1
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Capone M, Dell’Orletta G, Nicholls BT, Scholes GD, Hyster TK, Aschi M, Daidone I. Evidence of a Distinctive Enantioselective Binding Mode for the Photoinduced Radical Cyclization of α-Chloroamides in Ene-Reductases. ACS Catal 2023; 13:15310-15321. [PMID: 38058601 PMCID: PMC10696551 DOI: 10.1021/acscatal.3c03934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
We demonstrate here through molecular simulations and mutational studies the origin of the enantioselectivity in the photoinduced radical cyclization of α-chloroacetamides catalyzed by ene-reductases, in particular the Gluconobacter oxidans ene-reductase and the Old Yellow Enzyme 1, which show opposite enantioselectivity. Our results reveal that neither the π-facial selectivity model nor a protein-induced selective stabilization of the transition states is able to explain the enantioselectivity of the radical cyclization in the studied flavoenzymes. We propose a new enantioinduction scenario according to which enantioselectivity is indeed controlled by transition-state stability; however, the relative stability of the prochiral transition states is not determined by direct interaction with the protein but is rather dependent on an inherent degree of freedom within the substrate itself. This intrinsic degree of freedom, distinct from the traditional π-facial exposure mode, can be controlled by the substrate conformational selection upon binding to the enzyme.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
| | - Gianluca Dell’Orletta
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
| | - Bryce T. Nicholls
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Gregory D. Scholes
- Department
of Chemistry, Frick Laboratory, Princeton
University, Princeton, New Jersey 08544, United States
| | - Todd K. Hyster
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Massimiliano Aschi
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
| | - Isabella Daidone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, via
Vetoio (Coppito 1), L’Aquila 67010, Italy
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2
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Li YY, Long SS, Yu L, Liu AK, Gao SQ, Tan X, Lin YW. Effects of naturally occurring S47F/A mutations on the structure and function of human cytochrome c. J Inorg Biochem 2023; 246:112296. [PMID: 37356378 DOI: 10.1016/j.jinorgbio.2023.112296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/27/2023]
Abstract
The sequence and structure of human cytochrome c (hCyt c) exhibit evolutionary conservations, with only a limited number of naturally occurring mutations in humans. Herein, we investigated the effects of the naturally occurring S47F/A mutations on the structure and function of hCyt c in the oxidized form. Although the naturally occurring S47F/A mutations did not largely alter the protein structure, the S47F and S47A variants exhibited a small fraction of high-spin species. Kinetic studies showed that the peroxidase activity of the variants was enhanced by ∼2.5-fold under neutral pH conditions, as well as for the rate in reaction with H2O2, when compared to those of wild-type hCyt c. In addition, we evaluated the interaction between hCyt c and human neuroglobin (hNgb) by isothermal titration calorimetry (ITC) studies, which revealed that the binding constant was reduced by ∼8-fold as result of the mutation of the hydrophilic Ser to the hydrophobic Phe/Ala. These findings provide valuable insights into the role of Ser47 in Ω-loop C in sustaining the structure and function of hCyt c.
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Affiliation(s)
- Yan-Yan Li
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shuang-Shuang Long
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Ao-Kun Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Shu-Qin Gao
- Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China.
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3
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Capone M, Sirohiwal A, Aschi M, Pantazis DA, Daidone I. Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II. Angew Chem Int Ed Engl 2023; 62:e202216276. [PMID: 36791234 DOI: 10.1002/anie.202216276] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.
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Affiliation(s)
- Matteo Capone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.,Present Address: Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, 10691, Stockholm, Sweden
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy
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4
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Zanetti-Polzi L, Charchar P, Yarovsky I, Corni S. Origins of the pH-Responsive Photoluminescence of Peptide-Functionalized Au Nanoclusters. ACS NANO 2022; 16:20129-20140. [PMID: 36300936 DOI: 10.1021/acsnano.2c04335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ultrasmall peptide-protected gold nanoclusters are a promising class of bioresponsive material exhibiting pH-sensitive photoluminescence. We present a theoretical insight into the effect peptide-ligand environment has on pH-responsive fluorescence, with the aim of enhancing the rational design of gold nanoclusters for bioapplications. Employing a hybrid quantum/classical computational methodology, we systematically calculate deprotonation free energies of N-terminal cysteine amine groups in proximity to the inherently fluorescent core of Au25(Peptide)18 nanoclusters. We find that subtle changes in hexapeptide sequence alter the electrostatic environment and significantly shift the conventional N-terminal amine pKa expected for amino acids free-in-solution. Our findings provide an insight into how the deprotonation equilibrium of N-terminal amine and side chain carboxyl groups cooperatively respond to solution pH changes, explaining the experimentally observed, yet elusive, pH-responsive fluorescence of peptide-functionalized Au25 clusters.
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Affiliation(s)
- Laura Zanetti-Polzi
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125Modena, Italy
| | | | - Irene Yarovsky
- School of Engineering, RMIT University, Victoria3001, Australia
| | - Stefano Corni
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125Modena, Italy
- Dipartimento di Scienze Chimiche, Università di Padova, 35131Padova, Italy
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5
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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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6
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Capone M, Zanetti-Polzi L, Leonzi I, Spreti N, Daidone I. Evidence for a high pK a of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach. J Biomol Struct Dyn 2022:1-8. [PMID: 35593533 DOI: 10.1080/07391102.2022.2077834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Candida antarctica Lipase B (CALB) is a paradigm for the family of lipases. At pH 7, the optimal pH for catalysis, the protonation state of an aspartic acid of the active site (Asp134) could not be conclusively assigned. In fact, the pKa estimate provided by a widely used computational tool, namely PropKa, that predicts pKa values of ionizable groups in proteins based on the crystallographic structure, is only slightly above 7 (pKa = 7.25). This, along with the lack of an experimental evaluation, makes the assignment of its protonation state at neutral pH challenging. Here, we calculate the pKa of Asp134 by means of a fully atomistic multiscale computational approach based on classical molecular dynamics (MD) simulation and the perturbed matrix method (PMM), namely the MD-PMM approach. MD-PMM is able to take into account the dynamics of the system and, at the same time, to treat the deprotonation step at the quantum level. The calculations provide a pKa value of 8.9 ± 1.1, hence suggesting that Asp134 in CALB should be protonated at neutral, and even at slightly basic, pH.
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Affiliation(s)
- Matteo Capone
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Ilenia Leonzi
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Nicoletta Spreti
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
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7
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Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:13200227. [PMID: 33200115 PMCID: PMC7668740 DOI: 10.26434/chemrxiv.13200227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 11/06/2020] [Indexed: 12/21/2022]
Abstract
In this comutational work a hybrid quantum mechanics/molecular mechanics approach, the MD-PMM approach, is used to investigate the proton transfer reaction the activates the catalytic activity of SARS-CoV-2 main protease. The proton transfer thermodynamics is investigated for the apo ensyme (i.e., without any bound substrate or inhibitor) and in the presence of a inhibitor, N3, which was previously shown to covalently bind SARS-CoV-2 main protease.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Micholas Dean Smith
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Chris Chipot
- UMR 7019, Universite de Lorraine, Laboratoire International Associe CNRS
- University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, TN 37831, United States
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy
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8
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Zanetti-Polzi L, Daidone I, Amadei A. Fully Atomistic Multiscale Approach for p Ka Prediction. J Phys Chem B 2020; 124:4712-4722. [PMID: 32427481 DOI: 10.1021/acs.jpcb.0c01752] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The ionization state of titratable amino acids strongly affects proteins structure and functioning in a large number of biological processes. It is therefore essential to be able to characterize the pKa of ionizable groups inside proteins and to understand its microscopic determinants in order to gain insights into many functional properties of proteins. A big effort has been devoted to the development of theoretical approaches for the prediction of deprotonation free energies, yet the accurate theoretical/computational calculation of pKa values is recognized as a current challenge. A methodology based on a hybrid quantum/classical approach is here proposed for the computation of deprotonation free energies. The method is applied to calculate the pKa of formic acid, methylammonium, and methanethiol, providing results in good agreement with the corresponding experimental estimates. The pKa is also calculated for aspartic acid and lysine as single residues in solution and for three aspartic/glutamic acids inside a well-characterized protein: hen egg white lysozyme. While for small molecules the method is able to deal with multiple protonation states of all titratable groups, this becomes computationally very expensive for proteins. The calculated pKa values for the single amino acids (except for the zwitterionic aspartic acid) and inside the protein display a systematic shift with respect to the experimental values that suggests that the fine balance between hydrophobic and polar interactions might be not accurately reproduced by the usual classical force-fields, thus affecting the computation of deprotonation free energies. The calculated pKa shifts inside the protein are in good agreement with the corresponding experimental ones (within 1 pKa unit), well reproducing the pKa changes due to the protein environment even in the case of large pKa shifts.
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Affiliation(s)
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Via della Ricerca Scientifica, I-00185 Rome, Italy
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9
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Torres-Cuevas I, Corral-Debrinski M, Gressens P. Brain oxidative damage in murine models of neonatal hypoxia/ischemia and reoxygenation. Free Radic Biol Med 2019; 142:3-15. [PMID: 31226400 DOI: 10.1016/j.freeradbiomed.2019.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/26/2019] [Accepted: 06/10/2019] [Indexed: 02/08/2023]
Abstract
The brain is one of the main organs affected by hypoxia and reoxygenation in the neonatal period and one of the most vulnerable to oxidative stress. Hypoxia/ischemia and reoxygenation leads to impairment of neurogenesis, disruption of cortical migration, mitochondrial damage and neuroinflammation. The extent of the injury depends on the clinical manifestation in the affected regions. Preterm newborns are highly vulnerable, and they exhibit severe clinical manifestations such as intraventricular hemorrhage (IVH), retinopathy of prematurity (ROP) and diffuse white matter injury (DWMI) among others. In the neonatal period, the accumulation of high levels of reactive oxygen species exacerbated by the immature antioxidant defense systems in represents cellular threats that, if they exceed or bypass physiological counteracting mechanisms, are responsible of significant neuronal damage. Several experimental models in mice mimic the consequences of perinatal asphyxia and the use of oxygen in the reanimation process that produce brain injury. The aim of this review is to highlight brain damage associated with oxidative stress in different murine models of hypoxia/ischemia and reoxygenation.
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Affiliation(s)
| | | | - Pierre Gressens
- INSERM UMR1141, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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10
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Zanetti-Polzi L, Daidone I, Corni S. Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage. J Phys Chem Lett 2019; 10:1450-1456. [PMID: 30855973 DOI: 10.1021/acs.jpclett.9b00403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Redox proteins and enzymes are at risk of irreversible oxidative damage from highly oxidizing intermediates generated in the active site in the case of unsuccessful functional reaction. Chains of tyrosine and/or tryptophan residues have been recently proposed to provide protection to the active site and the whole protein by delivering oxidizing equivalents (holes) out of the protein via a multistep hopping mechanism. In the present work we use a hybrid quantum/classical theoretical-computational methodology based on the perturbed matrix method and on molecular dynamics simulations to calculate the oxidation potential difference along a chain of tyrosine and tryptophan residues in a human redox enzyme of major importance, a superoxide dismutase, which acts as antioxidant defense. We show that the hole hopping is thermodynamically favored along such a chain and that the hopping propensity is strongly affected by the protein environment and in particular by the active site and its second coordination sphere.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , via Vetoio (Coppito 1) , 67010 L'Aquila , Italy
| | - Stefano Corni
- Department of Chemical Sciences , University of Padova , I-35131 Padova , Italy
- Center S3 , CNR-Institute of Nanoscience , Via Campi 213/A , 41125 Modena , Italy
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11
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Kim J, Fukuda Y, Inoue T. Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade,
Ramazzottius varieornatus. FEBS J 2018; 286:1287-1304. [DOI: 10.1111/febs.14713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 01/05/2023]
Affiliation(s)
- JeeEun Kim
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
| | - Yohta Fukuda
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
- Graduate School of Pharmaceutical Science Suita Japan
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12
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Liu HX, Li L, He B, Gao SQ, Wen GB, Lin YW. Neuroglobin is capable of self-oxidation of methionine64 introduced at the heme axial position. Dalton Trans 2018; 47:10847-10852. [PMID: 30027178 DOI: 10.1039/c8dt02397b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Neuroglobin (Ngb), with its physiological role not fully understood, was found to be capable of self-oxidation of methionine64 introduced at the heme axial position (H64M Ngb), adopting a high-spin heme state and producing both methionine sulfoxide (SO-Met) and sulfone (SO2-Met), which represents the structure and function of cytochrome c in a non-native state.
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Affiliation(s)
- Hai-Xiao Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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13
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Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chem Sci 2018; 9:9002-9011. [PMID: 30647892 PMCID: PMC6301204 DOI: 10.1039/c8sc03786h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/02/2018] [Indexed: 11/23/2022] Open
Abstract
We break the barrier between simulation and experiment by comparing identical computed and experimental infrared observables.
For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I′ region at different frequencies. Next, the amide I′ spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
| | - Martin Gruebele
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , IL 61801 , USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences , University of Rome "Tor Vergata" , 00133 Rome , Italy
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
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14
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Van Acker ZP, Luyckx E, Dewilde S. Neuroglobin Expression in the Brain: a Story of Tissue Homeostasis Preservation. Mol Neurobiol 2018; 56:2101-2122. [DOI: 10.1007/s12035-018-1212-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 06/26/2018] [Indexed: 12/19/2022]
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15
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Rydzewski J, Nowak W. Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning. J Chem Phys 2018; 148:115101. [DOI: 10.1063/1.5013659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- J. Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - W. Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
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16
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Daidone I, Amadei A, Aschi M, Zanetti-Polzi L. On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:451-457. [PMID: 29212059 DOI: 10.1016/j.saa.2017.11.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/27/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.
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Affiliation(s)
- Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 00185 Rome, Italy
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy.
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17
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Bellei M, Bortolotti CA, Di Rocco G, Borsari M, Lancellotti L, Ranieri A, Sola M, Battistuzzi G. The influence of the Cys46/Cys55 disulfide bond on the redox and spectroscopic properties of human neuroglobin. J Inorg Biochem 2018; 178:70-86. [DOI: 10.1016/j.jinorgbio.2017.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
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18
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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19
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Carrillo-Parramon O, Del Galdo S, Aschi M, Mancini G, Amadei A, Barone V. Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. J Chem Theory Comput 2017; 13:5506-5514. [DOI: 10.1021/acs.jctc.7b00341] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
| | - Massimiliano Aschi
- Dipartimento
di Scienze Fisiche e Chimiche, Universitá di L’Aquila, Via
Vetoio s.n.c.67100, L’Aquila, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Andrea Amadei
- Dipartimento
di Scienze e Tecnologie Chimiche, Universitá di Roma ’Tor Vergata’, Via Della Ricerca Scientifica, 00100 Roma, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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20
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Zanetti Polzi L, Battistuzzi G, Borsari M, Pignataro M, Paltrinieri L, Daidone I, Bortolotti CA. Computational investigation of the electron transfer complex between neuroglobin and cytochrome c. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1377342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Laura Zanetti Polzi
- Department of Physical and Chemical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Gianantonio Battistuzzi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marco Borsari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Marcello Pignataro
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Licia Paltrinieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L’Aquila, L’Aquila, Italy
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