@article {2016|1687,
	title = {Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue},
	journal = {J. Phys. Chem. B},
	volume = {120},
	year = {2016},
	pages = {2721{\textendash}2730},
	abstract = {<p>Comparing homologous enzymes adapted to different thermal environments aids to shed light on their delicate stability/function trade-off. Protein mechanical rigidity was postulated to secure stability and high-temperature functionality of thermophilic proteins. In this work, we challenge the corresponding-state principle for a pair of homologous GTPase domains by performing extensive molecular dynamics simulations, applying conformational and kinetic clustering, as well as exploiting an enhanced sampling technique (REST2). While it was formerly shown that enhanced protein flexibility and high temperature stability can coexist in the apo hyperthermophilic variant, here we focus on the holo states of both homologues by mimicking the enzymatic turnover. We clearly show that the presence of the ligands affects the conformational landscape visited by the proteins, and that the corresponding state principle applies for some functional modes. Namely, in the hyperthermophilic species, the flexibility of the effec...</p>},
	issn = {15205207},
	doi = {10.1021/acs.jpcb.6b00306},
	author = {Katava, Marina and Kalimeri, Maria and Guillaume Stirnemann and Fabio Sterpone}
}
@article {2015|1668,
	title = {Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains.},
	journal = {J. Phys. Chem. B},
	volume = {119},
	year = {2015},
	month = {jul},
	pages = {8939{\textendash}49},
	abstract = {<p>In this work, we address the question of whether the enhanced stability of thermophilic proteins has a direct connection with internal hydration. Our model systems are two homologous G domains of different stability: the mesophilic G domain of the elongation factor thermal unstable protein from E. coli and the hyperthermophilic G domain of the EF-1α protein from S. solfataricus. Using molecular dynamics simulation at the microsecond time scale, we show that both proteins host water molecules in internal cavities and that these molecules exchange with the external solution in the nanosecond time scale. The hydration free energy of these sites evaluated via extensive calculations is found to be favorable for both systems, with the hyperthermophilic protein offering a slightly more favorable environment to host water molecules. We estimate that, under ambient conditions, the free energy gain due to internal hydration is about 1.3 kcal/mol in favor of the hyperthermophilic variant. However, we also find that, at the high working temperature of the hyperthermophile, the cavities are rather dehydrated, meaning that under extreme conditions other molecular factors secure the stability of the protein. Interestingly, we detect a clear correlation between the hydration of internal cavities and the protein conformational landscape. The emerging picture is that internal hydration is an effective observable to probe the conformational landscape of proteins. In the specific context of our investigation, the analysis confirms that the hyperthermophilic G domain is characterized by multiple states and it has a more flexible structure than its mesophilic homologue.</p>},
	issn = {1520-5207},
	doi = {10.1021/jp507571u},
	author = {Rahaman, Obaidur and Kalimeri, Maria and Melchionna, Simone and J{\'e}r{\^o}me H{\'e}nin and Fabio Sterpone}
}
@article {2014|1964,
	title = {Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase},
	journal = {Plos One},
	volume = {9},
	number = {12},
	year = {2014},
	month = {dec},
	pages = {e113895},
	url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0113895},
	author = {Kalimeri, Maria and Girard, Eric and Madern, Dominique and Sterpone, Fabio}
}
@article {2013|1926,
	title = {How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain},
	journal = {J. Phys. Chem. B},
	volume = {117},
	number = {44},
	year = {2013},
	month = {nov},
	pages = {13775{\textendash}13785},
	author = {Kalimeri, Maria and Rahaman, Obaidur and Melchionna, Simone and Sterpone, Fabio}
}
@article {2013|1892,
	title = {Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation},
	journal = {J. Chem. Theory Comput.},
	volume = {9},
	number = {10},
	year = {2013},
	month = {oct},
	pages = {4574{\textendash}4584},
	doi = {10.1021/ct4003493},
	author = {Sterpone, Fabio and Phuong Hoang Nguyen and Kalimeri, Maria and Philippe Derreumaux}
}
@inbook {2013|1533,
	title = {Inquiring Protein Thermostability: Is Resistance to Temperature Stress a Rigidity/Flexibility Trade-off?},
	booktitle = {Proceedings of the European Conference on Complex Systems 2012},
	year = {2013},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	author = {Kalimeri, Maria and Melchionna, Simone and Sterpone, Fabio}
}
