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De Sciscio ML, Nardi AN, Parisi G, Bulfaro G, Costanzo A, Gugole E, Exertier C, Freda I, Savino C, Vallone B, Montemiglio LC, D’Abramo M. Effect of Salts on the Conformational Dynamics of the Cytochrome P450 OleP. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020832. [PMID: 36677890 PMCID: PMC9867029 DOI: 10.3390/molecules28020832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Cytochrome P450 OleP catalytic activity is strongly influenced by its structural dynamic conformational behavior. Here, we combine equilibrium-binding experiments with all-atom molecular dynamics simulations to clarify how different environments affect OleP conformational equilibrium between the open and the closed-catalytic competent-forms. Our data clearly show that at high-ionic strength conditions, the closed form is favored, and, very interestingly, different mechanisms, depending on the chemistry of the cations, can be used to rationalize such an effect.
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Affiliation(s)
- Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | | | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, IIT, 00185 Rome, Italy
| | - Giovanni Bulfaro
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Antonella Costanzo
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Elena Gugole
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Ida Freda
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, CNR c/o Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
| | - Marco D’Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
- Correspondence: (B.V.); (L.C.M.); (M.D.)
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Del Galdo S, Chiarini M, Casieri C, Daidone I. High density water clusters observed at high concentrations of the macromolecular crowder PEG400. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Tao T, Gao Z, Fang C, Zhang J, Xu J, Yang H, Gong J. Enhancement of protein crystallization with the application of Taylor vortex and Poly(ionic liquid)s. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Savelyev A. Assessment of the DNA partial specific volume and hydration layer properties from CHARMM Drude polarizable and additive MD simulations. Phys Chem Chem Phys 2021; 23:10524-10535. [PMID: 33899879 PMCID: PMC8121142 DOI: 10.1039/d1cp00688f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study we report on the accurate computation of the biomolecular partial specific volume (PSV) from explicit-solvent molecular dynamics (MD) simulations. The case of DNA is considered, and the predictions from two state-of-the-art biomolecular force fields, the CHARMM36 additive (C36) and Drude polarizable models, are presented. Unlike most of the existing approaches to assess the biomolecular PSV, our proposed method bypasses the need for the arbitrarily defined volume partitioning scheme into the intrinsic solute and solvent contributions. At the same time, to assess the density of the hydration layer water, we combine our simulation analysis approach with some of the existing fixed-size methods to determine the solute's intrinsic volume, and also propose our own approach to compute all required quantities exclusively from MD simulations. Our findings provide useful insights into the properties of the hydration layer, specifically its size and density, parameters of great importance to the variety of techniques used to model hydrodynamic and structural properties of biological molecules. The computed PSV values are found to be in close agreement with the values obtained from analytical ultracentrifugation (AUC) experiments performed on canonical B-form duplex DNAs and single-stranded DNAs forming G-quadruplex structures. Since the biomolecular PSV represents an important quantitative measure of solute-solvent interactions, near quantitative agreement with AUC measurements is indicative of the quality of the all-atom models used in the MD simulations, particularly the reliability of the CHARMM force-field parameters for nucleic acids, water, mobile ions, and interactions among these entities.
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Affiliation(s)
- Alexey Savelyev
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA.
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D'Abramo M, Del Galdo S, Amadei A. Theoretical-computational modelling of the temperature dependence of the folding-unfolding thermodynamics and kinetics: the case of a Trp-cage. Phys Chem Chem Phys 2019; 21:23162-23168. [PMID: 31612180 DOI: 10.1039/c9cp03303c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we present a theoretical-computational study of the thermodynamics and kinetics of an aqueous Trp-cage, a 20-residue long miniprotein. The combined use of accurate molecular dynamics simulations rigorously reconstructing the proper isobar of the system and a sound statistical-mechanical model provides a quantitative description of the temperature dependence of the relevant physical-chemical properties and insights into the detailed mechanisms regulating the folding-unfolding properties.
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Affiliation(s)
- Marco D'Abramo
- Dept. of Chemistry, Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy.
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Tasca E, Alba J, Galantini L, D’Abramo M, Giuliani AM, Amadei A, Palazzo G, Giustini M. The self-association equilibria of doxorubicin at high concentration and ionic strength characterized by fluorescence spectroscopy and molecular dynamics simulations. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2019.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Del Galdo S, Mancini G, Daidone I, Zanetti Polzi L, Amadei A, Barone V. Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties. J Comput Chem 2018; 39:1747-1756. [DOI: 10.1002/jcc.25351] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Isabella Daidone
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Laura Zanetti Polzi
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma Tor Vergata, Via Della Ricerca Scientifica; Roma 00100 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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Schneider S, Paulsen H, Reiter KC, Hinze E, Schiene-Fischer C, Hübner CG. Single molecule FRET investigation of pressure-driven unfolding of cold shock protein A. J Chem Phys 2018; 148:123336. [DOI: 10.1063/1.5009662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sven Schneider
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Hauke Paulsen
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Kim Colin Reiter
- Institute of Physics, University of Lübeck, Lübeck D-23562, Germany
| | - Erik Hinze
- Max Planck Research Unit for Enzymology of Protein Folding Halle, Halle/Saale D-06120, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale D-06120, Germany
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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Amadei A, Aschi M. Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems. RSC Adv 2018; 8:27900-27918. [PMID: 35542751 PMCID: PMC9083445 DOI: 10.1039/c8ra03900c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/23/2018] [Indexed: 11/21/2022] Open
Abstract
In this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems. A theoretical-computational procedure, based on Molecular Dynamics simulations, is proposed for modelling the kinetics of non-adiabatic processes in very complex systems.![]()
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Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche
- Universita' di Roma ‘Tor Vergata’
- Roma
- Italy
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche
- Universita' di L'Aquila
- L'Aquila
- Italy
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