M. Marchi}
}
