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Sassi P, Comez L, D'Amico F, Rossi B, Bartolini G, Fioretto D, Paolantoni M. Ultraviolet Resonant Raman Scattering of Electrolyte Solutions. Appl Spectrosc 2024:37028241245443. [PMID: 38632936 DOI: 10.1177/00037028241245443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Saltwater stands as the most prevalent liquid on Earth. Consequently, substantial interest has been directed toward its characterization, both as an independent system and as a solvent for complex structures such as biomacromolecules. In the last few decades, special emphasis was placed on the investigation of the hydration properties of ions for the fundamental role they play in numerous chemical processes. In this study, we employed multi-wavelength Raman spectroscopy to examine the hydration shell surrounding bromide ions in solutions of simple electrolytes, specifically lithium bromide, potassium bromide, and cesium bromide, at two different concentrations. Cation-induced differences among electrolytes were observed in connection to their tendency to form ion pairs. An increased sensitivity to reveal the structure of the first hydration shell was evidenced when employing ultraviolet excitation in the 228-266 nm range, under resonance conditions with the charge transfer transition to the solvent peaked at about 200 nm. Other than a significant increase in the Raman cross-section for the OH stretching band when shifting from pure water to the solution, a larger enhancement for the Raman signal of the H-O-H bending mode over the stretching vibration was observed. Thus, the bending band plays a crucial role in monitoring the H-bond structure of water around the anions related to the charge distribution within the first hydration shell of anions, being an effective probe of hydration phenomena.
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Affiliation(s)
- Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Lucia Comez
- CNR-Istituto Officina dei Materiali (IOM), Perugia, Italy
| | - Francesco D'Amico
- Elettra-Sincrotrone Trieste S.C.p.A. di interesse nazionale, Trieste, Italy
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste S.C.p.A. di interesse nazionale, Trieste, Italy
| | - Gabriele Bartolini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
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2
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Bianconi E, Gidari A, Souma M, Sabbatini S, Grifagni D, Bigiotti C, Schiaroli E, Comez L, Paciaroni A, Cantini F, Francisci D, Macchiarulo A. The hope and hype of ellagic acid and urolithins as ligands of SARS-CoV-2 Nsp5 and inhibitors of viral replication. J Enzyme Inhib Med Chem 2023; 38:2251721. [PMID: 37638806 PMCID: PMC10464554 DOI: 10.1080/14756366.2023.2251721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 08/29/2023] Open
Abstract
Non-structural protein 5 (Nsp5) is a cysteine protease that plays a key role in SARS-CoV-2 replication, suppressing host protein synthesis and promoting immune evasion. The investigation of natural products as a potential strategy for Nsp5 inhibition is gaining attention as a means of developing antiviral agents. In this work, we have investigated the physicochemical properties and structure-activity relationships of ellagic acid and its gut metabolites, urolithins A-D, as ligands of Nsp5. Results allow us to identify urolithin D as promising ligand of Nsp5, with a dissociation constant in the nanomolar range of potency. Although urolithin D is able to bind to the catalytic cleft of Nsp5, the appraisal of its viral replication inhibition against SARS-CoV-2 in Vero E6 assay highlights a lack of activity. While these results are discussed in the framework of the available literature reporting conflicting data on polyphenol antiviral activity, they provide new clues for natural products as potential viral protease inhibitors.
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Affiliation(s)
- Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Anna Gidari
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Maria Souma
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Samuele Sabbatini
- Medical Microbiology Section, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Deborah Grifagni
- Centre for Magnetic Resonance, University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Carlo Bigiotti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Perugia, Italy
| | | | - Francesca Cantini
- Centre for Magnetic Resonance, University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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3
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Ceccarini M, Chiesa I, Ripanti F, Cardinali MA, Micalizzi S, Scattini G, De Maria C, Paciaroni A, Petrillo C, Comez L, Bertelli M, Sassi P, Pascucci L, Beccari T, Valentini L. Electrospun Nanofibrous UV Filters with Bidirectional Actuation Properties Based on Salmon Sperm DNA/Silk Fibroin for Biomedical Applications. ACS Omega 2023; 8:38233-38242. [PMID: 37867705 PMCID: PMC10586176 DOI: 10.1021/acsomega.3c04563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/23/2023] [Indexed: 10/24/2023]
Abstract
In this study, we dissolved Bombyx mori degummed silk [i.e., silk fibroin (SF)] and salmon sperm deoxyribonucleic acid (DNA) in water and used a bioinspired spinning process to obtain an electrospun nanofibrous SF-based patch (ESF). We investigated the bidirectional macroscale actuation behavior of ESF in response to water vapor and its UV-blocking properties as well as those of ESF/DNA films. Fourier transform infrared (FTIR) results suggest that the formation of β-sheet-rich structures promotes the actuation effect. ESF/DNA film with high-ordered and β-sheet-rich structures exhibits higher electrical conductivity and is water-insoluble. Given the intrinsic ability of both SF and DNA to absorb UV radiation, we performed biological experiments on the viability of keratinocyte HaCaT cells after exposure to solar spectrum components. Our findings indicate that the ESF/DNA patch is photoprotective and can increase the cellular viability of keratinocytes after UV exposure. Furthermore, we demonstrated that ESF/DNA patches treated with water vapor can serve as suitable scaffolds for tissue engineering and can improve tissue regeneration when cellularized with HaCaT cells. The 3D shape morphing capability of these patches, along with their potential as UV filters, could offer significant practical advantages in tissue engineering.
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Affiliation(s)
| | - Irene Chiesa
- Department
of Ingegneria dell’Informazione and Research Center E. Piaggio, University of Pisa, Largo Lucio Lazzarino 1, Pisa 56122, Italy
| | - Francesca Ripanti
- Dipartimento
di Fisica e Geologia, Università
degli Studi di Perugia, Via A. Pascoli, Perugia 06123, Italy
| | - Martina Alunni Cardinali
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, Perugia 06123, Italy
| | - Simone Micalizzi
- Department
of Ingegneria dell’Informazione and Research Center E. Piaggio, University of Pisa, Largo Lucio Lazzarino 1, Pisa 56122, Italy
| | - Gabriele Scattini
- Dipartimento
di Medicina Veterinaria, University of Perugia, Via S. Costanzo, 4, Perugia 06126, Italy
| | - Carmelo De Maria
- Department
of Ingegneria dell’Informazione and Research Center E. Piaggio, University of Pisa, Largo Lucio Lazzarino 1, Pisa 56122, Italy
| | - Alessandro Paciaroni
- Dipartimento
di Fisica e Geologia, Università
degli Studi di Perugia, Via A. Pascoli, Perugia 06123, Italy
| | - Caterina Petrillo
- Dipartimento
di Fisica e Geologia, Università
degli Studi di Perugia, Via A. Pascoli, Perugia 06123, Italy
| | - Lucia Comez
- Istituto
Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, Perugia 06123, Italy
| | | | - Paola Sassi
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, Perugia 06123, Italy
| | - Luisa Pascucci
- Dipartimento
di Medicina Veterinaria, University of Perugia, Via S. Costanzo, 4, Perugia 06126, Italy
| | - Tommaso Beccari
- Department
of Pharmaceutical Science, University of
Perugia, Perugia 06123, Italy
| | - Luca Valentini
- Civil
and Environmental Engineering Department and INSTM Research Unit, University of Perugia, Strada di Pentima 8, Terni 05100, Italy
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4
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Rosi BP, Libera V, Bertini L, Orecchini A, Corezzi S, Schirò G, Pernot P, Biehl R, Petrillo C, Comez L, De Michele C, Paciaroni A. Stacking Interactions and Flexibility of Human Telomeric Multimers. J Am Chem Soc 2023. [PMID: 37432645 PMCID: PMC10375521 DOI: 10.1021/jacs.3c04810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet under suitable and biologically relevant conditions, G4s undergo multimerization. Here, we investigate the stacking interactions and structural features of telomeric G4 multimers by means of a novel low-resolution structural approach that combines small-angle X-ray scattering (SAXS) with extremely coarse-grained (ECG) simulations. The degree of multimerization and the strength of the stacking interaction are quantitatively determined in G4 self-assembled multimers. We show that self-assembly induces a significant polydispersity of the G4 multimers with an exponential distribution of contour lengths, consistent with a step-growth polymerization. On increasing DNA concentration, the strength of the stacking interaction between G4 monomers increases, as well as the average number of units in the aggregates. We utilized the same approach to explore the conformational flexibility of a model single-stranded long telomeric sequence. Our findings indicate that its G4 units frequently adopt a beads-on-a-string configuration. We also observe that the interaction between G4 units can be significantly affected by complexation with benchmark ligands. The proposed methodology, which identifies the determinants that govern the formation and structural flexibility of G4 multimers, may be an affordable tool aiding in the selection and design of drugs that target G4s under physiological conditions.
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Affiliation(s)
- Benedetta Petra Rosi
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM, Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM, Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Silvia Corezzi
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Giorgio Schirò
- CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Petra Pernot
- European Synchrotron Radiation Facility (ESRF), 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Ralf Biehl
- Jülich Centre for Neutron Science and Institute of Biological Information Processing (JCNS-1/IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- CNR-IOM, Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Cristiano De Michele
- Department of Physics, University of Rome La Sapienza, Piazzale Aldo Moro 2, 00185 Rome, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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5
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Libera V, Ripanti F, Petrillo C, Sacchetti F, Ramos-Soriano J, Galan MC, Schirò G, Paciaroni A, Comez L. Stability of Human Telomeric G-Quadruplexes Complexed with Photosensitive Ligands and Irradiated with Visible Light. Int J Mol Sci 2023; 24:ijms24109090. [PMID: 37240437 DOI: 10.3390/ijms24109090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Guanine-rich DNA sequences can fold into non-canonical nucleic acid structures called G-quadruplexes (G4s). These nanostructures have strong implications in many fields, from medical science to bottom-up nanotechnologies. As a result, ligands interacting with G4s have attracted great attention as candidates in medical therapies, molecular probe applications, and biosensing. In recent years, the use of G4-ligand complexes as photopharmacological targets has shown significant promise for developing novel therapeutic strategies and nanodevices. Here, we studied the possibility of manipulating the secondary structure of a human telomeric G4 sequence through the interaction with two photosensitive ligands, DTE and TMPyP4, whose response to visible light is different. The effect of these two ligands on G4 thermal unfolding was also considered, revealing the occurrence of peculiar multi-step melting pathways and the different attitudes of the two molecules on the quadruplex stabilization.
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Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Javier Ramos-Soriano
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Maria Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Giorgio Schirò
- CNRS, CEA, IBS, c/o University Grenoble Alpes, 38400 Grenoble, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
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6
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Ceccarini MR, Ripanti F, Raggi V, Paciaroni A, Petrillo C, Comez L, Donato K, Bertelli M, Beccari T, Valentini L. Development of Salmon Sperm DNA/Regenerated Silk Bio-Based Films for Biomedical Studies on Human Keratinocyte HaCaT Cells under Solar Spectrum. J Funct Biomater 2023; 14:jfb14050280. [PMID: 37233390 DOI: 10.3390/jfb14050280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
In this study, we fabricated adhesive patches from silkworm-regenerated silk and DNA to safeguard human skin from the sun's rays. The patches are realized by exploiting the dissolution of silk fibers (e.g., silk fibroin (SF)) and salmon sperm DNA in formic acid and CaCl2 solutions. Infrared spectroscopy is used to investigate the conformational transition of SF when combined with DNA; the results indicated that the addition of DNA provides an increase in the SF crystallinity. UV-Visible absorption and circular dichroism spectroscopy showed strong absorption in the UV region and the presence of B-form of DNA once dispersed in the SF matrix, respectively. Water absorption measurements as well as thermal dependence of water sorption and thermal analysis, suggested the stability of the fabricated patches. Biological results on cellular viability (MTT assay) of keratinocyte HaCaT cells after exposures to the solar spectrum showed that both SF and SF/DNA patches are photo-protective by increasing the cellular viability of keratinocytes after UV component exposure. Overall, these SF/DNA patches promise applications in wound dressing for practical biomedical purposes.
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Affiliation(s)
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Veronica Raggi
- Polo Scientifico Didattico, University of Perugia, Strada di Pentima 4, 05100 Terni, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Kevin Donato
- MAGI EUREGIO SCS, Via Maso della Pieve, 60/A, 39100 Bolzano, Italy
- MAGISNAT, Atlanta Tech Park, 107 Technology Parkway, Peachtree Corners, GA 30092, USA
| | - Matteo Bertelli
- MAGI EUREGIO SCS, Via Maso della Pieve, 60/A, 39100 Bolzano, Italy
- MAGISNAT, Atlanta Tech Park, 107 Technology Parkway, Peachtree Corners, GA 30092, USA
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Luca Valentini
- Civil and Environmental Engineering Department, University of Perugia, Strada di Pentima 6, 05100 Terni, Italy
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7
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Paciaroni A, Libera V, Ripanti F, Orecchini A, Petrillo C, Francisci D, Schiaroli E, Sabbatini S, Gidari A, Bianconi E, Macchiarulo A, Hussain R, Silvestrini L, Moretti P, Belhaj N, Vercelli M, Roque Y, Mariani P, Comez L, Spinozzi F. Stabilization of the Dimeric State of SARS-CoV-2 Main Protease by GC376 and Nirmatrelvir. Int J Mol Sci 2023; 24:ijms24076062. [PMID: 37047038 PMCID: PMC10093836 DOI: 10.3390/ijms24076062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
The main protease (Mpro or 3CLpro) is an enzyme that is evolutionarily conserved among different genera of coronaviruses. As it is essential for processing and maturing viral polyproteins, Mpro has been identified as a promising target for the development of broad-spectrum drugs against coronaviruses. Like SARS-CoV and MERS-CoV, the mature and active form of SARS-CoV-2 Mpro is a dimer composed of identical subunits, each with a single active site. Individual monomers, however, have very low or no catalytic activity. As such, inhibition of Mpro can be achieved by molecules that target the substrate binding pocket to block catalytic activity or target the dimerization process. In this study, we investigated GC376, a transition-state analog inhibitor of the main protease of feline infectious peritonitis coronavirus, and Nirmatrelvir (NMV), an oral, bioavailable SARS-CoV-2 Mpro inhibitor with pan-human coronavirus antiviral activity. Our results show that both GC376 and NMV are capable of strongly binding to SARS-CoV-2 Mpro and altering the monomer-dimer equilibrium by stabilizing the dimeric state. This behavior is proposed to be related to a structured hydrogen-bond network established at the Mpro active site, where hydrogen bonds between Ser1' and Glu166/Phe140 are formed in addition to those achieved by the latter residues with GC376 or NMV.
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Affiliation(s)
- Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Samuele Sabbatini
- Department of Medicine and Surgery, Medical Microbiology Section, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Anna Gidari
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo, 06123 Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo, 06123 Perugia, Italy
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Lucia Silvestrini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Paolo Moretti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Norhan Belhaj
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Matteo Vercelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Yessica Roque
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
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8
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Bertini L, Libera V, Ripanti F, Natali F, Paolantoni M, Orecchini A, Nucara A, Petrillo C, Comez L, Paciaroni A. Polymorphism and Ligand Binding Modulate Fast Dynamics of Human Telomeric G-Quadruplexes. Int J Mol Sci 2023; 24:ijms24054280. [PMID: 36901712 PMCID: PMC10001961 DOI: 10.3390/ijms24054280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3)3 (Tel22) depends on the conformation. By using Fourier transform Infrared spectroscopy, we show that, in the hydrated powder state, Tel22 adopts parallel and mixed antiparallel/parallel topologies in the presence of K+ and Na+ ions, respectively. These conformational differences are reflected in the reduced mobility of Tel22 in Na+ environment in the sub-nanosecond timescale, as probed by elastic incoherent neutron scattering. These findings are consistent with the G4 antiparallel conformation being more stable than the parallel one, possibly due to the presence of ordered hydration water networks. In addition, we study the effect of Tel22 complexation with BRACO19 ligand. Despite the quite similar conformation in the complexed and uncomplexed state, the fast dynamics of Tel22-BRACO19 is enhanced compared to that of Tel22 alone, independently of the ions. We ascribe this effect to the preferential binding of water molecules to Tel22 against the ligand. The present results suggest that the effect of polymorphism and complexation on the G4 fast dynamics is mediated by hydration water.
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Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Francesca Natali
- CNR-IOM and INSIDE@ILL c/o OGG, 71 avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Nucara
- Department of Physics, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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9
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Bertini L, Libera V, Ripanti F, Seydel T, Paolantoni M, Orecchini A, Petrillo C, Comez L, Paciaroni A. Role of fast dynamics in the complexation of G-quadruplexes with small molecules. Phys Chem Chem Phys 2022; 24:29232-29240. [PMID: 36445842 DOI: 10.1039/d2cp03602a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-quadruplexes (G4s) formed by the human telomeric sequence AG3 (TTAG3)3 (Tel22) play a key role in cancer and aging. We combined elastic incoherent neutron scattering (EINS) and quasielastic incoherent neutron scattering (QENS) to characterize the internal dynamics of Tel22 G4s and to assess how it is affected by complexation with two standard ligands, Berberine and BRACO19. We show that the interaction with the two ligands induces an increase of the overall mobility of Tel22 as quantified by the mean squared displacements (MSD) of hydrogen atoms. At the same time, the complexes display a lower stiffness than G4 alone. Two different types of motion characterize the G4 nanosecond timescale dynamics. Upon complexation, an increasing fraction of G4 atomic groups participate in this fast dynamics, along with an increase in the relevant characteristic length scales. We suggest that the entropic contribution to the conformational free energy of these motions might be crucial for the complexation mechanisms.
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Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy. .,Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Tilo Seydel
- Institut Max von Laue - Paul Langevin (ILL) 71 avenue des Martyrs, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto, 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy.
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy.
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10
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Alunni Cardinali M, Cartechini L, Paolantoni M, Miliani C, Fioretto D, Pensabene Buemi L, Comez L, Rosi F. Microscale mechanochemical characterization of drying oil films by in situ correlative Brillouin and Raman spectroscopy. Sci Adv 2022; 8:eabo4221. [PMID: 35767625 PMCID: PMC9242584 DOI: 10.1126/sciadv.abo4221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Correlative Brillouin and Raman microspectroscopy (BRaMS) is applied for the in situ monitoring of the chemical and physical changes of linseed oil during polymerization. The viscoelastic properties of the drying oil throughout the phase transition were determined by Brillouin light scattering (BLS) and joined to the Raman spectroscopic information about the chemical process responsible for the oil hardening. A comparative study was then performed on an oil mock-up containing ZnO, one of the most common white pigments used in cultural heritage. The intriguing outcomes open new research perspectives for a deeper comprehension of the processes leading to the conversion of a fluid binder into a dry adhering film. The description of both chemical and structural properties of the polymeric network and their evolution are the basis for a better understanding of oil painting degradation. Last, as a feasibility test, BRaMS was applied to study a precious microfragment from J. Pollock's masterpiece Alchemy.
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Affiliation(s)
- Martina Alunni Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto, 6 06123 Perugia, Italy
| | - Laura Cartechini
- Institute of Chemical Sciences and Technologies-SCITEC, National Research Council-CNR, Via Elce di Sotto, Perugia I-06123, Italy
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto, 6 06123 Perugia, Italy
| | - Costanza Miliani
- Institute of Heritage Science-ISPC, National Research Council-CNR, Via Cardinale Guglielmo Sanfelice 8, 80134 Napoli (NA), Italy
| | - Daniele Fioretto
- Department of Physics and Geology, University of Perugia, Via Pascoli, Perugia I-06123, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Pascoli, Perugia I-06123, Italy
| | | | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Pascoli, Perugia I-06123, Italy
| | - Francesca Rosi
- Institute of Chemical Sciences and Technologies-SCITEC, National Research Council-CNR, Via Elce di Sotto, Perugia I-06123, Italy
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11
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Singh M, Gupta R, Comez L, Paciaroni A, Rani R, Kumar V. BCL2 G quadruplex-binding small molecules: Current status and prospects for the development of next-generation anticancer therapeutics. Drug Discov Today 2022; 27:2551-2561. [PMID: 35709931 DOI: 10.1016/j.drudis.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/03/2022]
Abstract
B cell lymphoma 2 (BCL2) overexpression in a range of human tumors is often related to chemotherapy resistance and poor prognosis. GC-rich regions upstream of the P1 promoter in human BCL2 can form G-quadruplex (G4) structures through the stacking of four Hoogsteen-paired guanine bases. Stabilizing the G4 fold implies the inhibition of BCL2 expression and, thus, small molecules that selectively bind to the G4 are promising anticancer candidates. In this review, we discuss the structural aspects, binding affinity, selectivity, and biological activity of well-characterized BCL2 G4 binding ligands in vitro and in vivo. We also explore future directions in the research and development of G4-based anticancer therapeutics.
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Affiliation(s)
- Mamta Singh
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Rajat Gupta
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Lucia Comez
- IOM-CNR National Research Council, Via Pascoli, Perugia I-06123, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Pascoli, 06123, Italy
| | - Reshma Rani
- Drug Discovery Unit, Jubilant Biosys Ltd, Sector 58, Noida, UP 201301, India.
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India.
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12
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Rosi BP, D’Angelo A, Buratti E, Zanatta M, Tavagnacco L, Natali F, Zamponi M, Noferini D, Corezzi S, Zaccarelli E, Comez L, Sacchetti F, Paciaroni A, Petrillo C, Orecchini A. Impact of the Environment on the PNIPAM Dynamical Transition Probed by Elastic Neutron Scattering. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benedetta P. Rosi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Arianna D’Angelo
- Laboratoire de Physique des Solides, CNRS, Université Paris-Saclay, 510 Rue André Rivière, 91405 Orsay, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Elena Buratti
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Marco Zanatta
- Dipartimento di Fisica, Università di Trento, via Sommarive 14, 38123 Trento, Italy
| | - Letizia Tavagnacco
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesca Natali
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, Cedex 9, France
- CNR-IOM, OGG, 71 Avenue des Martyrs, 38043 Grenoble, Cedex 9, France
| | - Michaela Zamponi
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany
- European Spallation Source ERIC, Box 176, 221 00 Lund, Sweden
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, CNR-ISC c/o Università di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Lucia Comez
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Dipartimento di Fisica e Geologia, CNR-IOM c/o Università di Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
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13
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Libera V, Bianchi F, Rossi B, D’Amico F, Masciovecchio C, Petrillo C, Sacchetti F, Paciaroni A, Comez L. Solvent Vibrations as a Proxy of the Telomere G-Quadruplex Rearrangements across Thermal Unfolding. Int J Mol Sci 2022; 23:ijms23095123. [PMID: 35563512 PMCID: PMC9100830 DOI: 10.3390/ijms23095123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical forms of DNA involved in many key genome functions. Here, we exploited UV Resonance Raman scattering to simultaneously explore the vibrational behavior of a human telomeric G4 (Tel22) and its aqueous solvent as the biomolecule underwent thermal melting. We found that the OH stretching band, related to the local hydrogen-bonded network of a water molecule, was in strict relation with the vibrational features of the G4 structure as a function of temperature. In particular, the modifications to the tetrahedral ordering of the water network were strongly coupled to the DNA rearrangements, showing changes in temperature that mirrored the multi-step melting process of Tel22. The comparison between circular dichroism and Raman results supported this view. The present findings provide novel insights into the impact of the molecular environment on G4 conformation. Improving current knowledge on the solvent structural properties will also contribute to a better understanding of the role played by water arrangement in the complexation of G4s with ligands.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Federico Bianchi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Francesco D’Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Claudio Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- Correspondence: (A.P.); (L.C.)
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: (A.P.); (L.C.)
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14
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Lupi L, Bracco B, Sassi P, Corezzi S, Morresi A, Fioretto D, Comez L, Paolantoni M. Hydration Dynamics of Model Peptides with Different Hydrophobic Character. Life (Basel) 2022; 12:life12040572. [PMID: 35455063 PMCID: PMC9031890 DOI: 10.3390/life12040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.
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Affiliation(s)
- Laura Lupi
- Dipartimento di Matematica e Fisica, Università Roma Tre, 00146 Rome, Italy;
| | - Brenda Bracco
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
| | - Assunta Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (S.C.); (D.F.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 060123 Perugia, Italy
- Correspondence: (L.C.); (M.P.)
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.); (A.M.)
- Correspondence: (L.C.); (M.P.)
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15
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Rosi BP, Tavagnacco L, Comez L, Sassi P, Ricci M, Buratti E, Bertoldo M, Petrillo C, Zaccarelli E, Chiessi E, Corezzi S. Thermoresponsivity of poly(N-isopropylacrylamide) microgels in water-trehalose solution and its relation to protein behavior. J Colloid Interface Sci 2021; 604:705-718. [PMID: 34280768 DOI: 10.1016/j.jcis.2021.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/21/2021] [Accepted: 07/01/2021] [Indexed: 11/18/2022]
Abstract
HYPOTHESES Additives are commonly used to tune macromolecular conformational transitions. Among additives, trehalose is an excellent bioprotectant and among responsive polymers, PNIPAM is the most studied material. Nevertheless, their interaction mechanism so far has only been hinted without direct investigation, and, crucially, never elucidated in comparison to proteins. Detailed insights would help understand to what extent PNIPAM microgels can effectively be used as synthetic biomimetic materials, to reproduce and study, at the colloidal scale, isolated protein behavior and its sensitivity to interactions with specific cosolvents or cosolutes. EXPERIMENTS The effect of trehalose on the swelling behavior of PNIPAM microgels was monitored by dynamic light scattering; Raman spectroscopy and molecular dynamics simulations were used to explore changes of solvation and dynamics across the swelling-deswelling transition at the molecular scale. FINDINGS Strongly hydrated trehalose molecules develop water-mediated interactions with PNIPAM microgels, thereby preserving polymer hydration below and above the transition while drastically inhibiting local motions of the polymer and of its hydration shell. Our study, for the first time, demonstrates that slowdown of dynamics and preferential exclusion are the principal mechanisms governing trehalose effect on PNIPAM microgels, at odds with preferential adsorption of alcohols, but in full analogy with the behavior observed in trehalose-protein systems.
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Affiliation(s)
- Benedetta Petra Rosi
- Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - Letizia Tavagnacco
- CNR-ISC, Sapienza Università di Roma, I-00185 Roma, Italy; Dipartimento di Fisica, Sapienza Università di Roma, I-00185 Roma, Italy
| | - Lucia Comez
- CNR-IOM, Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, I-06123 Perugia, Italy
| | - Maria Ricci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, I-06123 Perugia, Italy
| | - Elena Buratti
- CNR-ISC, Sapienza Università di Roma, I-00185 Roma, Italy; Dipartimento di Fisica, Sapienza Università di Roma, I-00185 Roma, Italy
| | - Monica Bertoldo
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie, Università di Ferrara, I-44121 Ferrara, Italy; CNR-ISOF, Area della Ricerca, I-40129 Bologna, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC, Sapienza Università di Roma, I-00185 Roma, Italy; Dipartimento di Fisica, Sapienza Università di Roma, I-00185 Roma, Italy
| | - Ester Chiessi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", I-00133 Roma, Italy.
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy.
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16
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Corezzi S, Bracco B, Sassi P, Paolantoni M, Comez L. Protein Hydration in a Bioprotecting Mixture. Life (Basel) 2021; 11:life11100995. [PMID: 34685367 PMCID: PMC8537178 DOI: 10.3390/life11100995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/10/2021] [Accepted: 09/18/2021] [Indexed: 11/16/2022] Open
Abstract
We combined broad-band depolarized light scattering and infrared spectroscopies to study the properties of hydration water in a lysozyme-trehalose aqueous solution, where trehalose is present above the concentration threshold (30% in weight) relevant for biopreservation. The joint use of the two different techniques, which were sensitive to inter-and intra-molecular degrees of freedom, shed new light on the molecular mechanism underlying the interaction between the three species in the mixture. Thanks to the comparison with the binary solution cases, we were able to show that, under the investigated conditions, the protein, through preferential hydration, remains strongly hydrated even in the ternary mixture. This supported the water entrapment scenario, for which a certain amount of water between protein and sugar protects the biomolecule from damage caused by external agents.
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Affiliation(s)
- Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy;
| | - Brenda Bracco
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.)
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.)
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy; (B.B.); (P.S.)
- Correspondence: (M.P.); (L.C.)
| | - Lucia Comez
- CNR-IOM at Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: (M.P.); (L.C.)
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17
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Libera V, Andreeva EA, Martel A, Thureau A, Longo M, Petrillo C, Paciaroni A, Schirò G, Comez L. Porphyrin Binding and Irradiation Promote G-Quadruplex DNA Dimeric Structure. J Phys Chem Lett 2021; 12:8096-8102. [PMID: 34406777 DOI: 10.1021/acs.jpclett.1c01840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nucleic acid sequences rich in guanines can organize into noncanonical DNA G-quadruplexes (G4s) of variable size. The design of small molecules stabilizing the structure of G4s is a rapidly growing area for the development of novel anticancer therapeutic strategies and bottom-up nanotechnologies. Among a multitude of binders, porphyrins are very attractive due to their light activation that can make them valuable conformational regulators of G4s. Here, a structure-based strategy, integrating complementary probes, is employed to study the interaction between TMPyP4 porphyrin and a 22-base human telomeric sequence (Tel22) before and after irradiation with blue light. Porphyrin binding is discovered to promote Tel22 dimerization, while light irradiation of the Tel22-TMPyP4 complex controls dimer fraction. Such a change in quaternary structure is found to be strictly correlated with modifications at the secondary structure level, thus providing an unprecedented link between the degree of dimerization and the underlying conformational changes in G4s.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Elena A Andreeva
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Aurelien Thureau
- Swing Beamline, Synchrotron SOLEIL, 91192 Gif sur Yvette, France
| | - Marialucia Longo
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Lucia Comez
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
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18
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Catalini S, Perinelli DR, Sassi P, Comez L, Palmieri GF, Morresi A, Bonacucina G, Foggi P, Pucciarelli S, Paolantoni M. Amyloid Self-Assembly of Lysozyme in Self-Crowded Conditions: The Formation of a Protein Oligomer Hydrogel. Biomacromolecules 2021; 22:1147-1158. [PMID: 33600168 PMCID: PMC8023603 DOI: 10.1021/acs.biomac.0c01652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A method
is designed to quickly form protein hydrogels, based on
the self-assembly of highly concentrated lysozyme solutions in acidic
conditions. Their properties can be easily modulated by selecting
the curing temperature. Molecular insights on the gelation pathway,
derived by in situ FTIR spectroscopy, are related to calorimetric
and rheological results, providing a consistent picture on structure–property
correlations. In these self-crowded samples, the thermal unfolding
induces the rapid formation of amyloid aggregates, leading to temperature-dependent
quasi-stationary levels of antiparallel cross β-sheet links,
attributed to kinetically trapped oligomers. Upon subsequent cooling,
thermoreversible hydrogels develop by the formation of interoligomer
contacts. Through heating/cooling cycles, the starting solutions can
be largely recovered back, due to oligomer-to-monomer dissociation
and refolding. Overall, transparent protein hydrogels can be easily
formed in self-crowding conditions and their properties explained,
considering the formation of interconnected amyloid oligomers. This
type of biomaterial might be relevant in different fields, along with
analogous systems of a fibrillar nature more commonly considered.
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Affiliation(s)
- Sara Catalini
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, 50019 Sesto Fiorentino, Italy
| | | | - Paola Sassi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, University of Perugia, 060123 Perugia, Italy
| | | | - Assunta Morresi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | - Paolo Foggi
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, 50019 Sesto Fiorentino, Italy.,Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy.,National Metrological Research Institute (INRIM), Strada delle Cacce 91, 10135 Torino, Italy
| | - Stefania Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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19
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Comez L, Bianchi F, Libera V, Longo M, Petrillo C, Sacchetti F, Sebastiani F, D'Amico F, Rossi B, Gessini A, Masciovecchio C, Amenitsch H, Sissi C, Paciaroni A. Polymorphism of human telomeric quadruplexes with drugs: a multi-technique biophysical study. Phys Chem Chem Phys 2020; 22:11583-11592. [PMID: 32400802 DOI: 10.1039/d0cp01483d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - V Libera
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - M Longo
- JCNS Forschungszentrum Jülich GmbH at Heinz Maier-Leibnitz Zentrum (MLZ), 85748 Garching, Germany
| | - C Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sebastiani
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - F D'Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - B Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - A Gessini
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - C Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - H Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - C Sissi
- Dipartimento di Scienze del Farmaco, Via Marzolo 5, 35131 Padova, Italy and Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, University of Padova, Italy
| | - A Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
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20
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Corezzi S, Paolantoni M, Sassi P, Morresi A, Fioretto D, Comez L. Trehalose-induced slowdown of lysozyme hydration dynamics probed by EDLS spectroscopy. J Chem Phys 2019; 151:015101. [DOI: 10.1063/1.5099588] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
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21
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Abstract
We characterize via small-angle neutron scattering the structural properties of a mixture of all-DNA particles with functionalities 4 (A) and 2 (B) constrained by design to reside close to the percolation threshold. DNA base sequences are selected such that A particles can only bind with B ones and that at the studied temperature (10 °C) all AB bonds are formed and long-lived, originating highly polydisperse persistent equilibrium clusters. The concentration dependence of the scattered intensity and its wavevector dependence is exploited to determine the fractal dimension and the size distribution of the clusters, which are found to be consistent with the critical exponents of the 3-D percolation universality class. The value of DNA nanoparticles as nanometric patchy colloids with well-defined functionality, bonding selectivity, and exquisite control of the interaction strength is demonstrated.
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Affiliation(s)
| | - M Zanatta
- Dipartimento di Informatica, Università di Verona, 37134 Verona, Italy
| | - L Comez
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - A Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A Radulescu
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, 85748 Garching, Germany
| | - F Sciortino
- Sapienza-Università di Roma, P.le A. Moro 5, 00185 Rome, Italy.,CNR-ISC, UOS Sapienza-Università di Roma, 00185 Rome, Italy
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22
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Bianchi F, Comez L, Biehl R, D’Amico F, Gessini A, Longo M, Masciovecchio C, Petrillo C, Radulescu A, Rossi B, Sacchetti F, Sebastiani F, Violini N, Paciaroni A. Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway. Nucleic Acids Res 2018; 46:11927-11938. [PMID: 30407585 PMCID: PMC6294516 DOI: 10.1093/nar/gky1092] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/28/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.
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Affiliation(s)
- Federico Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Ralf Biehl
- JCNS & ICS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
| | - Francesco D’Amico
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Marialucia Longo
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Aurel Radulescu
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Federico Sebastiani
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Nicolò Violini
- JCNS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
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23
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Corezzi S, Comez L, Zanatta M. A simple analysis of Brillouin spectra from opaque liquids and its application to aqueous suspensions of poly-N-isopropylacrylamide microgel particles. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.06.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Perticaroli S, Comez L, Sassi P, Morresi A, Fioretto D, Paolantoni M. Water-like Behavior of Formamide: Jump Reorientation Probed by Extended Depolarized Light Scattering. J Phys Chem Lett 2018; 9:120-125. [PMID: 29243934 DOI: 10.1021/acs.jpclett.7b02943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Water is a strong self-associated liquid with peculiar properties that crucially depend on H-bonding. As regards its molecular dynamics, only recently has water reorientation been successfully described based on a jump mechanism, which is responsible for the overall H-bonding exchange. Here, using high-resolution broad-band depolarized light scattering, we have investigated the reorientational dynamics of formamide (FA) as a function of concentration from the neat liquid to diluted aqueous solutions. Our main findings indicate that in the diluted regime the water rearrangement can trigger the motion of FA solute molecules, which are forced to reorient at the same rate as water. This highlights an exceptional behavior of FA, which perfectly substitutes water within its network. Besides other fundamental implications connected with the relevance of FA, its water-like behavior provides rare experimental evidence of a solute whose dynamics is completely slaved to the solvent.
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Affiliation(s)
- S Perticaroli
- Shull Wollan Center, a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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25
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Fernandez-Castanon J, Bomboi F, Rovigatti L, Zanatta M, Paciaroni A, Comez L, Porcar L, Jafta CJ, Fadda GC, Bellini T, Sciortino F. Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars. J Chem Phys 2017; 145:084910. [PMID: 27586949 DOI: 10.1063/1.4961398] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.
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Affiliation(s)
| | - F Bomboi
- Sapienza-Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
| | - L Rovigatti
- Rudolf Peierls C.T.P., University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - M Zanatta
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - A Paciaroni
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - L Comez
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - L Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - C J Jafta
- Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - G C Fadda
- Laboratoire Léon Brillouin, LLB, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - T Bellini
- Department of Medical Biotechnology and Translational Medicine, Università di Milano, I-20133 Milano, Italy
| | - F Sciortino
- Sapienza-Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
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26
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Bottari C, Comez L, Corezzi S, D'Amico F, Gessini A, Mele A, Punta C, Melone L, Pugliese A, Masciovecchio C, Rossi B. Correlation between collective and molecular dynamics in pH-responsive cyclodextrin-based hydrogels. Phys Chem Chem Phys 2017; 19:22555-22563. [DOI: 10.1039/c7cp04190j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The joint use of UV Raman and Brillouin scattering experiments is employed to explore phase evolutions in pH-responsive polysaccharide hydrogels.
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Affiliation(s)
- C. Bottari
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
- Department of Physics
- University of Trieste
| | - L. Comez
- IOM-CNR c/o Department of Physics and Geology
- University of Perugia
- 06123 Perugia
- Italy
| | - S. Corezzi
- Department of Physics and Geology
- University of Perugia
- 06123 Perugia
- Italy
| | - F. D'Amico
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
| | - A. Gessini
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
| | - A. Mele
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM Local Unit
- Milano
- Italy
| | - C. Punta
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM Local Unit
- Milano
- Italy
| | - L. Melone
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM Local Unit
- Milano
- Italy
| | - A. Pugliese
- Department of Chemistry
- Materials and Chemical Engineering “G. Natta”
- Politecnico di Milano and INSTM Local Unit
- Milano
- Italy
| | | | - B. Rossi
- Elettra – Sincrotrone Trieste
- 34149 Trieste
- Italy
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27
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Comez L, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. Soft Matter 2016; 12:5501-5514. [PMID: 27280176 DOI: 10.1039/c5sm03119b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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28
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Comez L, Paolantoni M, Corezzi S, Lupi L, Sassi P, Morresi A, Fioretto D. Aqueous solvation of amphiphilic molecules by extended depolarized light scattering: the case of trimethylamine-N-oxide. Phys Chem Chem Phys 2016; 18:8881-9. [PMID: 26958663 DOI: 10.1039/c5cp04357c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrophilic and hydrophobic interactions strongly affect the solvation dynamics of biomolecules. To understand their role, small model systems are generally employed to simplify the investigations. In this study the amphiphile trimethylamine N-oxide (TMAO) is chosen as an exemplar, and studied by means of extended frequency range depolarized light scattering (EDLS) experiments as a function of solute concentration. This technique proves to be a suitable tool for investigating different aspects of aqueous solvation, being able at the same time to provide information about relaxation processes and vibrational modes of solvent and solute. In the case study of TMAO, we find that the relaxation dynamics of hydration water is moderately retarded compared to the bulk, and the perturbation induced by the solute on surrounding water is confined to the first hydration shell. The results highlight the hydrophobic character of TMAO in its interaction with water. The number of molecules taking part in the solvation process decreases as the solute concentration increases, following a trend consistent with the hydration water-sharing model, and suggesting that aggregation between solute molecules is negligible. Finally, the analysis of the resonant modes in the THz region and the comparison with the corresponding results obtained for the isosteric molecule tert-butyl alcohol (TBA) allow us to provide new insights into the different solvating properties of these two biologically relevant molecules.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy. and Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - M Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - S Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - L Lupi
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - P Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - A Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - D Fioretto
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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29
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Mereu I, Liotta A, Comez L, Corezzi S. On the interplay between the slowdown of dynamics and the kinetics of aggregation: The case study of a reactive binary mixture. J Chem Phys 2016; 142:154905. [PMID: 25903908 DOI: 10.1063/1.4918743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Modeling the kinetics of aggregation requires a proper strategy to take into account not only the reactivity of reagents but also the ability they have to diffuse. The lack of direct information about diffusion represents the most serious experimental obstacle to the use of diffusion-corrected mean-field equations, which is usually overcome by using information on the structural relaxation dynamics. A very accurate description of the entire kinetics of aggregation can be made by introducing a single time scale of diffusion, set by the structural relaxation time τ of the system according to ∼τ(ξ), with ξ a fractional exponent. Here, we apply this modeling to the case of a reactive binary mixture made of diglycidyl ether of bisphenol-A and 1,3-phenylenediamine, where the reaction proceeds along an autocatalyic (hydroxyl catalyzed) and a non-catalytic (impurity catalyzed) pathway and find that a very small value of the exponent ξ = 0.27 ± 0.03 is needed to reproduce all the data. Our results help revise some preconceived ideas: contrary to widely held assumptions, we find that (i) the time scale of diffusion neither increases proportionally to the structural relaxation time nor is related to τ by a power law with the same fractional exponent as that relating τ to conductivity; (ii) no direct connection exists between the transition to diffusion-control and the development of a gel network or formation of a glassy phase; and (iii) there is no significant difference in the enthalpy barrier for bond formation in the presence of hydroxyl or other than hydroxyl catalyst groups.
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Affiliation(s)
- Isabella Mereu
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Andrea Liotta
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR, c/o Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Silvia Corezzi
- Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
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Comez L, Perticaroli S, Paolantoni M, Sassi P, Corezzi S, Morresi A, Fioretto D. Concentration dependence of hydration water in a model peptide. Phys Chem Chem Phys 2015; 16:12433-40. [PMID: 24829171 DOI: 10.1039/c4cp00840e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular dynamics of aqueous solutions of a model amphiphilic peptide is studied as a function of concentration by broad-band light scattering experiments. Similarly to protein aqueous solutions, a considerable retardation, of about a factor 6-8, of hydration water dynamics with respect to bulk water is found, showing a slight dependence on solute concentration. Conversely, the average number of water molecules perturbed by the presence of peptide, i.e. the hydration number, appears to be strongly modified by adding solute. Its behaviour, decreasing upon increasing concentration, can be interpreted considering the random close-to-contact condition experienced by solute particles. Overall, the present findings support the view of a "long range" effect of peptides on the surrounding water, extending beyond the first two hydration shells.
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Affiliation(s)
- Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy.
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32
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Perticaroli S, Russo D, Paolantoni M, Gonzalez MA, Sassi P, Nickels JD, Ehlers G, Comez L, Pellegrini E, Fioretto D, Morresi A. Painting biological low-frequency vibrational modes from small peptides to proteins. Phys Chem Chem Phys 2015; 17:11423-31. [DOI: 10.1039/c4cp05388e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We use experiments and simulation to investigate the validity of different model systems used to study the low-frequency vibrations of proteins.
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Affiliation(s)
- S. Perticaroli
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Chemical and Materials Sciences Division
| | - D. Russo
- CNR-IOM
- Italy c/o Institut Laue Langevin
- France
- Institut Lumière Matière
- Université de Lyon 1
| | - M. Paolantoni
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | | | - P. Sassi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
| | - J. D. Nickels
- Joint Institute for Neutron Sciences
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Chemistry
| | - G. Ehlers
- Quantum Condensed Matter Division
- Oak Ridge National Laboratory
- Oak Ridge
- USA
| | - L. Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Dipartimento di Fisica e Geologia
| | | | - D. Fioretto
- Dipartimento di Fisica e Geologia
- Università di Perugia
- I-06123 Perugia
- Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN)
| | - A. Morresi
- Dipartimento di Chimica
- Biologia e Biotecnologie
- Università di Perugia
- I-06123 Perugia
- Italy
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33
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Comez L, Paolantoni M, Lupi L, Sassi P, Corezzi S, Morresi A, Fioretto D. Hydrophobic Hydration in Water–tert-Butyl Alcohol Solutions by Extended Depolarized Light Scattering. J Phys Chem B 2014; 119:9236-43. [DOI: 10.1021/jp509854a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Comez
- IOM-CNR
c/o Dipartimento di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - M. Paolantoni
- Dipartimento
di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - L. Lupi
- Department
of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - P. Sassi
- Dipartimento
di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - S. Corezzi
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - A. Morresi
- Dipartimento
di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - D. Fioretto
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Centro
di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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34
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Corezzi S, Sassi P, Paolantoni M, Comez L, Morresi A, Fioretto D. Hydration and rotational diffusion of levoglucosan in aqueous solutions. J Chem Phys 2014; 140:184505. [DOI: 10.1063/1.4873575] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Sebastiani F, Pietrini A, Longo M, Comez L, Petrillo C, Sacchetti F, Paciaroni A. Melting of DNA Nonoriented Fibers: A Wide-Angle X-ray Diffraction Study. J Phys Chem B 2014; 118:3785-92. [DOI: 10.1021/jp411096d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Federico Sebastiani
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alberto Pietrini
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Marialucia Longo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Elettra − Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Lucia Comez
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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36
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Sassi P, Perticaroli S, Comez L, Giugliarelli A, Paolantoni M, Fioretto D, Morresi A. Volume properties and spectroscopy: A terahertz Raman investigation of hen egg white lysozyme. J Chem Phys 2013; 139:225101. [DOI: 10.1063/1.4838355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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37
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Comez L, Lupi L, Morresi A, Paolantoni M, Sassi P, Fioretto D. More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water. J Phys Chem Lett 2013; 4:1188-1192. [PMID: 26282040 DOI: 10.1021/jz400360v] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biological interfaces characterized by a complex mixture of hydrophobic, hydrophilic, or charged moieties interfere with the cooperative rearrangement of the hydrogen-bond network of water. In the present study, this solute-induced dynamical perturbation is investigated by extended frequency range depolarized light scattering experiments on an aqueous solution of a variety of systems of different nature and complexity such as small hydrophobic and hydrophilic molecules, amino acids, dipeptides, and proteins. Our results suggest that a reductionist approach is not adequate to describe the rearrangement of hydration water because a significant increase of the dynamical retardation and extension of the perturbation occurs when increasing the chemical complexity of the solute.
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Affiliation(s)
- Lucia Comez
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Laura Lupi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Assunta Morresi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Marco Paolantoni
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Paola Sassi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Daniele Fioretto
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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38
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Comez L, Lupi L, Paolantoni M, Picchiò F, Fioretto D. Hydration properties of small hydrophobic molecules by Brillouin light scattering. J Chem Phys 2013; 137:114509. [PMID: 22998273 DOI: 10.1063/1.4752732] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the relaxation of water molecules next to hydrophobic solutes with different functional groups by Brillouin light scattering. Evidence is given for (i) water activation energy in trimethylamine-N-oxide, proline and t-butyl alcohol diluted solutions which is comparable to that of neat water, almost independent from solute mole fraction and (ii) moderate slowdown of relaxation time of proximal water compared to the bulk, which is consistent with excluded volume models. Assuming that the main contribution to viscosity comes from bulk and hydration water, a rationale is given of the phenomenological Arrhenius' laws for the viscosity of diluted aqueous solutions.
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Affiliation(s)
- L Comez
- IOM-CNR, c/o Dipartimento di Fisica, Università di Perugia, I-06123, Perugia, Italy
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39
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Lupi L, Comez L, Paolantoni M, Perticaroli S, Sassi P, Morresi A, Ladanyi BM, Fioretto D. Hydration and Aggregation in Mono- and Disaccharide Aqueous Solutions by Gigahertz-to-Terahertz Light Scattering and Molecular Dynamics Simulations. J Phys Chem B 2012. [DOI: 10.1021/jp3079869] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Lupi
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123,
Perugia, Italy
| | - M. Paolantoni
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - S. Perticaroli
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - P. Sassi
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - A. Morresi
- Dipartimento
di Chimica, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy
| | - B. M. Ladanyi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872,
United States
| | - D. Fioretto
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Centro di
Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università of Perugia, via Elce di Sotto 8,
06123 Perugia, Italy
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40
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Comez L, Corezzi S, Orecchini A, Paciaroni A, Petrillo C, Santucci S, Sacchetti F, Fioretto D. A comparison between acoustic compliance and self-particle susceptibility in associated liquids: The case of water and glycerol. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2012.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Lupi L, Comez L, Paolantoni M, Fioretto D, Ladanyi BM. Dynamics of Biological Water: Insights from Molecular Modeling of Light Scattering in Aqueous Trehalose Solutions. J Phys Chem B 2012; 116:7499-508. [DOI: 10.1021/jp301988f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Laura Lupi
- Dipartimento di
Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Lucia Comez
- Dipartimento di
Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli,
I-06123, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Università di Perugia, via Elce di Sotto, I-06123
Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di
Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - Branka M. Ladanyi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872,
United States
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42
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Perticaroli S, Comez L, Paolantoni M, Sassi P, Morresi A, Fioretto D. Extended Frequency Range Depolarized Light Scattering Study of N-Acetyl-leucine-methylamide–Water Solutions. J Am Chem Soc 2011; 133:12063-8. [DOI: 10.1021/ja202272k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefania Perticaroli
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Lucia Comez
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Universitá di Perugia, Via Pascoli, I-06123, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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43
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Chumakov AI, Monaco G, Monaco A, Crichton WA, Bosak A, Rüffer R, Meyer A, Kargl F, Comez L, Fioretto D, Giefers H, Roitsch S, Wortmann G, Manghnani MH, Hushur A, Williams Q, Balogh J, Parliński K, Jochym P, Piekarz P. Equivalence of the boson peak in glasses to the transverse acoustic van Hove singularity in crystals. Phys Rev Lett 2011; 106:225501. [PMID: 21702612 DOI: 10.1103/physrevlett.106.225501] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Indexed: 05/31/2023]
Abstract
We compare the atomic dynamics of the glass to that of the relevant crystal. In the spectra of inelastic scattering, the boson peak of the glass appears higher than the transverse acoustic (TA) singularity of the crystal. However, the density of states shows that they have the same number of states. Increasing pressure causes the transformation of the boson peak of the glass towards the TA singularity of the crystal. Once corrected for the difference in the elastic medium, the boson peak matches the TA singularity in energy and height. This suggests the identical nature of the two features.
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Affiliation(s)
- A I Chumakov
- European Synchrotron Radiation Facility, Grenoble, France.
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44
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Comez L, Monaco G, Masciovecchio C, Paciaroni A, Gessini A, Scarponi F, Ruocco G, Fioretto D. Acoustic dissipation and density of states in liquid, supercooled, and glassy glycerol. Phys Rev Lett 2011; 106:155701. [PMID: 21568574 DOI: 10.1103/physrevlett.106.155701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 02/22/2011] [Indexed: 05/30/2023]
Abstract
Combined Brillouin spectra collected at visible, ultraviolet, and x-ray frequencies are used to reconstruct the imaginary part of the acoustic compliance J'' over a wide frequency range between 0.5 GHz and 5 THz. For liquid, supercooled, and glassy glycerol, J'' is found to be linearly dependent on the tagged-particle susceptibility measured by incoherent neutron scattering up to ≃1 THz, giving evidence of a clear relation between acoustic power dissipation and density of states. A simple but general formalism is presented to quantitatively explain this relation, thus clarifying the connection between the quasielastic component observed in neutron scattering experiments and the fast relaxation dynamics probed by Brillouin scattering.
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Affiliation(s)
- L Comez
- IOM-CNR, c/o Università di Perugia, I-06123, Perugia, Italy
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45
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Lupi L, Comez L, Masciovecchio C, Morresi A, Paolantoni M, Sassi P, Scarponi F, Fioretto D. Hydrophobic hydration of tert-butyl alcohol studied by Brillouin light and inelastic ultraviolet scattering. J Chem Phys 2011; 134:055104. [DOI: 10.1063/1.3529014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Perticaroli S, Comez L, Paolantoni M, Sassi P, Lupi L, Fioretto D, Paciaroni A, Morresi A. Broadband depolarized light scattering study of diluted protein aqueous solutions. J Phys Chem B 2010; 114:8262-9. [PMID: 20509696 DOI: 10.1021/jp101896f] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A broadband depolarized light scattering (DLS) study is performed on diluted lysozyme aqueous solutions as a function of temperature and concentration. The dynamical susceptibility, obtained in a wide spectral range (0.6-36000 GHz) through the coupled use of interferometric and dispersive devices, is interpreted and compared with neutron scattering and Raman-induced optical Kerr-effect literature data, thus giving a general picture of relaxation phenomena. We show that the proposed approach represents a suitable tool for investigating the hydration dynamics of protein-water solutions. A detailed analysis of the quasi-elastic scattering region evidences the existence of two distinct relaxational processes at picosecond time scales. The fast process (fractions of picosecond) is attributed to bulk water dynamics, while the slow one (few picoseconds) is attributed to dynamical rearrangements of water molecules strongly influenced by the protein (hydration water). The retardation effect here estimated of about 6-7 can be regarded as a direct measure of the increased protein-water and water-water hydrogen bond stability of the water molecules within the protein hydration shell. Interestingly, a similar effect was previously observed on small hydrophilic sugar molecules. Moreover, backbone and side chains torsional motions of the protein in the 600-5300 GHz frequency range are found to be insensitive to thermal variations and to eventual changes occurring in the premelting zone.
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Gallina ME, Comez L, Morresi A, Paolantoni M, Perticaroli S, Sassi P, Fioretto D. Rotational dynamics of trehalose in aqueous solutions studied by depolarized light scattering. J Chem Phys 2010; 132:214508. [DOI: 10.1063/1.3430555] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Esposito A, Comez L, Cinelli S, Scarponi F, Onori G. Influence of glycerol on the structure and thermal stability of lysozyme: a dynamic light scattering and circular dichroism study. J Phys Chem B 2010; 113:16420-4. [PMID: 19924849 DOI: 10.1021/jp906739v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Photon correlation spectroscopy and circular dichroism have been used to study the role of hydration in the structure and thermostability of the model protein lysozyme in water-glycerol mixtures. Two cases have been considered: water-rich and glycerol-rich regimes of concentrations. We follow the thermal denaturation both by optical spectral changes and hydrodynamic radius variations. This methodology allows us to emphasize the relevant role played by hydrophobic interactions during the process in aqueous solutions and, in glycerol, to distinguish the non-cooperative melting of secondary structure, supporting the view of a protein transition to a molten globule-like state.
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Affiliation(s)
- Alessandro Esposito
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
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Santucci SC, Comez L, Scarponi F, Monaco G, Verbeni R, Legrand JF, Masciovecchio C, Gessini A, Fioretto D. Onset of the α-relaxation in the glass-forming solution LiCl–6H2O revealed by Brillouin scattering techniques. J Chem Phys 2009; 131:154507. [DOI: 10.1063/1.3223537] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Affiliation(s)
- G. Monaco
- a Dipartimento di Fisica , Università dell'Aquila , I-67100 , L'Aquila , Italy
- b Istituto Nazionale per la Fisica della Materia , I-16152 , Genova , Italy
| | - L. Comez
- b Istituto Nazionale per la Fisica della Materia , I-16152 , Genova , Italy
- c Dipartimento di Fisica , Università di Perugia , I-06100 , Perugia , Italy
| | - D. Fioretto
- b Istituto Nazionale per la Fisica della Materia , I-16152 , Genova , Italy
- c Dipartimento di Fisica , Università di Perugia , I-06100 , Perugia , Italy
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