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Nobili G, Botticelli S, La Penna G, Morante S, Rossi G, Salina G. Probing protein stability: towards a computational atomistic, reliable, affordable, and improvable model. Front Mol Biosci 2023; 10:1122269. [PMID: 37325476 PMCID: PMC10267363 DOI: 10.3389/fmolb.2023.1122269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
We present an improved application of a recently proposed computational method designed to evaluate the change of free energy as a function of the average value of a suitably chosen collective variable in proteins. The method is based on a full atomistic description of the protein and its environment. The goal is to understand how the protein melting temperature changes upon single-point mutations, because the sign of the temperature variation will allow us to discriminate stabilizing vs. destabilizing mutations in protein sequences. In this refined application the method is based on altruistic well-tempered metadynamics, a variant of multiple-walkers metadynamics. The resulting metastatistics is then modulated by the maximal constrained entropy principle. The latter turns out to be especially helpful in free-energy calculations as it is able to alleviate the severe limitations of metadynamics in properly sampling folded and unfolded configurations. In this work we apply the computational strategy outlined above in the case of the bovine pancreatic trypsin inhibitor, a well-studied small protein, which is a reference for computer simulations since decades. We compute the variation of the melting temperature characterizing the folding-unfolding process between the wild-type protein and two of its single-point mutations that are seen to have opposite effect on the free energy changes. The same approach is used for free energy difference calculations between a truncated form of frataxin and a set of five of its variants. Simulation data are compared to in vitro experiments. In all cases the sign of the change of melting temperature is reproduced, under the further approximation of using an empirical effective mean-field to average out protein-solvent interactions.
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Affiliation(s)
- Germano Nobili
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Simone Botticelli
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Giovanni La Penna
- CNR-Istituto di Chimica Dei Composti Organometallici, Firenze, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
| | - Silvia Morante
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- CNR-Istituto di Chimica Dei Composti Organometallici, Firenze, Italy
| | - Giancarlo Rossi
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Roma, Italy
- INFN, Sezione di Roma Tor Vergata, Roma, Italy
- Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Roma, Italy
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Morante S, Botticelli S, Chiaraluce R, Consalvi V, La Penna G, Novak L, Pasquo A, Petrosino M, Proux O, Rossi G, Salina G, Stellato F. Metal Ion Binding in Wild-Type and Mutated Frataxin: A Stability Study. Front Mol Biosci 2022; 9:878017. [PMID: 35712353 PMCID: PMC9195147 DOI: 10.3389/fmolb.2022.878017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal.
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Affiliation(s)
- S. Morante
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
- *Correspondence: S. Morante ,
| | - S. Botticelli
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
| | - R. Chiaraluce
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universitá di Roma, Rome, Italy
| | - V. Consalvi
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universitá di Roma, Rome, Italy
| | - G. La Penna
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
- CNR—Istituto di Chimica dei Composti Organometallici, Firenze, Italy
| | - L. Novak
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universitá di Roma, Rome, Italy
| | - A. Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory FSN-TECFIS-DIM, Frascati, Italy
| | - M. Petrosino
- Chair of Pharmacology, Section of Medicine, University of Fribourg, Fribourg, Switzerland
| | - O. Proux
- Observatoire des Sciences de L’Univers de Grenoble, UAR 832 CNRS, Université Grenoble Alpes, Grenoble, France
| | - G. Rossi
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
- Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Roma, Italy
| | - G. Salina
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
| | - F. Stellato
- Dipartimento di Fisica, Universitá di Roma Tor Vergata, Rome, Italy
- INFN, Sezione di Roma Tor Vergata, Rome, Italy
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