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Rabah J, Nasrallah H, Wright K, Gérard I, Fensterbank H, Bui TTV, Marrot J, Tran TT, Fatima A, Ha-Thi MH, Méallet R, Burdzinski G, Clavier G, Boujday S, Cachet H, Debiemme-Chouvy C, Maisonhaute E, Vallée A, Allard E. Clicked BODIPY-Fullerene-Peptide Assemblies: Studies of Electron Transfer Processes in Self-Assembled Monolayers on Gold Surfaces. Chempluschem 2024; 89:e202300717. [PMID: 38406894 DOI: 10.1002/cplu.202300717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/30/2024] [Accepted: 02/23/2024] [Indexed: 02/27/2024]
Abstract
Two BODIPY-C60-peptide assemblies were synthesized by CuAAC reactions of BODIPY-C60 dyads and a helical peptide functionalized with a terminal alkyne group and an azide group, respectively. The helical peptide within these assemblies was functionalized at its other end by a disulfide group, allowing formation of self-assembled monolayers (SAMs) on gold surfaces. Characterizations of these SAMs, as well as those of reference molecules (BODIPY-C60-alkyl, C60-peptide and BODIPY-peptide), were carried out by PM-IRRAS and cyclic voltammetry. BODIPY-C60-peptide SAMs are more densely packed than BODIPY-C60-alkyl and BODIPY-peptide based SAMs. These findings were attributed to the rigid peptide helical conformation along with peptide-peptide and C60-C60 interactions within the monolayers. However, less dense monolayers were obtained with the target assemblies compared to the C60-peptide, as the BODIPY entity likely disrupts organization within the monolayers. Finally, electron transfer kinetics measurements by ultra-fast electrochemistry experiments demonstrated that the helical peptide is a better electron mediator in comparison to alkyl chains. This property was exploited along with those of the BODIPY-C60 dyads in a photo-current generation experiment by converting the resulting excited and/or charge separated states from photo-illumination of the dyad into electrical energy.
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Affiliation(s)
- Jad Rabah
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
| | - Houssein Nasrallah
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
| | - Karen Wright
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
| | - Isabelle Gérard
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
| | - Hélène Fensterbank
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
| | - Thi-Tuyet-Van Bui
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
| | - Jérôme Marrot
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
| | - Thu-Trang Tran
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - Anam Fatima
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - Minh-Huong Ha-Thi
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - Rachel Méallet
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - Gotard Burdzinski
- Adam Mickiewicz University, Poznan, Faculty of Physics Poznań, PL-61614, Poznan, Poland
| | - Gilles Clavier
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, PPSM, 91190, Gif-sur-Yvette, France
| | - Souhir Boujday
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), 4 place Jussieu, F-75005, Paris, France
| | - Hubert Cachet
- Laboratoire Interfaces et Systèmes Electrochimiques, Sorbonne Université, CNRS, 4 place Jussieu, 75005, Paris, France
| | - Catherine Debiemme-Chouvy
- Laboratoire Interfaces et Systèmes Electrochimiques, Sorbonne Université, CNRS, 4 place Jussieu, 75005, Paris, France
| | - Emmanuel Maisonhaute
- Laboratoire Interfaces et Systèmes Electrochimiques, Sorbonne Université, CNRS, 4 place Jussieu, 75005, Paris, France
| | - Anne Vallée
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), 4 place Jussieu, F-75005, Paris, France
| | - Emmanuel Allard
- Université Paris-Saclay, UVSQ, CNRS, Institut Lavoisier de Versailles, 78000, Versailles, France
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2
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Caramiello A, Bellucci MC, Cristina G, Castellano C, Meneghetti F, Mori M, Secundo F, Viani F, Sacchetti A, Volonterio A. Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics. J Org Chem 2023; 88:10381-10402. [PMID: 36226862 PMCID: PMC10407853 DOI: 10.1021/acs.joc.2c01903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.
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Affiliation(s)
- Alessio
M. Caramiello
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133Milano, Italy
| | - Gaetano Cristina
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Carlo Castellano
- Department
of Chemistry, Università degli Studi
di Milano, via Golgi
19, 20133Milano, Italy
| | - Fiorella Meneghetti
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Matteo Mori
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Francesco Secundo
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Fiorenza Viani
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
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3
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Elenewski JE, Velizhanin KA, Zwolak M. A spin-1 representation for dual-funnel energy landscapes. J Chem Phys 2018; 149:035101. [PMID: 30037251 PMCID: PMC7723752 DOI: 10.1063/1.5036677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model-left, right, and unstructured-can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.
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Affiliation(s)
- Justin E. Elenewski
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
| | | | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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4
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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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5
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Gerolin M, Zerbetto M, Moretto A, Formaggio F, Toniolo C, van Son M, Shabestari MH, Huber M, Calligari P, Polimeno A. Integrated Computational Approach to the Electron Paramagnetic Resonance Characterization of Rigid 3 10-Helical Peptides with TOAC Nitroxide Spin Labels. J Phys Chem B 2017; 121:4379-4387. [PMID: 28422504 PMCID: PMC5628910 DOI: 10.1021/acs.jpcb.7b01050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We address the interpretation, via
an integrated computational
approach, of the experimental continuous-wave electron paramagnetic
resonance (cw-EPR) spectra of a complete set of conformationally highly
restricted, stable 310-helical peptides from hexa- to nonamers,
each bis-labeled with nitroxide radical-containing TOAC (4-amino-1-oxyl-2,2,6,6-tetramethylpiperidine-4-carboxylic
acid) residues. The usefulness of TOAC for this type of analysis has
been shown already to be due to its cyclic piperidine side chain,
which is rigidly connected to the peptide backbone α-carbon.
The TOAC α-amino acids are separated by two, three, four, and
five intervening residues. This set of compounds has allowed us to
modulate both the radical···radical distance and the
relative orientation parameters. To further validate our conclusion,
a comparative analysis has been carried out on three singly TOAC-labeled
peptides of similar main-chain length.
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Affiliation(s)
- Marco Gerolin
- Department of Chemical Sciences, University of Padova , 35131 Padova, Italy.,Department of Chemistry, École Normale Supérieure, UPMC University of Paris 06, CNRS, Laboratory of Biomolecules , 75005 Paris, France
| | - Mirco Zerbetto
- Department of Chemical Sciences, University of Padova , 35131 Padova, Italy
| | - Alessandro Moretto
- Department of Chemical Sciences, University of Padova , 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova , 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova , 35131 Padova, Italy
| | - Martin van Son
- Huygens-Kamerlingh Onnes Laboratory, Leiden University , 2300RA Leiden, The Netherlands
| | | | - Martina Huber
- Huygens-Kamerlingh Onnes Laboratory, Leiden University , 2300RA Leiden, The Netherlands
| | - Paolo Calligari
- Department of Chemical Sciences, University of Padova , 35131 Padova, Italy
| | - Antonino Polimeno
- Department of Chemical Sciences, University of Padova , 35131 Padova, Italy
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6
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Salvadori A, Del Frate G, Pagliai M, Mancini G, Barone V. Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2016; 116:1731-1746. [PMID: 27867214 PMCID: PMC5101850 DOI: 10.1002/qua.25207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/21/2016] [Accepted: 06/24/2016] [Indexed: 05/31/2023]
Abstract
The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.
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Affiliation(s)
- Andrea Salvadori
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | | | - Marco Pagliai
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 Pisa I-56126 Italy
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7
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Piserchia A, Barone V. Toward a General Yet Effective Computational Approach for Diffusive Problems: Variable Diffusion Tensor and DVR Solution of the Smoluchowski Equation along a General One-Dimensional Coordinate. J Chem Theory Comput 2016; 12:3482-90. [PMID: 27403666 DOI: 10.1021/acs.jctc.6b00388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A generalization to arbitrary large amplitude motions of a recent approach to the evaluation of diffusion tensors [ J. Comput. Chem. , 2009 , 30 , 2 - 13 ] is presented and implemented in a widely available package for electronic structure computations. A fully black-box tool is obtained, which, starting from the generation of geometric structures along different kinds of paths, proceeds toward the evaluation of an effective diffusion tensor and to the solution of one-dimensional Smoluchowski equations by a robust numerical approach rooted in the discrete variable representation (DVR). Application to a number of case studies shows that the results issuing from our approach are identical to those delivered by previous software (in particular DiTe) for rigid scans along a dihedral angle, but can be improved by employing relaxed scans (i.e., constrained geometry optimizations) or even more general large amplitude paths. The theoretical and numerical background is robust and general enough to allow quite straightforward extensions in several directions (e.g., inclusion of reactive paths, solution of Fokker-Planck or stochastic Liouville equations, multidimensional problems, free-energy rather than electronic-energy driven processes).
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Affiliation(s)
- Andrea Piserchia
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy
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8
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Shabestari MH, van Son M, Moretto A, Crisma M, Toniolo C, Huber M. Conformation and EPR characterization of rigid, 310 -helical peptides with TOAC spin labels: Models for short distances. Biopolymers 2016; 102:244-51. [PMID: 24488683 DOI: 10.1002/bip.22467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 11/07/2022]
Abstract
For 3D-structure determination in biophysical systems EPR is rapidly gaining ground. Proteins labeled specifically with two nitroxide spin labels can be prepared, and several EPR methods are available for distance determination, which makes it possible to determine distance constraints. However, such methods require frozen solutions, potentially causing non-physiological states of the sample. Here, we target spin- spin interaction in liquid solution at room temperature using rigid model compounds. A series of 310 -helical peptides, based on α-aminoisobutyric acid (Aib), is synthesized with pairs of spin labels separated by three, four, and five amino acids. To avoid flexibility, the noncoded nitroxyl-containing α-amino acid TOAC that is rigidly connected with the peptide backbone, is used. The EPR spectra of the peptides show a decreasing amount of coupling between the two spin labels within this series. We suggest through-bond interaction as the dominating mechanism for exchange interaction (J) and find a stronger J-coupling than in the corresponding Ala-based TOAC-peptides investigated previously (Hanson, et al., J Am Chem Soc 1996, 118, 7618-7625). We speculate that stronger coupling in Aib- vs Ala- peptides is due to intrinsically stronger through-bond interaction in the Aib-based peptides.
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Affiliation(s)
- Maryam Hashemi Shabestari
- Department of Molecular Physics, Huygens Laboratory, Leiden University, 2300, RA Leiden, The Netherlands
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9
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Puzzarini C, Barone V. Theoretical Study of the X2NO Systems (X = F, Cl, Br, I): Effects of Halogen Substitution on Structural and Spectroscopic Properties. J Chem Theory Comput 2015; 5:2378-87. [PMID: 26616619 DOI: 10.1021/ct9001762] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Structural and spectroscopic properties of the X2 NO series of radicals, with X = F, Cl, Br, I, have been computed by the coupled cluster ansatz in conjunction with hierarchical series of basis sets, accounting for, in most cases, core correlation effects and extrapolation to the complete basis set limit. Namely, equilibrium structures, vibrational frequencies, and hyperfine coupling constants have been considered. Methods rooted into the density functional theory have been used to estimate anharmonic and, in conjunction with the polarizable continuum model, environmental effects. The remarkable agreement with the available experimental data, limited to the lighter member of the series, confirms the reliability of our computational approach and suggests that the data for heavier species represent reliable benchmarks for future experimental data and/or cheaper computational methods devised for larger systems.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy, and Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy, IPCF-CNR, via Moruzzi 1, 56124 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy, and Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy, IPCF-CNR, via Moruzzi 1, 56124 Pisa, Italy
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10
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Bocchinfuso G, Conflitti P, Raniolo S, Caruso M, Mazzuca C, Gatto E, Placidi E, Formaggio F, Toniolo C, Venanzi M, Palleschi A. Aggregation propensity of Aib homo-peptides of different length: an insight from molecular dynamics simulations. J Pept Sci 2014; 20:494-507. [DOI: 10.1002/psc.2648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Gianfranco Bocchinfuso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Paolo Conflitti
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Stefano Raniolo
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Mario Caruso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Claudia Mazzuca
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Emanuela Gatto
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Ernesto Placidi
- Department of Physics; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
- CNR-ISM; Via Fosso del Cavaliere 100 I-00133 Roma Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
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11
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Hermosilla L, Prampolini G, Calle P, García de la Vega JM, Brancato G, Barone V. Extension of the AMBER Force Field for Nitroxide Radicals and Combined QM/MM/PCM Approach to the Accurate Determination of EPR Parameters of DMPO-H in Solution. J Chem Theory Comput 2013; 9:3626-36. [PMID: 26584116 PMCID: PMC4660035 DOI: 10.1021/ct4003256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO-moiety. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second-order vibrational perturbation theory involving semidiagonal third energy derivatives together first and second property derivatives.
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Affiliation(s)
- Laura Hermosilla
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid (Spain)
| | - Giacomo Prampolini
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Area della Ricerca, via Moruzzi 1, I-56124, Pisa (Italy)
| | - Paloma Calle
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid (Spain)
| | | | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa (Italy)
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa (Italy)
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12
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Grubišić S, Brancato G, Barone V. An improved AMBER force field for α,α-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems. Phys Chem Chem Phys 2013; 15:17395-407. [DOI: 10.1039/c3cp52721b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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13
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Casati C, Franchi P, Pievo R, Mezzina E, Lucarini M. Unraveling unidirectional threading of α-cyclodextrin in a [2]rotaxane through spin labeling approach. J Am Chem Soc 2012; 134:19108-17. [PMID: 23106205 DOI: 10.1021/ja3073484] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present here the results of a CW-ESR investigation of a double spin labeled α-cyclodextrin-based [2]rotaxane that is characterized by the presence of nitroxide labels both at the wheel and at the dumbbell. This was accomplished by synthesizing a spin labeled α-CD (the wheel) that was mechanically blocked on a thread containing a nitroxide unit by a Cu(I) catalyzed azide-alkyne cycloaddition (CuAAC). Both ESI-MS analysis and NMR spectroscopy were used to provide evidence of the threading processes. Because of the unsymmetrical structure of both the wheel and the axle, two different geometrical isomers could be predicted on the basis of the orientation of the CD along the thread. By combining molecular dynamic calculations and information extracted from the CW-ESR spectra, we were able to determine the geometrical nature of the isomer that was isolated as the only species. The ESR spectra showed J-coupling between the two mechanically connected nitroxide units and were analyzed by a model assuming three main molecular states. The intramolecular noncovalent nature of spin exchange was confirmed by reversibly switching the magnetic interaction on-off by changing the pH of the solution in the presence of a competing macrocyclic host.
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Affiliation(s)
- Costanza Casati
- Department of Organic Chemistry A. Mangini, University of Bologna, Via San Giacomo 11, I-40126 Bologna, Italy
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14
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The spin label amino acid TOAC and its uses in studies of peptides: chemical, physicochemical, spectroscopic, and conformational aspects. Biophys Rev 2012; 4:45-66. [PMID: 22347893 PMCID: PMC3271205 DOI: 10.1007/s12551-011-0064-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/20/2011] [Indexed: 01/21/2023] Open
Abstract
We review work on the paramagnetic amino acid 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid, TOAC, and its applications in studies of peptides and peptide synthesis. TOAC was the first spin label probe incorporated in peptides by means of a peptide bond. In view of the rigid character of this cyclic molecule and its attachment to the peptide backbone via a peptide bond, TOAC incorporation has been very useful to analyze backbone dynamics and peptide secondary structure. Many of these studies were performed making use of EPR spectroscopy, but other physical techniques, such as X-ray crystallography, CD, fluorescence, NMR, and FT-IR, have been employed. The use of double-labeled synthetic peptides has allowed the investigation of their secondary structure. A large number of studies have focused on the interaction of peptides, both synthetic and biologically active, with membranes. In the latter case, work has been reported on ligands and fragments of GPCR, host defense peptides, phospholamban, and β-amyloid. EPR studies of macroscopically aligned samples have provided information on the orientation of peptides in membranes. More recent studies have focused on peptide–protein and peptide–nucleic acid interactions. Moreover, TOAC has been shown to be a valuable probe for paramagnetic relaxation enhancement NMR studies of the interaction of labeled peptides with proteins. The growth of the number of TOAC-related publications suggests that this unnatural amino acid will find increasing applications in the future.
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Grubišić S, Brancato G, Pedone A, Barone V. Extension of the AMBER force field to cyclic α,α dialkylated peptides. Phys Chem Chem Phys 2012; 14:15308-20. [DOI: 10.1039/c2cp42713c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Rinkevicius Z, Frecuş B, Murugan NA, Vahtras O, Kongsted J, Ågren H. Encapsulation Influence on EPR Parameters of Spin-Labels: 2,2,6,6-Tetramethyl-4-methoxypiperidine-1-oxyl in Cucurbit[8]uril. J Chem Theory Comput 2011; 8:257-63. [DOI: 10.1021/ct200816z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Zilvinas Rinkevicius
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Swedish e-Science Research Center (SeRC), Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Bogdan Frecuş
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - N. Arul Murugan
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Olav Vahtras
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Hans Ågren
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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Carlotto S, Zerbetto M, Shabestari MH, Moretto A, Formaggio F, Crisma M, Toniolo C, Huber M, Polimeno A. In silico interpretation of cw-ESR at 9 and 95 GHz of mono- and bis- TOAC-labeled Aib-homopeptides in fluid and frozen acetonitrile. J Phys Chem B 2011; 115:13026-36. [PMID: 21970372 DOI: 10.1021/jp2063645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we address the interpretation of molecular properties of selected singly and doubly spin-labeled peptides from continuous-wave electron spin resonance (cw-ESR) spectroscopy. This study is performed by means of an integrated computational approach that merges a stochastic treatment of long-term dynamics to ad hoc methodologies for the calculation of structural properties. In particular, our method is based on (i) the determination of geometric and local magnetic parameters of the peptides by quantum mechanical density functional calculations by taking into account solvent contribution; (ii) the hydrodynamic evaluation of dissipative properties; and (iii) molecular dynamics including equilibrium distribution of molecular conformations. The system is then described by a stochastic Liouville equation in which the spin Hamiltonian for the two electron spins, interacting with each other and coupled to two (14)N nuclear spins, is coupled to the diffusive operator describing the time evolution of slow coordinates. cw-ESR spectra are simulated for selected peptides built from the non-natural α-aminoacids α-aminoisobutyric acid (Aib) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, we study the -Aib-TOAC-Aib- singly labeled tripeptide and the -Aib-TOAC-(Aib)(7)- singly labeled and -Aib-TOAC-(Aib)(5)-TOAC-Aib- doubly labeled nonapeptides. We show that good agreement is obtained with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling is a powerful approach to the investigation of both molecular dynamics and 3D-structural properties.
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Affiliation(s)
- Silvia Carlotto
- Department of Chemistry, University of Padova, Padova, Italy
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Rinkevicius Z, Murugan NA, Kongsted J, Frecuş B, Steindal AH, Ågren H. Density Functional Restricted–Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution. J Chem Theory Comput 2011; 7:3261-71. [DOI: 10.1021/ct2003572] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zilvinas Rinkevicius
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Swedish e-Science Research Center (SeRC), Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - N. Arul Murugan
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Bogdan Frecuş
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Arnfinn Hykkerud Steindal
- Centre of Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Hans Ågren
- Department of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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Shapiro YE, Polimeno A, Freed JH, Meirovitch E. Methyl dynamics of a Ca2+-calmodulin-peptide complex from NMR/SRLS. J Phys Chem B 2011; 115:354-65. [PMID: 21166433 PMCID: PMC3062514 DOI: 10.1021/jp107130m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS accounts for dynamical coupling between the tumbling of the protein and the local motion of the probe and for general tensorial properties. It is the generalization of the traditional model-free (MF) method, which does not account for mode-coupling and treats only simple tensorial properties. SRLS is applied herein to ²H relaxation of ¹³CDH₂ groups in the complex of Ca(2+)-calmodulin with the peptide smMLCKp. Literature data comprising ²H T₁ and T₂ acquired at 14.1 and 17.6 T, and 288, 295, 308, and 320 K, are used. We find that mode-coupling is a small effect for methyl dynamics. On the other hand, general tensorial properties are important. In particular, it is important to allow for the asymmetry of the local spatial restrictions, which can be represented in SRLS by a rhombic local ordering tensor with components S(0)(2) and S(2)(2). The principal axes frame of this tensor is obviously different from the axial frames of the magnetic tensors. Here, we find that -0.2 ≤ S(0)(2) ≤ 0.5 and -0.4 ≤ S(2)(2) ≤ 0. MF features a single "generalized" order parameter, S, confined to the 0-0.316 range; the local geometry is inherently simple. The parameter S is inaccurate, having absorbed unaccounted for effects, notably S(2)(2) ≠ 0. We find that the methionine methyls (the other methyl types) reorient with rates of 8.6 × 10⁹ to 21.4 × 10⁹ (0.67 × 10⁹ to 6.5 × 10⁹) 1/s. The corresponding activation energies are 10 (10-27) kJ/mol. By contrast, MF yields inaccurate effective local motional correlation times, τ(e), with nonphysical temperature dependence. Thus, the problematic S- and τ(e)-based MF picture of methyl dynamics has been replaced with an insightful physical picture based on a local ordering tensor related to structural features, and a local diffusion tensor that yields accurate activation energies.
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Affiliation(s)
- Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
| | - Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900 Israel
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Meirovitch E, Zerbetto M, Polimeno A, Freed JH. Backbone dynamics of deoxy and carbonmonoxy hemoglobin by NMR/SRLS. J Phys Chem B 2011; 115:143-57. [PMID: 21162544 PMCID: PMC3071157 DOI: 10.1021/jp107553j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The slowly relaxing local structure (SRLS) approach, developed for NMR spin relaxation analysis in proteins, is applied herein to amide ¹⁵N relaxation in deoxy and carbonmonoxy hemoglobin. Experimental data including ¹⁵N T₁, T₂ and ¹⁵N-{¹H} NOE, acquired at 11.7 and 14.1 T, and 29 and 34 °C, are analyzed. The restricted local motion of the N-H bond is described in terms of the principal value (S(0)(2)) and orientation (β(D)) of an axial local ordering tensor, S, and the principal values (R(||)(L) and R(⊥)(L)) and orientation (β(O)) of an axial local diffusion tensor, R(L). The parameters c₀² (the potential coefficient in terms of which S(0)(2) is defined), R(||)(L), β(D), and β(O) are determined by data fitting; R(⊥)(L) is set equal to the global motional rate, R(C), found previously to be (5.2-5.8) × 10⁶ 1/s in the temperature range investigated. The principal axis of S is (nearly) parallel to the C(i-1)(α)-C(i)(α) axis; when the two axes are parallel, β(D) = -101.3° (in the frame used). The principal axis of R(L) is (nearly) parallel to the N-H bond; when the two axes are parallel, β(O) = -101.3°. For "rigid" N-H bonds located in secondary structure elements the best-fit parameters are S(0)(2) = 0.88-0.95 (corresponding to local potentials of 8.6-19.9 k(B)T), R(||)(L) = 10⁹-10¹⁰ 1/s, β(D) = -101.3° ± 2.0°, and β(O) = -101.3° ± 4°. For flexible N-H bonds located in loops the best-fit values are S(0)(2) = 0.75-0.80 (corresponding to local potentials of 4.5-5.5 k(B)T), R(||)(L) = (1.0-6.3) × 10⁸ 1/s, β(D) = -101.3° ± 4.0°, and β(O) = -101.3° ± 10°. These results are important in view of their physical clarity, inherent potential for further interpretation, consistency, and new qualitative insights provided (vide infra).
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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21
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Barone V, Cimino P, Pedone A. An integrated computational protocol for the accurate prediction of EPR and PNMR parameters of aminoxyl radicals in solution. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48 Suppl 1:S11-S22. [PMID: 20625984 DOI: 10.1002/mrc.2640] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Magnetic spectroscopic techniques such as electron paramagnetic resonance (EPR) and paramagnetic NMR (PNMR) are valuable tools for understanding the structure and dynamics of complex systems such as, for example, biomolecules or nanomaterials labeled with suitable free radicals. Unfortunately, such spectra do not give direct access to the radical structure because of the subtle interplay between several different effects not easily separable and evaluable by experimentalists alone. In this respect, computational spectroscopy is becoming an essential and versatile tool for the assignment and interpretation of experimental spectra. In this article, the new integrated computational approaches developed in the recent years in our research group are reviewed. Such approaches have been applied to two widely used spin probes showing that proper account of stereo-electronic, environmental and dynamical effects leads to magnetic properties in remarkable agreement with experimental results.
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22
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Meirovitch E, Shapiro YE, Polimeno A, Freed JH. Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 56:360-405. [PMID: 20625480 PMCID: PMC2899824 DOI: 10.1016/j.pnmrs.2010.03.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Yury E. Shapiro
- The Mina and Everard Goodman Faculty of Life Sciences, Bar–Ilan University, Ramat-Gan 52900 Israel
| | - Antonino Polimeno
- Department of Physical Chemistry, University of Padua, 35131 Padua, Italy
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, U.S.A
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23
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Barone V, Biczysko M, Brancato G. Extending the Range of Computational Spectroscopy by QM/MM Approaches: Time-Dependent and Time-Independent Routes. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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24
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Stendardo E, Pedone A, Cimino P, Cristina Menziani M, Crescenzi O, Barone V. Extension of the AMBER force-field for the study of large nitroxides in condensed phases: an ab initio parameterization. Phys Chem Chem Phys 2010; 12:11697-709. [DOI: 10.1039/c001481h] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Zerbetto M, Polimeno A, Meirovitch E. General theoretical/computational tool for interpreting NMR spin relaxation in proteins. J Phys Chem B 2009; 113:13613-25. [PMID: 19775101 DOI: 10.1021/jp9046819] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed in recent years the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS is a two-body coupled rotator model which accounts rigorously for mode-coupling between the global motion of the protein and the local motion of the spin-bearing probe and allows for general properties of the second rank tensors involved. We showed that a general tool of data analysis requires both capabilities. Several important functionalities were missing in our previous implementations of SRLS in data fitting schemes, and in some important cases, the calculations were tedious. Here we present a general implementation which allows for asymmetric local and global diffusion tensors, distinct local ordering and local diffusion frames, and features a rhombic local potential which includes Wigner matrix element terms of ranks 2 and 4. A recently developed hydrodynamics-based approach for calculating global diffusion tensors has been incorporated into the data-fitting scheme. The computational efficiency of the latter has been increased significantly through object-oriented programming within the scope of the C++ programming language, and code parallelization. A convenient graphical user interface is provided. Currently autocorrelated (15)N spin relaxation data can be analyzed effectively. Adaptation to any autocorrelated and cross-correlated relaxation analysis is straightforward. New physical insight is gleaned on largely preserved local structure in solution, even in chain segments which experience slow local motion. Prospects associated with improved dynamic models, and new applications made possible by the current implementation of SRLS, are delineated.
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Affiliation(s)
- Mirco Zerbetto
- Dipartimento di Scienze Chimiche, Università di Padova, Padova, Italy
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26
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Puzzarini C, Barone V. On the stability of X2NO radicals (X = F, Cl, Br, I). Phys Chem Chem Phys 2009; 11:11463-70. [PMID: 20024417 DOI: 10.1039/b917446j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The stability of X(2)NO radicals has been studied by investigating the three possible dissociative channels, namely X+XNO, X(2)+NO, and NX(2)+O. While all the radicals have been found stable with respect to the latter, the second pathway shows that Br(2)NO and I(2)NO are unstable with respect to dissociation. The first dissociative channel has been thoroughly investigated with the aim of understanding whether F(2)NO and Cl(2)NO are stable and how much. This implied the molecular structures and energies of X(2)NO and XNO, with X = F, Cl, to be computed at high level of theory. The coupled cluster ansatz in conjunction with hierarchical series of basis sets has been employed, thus accounting for extrapolation to the complete basis-set limit. Core correlation as well as higher excitations in the electronic-correlation treatment have also been taken into account. It is particularly noteworthy that explicit inclusion of quadruple excitations allowed to obtain for the first time equilibrium geometries of FNO and ClNO in full quantitative agreement with their experimental counterparts.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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27
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Williams F, Chen GF, Mattar SM, Scudder PH, Trieber DA, Saven JG, Whritenour DC, Cimino P, Barone V. Magneto-structural relationships for radical cation and neutral pyridinophane structures with intrabridgehead nitrogen atoms. An integrated experimental and quantum mechanical study. J Phys Chem B 2009; 113:9026-34. [PMID: 19507811 DOI: 10.1021/jp902493e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An integrated experimental and computational approach was used to compare the properties of representative molecules containing intrabridgehead nitrogen atoms with those of the corresponding radical cations issuing from one-electron oxidation with the aim of unraveling the characteristics of the three-electron sigma-bonds formed in the open-shell species. From a quantitative point of view, last-generation density functional methods coupled with proper basis sets and, when needed, continuum models for describing bulk solvent effects confirm their reliability for the computation of structures and magnetic properties of organic free radicals. From an interpretative point of view, different hybridizations of nitrogen atoms tuned by their chemical environment lead to markedly different magnetic properties that represent reliable and sensitive probes of structural and electronic characteristics.
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Affiliation(s)
- Ffrancon Williams
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996-1600, USA.
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28
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Barone V, Zerbetto M, Polimeno A. Hydrodynamic modeling of diffusion tensor properties of flexible molecules. J Comput Chem 2008; 30:2-13. [PMID: 18496840 DOI: 10.1002/jcc.21007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a computationally efficient implementation of hydrodynamic modeling for the evaluation of diffusion tensors of molecules with internal degrees of freedom, adapted to take into account information from linear scaling computations of solvent accessible surfaces implemented in the framework of last generation continuum solvent models. Torsional angles are taken also explicitly into account, while retaining correct hydrodynamic interactions. A comparison with literature data is presented to prove the effectiveness of the approach for a wide range of molecular dimensions and solvent environments.
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Affiliation(s)
- Vincenzo Barone
- Dipartimento di Chimica and INSTM-Village, Università di Napoli Federico II Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Napoli, Italy.
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Barone V, Cimino P. Validation of the B3LYP/N07D and PBE0/N07D Computational Models for the Calculation of Electronic g-Tensors. J Chem Theory Comput 2008; 5:192-9. [DOI: 10.1021/ct800279g] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Vincenzo Barone
- Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte don Melillo, I-84084 Fisciano (Sa), Italy
| | - Paola Cimino
- Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte don Melillo, I-84084 Fisciano (Sa), Italy
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30
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Shafer AM, Nakaie CR, Deupi X, Bennett VJ, Voss JC. Characterization of a conformationally sensitive TOAC spin-labeled substance P. Peptides 2008; 29:1919-29. [PMID: 18775458 DOI: 10.1016/j.peptides.2008.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 07/31/2008] [Accepted: 08/01/2008] [Indexed: 11/23/2022]
Abstract
To probe the binding of a peptide agonist to a G-protein coupled receptor in native membranes, the spin-labeled amino acid analogue 4-amino-4-carboxy-2,2,6,6-tetramethylpiperidino-1-oxyl (TOAC) was substituted at either position 4 or 9 within the substance P peptide (RPKPQQFFGLM-NH2), a potent agonist of the neurokinin-1 receptor. The affinity of the 4-TOAC analog is comparable to the native peptide while the affinity of the 9-TOAC derivative is approximately 250-fold lower. Both peptides activate receptor signaling, though the potency of the 9-TOAC peptide is substantially lower. The utility of these modified ligands for reporting conformational dynamics during the neurokinin-1 receptor activation was explored using EPR spectroscopy, which can determine the real-time dynamics of the TOAC nitroxides in solution. While the binding of both the 4-TOAC substance P and 9-TOAC substance P peptides to isolated cell membranes containing the neurokinin-1 receptor is detected, a bound signal for the 9-TOAC peptide is only obtained under conditions that maintain the receptor in its high-affinity binding state. In contrast, 4-TOAC substance P binding is observed by solution EPR under both low- and high-affinity receptor states, with evidence of a more strongly immobilized peptide in the presence of GDP. In addition, to better understand the conformational consequences of TOAC substitution into substance P as it relates to receptor binding and activation, atomistic models for both the 4- and 9-TOAC versions of the peptide were constructed, and the molecular dynamics calculated via simulated annealing to explore the influence of the TOAC substitutions on backbone structure.
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Affiliation(s)
- Aaron M Shafer
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, United States
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31
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Hermosilla L, Sieiro C, Calle P, Zerbetto M, Polimeno A. Modeling of cw-EPR Spectra of Propagating Radicals in Methacrylic Polymerization at Different Temperatures. J Phys Chem B 2008; 112:11202-8. [DOI: 10.1021/jp804675q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Hermosilla
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain, and Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, I-35131, Padova, Italy
| | - Carlos Sieiro
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain, and Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, I-35131, Padova, Italy
| | - Paloma Calle
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain, and Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, I-35131, Padova, Italy
| | - Mirco Zerbetto
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain, and Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, I-35131, Padova, Italy
| | - Antonino Polimeno
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain, and Dipartimento di Scienze Chimiche, Università degli Studi di Padova, via Marzolo 1, I-35131, Padova, Italy
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32
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Barone V, Improta R, Rega N. Quantum mechanical computations and spectroscopy: from small rigid molecules in the gas phase to large flexible molecules in solution. Acc Chem Res 2008; 41:605-16. [PMID: 18307319 DOI: 10.1021/ar7002144] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Interpretation of structural properties and dynamic behavior of molecules in solution is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle interplay of several different effects, whose specific role is not easy to separate and evaluate. In such a complex scenario, theoretical studies can be very helpful at two different levels: (i) supporting and complementing experimental results to determine the structure of the target molecule starting from its spectral properties; (ii) dissecting and evaluating the role of different effects in determining the observed spectroscopic properties. This is the reason why computational spectroscopy is rapidly evolving from a highly specialized research field into a versatile and widespread tool for the assignment of experimental spectra and their interpretation in terms of chemical physical effects. In such a situation, it becomes important that both computationally and experimentally oriented chemists are aware that new methodological advances and integrated computational strategies are available, providing reliable estimates of fundamental spectral parameters not only for relatively small molecules in the gas phase but also for large and flexible molecules in condensed phases. In this Account, we review the most significant methodological contributions from our research group in this field, and by exploiting some recent results of their application to the computation of IR, UV-vis, NMR, and EPR spectral parameters, we discuss the microscopic mechanisms underlying solvent and vibrational effects on the spectral parameters. After reporting some recent achievements for the study of excited states by first principle quantum mechanical approaches, we focus on the treatment of environmental effects by means of mixed discrete-continuum solvent models and on effective methods for computing vibronic contributions to the spectra. We then discuss some new developments, mainly based on time-dependent approaches, allowing us to go beyond the determination of spectroscopic parameters toward the simulation of line widths and shapes. Although further developments are surely needed to improve the accuracy and effectiveness of several items in the proposed approach, we try to show that the first important steps toward a direct comparison between the results obtained in vitro and those obtained in silico have been made, making easier fruitful crossovers among experiments, computations and theoretical models, which would be decisive for a deeper understanding of the spectral behavior associated with complex systems and processes.
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Affiliation(s)
- Vincenzo Barone
- LSDM and CR-INSTM VILLAGE, Chemistry Department Paolo Corradini, University Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Roberto Improta
- LSDM and CR-INSTM VILLAGE, Chemistry Department Paolo Corradini, University Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Nadia Rega
- LSDM and CR-INSTM VILLAGE, Chemistry Department Paolo Corradini, University Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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Choi SH, Guzei IA, Spencer LC, Gellman SH. Crystallographic Characterization of Helical Secondary Structures in α/β-Peptides with 1:1 Residue Alternation. J Am Chem Soc 2008; 130:6544-50. [DOI: 10.1021/ja800355p] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Soo Hyuk Choi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Lara C. Spencer
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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Barone V, Causà M. Structure and ESR features of a radiation-induced radical in α-glycine crystals. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2007.12.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zerbetto M, Polimeno A, Cimino P, Barone V. On the interpretation of continuous wave electron spin resonance spectra of tempo-palmitate in 5-cyanobiphenyl. J Chem Phys 2008; 128:024501. [DOI: 10.1063/1.2812280] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Brancato G, Rega N, Barone V. Unraveling the Role of Stereo-electronic, Dynamical, and Environmental Effects in Tuning the Structure and Magnetic Properties of Glycine Radical in Aqueous Solution at Different pH Values. J Am Chem Soc 2007; 129:15380-90. [DOI: 10.1021/ja074910t] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Giuseppe Brancato
- Contribution from the Chemistry Department Paolo Corradini, University Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Nadia Rega
- Contribution from the Chemistry Department Paolo Corradini, University Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Vincenzo Barone
- Contribution from the Chemistry Department Paolo Corradini, University Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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