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Your search keyword '"Daidone, Isabella"' showing total 15 results
Start Over Author "Daidone, Isabella" Publisher royal society of chemistry (rsc)
15 results on '"Daidone, Isabella"'

3. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Author

Pavlova, Anna, primary, Lynch, Diane L., additional, Daidone, Isabella, additional, Zanetti-Polzi, Laura, additional, Smith, Micholas Dean, additional, Chipot, Chris, additional, Kneller, Daniel W., additional, Kovalevsky, Andrey, additional, Coates, Leighton, additional, Golosov, Andrei A., additional, Dickson, Callum J., additional, Velez-Vega, Camilo, additional, Duca, José S., additional, Vermaas, Josh V., additional, Pang, Yui Tik, additional, Acharya, Atanu, additional, Parks, Jerry M., additional, Smith, Jeremy C., additional, and Gumbart, James C., additional

Published
2021
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15. Modeling amino-acid side chain infrared spectra: the case of carboxylic residues

Author

Nicola Tasinato, Vincenzo Barone, Isabella Daidone, Laura Zanetti-Polzi, Sandra Mónica Vieira Pinto, Andrea Amadei, VIEIRA PINTO, Sandra Mónica, Tasinato, Nicola, Barone, Vincenzo, Amadei, Andrea, Zanetti-Polzi, Laura, and Daidone, Isabella

Subjects
Materials science, Spectrophotometry, Infrared, Infrared, Glutamic Acid, General Physics and Astronomy, Infrared spectroscopy, Protonation, Molecular Dynamics Simulation, Spectral line, Molecular dynamics, Protein structure, Settore CHIM/02, Side chain, Amino Acids, Physical and Theoretical Chemistry, Spectroscopy, Aspartic Acid, Quantitative Biology::Biomolecules, Protein, Proteins, Quantum Theory, Amino Acid, Crystallography, Spectrophotometry
Abstract

Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes. While the amide I band provides information on protein secondary structures, amino acid side chains are used as IR probes for the investigation of protein reactions, such as proton pumping in rhodopsins. In this work, we calculate the IR spectra of the solvated aspartic acid, with both zwitterionic and protonated backbones, and of a capped form, i.e. mimicking the aspartic acid residue in proteins, by means of molecular dynamics (MD) simulations and the perturbed matrix method (PMM). This methodology has already proved its good modeling capabilities for the amide I mode and is here extended to the treatment of protein side chains. The computed side chain vibrational signal is in very good agreement with the experimental one, well reproducing both the peak frequency position and the bandwidth. In addition, the MD-PMM approach proposed here is able to reproduce the small frequency shift (5-10 cm-1) experimentally observed between the protonated and zwitterionic forms, showing that such a shift depends on the excitonic coupling between the modes localized on the side chain and on the backbone in the protonated form. The spectrum of the capped form, in which the amide I band is also calculated, agrees well with the corresponding experimental spectrum. The reliable calculation of the vibrational bands of carboxyl-containing side chains provides a useful tool for the interpretation of experimental spectra.

Published
2020

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