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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Exertier C, Sebastiani F, Freda I, Gugole E, Cerutti G, Parisi G, Montemiglio LC, Becucci M, Viappiani C, Bruno S, Savino C, Zamparelli C, Anselmi M, Abbruzzetti S, Smulevich G, Vallone B. Probing the Role of Murine Neuroglobin CDloop-D-Helix Unit in CO Ligand Binding and Structural Dynamics. ACS Chem Biol 2022; 17:2099-2108. [PMID: 35797699 PMCID: PMC9396615 DOI: 10.1021/acschembio.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We produced a neuroglobin variant, namely, Ngb CDless,
with the
excised CDloop- and D-helix, directly joining the C- and E-helices.
The CDless variant retained bis-His hexacoordination, and we investigated
the role of the CDloop–D-helix unit in controlling the CO binding
and structural dynamics by an integrative approach based on X-ray
crystallography, rapid mixing, laser flash photolysis, resonance Raman
spectroscopy, and molecular dynamics simulations. Rapid mixing and
laser flash photolysis showed that ligand affinity was unchanged with
respect to the wild-type protein, albeit with increased on and off
constants for rate-limiting heme iron hexacoordination by the distal
His64. Accordingly, resonance Raman spectroscopy highlighted a more
open distal pocket in the CO complex that, in agreement with MD simulations,
likely involves His64 swinging inward and outward of the distal heme
pocket. Ngb CDless displays a more rigid overall structure with respect
to the wild type, abolishing the structural dynamics of the CDloop–D-helix
hypothesized to mediate its signaling role, and it retains ligand
binding control by distal His64. In conclusion, this mutant may represent
a tool to investigate the involvement of CDloop–D-helix in
neuroprotective signaling in a cellular or animal model.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Federico Sebastiani
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, 3227 Broadway, New York, New York 10027, United States
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, I-00161 Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
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3
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Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus. SENSORS 2020; 20:s20174977. [PMID: 32887407 PMCID: PMC7506613 DOI: 10.3390/s20174977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/29/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
The urgent need to develop a detection system for Staphylococcus aureus, one of the most common causes of infection, is prompting research towards novel approaches and devices, with a particular focus on point-of-care analysis. Biosensors are promising systems to achieve this aim. We coupled the selectivity and affinity of aptamers, short nucleic acids sequences able to recognize specific epitopes on bacterial surface, immobilized at high density on a nanostructured zirconium dioxide surface, with the rational design of specifically interacting fluorescent peptides to assemble an easy-to-use detection device. We show that the displacement of fluorescent peptides upon the competitive binding of S. aureus to immobilized aptamers can be detected and quantified through fluorescence loss. This approach could be also applied to the detection of other bacterial species once aptamers interacting with specific antigens will be identified, allowing the development of a platform for easy detection of a pathogen without requiring access to a healthcare environment.
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4
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Gianquinto E, Moscetti I, De Bei O, Campanini B, Marchetti M, Luque FJ, Cannistraro S, Ronda L, Bizzarri AR, Spyrakis F, Bettati S. Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight. Sci Rep 2019; 9:18629. [PMID: 31819099 PMCID: PMC6901573 DOI: 10.1038/s41598-019-54970-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Among multidrug-resistant bacteria, methicillin-resistant Staphylococcus aureus is emerging as one of the most threatening pathogens. S. aureus exploits different mechanisms for its iron supply, but the preferred one is acquisition of organic iron through the expression of hemoglobin (Hb) receptors. One of these, IsdB, belonging to the Isd (Iron-Regulated Surface Determinant) system, was shown to be essential for bacterial growth and virulence. Therefore, interaction of IsdB with Hb represents a promising target for the rational design of a new class of antibacterial molecules. However, despite recent investigations, many structural and mechanistic details of complex formation and heme extraction process are still elusive. By combining site-directed mutagenesis, absorption spectroscopy, surface plasmon resonance and molecular dynamics simulations, we tackled most of the so far unanswered questions: (i) the exact complex stoichiometry, (ii) the microscopic kinetic rates of complex formation, (iii) the IsdB selectivity for binding to, and extracting heme from, α and β subunits of Hb, iv) the role of specific amino acid residues and structural regions in driving complex formation and heme transfer, and (v) the structural/dynamic effect played by the hemophore on Hb.
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Affiliation(s)
- Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy
| | - Ilaria Moscetti
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Omar De Bei
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, Parma, 43124, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - Marialaura Marchetti
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet, 08921, Spain
| | - Salvatore Cannistraro
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Luca Ronda
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy.,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy.,Institute of Biophysics, National Research Council, Pisa, 56124, Italy
| | - Anna Rita Bizzarri
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.
| | - Stefano Bettati
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy. .,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy. .,Institute of Biophysics, National Research Council, Pisa, 56124, Italy.
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5
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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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6
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Russo R, Giordano D, Paredi G, Marchesani F, Milazzo L, Altomonte G, Del Canale P, Abbruzzetti S, Ascenzi P, di Prisco G, Viappiani C, Fago A, Bruno S, Smulevich G, Verde C. The Greenland shark Somniosus microcephalus-Hemoglobins and ligand-binding properties. PLoS One 2017; 12:e0186181. [PMID: 29023598 PMCID: PMC5638460 DOI: 10.1371/journal.pone.0186181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 09/26/2017] [Indexed: 11/18/2022] Open
Abstract
A large amount of data is currently available on the adaptive mechanisms of polar bony fish hemoglobins, but structural information on those of cartilaginous species is scarce. This study presents the first characterisation of the hemoglobin system of one of the longest-living vertebrate species (392 ± 120 years), the Arctic shark Somniosus microcephalus. Three major hemoglobins are found in its red blood cells and are made of two copies of the same α globin combined with two copies of three very similar β subunits. The three hemoglobins show very similar oxygenation and carbonylation properties, which are unaffected by urea, a very important compound in marine elasmobranch physiology. They display identical electronic absorption and resonance Raman spectra, indicating that their heme-pocket structures are identical or highly similar. The quaternary transition equilibrium between the relaxed (R) and the tense (T) states is more dependent on physiological allosteric effectors than in human hemoglobin, as also demonstrated in polar teleost hemoglobins. Similar to other cartilaginous fishes, we found no evidence for functional differentiation among the three isoforms. The very similar ligand-binding properties suggest that regulatory control of O2 transport may be at the cellular level and that it may involve changes in the cellular concentrations of allosteric effectors and/or variations of other systemic factors. The hemoglobins of this polar shark have evolved adaptive decreases in O2 affinity in comparison to temperate sharks.
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Affiliation(s)
- Roberta Russo
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, Naples, Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, Naples, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Gianluca Paredi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parco Area delle Scienze 23/A, Parma, Italy
| | - Francesco Marchesani
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parco Area delle Scienze 23/A, Parma, Italy
| | - Lisa Milazzo
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3–13, Sesto Fiorentino (FI), Italy
| | - Giovanna Altomonte
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, Naples, Italy
- Dipartimento di Biologia, Università Roma 3, Viale Marconi 448, Roma, Italy
| | - Pietro Del Canale
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, Parma, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, Parma, Italy
- NEST Istituto Nanoscienze, CNR, Piazza San Silvestro 12, Pisa, Italy
| | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università RomaTre, Via della Vasca Navale 79, Roma, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, Naples, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, Parma, Italy
- NEST Istituto Nanoscienze, CNR, Piazza San Silvestro 12, Pisa, Italy
| | - Angela Fago
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parco Area delle Scienze 23/A, Parma, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3–13, Sesto Fiorentino (FI), Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, Naples, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
- Dipartimento di Biologia, Università Roma 3, Viale Marconi 448, Roma, Italy
- * E-mail: ,
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7
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Calvo-Begueria L, Cuypers B, Van Doorslaer S, Abbruzzetti S, Bruno S, Berghmans H, Dewilde S, Ramos J, Viappiani C, Becana M. Characterization of the Heme Pocket Structure and Ligand Binding Kinetics of Non-symbiotic Hemoglobins from the Model Legume Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2017; 8:407. [PMID: 28421084 PMCID: PMC5378813 DOI: 10.3389/fpls.2017.00407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 05/04/2023]
Abstract
Plant hemoglobins (Hbs) are found in nodules of legumes and actinorhizal plants but also in non-symbiotic organs of monocots and dicots. Non-symbiotic Hbs (nsHbs) have been classified into two phylogenetic groups. Class 1 nsHbs show an extremely high O2 affinity and are induced by hypoxia and nitric oxide (NO), whereas class 2 nsHbs have moderate O2 affinity and are induced by cold and cytokinins. The functions of nsHbs are still unclear, but some of them rely on the capacity of hemes to bind diatomic ligands and catalyze the NO dioxygenase (NOD) reaction (oxyferrous Hb + NO → ferric Hb + nitrate). Moreover, NO may nitrosylate Cys residues of proteins. It is therefore important to determine the ligand binding properties of the hemes and the role of Cys residues. Here, we have addressed these issues with the two class 1 nsHbs (LjGlb1-1 and LjGlb1-2) and the single class 2 nsHb (LjGlb2) of Lotus japonicus, which is a model legume used to facilitate the transfer of genetic and biochemical information into crops. We have employed carbon monoxide (CO) as a model ligand and resonance Raman, laser flash photolysis, and stopped-flow spectroscopies to unveil major differences in the heme environments and ligand binding kinetics of the three proteins, which suggest non-redundant functions. In the deoxyferrous state, LjGlb1-1 is partially hexacoordinate, whereas LjGlb1-2 shows complete hexacoordination (behaving like class 2 nsHbs) and LjGlb2 is mostly pentacoordinate (unlike other class 2 nsHbs). LjGlb1-1 binds CO very strongly by stabilizing it through hydrogen bonding, but LjGlb1-2 and LjGlb2 show lower CO stabilization. The changes in CO stabilization would explain the different affinities of the three proteins for gaseous ligands. These affinities are determined by the dissociation rates and follow the order LjGlb1-1 > LjGlb1-2 > LjGlb2. Mutations LjGlb1-1 C78S and LjGlb1-2 C79S caused important alterations in protein dynamics and stability, indicating a structural role of those Cys residues, whereas mutation LjGlb1-1 C8S had a smaller effect. The three proteins and their mutant derivatives exhibited similarly high rates of NO consumption, which were due to NOD activity of the hemes and not to nitrosylation of Cys residues.
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Affiliation(s)
- Laura Calvo-Begueria
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Bert Cuypers
- Department of Physics, University of AntwerpAntwerp, Belgium
| | | | - Stefania Abbruzzetti
- Dipartimento di Bioscienze, Università degli Studi di ParmaParma, Italy
- NEST, Istituto Nanoscienze, Consiglio Nazionale delle RicerchePisa, Italy
| | - Stefano Bruno
- Dipartimento di Farmacia, Università degli Studi di ParmaParma, Italy
| | - Herald Berghmans
- Department of Biomedical Sciences, University of AntwerpAntwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of AntwerpAntwerp, Belgium
| | - Javier Ramos
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Cristiano Viappiani
- NEST, Istituto Nanoscienze, Consiglio Nazionale delle RicerchePisa, Italy
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di ParmaParma, Italy
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
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8
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9
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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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10
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Spyrakis F, Lucas F, Bidon-Chanal A, Viappiani C, Guallar V, Luque FJ. Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1957-67. [PMID: 23583621 DOI: 10.1016/j.bbapap.2013.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/30/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
Abstract
This study reports a comparative analysis of the topological properties of inner cavities and the intrinsic dynamics of non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana. The two proteins belong to the 3/3 globin fold and have a sequence identity of about 60%. However, it is widely assumed that they have distinct physiological roles. In order to investigate the structure-function relationships in these proteins, we have examined the bis-histidyl and ligand-bound hexacoordinated states by atomistic simulations using in silico structural models. The results allow us to identify two main pathways to the distal cavity in the bis-histidyl hexacoordinated proteins. Nevertheless, a larger accessibility to small gaseous molecules is found in AHb2. This effect can be attributed to three factors: the mutation Leu35(AHb1)→Phe32(AHb2), the enhanced flexibility of helix B, and the more favorable energetic profile for ligand migration to the distal cavity. The net effect of these factors would be to facilitate the access of ligands, thus compensating the preference for the fully hexacoordination of AHb2, in contrast to the equilibrium between hexa- and pentacoordinated species in AHb1. On the other hand, binding of the exogenous ligand introduces distinct structural changes in the two proteins. A well-defined tunnel is formed in AHb1, which might be relevant to accomplish the proposed NO detoxification reaction. In contrast, no similar tunnel is found in AHb2, which can be ascribed to the reduced flexibility of helix E imposed by the larger number of salt bridges compared to AHb1. This feature would thus support the storage and transport functions proposed for AHb2. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy.
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11
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Mukhi N, Dhindwal S, Uppal S, Kumar P, Kaur J, Kundu S. X-ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1944-56. [PMID: 23485912 DOI: 10.1016/j.bbapap.2013.02.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/16/2013] [Accepted: 02/19/2013] [Indexed: 11/24/2022]
Abstract
Genome of the model dicot flowering plant, Arabidopsis thaliana, a popular tool for understanding molecular biology of plant physiology, encodes all three classes of plant hemoglobins that differ in their sequence, ligand binding and spectral properties. As such these globins are of considerable attention. Crystal structures of few members of plant class I nonsymbiotic hemoglobin have been described earlier. Here we report the crystal structure of Arabidopsis class I hemoglobin (AHb1) to 2.2Ǻ and compare its key features with the structures of similar nonsymbiotic hemoglobin from other species. Crystal structure of AHb1 is homologous to the related members with similar globin fold and heme pocket architecture. The structure is homodimeric in the asymmetric unit with both distal and proximal histidines coordinating to the heme iron atom. Residues lining the dimeric interface are also conserved in AHb1 with the exception of additional electrostatic interaction between H112 and E113 of each subunit and that involving Y119 through two water molecules. In addition, differences in heme pocket non-covalent interactions, a novel Ser residue at F7 position, Xe binding site variability, internal cavity topology differences, CD loop conformation and stability and other such properties might explain kinetic variability in AHb1. Detailed cavity analysis of AHb1 showed the presence of a novel long tunnel connecting the distal pockets of both the monomers. Presence of such tunnel, along with conformational heterogeneity observed in the two chains, might suggest cooperative ligand binding and support its role in NO scavenging. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Nitika Mukhi
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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12
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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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13
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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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14
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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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Hill RD. Non-symbiotic haemoglobins-What's happening beyond nitric oxide scavenging? AOB PLANTS 2012; 2012:pls004. [PMID: 22479675 PMCID: PMC3292739 DOI: 10.1093/aobpla/pls004] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 01/25/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Non-symbiotic haemoglobins have been an active research topic for over 30 years, during which time a considerable portfolio of knowledge has accumulated relative to their chemical and molecular properties, and their presence and mode of induction in plants. While progress has been made towards understanding their physiological role, there remain a number of unanswered questions with respect to their biological function. This review attempts to update recent progress in this area and to introduce a hypothesis as to how non-symbiotic haemoglobins might participate in regulating hormone signal transduction. PRINCIPAL RESULTS Advances have been made towards understanding the structural nuances that explain some of the differences in ligand association characteristics of class 1 and class 2 non-symbiotic haemoglobins. Non-symbiotic haemoglobins have been found to function in seed development and germination, flowering, root development and differentiation, abiotic stress responses, pathogen invasion and symbiotic bacterial associations. Microarray analyses under various stress conditions yield uneven results relative to non-symbiotic haemoglobin expression. Increasing evidence of the role of nitric oxide (NO) in hormone responses and the known involvement of non-symbiotic haemoglobins in scavenging NO provide opportunities for fruitful research, particularly at the cellular level. CONCLUSIONS Circumstantial evidence suggests that non-symbiotic haemoglobins may have a critical function in the signal transduction pathways of auxin, ethylene, jasmonic acid, salicylic acid, cytokinin and abscisic acid. There is a strong need for research on haemoglobin gene expression at the cellular level relative to hormone signal transduction.
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16
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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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17
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Spyrakis F, Bruno S, Bidon-Chanal A, Luque FJ, Abbruzzetti S, Viappiani C, Dominici P, Mozzarelli A. Oxygen binding to Arabidopsis thaliana AHb2 nonsymbiotic hemoglobin: evidence for a role in oxygen transport. IUBMB Life 2011; 63:355-62. [PMID: 21618402 DOI: 10.1002/iub.470] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nonsymbiotic hemoglobins AHb1 and AHb2 discovered in Arabidopsis thaliana are likely to carry out distinct physiological roles, in consideration of their differences in sequence, structure, expression pattern, and tissue localization. Despite a relatively fast autoxidation in the presence of O(2) , we were able to collect O(2) -binding curves for AHb2 in the presence of a reduction enzymatic system. AHb2 binds O(2) noncooperatively with a p50 of 0.021 ± 0.003 Torr, a value consistent with a recently proposed role in O(2) transport. The analysis of the internal cavities derived from the structures sampled in molecular dynamics simulations confirms strong differences with AHb1, proposed to work as a NO deoxygenase in vivo. Overall, our results are consistent with a role for AHb2 as an oxygen carrier, as recently proposed on the basis of experiments on AHb2-overexpressing mutants of A. thaliana.
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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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18
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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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19
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Igamberdiev AU, Bykova NV, Hill RD. Structural and functional properties of class 1 plant hemoglobins. IUBMB Life 2011; 63:146-52. [DOI: 10.1002/iub.439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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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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21
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Nienhaus K, Dominici P, Astegno A, Abbruzzetti S, Viappiani C, Nienhaus GU. Ligand migration and binding in nonsymbiotic hemoglobins of Arabidopsis thaliana. Biochemistry 2010; 49:7448-58. [PMID: 20666470 DOI: 10.1021/bi100768g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We have studied carbon monoxide (CO) migration and binding in the nonsymbiotic hemoglobins AHb1 and AHb2 of Arabidopsis thaliana using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures. Both proteins have similar amino acid sequences but display pronounced differences in ligand binding properties, at both physiological and cryogenic temperatures. Near neutral pH, the distal HisE7 side chain is close to the heme-bound ligand in the majority of AHb1-CO molecules, as indicated by a low CO stretching frequency at 1921 cm(-1). In this fraction, two CO docking sites can be populated, the primary site B and the secondary site C. When the pH is lowered, a high-frequency stretching band at approximately 1964 cm(-1) grows at the expense of the low-frequency band, indicating that HisE7 protonates and, concomitantly, moves away from the bound ligand. Geminate rebinding barriers are markedly different for the two conformations, and docking site C is not accessible in the low-pH conformation. Rebinding of NO ligands was observed only from site B of AHb1, regardless of conformation. In AHb2, the HisE7 side chain is removed from the bound ligand; rebinding barriers are low, and CO molecules can populate only primary docking site B. These results are interpreted in terms of differences in the active site structures and physiological functions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
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22
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Orzeł Ł, Jańczyk A, Brindell M, Stopa G, Stochel G. New trends in the application of laser flash photolysis – case studies. J COORD CHEM 2010. [DOI: 10.1080/00958972.2010.507271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ł. Orzeł
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - A. Jańczyk
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - M. Brindell
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - G. Stopa
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - G. Stochel
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
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23
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Nienhaus K, Nienhaus GU. Ligand dynamics in heme proteins observed by Fourier transform infrared-temperature derivative spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1030-41. [PMID: 20656073 DOI: 10.1016/j.bbapap.2010.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a powerful tool for the investigation of protein-ligand interactions in heme proteins. Nitric oxide and carbon monoxide are attractive physiologically relevant ligands because their bond stretching vibrations give rise to strong mid-infrared absorption bands that can be measured with exquisite sensitivity and precision using photolysis difference spectroscopy at cryogenic temperatures. These stretching bands are fine-tuned by electrostatic interactions with the environment and, therefore, ligands can be utilized as local probes of structure and dynamics. Bound to the heme iron, the ligand stretching bands are susceptible to changes in the iron-ligand bond and the electric field at the active site. Upon photolysis, the vibrational bands display changes due to ligand relocation to docking sites within the protein, rotational motions of the ligand in these sites and protein conformational changes. Photolysis difference spectra taken over a wide temperature range (3-300K) using specific temperature protocols for sample photodissociation can provide detailed insights into both protein and ligand dynamics. Moreover, temperature-derivative spectroscopy (TDS) has proven to be a particularly powerful technique to study protein-ligand interactions. The FTIR-TDS technique has been extensively applied to studies of carbon monoxide binding to heme proteins, whereas measurements with nitric oxide are still scarce. Here we describe infrared cryo-spectroscopy and present a variety of applications to the study of protein-ligand interactions in heme proteins. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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24
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Scorciapino MA, Robertazzi A, Casu M, Ruggerone P, Ceccarelli M. Breathing motions of a respiratory protein revealed by molecular dynamics simulations. J Am Chem Soc 2009; 131:11825-32. [PMID: 19653680 DOI: 10.1021/ja9028473] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Internal cavities, which are central to the biological functions of myoglobin, are exploited by gaseous ligands (e.g., O(2), NO, CO, etc.) to migrate inside the protein matrix. At present, it is not clear whether the ligand makes its own way inside the protein or instead the internal cavities are an intrinsic feature of myoglobin. To address this issue, standard molecular dynamics simulations were performed on horse-heart met-myoglobin with no ligand migrating inside the protein matrix. To reveal intrinsic internal pathways, the use of a statistical approach was applied to the cavity calculation, with special emphasis on the major pathway from the distal pocket to Xe1. Our study points out the remarkable dynamical behavior of Xe4, whose "breathing motions" may facilitate migration of ligands through the distal region. Additionally, our results highlight a two-way path for a ligand to diffuse through the proximal region, possibly allowing an alternative route in case Xe1 is occupied. Finally, our approach has led us to the identification of key residues, such as leucines, that may work as switches between cavities.
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Affiliation(s)
- Mariano Andrea Scorciapino
- Department of Chemical Sciences, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (Ca), Italy
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25
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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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26
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Dordas C. Nonsymbiotic hemoglobins and stress tolerance in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2009; 176:433-40. [PMID: 26493132 DOI: 10.1016/j.plantsci.2009.01.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/09/2009] [Accepted: 01/09/2009] [Indexed: 05/24/2023]
Abstract
Hemoglobins (Hbs) are heme containing proteins found in most organisms including animals, bacteria, and plants. Their structure, size, and function are quite diverse among the different organisms. There are three different types of hemoglobins in plants: symbiotic (sHb), nonsymbiotic (nsHb), and truncated hemoglobins (trHb). The nonsymbiotic hemoglobins are divided into: class 1 hemoglobins (nsHb-1s), which have a very high affinity for oxygen: and class 2 hemoglobins (nsHb-2s), which have lower affinity for oxygen, are similar to the sHbs. nsHb-1s are expressed under hypoxia, osmotic stress, nutrient deprivation, cold stress, rhizobial infection, nitric oxide exposure, and fungal infection. Tolerance to stress is very important for the survival of the plant. Hemoglobins are one of many different strategies that plants have evolved to overcome stress conditions and survive. Hbs also react with NO produced under different stress conditions. Class 1 nsHbs are involved in a metabolic pathway involving NO. Those hemoglobins provide an alternative type of respiration to mitochondrial electron transport under limiting oxygen concentrations. Class 1 nsHbs in hypoxic plants act as part of a soluble, terminal, NO dioxygenase system, yielding nitrate from the reaction of oxyHb with NO. The overall reaction sequence, referred to as the nsHb/NO cycle, consumes NADH and maintains ATP levels via an as yet unknown mechanism. Class 2 nsHbs seem to scavenge NO in a similar fashion as class 1 Hbs and are involved in reducing flowering time in Arabidopsis. nsHbs also show peroxidase-like activity and NO metabolism and possibly protect against nitrosative stress in plant-pathogen interaction and in symbiotic interactions. nsHbs may be involved in other stress conditions such as osmotic, nutrient and cold stress together with NO and the function of nsHbs can be in NO metabolism and signal transduction. However, other possible functions cannot be precluded as Hbs have many different functions in other organisms.
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Affiliation(s)
- Christos Dordas
- Aristotle University of Thessaloniki, Faculty of Agriculture, Laboratory of Agronomy, 54124 Thessaloniki, Greece.
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