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4. Se non strozza ingrassa?

Author

Donini, Lorenzo M., Sorabella, Daniele, Frigerio, Francesco, Mocini, Edoardo, Muzzioli, Luca, Pinto, Alessandro, Poggiogalle, Eleonora, and Giusti, Anna Maria

Published
2023
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5. Indoor noise level measurements and subjective comfort: feasibility of smartphone-based participatory experiments

Author

Rozzi, Carlo Andrea, Frigerio, Francesco, Balletti, Luca, Mattoni, Silvia, Grasso, Daniele, and Fogola, Jacopo

Subjects
Physics - Physics and Society
Abstract

We designed and performed a participatory sensing initiative to explore the reliability and effectiveness of a distributed network of citizen-operated smartphones in evaluating the impact of environmental noise in residential areas. We asked participants to evaluate the comfort of their home environment in different situations and at different times, to select the most and least comfortable states and to measure noise levels with their smartphones. We then correlated comfort ratings with noise measurements and additional contextual information provided by participants. We discuss how to strengthen methods and procedures, particularly regarding the calibration of the devices, in order to make similar citizen-science efforts effective at monitoring environmental noise and planning long-term solutions to human well-being.

Published
2021
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8. Sarcopenic obesity research perspectives outlined by the sarcopenic obesity global leadership initiative (SOGLI) – Proceedings from the SOGLI consortium meeting in Rome November 2022

Author

Bosy-Westphal, Anja, Brunani, Amelia, Capodaglio, Paolo, Coletti, Dario, Ferretti, Elisabetta, Frigerio, Francesco, Giustina, Andrea, Lenzi, Andrea, Marini, Elisabetta, Migliaccio, Silvia, Minnetti, Marianna, Mocini, Edoardo, Moro, Tatiana, Muscaritoli, Maurizio, Noirez, Philippe, Paoli, Antonio, Rondanelli, Mariangela, Rughetti, Auralia, Schoufour, Josje D., Skalska, Anna, Topinkova, Eva, Wakabayashi, Hidekata, Yu, Jianchun, Gortan Cappellari, Gianluca, Guillet, Christelle, Poggiogalle, Eleonora, Ballesteros Pomar, Maria D., Batsis, John A., Boirie, Yves, Breton, Irene, Frara, Stefano, Genton, Laurence, Gepner, Yftach, Gonzalez, Maria Cristina, Heymsfield, Steven B., Kiesswetter, Eva, Laviano, Alessandro, Prado, Carla M., Santini, Ferruccio, Serlie, Mireille J., Siervo, Mario, Villareal, Dennis T., Volkert, Dorothee, Voortman, Trudy, Weijs, Peter JM., Zamboni, Mauro, Bischoff, Stephan C., Busetto, Luca, Cederholm, Tommy, Barazzoni, Rocco, and Donini, Lorenzo M.

Published
2023
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12. Integrating Molecular Dynamics and Machine Learning Algorithms to Predict the Functional Profile of Kinase Ligands

Author

Frasnetti, Elena, Cucchi, Ivan, Pavoni, Silvia, Frigerio, Francesco, Cinquini, Fabrizio, Serapian, Stefano A., Pavarino, Luca F., and Colombo, Giorgio

Abstract

The modulation of protein function via designed small molecules is providing new opportunities in chemical biology and medicinal chemistry. While drugs have traditionally been developed to block enzymatic activities through active site occupation, a growing number of strategies now aim to control protein functions in an allosteric fashion, allowing for the tuning of a target’s activation or deactivation via the modulation of the populations of conformational ensembles that underlie its function. In the context of the discovery of new active leads, it would be very useful to generate hypotheses for the functional impact of new ligands. Since the discovery and design of allosteric modulators (inhibitors/activators) is still a challenging and often serendipitous target, the development of a rapid and robust approach to predict the functional profile of a new ligand would significantly speed up candidate selection. Herein, we present different machine learning (ML) classifiers to distinguish between potential orthosteric and allosteric binders. Our approach integrates information on the chemical fingerprints of the ligands with descriptors that recapitulate ligand effects on protein functional motions. The latter are derived from molecular dynamics (MD) simulations of the target protein in complex with orthosteric or allosteric ligands. In this framework, we train and test different ML architectures, which are initially probed on the classification of orthosteric versus allosteric ligands for cyclin-dependent kinases (CDKs). The results demonstrate that different ML methods can successfully partition allosteric versus orthosteric effectors (although to different degrees). Next, we further test the models with FDA-approved CDK drugs, not included in the original dataset, as well as ligands that target other kinases, to test the range of applicability of these models outside of the domain on which they were developed. Overall, the results show that enriching the training dataset with chemical physics-based information on the protein–ligand dynamic cross-talk can significantly expand the reach and applicability of approaches for the prediction and classification of the mode of action of small molecules.

Published
2024
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18. Molecular mechanisms of chaperone‐directed protein folding: Insights from atomistic simulations.

Author

Castelli, Matteo, Magni, Andrea, Bonollo, Giorgio, Pavoni, Silvia, Frigerio, Francesco, Oliveira, A. Sofia F., Cinquini, Fabrizio, Serapian, Stefano A., and Colombo, Giorgio

Abstract

Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task‐specific co‐chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co‐chaperone Hop client‐loading and the GR:Hsp90:co‐chaperone p23 client‐maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide‐encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross‐talk emerges between the chaperone dynamics states and remodeling of client‐interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences

Author

Triveri, Alice, primary, Casali, Emanuele, additional, Frasnetti, Elena, additional, Doria, Filippo, additional, Frigerio, Francesco, additional, Cinquini, Fabrizio, additional, Pavoni, Silvia, additional, Moroni, Elisabetta, additional, Marchetti, Filippo, additional, Serapian, Stefano A., additional, and Colombo, Giorgio, additional

Published
2023
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23. Sarcopenic obesity research perspectives outlined by the sarcopenic obesity global leadership initiative (SOGLI) – Proceedings from the SOGLI consortium meeting in rome November 2022

Author

Gortan Cappellari, Gianluca, primary, Guillet, Christelle, additional, Poggiogalle, Eleonora, additional, Ballesteros Pomar, Maria D., additional, Batsis, John A., additional, Boirie, Yves, additional, Breton, Irene, additional, Frara, Stefano, additional, Genton, Laurence, additional, Gepner, Yftach, additional, Gonzalez, Maria Cristina, additional, Heymsfield, Steven B., additional, Kiesswetter, Eva, additional, Laviano, Alessandro, additional, Prado, Carla M., additional, Santini, Ferruccio, additional, Serlie, Mireille J., additional, Siervo, Mario, additional, Villareal, Dennis T., additional, Volkert, Dorothee, additional, Voortman, Trudy, additional, Weijs, Peter JM., additional, Zamboni, Mauro, additional, Bischoff, Stephan C., additional, Busetto, Luca, additional, Cederholm, Tommy, additional, Barazzoni, Rocco, additional, Donini, Lorenzo M., additional, Bosy-Westphal, Anja, additional, Brunani, Amelia, additional, Capodaglio, Paolo, additional, Coletti, Dario, additional, Ferretti, Elisabetta, additional, Frigerio, Francesco, additional, Giustina, Andrea, additional, Lenzi, Andrea, additional, Marini, Elisabetta, additional, Migliaccio, Silvia, additional, Minnetti, Marianna, additional, Mocini, Edoardo, additional, Moro, Tatiana, additional, Muscaritoli, Maurizio, additional, Noirez, Philippe, additional, Paoli, Antonio, additional, Rondanelli, Mariangela, additional, Rughetti, Auralia, additional, Schoufour, Josje D., additional, Skalska, Anna, additional, Topinkova, Eva, additional, Wakabayashi, Hidekata, additional, and Yu, Jianchun, additional

Published
2023
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24. New Advances in Metabolic Syndrome, from Prevention to Treatment: The Role of Diet and Food

Author

Ambroselli, Donatella, primary, Masciulli, Fabrizio, additional, Romano, Enrico, additional, Catanzaro, Giuseppina, additional, Besharat, Zein Mersini, additional, Massari, Maria Chiara, additional, Ferretti, Elisabetta, additional, Migliaccio, Silvia, additional, Izzo, Luana, additional, Ritieni, Alberto, additional, Grosso, Michela, additional, Formichi, Caterina, additional, Dotta, Francesco, additional, Frigerio, Francesco, additional, Barbiera, Eleonora, additional, Giusti, Anna Maria, additional, Ingallina, Cinzia, additional, and Mannina, Luisa, additional

Published
2023
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26. Characterisation of the Surfactant Shell Stabilising Calcium Carbonate Dispersions in Overbased Detergent Additives: Molecular Modelling and Spin-Probe-ESR Studies

Author

Frigerio, Francesco, Montanari, Luciano, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Rangan, C. Pandu, editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Shi, Yong, editor, van Albada, Geert Dick, editor, Dongarra, Jack, editor, and Sloot, Peter M. A., editor

Published
2007
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34. Computational Studies of SARS-CoV-2 3CLpro : Insights from MD Simulations

Author

Grottesi, Alessandro, Bešker, Neva, Emerson, Andrew, Manelfi, Candida, Beccari, Andrea R., Frigerio, Francesco, Lindahl, Erik, Cerchia, Carmen, Talarico, Carmine, Grottesi, Alessandro, Bešker, Neva, Emerson, Andrew, Manelfi, Candida, Beccari, Andrea R., Frigerio, Francesco, Lindahl, Erik, Cerchia, Carmen, and Talarico, Carmine

Abstract

Given the enormous social and health impact of the pandemic triggered by severe acute respiratory syndrome 2 (SARS-CoV-2), the scientific community made a huge effort to provide an immediate response to the challenges posed by Coronavirus disease 2019 (COVID-19). One of the most important proteins of the virus is an enzyme, called 3CLpro or main protease, already identified as an important pharmacological target also in SARS and Middle East respiratory syndrome virus (MERS) viruses. This protein triggers the production of a whole series of enzymes necessary for the virus to carry out its replicating and infectious activities. Therefore, it is crucial to gain a deeper understanding of 3CLpro structure and function in order to effectively target this enzyme. All-atoms molecular dynamics (MD) simulations were performed to examine the different conformational behaviors of the monomeric and dimeric form of SARS-CoV-2 3CLpro apo structure, as revealed by microsecond time scale MD simulations. Our results also shed light on the conformational dynamics of the loop regions at the entry of the catalytic site. Studying, at atomic level, the characteristics of the active site and obtaining information on how the protein can interact with its substrates will allow the design of molecules able to block the enzymatic function crucial for the virus.

Published
2020
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39. Reconstituted high-density lipoproteins with a disulfide-linked apolipoprotein A-I dimer: evidence for restricted particle size heterogeneity

Author

Calabresi, Laura, Vecchio, Guiseppe, Frigerio, Francesco, Vavassori, Laura, Sirtori, Cesare R., and Francheschini, Guido

Subjects
High density lipoproteins -- Analysis, Apolipoproteins -- Analysis, Biological sciences, Chemistry
Abstract

The lipid-binding properties of apolipopotein recombinant homodimer (A-I(sub M)/A-I(sub M)) and normal apolipoprotein (apoA-I) were comparatively studied. The dimerization of apoA-I did not affect the rate off association of apoA-I with phospholipids. The introduction of an interchain disulfide bridge in apoA-I limited the high-density lipoprotein heterogeneity. A-I(sub M)/A-I(sub M) behaved as a stable form of apoA-I.

Published
1997

45. Macular degeneration: peculiar sunlight exposure in an agricultural worker.

Author

ODDONE, ENRICO, TAINO, GIUSEPPE, VITA, SILVIA, SCHIMD, MONICA, FRIGERIO, FRANCESCO, and IMBRIANI, MARCELLO

Abstract

Copyright of La Medicina del Lavoro is the property of Mattioli 1885 SpA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2019
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46. Design and Test of Molecules that Interfere with the Recognition Mechanisms between the SARS-CoV-2 Spike Protein and Its Host Cell Receptors

Author

Scantamburlo, Francesca, Masgras, Ionica, Ciscato, Francesco, Laquatra, Claudio, Frigerio, Francesco, Cinquini, Fabrizio, Pavoni, Silvia, Triveri, Alice, Frasnetti, Elena, Serapian, Stefano A., Colombo, Giorgio, Rasola, Andrea, and Moroni, Elisabetta

Abstract

The disruptive impact of the COVID-19 pandemic has led the scientific community to undertake an unprecedented effort to characterize viral infection mechanisms. Among these, interactions between the viral glycosylated Spike and the human receptors ACE2 and TMPRSS2 are key to allowing virus invasion. Here, we report and test a fully rational methodology to design molecules that are capable of perturbing the interactions between these critical players in SARS-CoV-2 pathogenicity. To this end, we computationally identify substructures on the fully glycosylated Spike protein that are not intramolecularly optimized and are thus prone to being stabilized by forming complexes with ACE2 and TMPRSS2. With the aim of competing with the Spike-mediated cell entry mechanisms, we have engineered the predicted putative interaction regions in the form of peptide mimics that could compete with Spike for interaction with ACE2 and/or TMPRSS2. Experimental models of viral entry demonstrate that the designed molecules are able to interfere with viral entry into ACE2/TMPRSS2 expressing cells, while they have no effects on the entry of control viral particles that do not harbor the Spike protein or on the entry of Spike-presenting viral particles into cells that do not display its receptors on their surface.

Published
2024
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47. Control measurements for lasers in physiotherapy.

Author

Bivona, Rosanna, Tomaselli, Alessandra, and Frigerio, Francesco

Subjects
PHYSICAL therapy, SKIN diseases, MITOCHONDRIA, PHYSIOLOGICAL effects of radiation, PULSED lasers
Abstract

Copyright of Giornale Italiano di Medicina del Lavoro ed Ergonomia is the property of Giornale Italiano di Medicina del Lavoro ed Ergonomia Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2017

49. Tu1168 Identical Diagnostic Performance of Two Commercially Available Tests for Infliximab Trough Levels (IFX-Tl) and Antibodies to Infliximab (ATI) Titration in Inflammatory Bowel Disease (IBD): Promonitor and Immunodiagnostik Tests

Author

Daperno, Marco, primary, Frigerio, Francesco, additional, Guiotto, Cristina, additional, Germano, Laura, additional, Ercole, Elena, additional, Aricò, Sarino, additional, Fracchia, Mario, additional, Rigazio, Caterina, additional, Lavagna, Alessandro, additional, Pellerito, Raffaele, additional, Migliardi, Marco, additional, and Rocca, Rodolfo, additional

Published
2013
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