1
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de Armiño DJA, Di Lella S, Montepietra D, Delcanale P, Bruno S, Giordano D, Verde C, Estrin DA, Viappiani C, Abbruzzetti S. Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Protein Sci 2024; 33:e5064. [PMID: 38864722 PMCID: PMC11168075 DOI: 10.1002/pro.5064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024]
Abstract
Due to the low temperature, the Antarctic marine environment is challenging for protein functioning. Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologs, resulting in enhanced reaction rates at low temperatures. The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) genome is one of the few examples of coexistence of multiple hemoglobin genes encoding, among others, two constitutively transcribed 2/2 hemoglobins (2/2Hbs), also named truncated Hbs (TrHbs), belonging to the Group II (or O), annotated as PSHAa0030 and PSHAa2217. In this work, we describe the ligand binding kinetics and their interrelationship with the dynamical properties of globin Ph-2/2HbO-2217 by combining experimental and computational approaches and implementing a new computational method to retrieve information from molecular dynamic trajectories. We show that our approach allows us to identify docking sites within the protein matrix that are potentially able to transiently accommodate ligands and migration pathways connecting them. Consistently with ligand rebinding studies, our modeling suggests that the distal heme pocket is connected to the solvent through a low energy barrier, while inner cavities play only a minor role in modulating rebinding kinetics.
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Affiliation(s)
- Diego Javier Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Santiago Di Lella
- Departamento de Química Biológica and IQUIBICEN‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Daniele Montepietra
- Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Nanoscience Institute—CNR‐NANOModenaItaly
| | - Pietro Delcanale
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
| | - Stefano Bruno
- Department of Food and Drug SciencesUniversity of ParmaParmaItaly
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNRNaplesItaly
- Department of Ecosustainable Marine BiotechnologyStazione Zoologica Anton DohrnNaplesItaly
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNRNaplesItaly
- Department of Ecosustainable Marine BiotechnologyStazione Zoologica Anton DohrnNaplesItaly
| | - Dario A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
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2
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Unusually Fast bis-Histidyl Coordination in a Plant Hemoglobin. Int J Mol Sci 2021; 22:ijms22052740. [PMID: 33800498 PMCID: PMC7962945 DOI: 10.3390/ijms22052740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/16/2021] [Accepted: 03/02/2021] [Indexed: 11/17/2022] Open
Abstract
The recently identified nonsymbiotic hemoglobin gene MtGlb1-2 of the legume Medicago truncatula possesses unique properties as it generates four alternative splice forms encoding proteins with one or two heme domains. Here we investigate the ligand binding kinetics of MtGlb1-2.1 and MtGlb1-2.4, bearing two hemes and one heme, respectively. Unexpectedly, the overall time-course of ligand rebinding was unusually fast. Thus, we complemented nanosecond laser flash photolysis kinetics with data collected with a hybrid femtosecond–nanosecond pump–probe setup. Most photodissociated ligands are rebound geminately within a few nanoseconds, which leads to rates of the bimolecular rebinding to pentacoordinate species in the 108 M−1s−1 range. Binding of the distal histidine to the heme competes with CO rebinding with extremely high rates (kh ~ 105 s−1). Histidine dissociation from the heme occurs with comparable rates, thus resulting in moderate equilibrium binding constants (KH ~ 1). The rate constants for ligation and deligation of distal histidine to the heme are the highest reported for any plant or vertebrate globin. The combination of microscopic rates results in unusually high overall ligand binding rate constants, a fact that contributes to explaining at the mechanistic level the extremely high reactivity of these proteins toward the physiological ligands oxygen, nitric oxide and nitrite.
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3
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Boubeta FM, Boechi L, Estrin D, Patrizi B, Di Donato M, Iagatti A, Giordano D, Verde C, Bruno S, Abbruzzetti S, Viappiani C. Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125. J Phys Chem B 2018; 122:11649-11661. [PMID: 30230844 DOI: 10.1021/acs.jpcb.8b07682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologues, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their weaker interactions at protein active sites have been associated with cold adaptation. In this work, we tested this hypothesis on truncated hemoglobins (a family of microbial heme-proteins of yet-unclear function) applying molecular dynamics simulations and ligand-rebinding kinetics on a protein from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in comparison with its thermophilic Thermobifida fusca homologue. The CO rebinding kinetics of the former highlight several geminate phases, with an unusually long-lived geminate intermediate. An articulated tunnel with at least two distinct docking sites was identified by analysis of molecular dynamics simulations and was suggested to be at the origin of the unusual geminate rebinding phase. Water molecules are present in the distal pocket, but their stabilization by TrpG8, TyrB10, and HisCD1 is much weaker than in thermophilic Thermobifida fusca truncated hemoglobin, resulting in a faster geminate rebinding. Our results support the hypothesis that weaker water-molecule interactions at the reaction site are associated with cold adaptation.
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Affiliation(s)
- Fernando M Boubeta
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Leonardo Boechi
- Instituto de Calculo, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , C1428EGA Buenos Aires , Argentina
| | - Dario Estrin
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Barbara Patrizi
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Mariangela Di Donato
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Alessandro Iagatti
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , Parco Area delle Scienze 23A , 43124 , Parma , Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
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4
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Tilleman L, Abbruzzetti S, Ciaccio C, De Sanctis G, Nardini M, Pesce A, Desmet F, Moens L, Van Doorslaer S, Bruno S, Bolognesi M, Ascenzi P, Coletta M, Viappiani C, Dewilde S. Structural Bases for the Regulation of CO Binding in the Archaeal Protoglobin from Methanosarcina acetivorans. PLoS One 2015; 10:e0125959. [PMID: 26047471 PMCID: PMC4457829 DOI: 10.1371/journal.pone.0125959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 03/28/2015] [Indexed: 12/02/2022] Open
Abstract
Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20)101 was mutated to Ser). The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the “more reactive” and “less reactive” conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60)B9, Tyr(61)B10, and Phe(93)E11. Trp(60)B9 and Tyr(61)B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93)E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60)B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60)B9, Tyr(61)B10, and Phe(93)E11 play a role in regulating heme/ligand affinity.
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Affiliation(s)
- Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Giampiero De Sanctis
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | | | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Stefano Bruno
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | - Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | - Cristiano Viappiani
- Department of Physics and Earth Sciences, University of Parma, Parma, Italy
- * E-mail: (SD); (CV)
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- * E-mail: (SD); (CV)
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5
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Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ. Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7. F1000Res 2015; 4:45. [PMID: 26167269 PMCID: PMC4482215 DOI: 10.12688/f1000research.6060.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 11/20/2022] Open
Abstract
Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.
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Affiliation(s)
- Markus Knipp
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Hideaki Ogata
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Giancarlo Soavi
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Alessandro Allegri
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Bioscienze, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Stefano Bruno
- Dipartimento di Farmacia, Università di Parma, Parma, 43124, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
| | - F Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
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6
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Engineered chimeras reveal the structural basis of hexacoordination in globins: A case study of neuroglobin and myoglobin. Biochim Biophys Acta Gen Subj 2015; 1850:169-77. [DOI: 10.1016/j.bbagen.2014.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/12/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022]
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7
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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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8
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Gabba M, Abbruzzetti S, Spyrakis F, Forti F, Bruno S, Mozzarelli A, Luque FJ, Viappiani C, Cozzini P, Nardini M, Germani F, Bolognesi M, Moens L, Dewilde S. CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin. PLoS One 2013; 8:e49770. [PMID: 23308092 PMCID: PMC3537629 DOI: 10.1371/journal.pone.0049770] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/12/2012] [Indexed: 12/03/2022] Open
Abstract
Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate. Ligand exit to the solvent occurs through distinct pathways, some of which exploit temporary docking sites. The remarkable change in energetic barriers, linked to heme bis-histidyl hexacoordination by HisE7, may be responsible for active regulation of the flux of reactants and products to and from the reaction site on the distal side of the heme. A substantial change in both protein dynamics and inner cavities is observed upon transition from the CO-liganded to the pentacoordinated and bis-histidyl hexacoordinated species, which could be exploited as a signalling state. These findings are consistent with the expected versatility of the molecular activity of this protein.
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Affiliation(s)
- Matteo Gabba
- Institute of Complex Systems - Molekulare Biophysik (ICS-5) Forschungszentrum Jülich, Jülich, Germany
| | - Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, Parma, Italy
| | - Francesca Spyrakis
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy
- INBB, Biostructures and Biosystems National Institute, Rome, Italy
| | - Flavio Forti
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Stefano Bruno
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
- * E-mail:
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy
- INBB, Biostructures and Biosystems National Institute, Rome, Italy
| | - Marco Nardini
- Dipartimento di BioScienze, CNR-IBF, and CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Martino Bolognesi
- Dipartimento di BioScienze, CNR-IBF, and CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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9
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Marcelli A, Abbruzzetti S, Bustamante JP, Feis A, Bonamore A, Boffi A, Gellini C, Salvi PR, Estrin DA, Bruno S, Viappiani C, Foggi P. Following ligand migration pathways from picoseconds to milliseconds in type II truncated hemoglobin from Thermobifida fusca. PLoS One 2012; 7:e39884. [PMID: 22792194 PMCID: PMC3391200 DOI: 10.1371/journal.pone.0039884] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/28/2012] [Indexed: 11/18/2022] Open
Abstract
CO recombination kinetics has been investigated in the type II truncated hemoglobin from Thermobifida fusca (Tf-trHb) over more than 10 time decades (from 1 ps to ∼100 ms) by combining femtosecond transient absorption, nanosecond laser flash photolysis and optoacoustic spectroscopy. Photolysis is followed by a rapid geminate recombination with a time constant of ∼2 ns representing almost 60% of the overall reaction. An additional, small amplitude geminate recombination was identified at ∼100 ns. Finally, CO pressure dependent measurements brought out the presence of two transient species in the second order rebinding phase, with time constants ranging from ∼3 to ∼100 ms. The available experimental evidence suggests that the two transients are due to the presence of two conformations which do not interconvert within the time frame of the experiment. Computational studies revealed that the plasticity of protein structure is able to define a branched pathway connecting the ligand binding site and the solvent. This allowed to build a kinetic model capable of describing the complete time course of the CO rebinding kinetics to Tf-trHb.
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Affiliation(s)
- Agnese Marcelli
- LENS, European Laboratory for Non-linear Spectroscopy, Florence, Italy.
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10
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Abbruzzetti S, He C, Ogata H, Bruno S, Viappiani C, Knipp M. Heterogeneous kinetics of the carbon monoxide association and dissociation reaction to nitrophorin 4 and 7 coincide with structural heterogeneity of the gate-loop. J Am Chem Soc 2012; 134:9986-98. [PMID: 22594621 DOI: 10.1021/ja2121662] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
NO is an important signaling molecule in human tissue. However, the mechanisms by which this molecule is controlled and directed are currently little understood. Nitrophorins (NPs) comprise a group of ferriheme proteins originating from blood-sucking insects that are tailored to protect and deliver NO via coordination to and release from the heme iron. Therefore, the kinetics of the association and dissociation reactions were studied in this work using the ferroheme-CO complexes of NP4, NP4(D30N), and NP7 as isoelectronic models for the ferriheme-NO complexes. The kinetic measurements performed by nanosecond laser-flash-photolysis and stopped-flow are accompanied by resonance Raman and FT-IR spectroscopy to characterize the carbonyl species. Careful analysis of the CO rebinding kinetics reveals that in NP4 and, to a larger extent, NP7 internal gas binding cavities are located, which temporarily trap photodissociated ligands. Moreover, changes in the free energy barriers throughout the rebinding and release pathway upon increase of the pH are surprisingly small in case of NP4. Also in case of NP4, a heterogeneous kinetic trace is obtained at pH 7.5, which corresponds to the presence of two carbonyl species in the heme cavity that are seen in vibrational spectroscopy and that are due to the change of the distal heme pocket polarity. Quantification of the two species from FT-IR spectra allowed the fitting of the kinetic traces as two processes, corresponding to the previously reported open and closed conformation of the A-B and G-H loops. With the use of the A-B loop mutant NP4(D30N), it was confirmed that the kinetic heterogeneity is controlled by pH through the disruption of the H-bond between the Asp30 side chain and the Leu130 backbone carbonyl. Overall, this first study on the slow phase of the dynamics of diatomic gas molecule interaction with NPs comprises an important experimental contribution for the understanding of the dynamics involved in the binding/release processes of NO/CO in NPs.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica, Università degli Studi di Parma, viale delle Scienze 7A, I-43124, Parma, Italy
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11
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Abbruzzetti S, Tilleman L, Bruno S, Viappiani C, Desmet F, Van Doorslaer S, Coletta M, Ciaccio C, Ascenzi P, Nardini M, Bolognesi M, Moens L, Dewilde S. Ligation tunes protein reactivity in an ancient haemoglobin: kinetic evidence for an allosteric mechanism in Methanosarcina acetivorans protoglobin. PLoS One 2012; 7:e33614. [PMID: 22479420 PMCID: PMC3313925 DOI: 10.1371/journal.pone.0033614] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/13/2012] [Indexed: 11/19/2022] Open
Abstract
Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Filip Desmet
- Department of Physics, University of Antwerp, Antwerp, Belgium
| | | | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Chiara Ciaccio
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Roma, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Bari, Italy
| | - Paolo Ascenzi
- Dipartimento di Biologia, Università Roma Tre, Roma, Italy
| | - Marco Nardini
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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12
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Abbruzzetti S, Faggiano S, Spyrakis F, Bruno S, Mozzarelli A, Astegno A, Dominici P, Viappiani C. Oxygen and nitric oxide rebinding kinetics in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana. IUBMB Life 2011; 63:1094-100. [PMID: 22034287 DOI: 10.1002/iub.546] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 07/02/2011] [Indexed: 01/26/2023]
Abstract
Type 1 nonsymbiotic hemoglobin from Arabidopsis thaliana (AHb1) shows a partial bis-histidyl hexacoordination but can reversibly bind diatomic ligands. The physiological function is still unclear, but the high oxygen affinity rules out a function related to O2 sensing, carrying, or storing. To gain insight into its possible functional roles, we have investigated its O2 and NO rebinding kinetics after laser flash photolysis. The rate constants of the rebinding from the primary docking site for both O2 and NO are higher than CO, with lower photolysis yields. Moreover, the amplitude of the geminate phase increases and, as for CO, the numerical analysis of the experimental curves suggests the existence of an internal pathway leading, with high rate, to an additional docking site. However, the accessibility to this site seems to be strongly ligand-dependent, being lower for O2 and higher for NO.
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13
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Spyrakis F, Luque FJ, Viappiani C. Structural analysis in nonsymbiotic hemoglobins: what can we learn from inner cavities? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:8-13. [PMID: 21600392 DOI: 10.1016/j.plantsci.2011.03.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/24/2011] [Accepted: 03/29/2011] [Indexed: 05/09/2023]
Abstract
Plants contain three classes of hemoglobins which are not associated with nitrogen fixing bacteria, and have been accordingly termed nonsymbiotic hemoglobins. The function of nonsymbiotic hemoglobins is as yet mostly unknown. A NO dioxygenase activity has been proposed and demonstrated for some of them in vitro. In this context, a sound molecular mechanism that relates the structure with the biological activity is crucial to suggest a given physiological role. Insight into such a mechanism is now facilitated by recent progress made in both experimental and computational techniques. These studies have highlighted a number of key structural features implicated in the function of nonsymbiotic hemoglobins. The bis-histidyl hexacoordination of the heme in both its ferric and ferrous states provides a powerful and general tool to modulate reactivity, protein dynamics, and shape of the cavities. In addition, the specific arrangement of distal cavity residues provides effective protection against autoxidation. Inspection of the static crystal structures available for both liganded and unliganded states seems unsufficient to explain the function of these proteins. Function appears to be intimately linked with protein flexibility, which influences the dynamical behavior of inner cavities, capable of delivering apolar reactants to the reaction site, and removing charged reaction products. In this mini review, we demonstrate how the integration of information derived from experimental assays and computational studies is valuable and can shed light into the linkage between structural plasticity of nonsymbiotic hemoglobins and their biological role.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica, Chimica Fisica, Università degli Studi di Parma, Italy
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14
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Bisht NK, Abbruzzetti S, Uppal S, Bruno S, Spyrakis F, Mozzarelli A, Viappiani C, Kundu S. Ligand migration and hexacoordination in type 1 non-symbiotic rice hemoglobin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1042-53. [PMID: 20940062 DOI: 10.1016/j.bbapap.2010.09.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 09/26/2010] [Accepted: 09/28/2010] [Indexed: 10/19/2022]
Abstract
Type 1 non-symbiotic rice hemoglobin (rHb1) shows bis-histidyl heme hexacoordination and is capable of binding diatomic ligands reversibly. The biological function is as yet unclear, but the high oxygen affinity makes it unlikely to be involved in oxygen transport. In order to gain insight into possible physiological roles, we have studied CO rebinding kinetics after laser flash photolysis of rHb1 in solution and encapsulated in silica gel. CO rebinding to wt rHb1 in solution occurs through a fast geminate phase with no sign of rebinding from internal docking sites. Encapsulation in silica gel enhances migration to internal cavities. Site-directed mutagenesis of FB10, a residue known to have a key role in the regulation of hexacoordination and ligand affinity, resulted in substantial effects on the rebinding kinetics, partly inhibiting ligand exit to the solvent, enhancing geminate rebinding and enabling ligand migration within the internal cavities. The mutation of HE7, one of the histidyl residues involved in the hexacoordination, prevents hexacoordination, as expected, but also exposes ligand migration through a complex system of cavities. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Nitin Kumar Bisht
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
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15
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Merlino A, Vergara A, Sica F, Aschi M, Amadei A, Di Nola A, Mazzarella L. Free-Energy Profile for CO Binding to Separated Chains of Human and Trematomus newnesi Hemoglobin: Insights from Molecular Dynamics Simulations and Perturbed Matrix Method. J Phys Chem B 2010; 114:7002-8. [DOI: 10.1021/jp908525s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antonello Merlino
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Alessandro Vergara
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Filomena Sica
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Massimiliano Aschi
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Andrea Amadei
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Alfredo Di Nola
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
| | - Lelio Mazzarella
- Dipartimento di Chimica, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali, University of L’Aquila, Via Vetoio, I-67010, L’Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Via della Ricerca scientifica 1, I-00133 Roma, Italy, and Dipartimento di Chimica,
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16
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Ligand migration through the internal hydrophobic cavities in human neuroglobin. Proc Natl Acad Sci U S A 2009; 106:18984-9. [PMID: 19850865 DOI: 10.1073/pnas.0905433106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuroglobin (Ngb), a member of the globin superfamily, was found in the brain of vertebrates and is suggested to play a neuroprotective function under hypoxic conditions by scavenging nitrogen monoxide (NO) through a dioxygenase activity. In order for such a reaction to efficiently take place and to minimize the release of reactive intermediates in the cytosol, the cosubstrates O(2) and NO and other unstable reaction intermediates should bind sequentially to docking sites in the protein matrix. We have characterized the accessibility of these sites by analyzing the geminate CO rebinding kinetics to the heme moiety observed upon nanosecond flash photolysis of the Ngb-CO complex encapsulated in silica gels. The geminate rebinding phase showed a remarkable complexity, revealing the presence of a system of secondary docking sites where ligands are stored for hundreds of microseconds. Most kinetics steps display little temperature dependence, demonstrating that ligands can easily migrate through the cavities, except for the slowest reaction intermediate, possibly reflecting a structural conformational change reshaping the system of cavities. This conformational change is unrelated with distal His E7 binding to the heme, as it persists for the HE7L mutant. Overall, data are consistent with the presence of a discrete system of docking sites, possibly acting as reservoirs for the putative cosubstrates and for other reactive species involved in the physiologically relevant reaction.
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17
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Bettati S, Viappiani C, Mozzarelli A. Hemoglobin, an “evergreen” red protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1317-24. [DOI: 10.1016/j.bbapap.2009.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 03/23/2009] [Indexed: 10/20/2022]
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18
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Caccia D, Ronda L, Frassi R, Perrella M, Del Favero E, Bruno S, Pioselli B, Abbruzzetti S, Viappiani C, Mozzarelli A. PEGylation Promotes Hemoglobin Tetramer Dissociation. Bioconjug Chem 2009; 20:1356-66. [DOI: 10.1021/bc900130f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dario Caccia
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Luca Ronda
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Raffaella Frassi
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Michele Perrella
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Elena Del Favero
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Stefano Bruno
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Barbara Pioselli
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze e Tecnologie Biomediche, Dipartimento di Chimica, Biochimica e Biotecnologie per la Medicina, Università degli Studi di Milano, and LITA (Laboratorio Interdisciplinare di Tecnologie Avanzate), 20090 Segrate, Milano, Italy, and Dipartimento di Biochimica e Biologia Molecolare, Dipartimento di Fisica, Università di Parma, and NEST CNR-INFM, Istituto Nazionale di Biostrutture e Biosistemi, 43100 Parma, Italy
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19
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Ronda L, Abbruzzetti S, Bruno S, Bettati S, Mozzarelli A, Viappiani C. Ligand-Induced Tertiary Relaxations During the T-to-R Quaternary Transition in Hemoglobin. J Phys Chem B 2008; 112:12790-4. [DOI: 10.1021/jp803040j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luca Ronda
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefania Abbruzzetti
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Stefano Bettati
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
| | - Cristiano Viappiani
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, CNISM, and Dipartimento di Fisica, Università degli Studi di Parma, CNISM, and NEST CNR-INFM
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20
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21
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Abbruzzetti S, Bruno S, Faggiano S, Ronda L, Grandi E, Mozzarelli A, Viappiani C. Characterization of ligand migration mechanisms inside hemoglobins from the analysis of geminate rebinding kinetics. Methods Enzymol 2008; 437:329-45. [PMID: 18433636 DOI: 10.1016/s0076-6879(07)37017-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The presence of internal hydrophobic cavities and packing defects has been demonstrated for several small globular proteins, including hemoglobins. The reduced thermodynamic stability appears to be compensated for by the capability of controlling ligand diffusion through the protein matrix to the active site, possibly by stocking more than one reactant molecule in selected sites. Photolysis of carbon monoxide complexes of hemoglobins encapsulated in silica gels leads to multiphasic geminate rebinding kinetics at room temperature, reflecting rebinding also from different temporary docking sites inside the protein matrix. A careful analysis of the ligand rebinding kinetics allows the determination of the microscopic rates for the underlying reactions, including those governing the migration to and from the docking sites. This chapter describes the experimental approach used to characterize the ligand rebinding kinetics for heme proteins in silica gels after nanosecond laser flash photolysis and the computational methods necessary to retrieve the kinetic parameters.
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22
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Samuni U, Dantsker D, Roche C, Friedman JM. Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins. Gene 2007; 398:234-48. [PMID: 17570619 PMCID: PMC1975397 DOI: 10.1016/j.gene.2007.04.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ligand recombination studies play a central role both for characterizing different hemeproteins and their conformational states but also for probing fundamental biophysical processes. Consequently, there is great importance to providing a foundation from which one can understand the physical processes that give rise to and modulate the large range of kinetic patterns associated with ligand recombination in myoglobins and hemoglobins. In this work, an overview of cryogenic and solution phase recombination phenomena for COMb is first reviewed and then a new paradigm is presented for analyzing the temperature and viscosity dependent features of kinetic traces in terms of multiple phases that reflect which tier(s) of solvent slaved protein dynamics is (are) operative on the photoproduct population during the time course of the measurement. This approach allows for facile inclusion of both ligand diffusion among accessible cavities and conformational relaxation effects. The concepts are illustrated using kinetic traces and MEM populations derived from the CO recombination process for wild type and mutant myoglobins either in sol-gel matrices bathed in glycerol or in trehalose-derived glassy matrices.
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Affiliation(s)
- Uri Samuni
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - David Dantsker
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - Camille Roche
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
| | - Joel M. Friedman
- Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA
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23
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Bruno S, Faggiano S, Spyrakis F, Mozzarelli A, Cacciatori E, Dominici P, Grandi E, Abbruzzetti S, Viappiani C. Different roles of protein dynamics and ligand migration in non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. Gene 2007; 398:224-33. [PMID: 17555890 DOI: 10.1016/j.gene.2007.02.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Revised: 02/20/2007] [Accepted: 02/21/2007] [Indexed: 10/23/2022]
Abstract
The ligand rebinding kinetics after photolysis of the CO complexes of Arabidopsis thaliana hemoglobins AHb1 and AHb2 in solution show very different amplitudes in the geminate phase, reflecting different migration pathways of the photodissociated ligand in the system of internal cavities accessible from the heme. The dependence of the geminate phase on CO concentration, temperature, encapsulation in silica gels and presence of glycerol confirms a remarkable difference in the internal structure of the two proteins and a dramatically different role of protein dynamics in regulating the reactivity with CO. This finding strongly supports the idea that they have distinct physiological functions.
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Affiliation(s)
- Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Italy
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24
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Bruno S, Faggiano S, Spyrakis F, Mozzarelli A, Abbruzzetti S, Grandi E, Viappiani C, Feis A, Mackowiak S, Smulevich G, Cacciatori E, Dominici P. The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities. J Am Chem Soc 2007; 129:2880-9. [PMID: 17298064 DOI: 10.1021/ja066638d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nonsymbiotic hemoglobins, AHb1 and AHb2, have recently been isolated from Arabidopsis thaliana. Using steady-state and time-resolved spectroscopic methods, we show that Fe2+ AHb1 contains a mixture of penta- and hexacoordinated heme, while Fe2+ AHb2 is fully hexacoordinated. In the CO complexes, polar interactions and H-bonds with the ligand are stronger for AHb1 than for AHb2. The ligand binding kinetics are substantially different, reflecting the distribution between the penta- and hexacoordinated species, and indicate that protein dynamics and ligand migration pathways are very specific for each of the two proteins. In particular, a very small, non-exponential geminate rebinding observed in AHb1 suggests that the distal heme cavity is connected with the exterior by a relatively open channel. The large, temperature-dependent geminate rebinding observed for AHb2 implies a major role of protein dynamics in the ligand migration from the distal cavity to the solvent. The structures of AHb1 and AHb2, modeled on the basis of the homologous rice hemoglobin, exhibit a different cavity system that is fully compatible with the observed ligand binding kinetics. Overall, these kinetic and structural data are consistent with the putative NO-dioxygenase activity previously attributed to AHb1, whereas the role of AHb2 remains elusive.
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Affiliation(s)
- Stefano Bruno
- Dipartimento di Biochimica e Biologia Molecolare, UniversitA degli Studi di Parma, Parma, Italy
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25
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Amadei A, D’Abramo M, Daidone I, D’Alessandro M, Nola AD, Aschi M. Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0197-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abbruzzetti S, Bruno S, Faggiano S, Grandi E, Mozzarelli A, Viappiani C. Time-resolved methods in Biophysics. 2. Monitoring haem proteins at work with nanosecond laser flash photolysis. Photochem Photobiol Sci 2006; 5:1109-20. [PMID: 17136275 DOI: 10.1039/b610236k] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Haem proteins have long been the most studied proteins in biophysics, and have become paradigms for the characterization of fundamental biomolecular processes as ligand binding and regulatory conformational transitions. The presence of the haem prosthetic group, the absorbance spectrum of which has a ligation sensitive region conveniently located in the UV-visible range, has offered a powerful and sensitive tool for the investigation of molecular functions. The central Fe atom is capable of reversibly binding diatomic ligands, including O(2), CO, and NO. The Fe-ligand bond is photolabile, and a reactive unligated state can be transiently generated with a pulsed laser. The photodissociated ligands quickly rebind to the haem and the process can be monitored by transient absorbance methods. The ligand rebinding kinetics reflects protein dynamics and ligand migration within the protein inner cavities. The characterization of these processes was done in the past mainly by low temperature experiments. The use of silica gels to trap proteins allows the characterization of internal ligand dynamics at room temperature. In order to show the potential of the laser flash photolysis techniques, combined with modern numerical analysis methods, we report experiments conducted on two non-symbiotic haemoglobins from Arabidopsis thaliana. The comparison between time courses recorded on haemoglobins in solution and encapsulated in silica gels allows for the highlighting of different interplays between protein dynamics and ligand migration.
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Gensch T, Viappiani C. Introducing the Time-resolved methods in biophysics series. Photochem Photobiol Sci 2006; 5:1101-2. [PMID: 17136273 DOI: 10.1039/b615863n] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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