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Mir B, Serrano-Chacón I, Medina P, Macaluso V, Terrazas M, Gandioso A, Garavís M, Orozco M, Escaja N, González C. Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells. Nucleic Acids Res 2024; 52:3375-3389. [PMID: 38366792 PMCID: PMC11014255 DOI: 10.1093/nar/gkae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 01/17/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
The i-motif is an intriguing non-canonical DNA structure, whose role in the cell is still controversial. Development of methods to study i-motif formation under physiological conditions in living cells is necessary to study its potential biological functions. The cytosine analog 1,3-diaza-2-oxophenoxazine (tCO) is a fluorescent nucleobase able to form either hemiprotonated base pairs with cytosine residues, or neutral base pairs with guanines. We show here that when tCO is incorporated in the proximity of a G:C:G:C minor groove tetrad, it induces a strong thermal and pH stabilization, resulting in i-motifs with Tm of 39ºC at neutral pH. The structural determination by NMR methods reveals that the enhanced stability is due to a large stacking interaction between the guanines of the tetrad with the tCO nucleobase, which forms a tCO:C+ in the folded structure at unusually-high pHs, leading to an increased quenching in its fluorescence at neutral conditions. This quenching is much lower when tCO is base-paired to guanines and totally disappears when the oligonucleotide is unfolded. By taking profit of this property, we have been able to monitor i-motif folding in cells.
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Affiliation(s)
- Bartomeu Mir
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Israel Serrano-Chacón
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Pedro Medina
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia. Universitat de Barcelona. 08028 Barcelona. Spain
| | - Veronica Macaluso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Albert Gandioso
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
| | - Miguel Garavís
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). 08028 Barcelona. Spain
- Departament de Bioquímica i Biomedicina. Facultat de Biologia. Universitat de Barcelona. 08028 Barcelona. Spain
| | - Núria Escaja
- Inorganic and Organic Chemistry Department. Organic Chemistry Section and IBUB. University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona. Spain
| | - Carlos González
- Instituto de Química Física ‘Blas Cabrera’. CSIC. Serrano 119. 28006 Madrid. Spain
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2
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Hashem S, Macaluso V, Nottoli M, Lipparini F, Cupellini L, Mennucci B. From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain. Chem Sci 2021; 12:13331-13342. [PMID: 34777752 PMCID: PMC8528011 DOI: 10.1039/d1sc03000k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/01/2021] [Indexed: 12/28/2022] Open
Abstract
Photoreceptor proteins bind a chromophore, which, upon light absorption, modifies its geometry or its interactions with the protein, finally inducing the structural change needed to switch the protein from an inactive to an active or signaling state. In the Blue Light-Using Flavin (BLUF) family of photoreceptors, the chromophore is a flavin and the changes have been connected with a rearrangement of the hydrogen bond network around it on the basis of spectroscopic changes measured for the dark-to-light conversion. However, the exact conformational change triggered by the photoexcitation is still elusive mainly because a clear consensus on the identity not only of the light activated state but also of the dark one has not been achieved. Here, we present an integrated investigation that combines microsecond MD simulations starting from the two conflicting crystal structures available for the AppA BLUF domain with calculations of NMR, IR and UV-Vis spectra using a polarizable QM/MM approach. Thanks to such a combined analysis of the three different spectroscopic responses, a robust characterization of the structure of the dark state in solution is given together with the uncovering of important flaws of the most popular molecular mechanisms present in the literature for the dark-to-light activation.
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Affiliation(s)
- Shaima Hashem
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Veronica Macaluso
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
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3
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Macaluso V, Hashem S, Nottoli M, Lipparini F, Cupellini L, Mennucci B. Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics. J Phys Chem B 2021; 125:10282-10292. [PMID: 34476939 PMCID: PMC8450903 DOI: 10.1021/acs.jpcb.1c05753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Indexed: 01/02/2023]
Abstract
Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.
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Affiliation(s)
| | | | - Michele Nottoli
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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4
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Macaluso V, Salvadori G, Cupellini L, Mennucci B. The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation. Chem Sci 2021; 12:5555-5565. [PMID: 34168792 PMCID: PMC8179611 DOI: 10.1039/d1sc00186h] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 12/28/2022] Open
Abstract
Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chromophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive molecular dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway.
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Affiliation(s)
- Veronica Macaluso
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa 56124 Pisa Italy
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5
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Martin Somer A, Macaluso V, Barnes GL, Yang L, Pratihar S, Song K, Hase WL, Spezia R. Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces. J Am Soc Mass Spectrom 2020; 31:2-24. [PMID: 32881516 DOI: 10.1021/jasms.9b00062] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.
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Affiliation(s)
- Ana Martin Somer
- Departamento de Química, Facultad de Ciencias, Módulo 13 Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain
| | - Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Evry, France
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Li Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P.R. China
| | - Subha Pratihar
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Kihyung Song
- Department of Chemistry, Korea National University of Education, Chungbuk 28644, Republic of Korea
| | - William L Hase
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, 4, Place Jussieu, Paris, 75252 Cedex 05, France
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6
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Macaluso V, Cupellini L, Salvadori G, Lipparini F, Mennucci B. Elucidating the role of structural fluctuations, and intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome. Phys Chem Chem Phys 2020; 22:8585-8594. [DOI: 10.1039/d0cp00372g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular dynamics and a multiscale polarizable QM/MM strategy allow reproducing absorption, circular dichroism, and resonance Raman spectra of a bacteriophytochrome.
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Affiliation(s)
- Veronica Macaluso
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Filippo Lipparini
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry
- University of Pisa
- Pisa
- Italy
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7
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Carrà A, Macaluso V, Villalta PW, Spezia R, Balbo S. Fragmentation Spectra Prediction and DNA Adducts Structural Determination. J Am Soc Mass Spectrom 2019; 30:2771-2784. [PMID: 31696434 DOI: 10.1007/s13361-019-02348-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/04/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
In this work, chemical dynamics simulations were optimized and used to predict fragmentation mass spectra for DNA adduct structural determination. O6-methylguanine (O6-Me-G) was used as a simple model adduct to calculate theoretical spectra for comparison with measured high-resolution fragmentation data. An automatic protocol was established to consider the different tautomers accessible at a given energy and obtain final theoretical spectra by insertion of an initial tautomer. In the work reported here, the most stable tautomer was chosen as the initial structure, but in general, any structure could be considered. Allowing for the formation of the various possible tautomers during simulation calculations was found to be important to getting a more complete fragmentation spectrum. The calculated theoretical results reproduce the experimental peaks such that it was possible to determine reaction pathways and product structures. The calculated tautomerization network was crucial to correctly identifying all the observed ion peaks, showing that a mobile proton model holds not only for peptide fragmentation but also for nucleobases. Finally, first principles results were compared to simple machine learning fragmentation models.
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Affiliation(s)
- Andrea Carrà
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Veronica Macaluso
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry, CEA, CNRS, Université Paris Saclay, Bd. F. Mitterrand, 91025, Evry Cedex, France
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique, LCT, CNRS, Sorbonne Université, F. 75005, Paris, France.
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, Minneapolis, MN, 55455, USA.
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8
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Macaluso V, Scuderi D, Crestoni ME, Fornarini S, Corinti D, Dalloz E, Martinez-Nunez E, Hase WL, Spezia R. l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations. J Phys Chem A 2019; 123:3685-3696. [DOI: 10.1021/acs.jpca.9b01779] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
| | - Debora Scuderi
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Enzo Dalloz
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Emilio Martinez-Nunez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, 4, Place Jussieu, 75252 Paris Cedex 05, France
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9
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Homayoon Z, Macaluso V, Martin-Somer A, Muniz MCNB, Borges I, Hase WL, Spezia R. Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H +) 2 and TLK(H +) 2 fragmentation dynamics, and with thermal simulations. Phys Chem Chem Phys 2018; 20:3614-3629. [PMID: 29340378 DOI: 10.1039/c7cp06818b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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
Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N2, and previous thermal activation simulation results; Z. Homayoon, S. Pratihar, E. Dratz, R. Snider, R. Spezia, G. L. Barnes, V. Macaluso, A. Martin-Somer and W. L. Hase, J. Phys. Chem. A, 2016, 120, 8211-8227. Upon thermal activation unimolecular fragmentation is statistical and in accord with RRKM unimolecular rate theory. Simulations show that in collisional activation some non-statistical fragmentation occurs, including shattering, which is not present when the ions dissociate statistically. Products formed by non-statistical shattering mechanisms may be related to characteristic mass spectrometry peaks which distinguish the two isomers I and L.
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Affiliation(s)
- Zahra Homayoon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 USA.
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Macaluso V, Homayoon Z, Spezia R, Hase WL. Threshold for shattering fragmentation in collision-induced dissociation of the doubly protonated tripeptide TIK(H+)2. Phys Chem Chem Phys 2018; 20:19744-19749. [DOI: 10.1039/c8cp02577k] [Citation(s) in RCA: 11] [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: 12/14/2022]
Abstract
Determination of shattering threshold for unimolecular dissociation of a model tripeptide.
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Affiliation(s)
| | - Zahra Homayoon
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | | | - William L. Hase
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
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11
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Homayoon Z, Pratihar S, Dratz E, Snider R, Spezia R, Barnes GL, Macaluso V, Martin Somer A, Hase WL. Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters. J Phys Chem A 2016; 120:8211-8227. [DOI: 10.1021/acs.jpca.6b05884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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)
- Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | | | | | - Riccardo Spezia
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Veronica Macaluso
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - Ana Martin Somer
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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12
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Spezia R, Martin-Somer A, Macaluso V, Homayoon Z, Pratihar S, Hase WL. Unimolecular dissociation of peptides: statistical vs. non-statistical fragmentation mechanisms and time scales. Faraday Discuss 2016; 195:599-618. [DOI: 10.1039/c6fd00126b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present work we have investigated mechanisms of gas phase unimolecular dissociation of a relatively simple dipeptide, the di-proline anion, by means of chemical dynamics simulations, using the PM3 semi-empirical Hamiltonian. In particular, we have considered two activation processes that are representative limits of what occurs in collision induced dissociation experiments: (i) thermal activation, corresponding to several low energy collisions, in which the system is prepared with a microcanonical distribution of energy; (ii) collisional activation where a single shock of hundreds of kcal mol−1 (300 kcal mol−1 in the present case) can transfer sufficient energy to allow dissociation. From these two activation processes we obtained different product abundances, and for one particular fragmentation pathway a clear mechanistic difference for the two activation processes. This mechanism corresponds to the leaving of an OH− group and subsequent formation of water by taking a proton from the remaining molecule. This last reaction is always observed in thermal activation while in collisional activation it is less favoured and the formation of OH− as a final product is observed. More importantly, we show that while in thermal activation unimolecular dissociation follows exponential decay, in collision activation the initial population decays with non-exponential behaviour. Finally, from the thermal activation simulations it was possible to obtain rate constants as a function of temperature that show Arrhenius behaviour. Thus activation energies have also been extracted from these simulations.
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Affiliation(s)
- Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement
- CEA CNRS
- Université Paris Saclay
- 91025 Evry
- France
| | - Ana Martin-Somer
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement
- CEA CNRS
- Université Paris Saclay
- 91025 Evry
- France
| | - Veronica Macaluso
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement
- CEA CNRS
- Université Paris Saclay
- 91025 Evry
- France
| | - Zahra Homayoon
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | - Subha Pratihar
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | - William L. Hase
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
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13
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Bodo E, Macaluso V, Spezia R. Solvent Structure around Lanthanoid(III) Ions in Liquid DMSO As Revealed by Polarizable Molecular Dynamics Simulations. J Phys Chem B 2015; 119:13347-57. [DOI: 10.1021/acs.jpcb.5b06317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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)
- Enrico Bodo
- Department
of Chemistry, University of Rome “La Sapienza”, Rome, Italy
| | - Veronica Macaluso
- Department
of Chemistry, University of Rome “La Sapienza”, Rome, Italy
| | - Riccardo Spezia
- LAMBE
CNRS UMR8587, Universite dEvry val dEssonne, Blvd F. Mitterrand, Bat̂ Maupertuis, 91025 Evry, France
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Cavalloni L, Macaluso V. [Frequency of experimental gastric ulcer in relation to the experimental composition of the light]. Dent Cadmos 1970; 38:1702-4. [PMID: 5275764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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