1
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Messias A, Pasquadibisceglie A, Alonso de Armiño D, De Simone G, Polticelli F, Coletta M, Ascenzi P, Estrin DA. Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation. J Inorg Biochem 2023; 248:112336. [PMID: 37572543 DOI: 10.1016/j.jinorgbio.2023.112336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/28/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Nitrobindins (Nbs) represent an evolutionary conserved all-β-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom, coordinated by a proximal His residue. Interestingly, even if the distal side is exposed to the solvent, the value of the second order rate constants for ligand binding to the ferrous derivative is almost one order of magnitude lower than those reported for myoglobins (Mbs). Noteworthy, nitric oxide binding to the sixth coordination position of the heme-Fe(II)-atom causes the cleavage or the severe weakening of the proximal His-Fe(II) bond. Here, we provide a computer simulation investigation to shed light on the molecular basis of ligand binding kinetics, by dissecting the ligand binding process into the ligand migration and the bond formation steps. Classical molecular dynamics simulations were performed employing a steered molecular dynamics approach and the Jarzinski equality to obtain ligand migration free energy profiles. The formation of the heme-Fe(II)-NO bond took into consideration the iron atom displacement from the heme plane. The ligand migration is almost unhindered, and the low rate constant for NO binding is due to the large displacement of the Fe(II) atom with respect to the heme plane responsible for the barrier for the Fe(II)-NO bond formation. In addition, we investigated the weakening and breaking of the proximal His-Fe(II) bond, observed experimentally upon NO binding, by means of a combination of classical molecular dynamics simulations and quantum-classical (QM-MM) optimizations. In both human and M. tuberculosis Nbs, a stable alternative conformation of the proximal His residue interacting with a network of water molecules was observed.
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Affiliation(s)
- Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | | | - Diego Alonso de Armiño
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146 Roma, Italy
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146 Roma, Italy
| | | | - Paolo Ascenzi
- Accademia Nazionale dei Lincei, Via della Lungara 10, 00165 Roma, Italy
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
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2
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Nardini M, Pesce A, Bolognesi M. Truncated (2/2) hemoglobin: Unconventional structures and functional roles in vivo and in human pathogenesis. Mol Aspects Med 2021; 84:101049. [PMID: 34776271 DOI: 10.1016/j.mam.2021.101049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022]
Abstract
Truncated hemoglobins (trHbs) build a sub-class of the globin family, found in eubacteria, cyanobacteria, unicellular eukaryotes, and in higher plants; among these, selected human pathogens are found. The trHb fold is based on a 2/2 α-helical sandwich, consisting of a simplified and reduced-size version of the classical 3/3 α-helical sandwich of vertebrate and invertebrate globins. Phylogenetic analysis indicates that trHbs further branch into three groups: group I (or trHbN), group II (or trHbO), and group III (or trHbP), each group being characterized by specific structural features. Among these, a protein matrix tunnel, or a cavity system implicated in diatomic ligand diffusion through the protein matrix, is typical of group I and group II, respectively. In general, a highly intertwined network of hydrogen bonds stabilizes the heme bound ligand, despite variability of the heme distal residues in the different trHb groups. Notably, some organisms display genes from more than one trHb group, suggesting that trHbN, trHbO, and trHbP may support different functions in vivo, such as detoxification of reactive nitrogen and oxygen species, respiration, oxygen storage/sensoring, thus aiding survival of an invading microorganism. Here, structural features and proposed functions of trHbs from human pathogens are reviewed.
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Affiliation(s)
- Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
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3
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Bringas M, Lombardi LE, Luque FJ, Estrin DA, Capece L. Ligand Binding Rate Constants in Heme Proteins Using Markov State Models and Molecular Dynamics Simulations. Chemphyschem 2019; 20:2451-2460. [PMID: 31365183 DOI: 10.1002/cphc.201900589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/30/2019] [Indexed: 11/07/2022]
Abstract
Computer simulation studies of the molecular basis for ligand migration in proteins allow the description of key events such as the transition between docking sites, displacement of existing ligands and solvent molecules, and open/closure of specific "gates", among others. In heme proteins, ligand migration from the solvent to the active site preludes the binding to the heme iron and triggers different functions. In this work, molecular dynamics simulations, a Markov State Model of migration and empirical kinetic equations are combined to study the migration of O2 and NO in two truncated hemoglobins of Mycobacterium tuberculosis (Mt-TrHbN and Mt-TrHbO). For Mt-TrHbN, we show that the difference in the association constant in the oxy and deoxy states relies mainly in the displacement of water molecules anchored in the distal cavity in the deoxy form. The results here provide a valuable approach to study ligand migration in globins.
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Affiliation(s)
- Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.,Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Buenos Aires, Argentina
| | - Leandro E Lombardi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires - CONICET, C1428EGA, Buenos Aires, Argentina
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences, University of Barcelona, Campus Torribera, 08921, Santa Coloma de Gramenet, Spain.,Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028, Barcelona, Spain
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.,Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Buenos Aires, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.,Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Buenos Aires, Argentina
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4
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Boubeta FM, Contestín García RM, Lorenzo EN, Boechi L, Estrin D, Sued M, Arrar M. Lessons learned about steered molecular dynamics simulations and free energy calculations. Chem Biol Drug Des 2019; 93:1129-1138. [PMID: 30793836 DOI: 10.1111/cbdd.13485] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/18/2018] [Accepted: 12/22/2018] [Indexed: 01/30/2023]
Abstract
The calculation of free energy profiles is central in understanding differential enzymatic activity, for instance, involving chemical reactions that require QM-MM tools, ligand migration, and conformational rearrangements that can be modeled using classical potentials. The use of steered molecular dynamics (sMD) together with the Jarzynski equality is a popular approach in calculating free energy profiles. Here, we first briefly review the application of the Jarzynski equality to sMD simulations, then revisit the so-called stiff-spring approximation and the consequent expectation of Gaussian work distributions and, finally, reiterate the practical utility of the second-order cumulant expansion, as it coincides with the parametric maximum-likelihood estimator in this scenario. We illustrate this procedure using simulations of CO, both in aqueous solution and in a carbon nanotube as a model system for biologically relevant nanoheterogeneous environments. We conclude the use of the second-order cumulant expansion permits the use of faster pulling velocities in sMD simulations, without introducing bias due to large dispersion in the non-equilibrium work distribution.
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Affiliation(s)
- Fernando Martín Boubeta
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rocío María Contestín García
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ezequiel Norberto Lorenzo
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Boechi
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario Estrin
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Sued
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Cálculo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mehrnoosh Arrar
- CONICET-Facultad de Ciencias Exactas y Naturales, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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5
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Boubeta FM, Bieza SA, Bringas M, Estrin DA, Boechi L, Bari SE. Mechanism of Sulfide Binding by Ferric Hemeproteins. Inorg Chem 2018; 57:7591-7600. [DOI: 10.1021/acs.inorgchem.8b00478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fernando M. Boubeta
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Silvina A. Bieza
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Mauro Bringas
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | - Darío A. Estrin
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
| | | | - Sara E. Bari
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET and Universidad de Buenos Aires, Buenos Aires 1053, Argentina
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6
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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7
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Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations. Sci Rep 2017; 7:10926. [PMID: 28883619 PMCID: PMC5589765 DOI: 10.1038/s41598-017-11259-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Abstract
Human hemoglobin (Hb) is a benchmark protein of structural biology that shaped our view of allosterism over 60 years ago, with the introduction of the MWC model based on Perutz structures of the oxy(R) and deoxy(T) states and the more recent Tertiary Two-State model that proposed the existence of individual subunit states -“r” and “t”-, whose structure is yet unknown. Cooperative oxygen binding is essential for Hb function, and despite decades of research there are still open questions related to how tertiary and quaternary changes regulate oxygen affinity. In the present work, we have determined the free energy profiles of oxygen migration and for HisE7 gate opening, with QM/MM calculations of the oxygen binding energy in order to address the influence of tertiary differences in the control of oxygen affinity. Our results show that in the α subunit the low to high affinity transition is achieved by a proximal effect that mostly affects oxygen dissociation and is the driving force of the allosteric transition, while in the β subunit the affinity change results from a complex interplay of proximal and distal effects, including an increase in the HE7 gate opening, that as shown by free energy profiles promotes oxygen uptake.
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8
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Rydzewski J, Nowak W. Ligand diffusion in proteins via enhanced sampling in molecular dynamics. Phys Life Rev 2017; 22-23:58-74. [PMID: 28410930 DOI: 10.1016/j.plrev.2017.03.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 10/28/2016] [Accepted: 03/28/2017] [Indexed: 01/17/2023]
Abstract
Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.
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Affiliation(s)
- J Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland.
| | - W Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland.
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9
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Nategholeslam M, Gray CG, Tomberli B. Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories. J Phys Chem B 2017; 121:391-403. [DOI: 10.1021/acs.jpcb.6b08701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - C. G. Gray
- Guelph-Waterloo
Physics Institute and Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Bruno Tomberli
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Physics, Capilano University, North Vancouver, British
Columbia V7J 3H5, Canada
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10
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Boubeta FM, Bari SE, Estrin DA, Boechi L. Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata. J Phys Chem B 2016; 120:9642-53. [DOI: 10.1021/acs.jpcb.6b06686] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fernando M. Boubeta
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Sara E. Bari
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Dario A. Estrin
- Departamento de
Química Inorgánica, Analítica y Química
Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo/CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires,
Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
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11
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Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:59-80. [PMID: 27567484 DOI: 10.1016/bs.apcsb.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the impact of differences in amino acid sequence on the topological features of docking sites and cavities and to the influence of conformational flexibility in facilitating the migration of small ligands through these cavities. Often, tunnels are carved in the interior of globins, and ligand exchange is regulated by gating residues. Understanding the subtle intricacies that relate the differences in sequence with the structural and dynamical features of globins with the ultimate aim of rationalizing the thermodynamics and kinetics of ligand binding continues to be a major challenge in the field. Due to the evolution of computational techniques, significant advances into our understanding of these questions have been made. In this review we focus our attention on the analysis of the ligand migration pathways as well as the function of the structural cavities and tunnels in a series of representative globins, emphasizing the synergy between experimental and theoretical approaches to gain a comprehensive knowledge into the molecular mechanisms of this diverse family of proteins.
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12
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Abstract
If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.
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Affiliation(s)
- Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche “Alessandro Rossi Fanelli” and Istituto Pasteur — Fondazione Cenci, Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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13
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Mukhi N, Dhindwal S, Uppal S, Kapoor A, Arya R, Kumar P, Kaur J, Kundu S. Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin. Biochemistry 2016; 55:1724-40. [PMID: 26913482 DOI: 10.1021/acs.biochem.5b01013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plant hemoglobins constitute three distinct groups: symbiotic, nonsymbiotic, and truncated hemoglobins. Structural investigation of symbiotic and nonsymbiotic (class I) hemoglobins revealed the presence of a vertebrate-like 3/3 globin fold in these proteins. In contrast, plant truncated hemoglobins are similar to bacterial truncated hemoglobins with a putative 2/2 α-helical globin fold. While multiple structures have been reported for plant hemoglobins of the first two categories, for plant truncated globins only one structure has been reported of late. Here, we report yet another crystal structure of the truncated hemoglobin from Arabidopsis thaliana (AHb3) with two water molecules in the heme pocket, of which one is distinctly coordinated to the heme iron, unlike the only available crystal structure of AHb3 with a hydroxyl ligand. AHb3 was monomeric in its crystallographic asymmetric unit; however, dimer was evident in the crystallographic symmetry, and the globin indeed existed as a stable dimer in solution. The tertiary structure of the protein exhibited a bacterial-like 2/2 α-helical globin fold with an additional N-terminal α-helical extension and disordered C-termini. To address the role of these extended termini in AHb3, which is yet unknown, N- and C-terminal deletion mutants were created and characterized and molecular dynamics simulations performed. The C-terminal deletion had an insignificant effect on most properties but perturbed the dimeric equilibrium of AHb3 and significantly influenced azide binding kinetics in the ferric state. These results along with the disordered nature of the C-terminus indicated its putative role in intramolecular or intermolecular interactions probably regulating protein-ligand and protein-protein interactions. While the N-terminal deletion did not change the overall globin fold, stability, or ligand binding kinetics, it seemed to have influenced coordination at the heme iron, the hydration status of the active site, and the quaternary structure of AHb3. Evidence indicated that the N-terminus is the predominant factor regulating the quaternary interaction appropriate to physiological requirements, dynamics of the side chains in the heme pocket, and tunnel organization in the protein matrix.
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Affiliation(s)
- Nitika Mukhi
- Department of Genetics, University of Delhi South Campus , New Delhi 110021, India
| | - Sonali Dhindwal
- Department of Biotechnology, Indian Institute of Technology , Roorkee, Uttarakhand 247667, India
| | - Sheetal Uppal
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Abhijeet Kapoor
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology , Roorkee, Uttarakhand 247667, India
| | - Jagreet Kaur
- Department of Genetics, University of Delhi South Campus , New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus , New Delhi 110021, India
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14
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Bustamante JP, Szretter ME, Sued M, Martí MA, Estrin DA, Boechi L. A quantitative model for oxygen uptake and release in a family of hemeproteins. Bioinformatics 2016; 32:1805-13. [PMID: 27153569 DOI: 10.1093/bioinformatics/btw083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/30/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. RESULTS We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. CONTACT lboechi@ic.fcen.uba.ar SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - María E Szretter
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires Departamento De Matemática, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Mariela Sued
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Marcelo A Martí
- Departamento De Química Biológica E Instituto De Química Biológica De La Facultad De Ciencias Exactas Y Naturales (IQUIBICEN), Universidad De Buenos Aires, Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Leonardo Boechi
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
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15
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Estarellas Martin C, Seira Castan C, Luque Garriga FJ, Bidon-Chanal Badia A. Understanding the kinetics of ligand binding to globins with molecular dynamics simulations: the necessity of multiple state models. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 17:22-27. [PMID: 26724333 DOI: 10.1016/j.ddtec.2015.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
Residue conformational changes and internal cavity migration processes play a key role in regulating the kinetics of ligand migration and binding events in globins. Molecular dynamics simulations have demonstrated their value in the study of these processes in different haemoglobins, but derivation of kinetic data demands the use of more complex techniques like enhanced sampling molecular dynamics methods. This review discusses the different methodologies that are currently applied to study the ligand migration process in globins and highlight those specially developed to derive kinetic data.
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Affiliation(s)
- Carolina Estarellas Martin
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Constantí Seira Castan
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - F Javier Luque Garriga
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Axel Bidon-Chanal Badia
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain.
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16
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Giordano D, Pesce A, Boechi L, Bustamante JP, Caldelli E, Howes BD, Riccio A, di Prisco G, Nardini M, Estrin D, Smulevich G, Bolognesi M, Verde C. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. FEBS J 2015; 282:2948-65. [PMID: 26040838 DOI: 10.1111/febs.13335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/17/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022]
Abstract
Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two α-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21 Å resolution) shows typical features of group-II truncated hemoglobins, namely the two-on-two α-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | | | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Juan Pablo Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Elena Caldelli
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Barry D Howes
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Alessia Riccio
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Italy
| | - Dario Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Argentina
| | - Giulietta Smulevich
- Department of Chemistry 'Ugo Schiff', University of Firenze, Sesto Fiorentino, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Italy.,CNR-Institute of Biophysics and CIMAINA, University of Milano, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources, National Research Council, Napoli, Italy.,Department of Biology, Roma 3 University, Italy
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17
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Boron I, Bustamante JP, Davidge KS, Singh S, Bowman LAH, Tinajero-Trejo M, Carballal S, Radi R, Poole RK, Dikshit K, Estrin DA, Marti MA, Boechi L. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules. F1000Res 2015; 4:22. [PMID: 26478812 PMCID: PMC4591903 DOI: 10.12688/f1000research.5921.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2015] [Indexed: 11/23/2022] Open
Abstract
Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and •NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels interrupted by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify •NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, •NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.
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Affiliation(s)
- Ignacio Boron
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Juan Pablo Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Kelly S Davidge
- Centre for Biomolecular Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sandip Singh
- Institute of Microbial Technology, CSIR, Chandigarh, 160036, India
| | - Lesley AH Bowman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Mariana Tinajero-Trejo
- Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Sebastián Carballal
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, 11100, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, 11100, Uruguay
| | - Robert K Poole
- Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Kanak Dikshit
- Institute of Microbial Technology, CSIR, Chandigarh, 160036, India
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
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18
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Boron I, Bustamante JP, Davidge KS, Singh S, Bowman LAH, Tinajero-Trejo M, Carballal S, Radi R, Poole RK, Dikshit K, Estrin DA, Marti MA, Boechi L. Ligand uptake in Mycobacterium tuberculosis truncated hemoglobins is controlled by both internal tunnels and active site water molecules. F1000Res 2015; 4:22. [PMID: 26478812 PMCID: PMC4591903 DOI: 10.12688/f1000research.5921.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/19/2015] [Indexed: 06/04/2024] Open
Abstract
Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and (•)NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels that are partially blocked by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify (•)NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, (•)NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations introduce modifications in both tunnel topologies and affect the incoming ligand capacity to displace retained water molecules at the active site. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.
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Affiliation(s)
- Ignacio Boron
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Juan Pablo Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Kelly S Davidge
- Centre for Biomolecular Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sandip Singh
- Institute of Microbial Technology, CSIR, Chandigarh, 160036, India
| | - Lesley AH Bowman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Mariana Tinajero-Trejo
- Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Sebastián Carballal
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, 11100, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, 11100, Uruguay
| | - Robert K Poole
- Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Kanak Dikshit
- Institute of Microbial Technology, CSIR, Chandigarh, 160036, India
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, C1428EGA, Argentina
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19
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Howes BD, Boechi L, Boffi A, Estrin DE, Smulevich G. Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO. Adv Microb Physiol 2015; 67:85-126. [PMID: 26616516 DOI: 10.1016/bs.ampbs.2015.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this chapter, we will discuss the paradigmatic case of Thermobifida fusca (Tf-trHb) HbO in its ferrous and ferric states and its behaviour towards a battery of possible ligands. This choice was dictated by the fact that it has been one of the most extensively studied truncated haemoglobins, both in terms of spectroscopic and molecular dynamics studies. Tf-trHb typifies the structural properties of group II trHbs, as the active site is characterized by a highly polar distal environment in which TrpG8, TyrCD1, and TyrB10 provide three potential H-bond donors in the distal cavity capable of stabilizing the incoming ligands. The role of these residues in key topological positions, and their interplay with the iron-bound ligands, has been addressed in studies carried out on the CO, F(-), OH(-), CN(-), and HS(-) adducts formed with the wild-type protein and a combinatorial set of mutants, in which the distal polar residues, TrpG8, TyrCD1, and TyrB10, have been singly, doubly, or triply replaced by a Phe residue. In this context, such a complete analysis provides an excellent benchmark for the investigation of the relationship between protein structure and function, allowing one to translate physicochemical properties of the active site into the observed functional behaviour. Tf-trHb will be compared with other members of the group II trHbs and, more generally, with members of the other trHb subgroups.
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Affiliation(s)
- Barry D Howes
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Alberto Boffi
- Dipartimento di Scienze Biochimiche, Università "Sapienza", Rome, Italy
| | - Dario E Estrin
- Departamento de Química Inorgánica, Analítica y Química Física and Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy.
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20
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Nategholeslam M, Gray CG, Tomberli B. Implementation of the Forward–Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol. J Phys Chem B 2014; 118:14203-14. [DOI: 10.1021/jp504942t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mostafa Nategholeslam
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - C. G. Gray
- Guelph-Waterloo
Physics Institute and Department of Physics, University of Guelph, Guelph, Ontario, Canada
| | - Bruno Tomberli
- Department
of Physics, Capilano University, North Vancouver, British
Columbia, Canada
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21
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Abstract
Small size globins that have been defined as 'truncated haemoglobins' or as '2/2 haemoglobins' have increasingly been discovered in microorganisms since the early 1990s. Analysis of amino acid sequences allowed to distinguish three groups that collect proteins with specific and common structural properties. All three groups display 3D structures that are based on four main α-helices, which are a subset of the conventional eight-helices globin fold. Specific features, such as the presence of protein matrix tunnels that are held to promote diffusion of functional ligands to/from the haem, distinguish members of the three groups. Haem distal sites vary for their accessibility, local structures, polarity, and ligand stabilization mechanisms, suggesting functional roles that are related to O2/NO chemistry. In a few cases, such activities have been proven in vitro and in vivo through deletion mutants. The issue of 2/2 haemoglobin varied biological functions throughout the three groups remains however fully open.
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22
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Abstract
The genus Mycobacterium is comprised of Gram-positive bacteria occupying a wide range of natural habitats and includes species that range from severe intracellular pathogens to economically useful and harmless microbes. The recent upsurge in the availability of microbial genome data has shown that genes encoding haemoglobin-like proteins are ubiquitous among Mycobacteria and that multiple haemoglobins (Hbs) of different classes may be present in pathogenic and non-pathogenic species. The occurrence of truncated haemoglobins (trHbs) and flavohaemoglobins (flavoHbs) showing distinct haem active site structures and ligand-binding properties suggests that these Hbs may be playing diverse functions in the cellular metabolism of Mycobacteria. TrHbs and flavoHbs from some of the severe human pathogens such as Mycobacterium tuberculosis and Mycobacterium leprae have been studied recently and their roles in effective detoxification of reactive nitrogen and oxygen species, electron cycling, modulation of redox state of the cell and facilitation of aerobic respiration have been proposed. This multiplicity in the function of Hbs may aid these pathogens to cope with various environmental stresses and survive during their intracellular regime. This chapter provides recent updates on genomic, structural and functional aspects of Mycobacterial Hbs to address their role in Mycobacteria.
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23
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Bustamante JP, Abbruzzetti S, Marcelli A, Gauto D, Boechi L, Bonamore A, Boffi A, Bruno S, Feis A, Foggi P, Estrin DA, Viappiani C. Ligand uptake modulation by internal water molecules and hydrophobic cavities in hemoglobins. J Phys Chem B 2014; 118:1234-45. [PMID: 24410478 DOI: 10.1021/jp410724z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal water molecules play an active role in ligand uptake regulation, since displacement of retained water molecules from protein surfaces or cavities by incoming ligands can promote favorable or disfavorable effects over the global binding process. Detection of these water molecules by X-ray crystallography is difficult given their positional disorder and low occupancy. In this work, we employ a combination of molecular dynamics simulations and ligand rebinding over a broad time range to shed light into the role of water molecules in ligand migration and binding. Computational studies on the unliganded structure of the thermostable truncated hemoglobin from Thermobifida fusca (Tf-trHbO) show that a water molecule is in the vicinity of the iron heme, stabilized by WG8 with the assistance of YCD1, exerting a steric hindrance for binding of an exogenous ligand. Mutation of WG8 to F results in a significantly lower stabilization of this water molecule and in subtle dynamical structural changes that favor ligand binding, as observed experimentally. Water is absent from the fully hydrophobic distal cavity of the triple mutant YB10F-YCD1F-WG8F (3F), due to the lack of residues capable of stabilizing it nearby the heme. In agreement with these effects on the barriers for ligand rebinding, over 97% of the photodissociated ligands are rebound within a few nanoseconds in the 3F mutant case. Our results demonstrate the specific involvement of water molecules in shaping the energetic barriers for ligand migration and binding.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina
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24
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Dumas VG, Defelipe LA, Petruk AA, Turjanski AG, Marti MA. QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential cytochrome p450 of Mycobacterium tuberculosis. Proteins 2013; 82:1004-21. [PMID: 24356896 DOI: 10.1002/prot.24474] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/15/2013] [Accepted: 11/04/2013] [Indexed: 11/06/2022]
Abstract
Among 20 p450s of Mycobacterium tuberculosis (Mt), CYP121 has received an outstanding interest, not only due to its essentiality for bacterial viability but also because it catalyzes an unusual carbon-carbon coupling reaction. Based on the structure of the substrate bound enzyme, several reaction mechanisms were proposed involving first Tyr radical formation, second Tyr radical formation, and C-C coupling. Key and unknown features, being the nature of the species that generate the first and second radicals, and the role played by the protein scaffold each step. In the present work we have used classical and quantum based computer simulation methods to study in detail its reaction mechanism. Our results show that substrate binding promotes formation of the initial oxy complex, Compound I is the responsible for first Tyr radical formation, and that the second Tyr radical is formed subsequently, through a PCET reaction, promoted by the presence of key residue Arg386. The final C-C coupling reaction possibly occurs in bulk solution, thus yielding the product in one oxygen reduction cycle. Our results thus contribute to a better comprehension of MtCYP121 reaction mechanism, with direct implications for inhibitor design, and also contribute to our general understanding of these type of enzymes.
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Affiliation(s)
- Victoria G Dumas
- Departamento de Quimica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Química Física de los Materiales Medio Ambiente y Energia (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Güiraldes, 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
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25
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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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26
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Small ligand-globin interactions: reviewing lessons derived from computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1722-38. [PMID: 23470499 DOI: 10.1016/j.bbapap.2013.02.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/22/2013] [Accepted: 02/26/2013] [Indexed: 11/24/2022]
Abstract
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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27
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Boechi L, Arrar M, Martí MA, Olson JS, Roitberg AE, Estrin DA. Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7. J Biol Chem 2013; 288:6754-62. [PMID: 23297402 DOI: 10.1074/jbc.m112.426056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis.
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Affiliation(s)
- Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física/Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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Ferreiro DN, Boechi L, Estrin DA, Martí MA. The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin. J Inorg Biochem 2012; 119:75-84. [PMID: 23220591 DOI: 10.1016/j.jinorgbio.2012.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
Abstract
Flavohemoglobins (FHbs) are members of the globin superfamily, widely distributed among prokaryotes and eukaryotes that have been shown to carry out nitric oxide dioxygenase (NOD) activity. In prokaryotes, such as Escherichia coli, NOD activity is a defence mechanism against the NO release by the macrophages of the hosts' immune system during infection. Because of that, FHbs have been studied thoroughly and several drugs have been developed in an effort to fight infectious processes. Nevertheless, the protein's structural determinants involved in the NOD activity are still poorly understood. In this context, the aim of the present work is to unravel the molecular basis of FHbs structural dynamics-to-function relationship using state of the art computer simulation tools. In an effort to fulfill this goal, we studied three key processes that determine NOD activity, namely i) ligand migration into the active site ii) stabilization of the coordinated oxygen and iii) intra-protein electron transfer (ET). Our results allowed us to determine key factors related to all three processes like the presence of a long hydrophobic tunnel for ligand migration, the presence of a water mediated hydrogen bond to stabilize the coordinated oxygen and therefore achieve a high affinity, and the best possible ET paths between the FAD and the heme, where water molecules play an important role. Taken together the presented results close an important gap in our understanding of the wide and diverse globin structural-functional relationships.
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Affiliation(s)
- Dardo N Ferreiro
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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29
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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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30
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Balsamo A, Sannino F, Merlino A, Parrilli E, Tutino ML, Mazzarella L, Vergara A. Role of the tertiary and quaternary structure in the formation of bis-histidyl adducts in cold-adapted hemoglobins. Biochimie 2012; 94:953-60. [DOI: 10.1016/j.biochi.2011.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
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31
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Jasaitis A, Ouellet H, Lambry JC, Martin JL, Friedman JM, Guertin M, Vos MH. Ultrafast heme–ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Nicoletti FP, Droghetti E, Boechi L, Bonamore A, Sciamanna N, Estrin DA, Feis A, Boffi A, Smulevich G. Fluoride as a Probe for H-Bonding Interactions in the Active Site of Heme Proteins: The Case of Thermobifida fusca Hemoglobin. J Am Chem Soc 2011; 133:20970-80. [DOI: 10.1021/ja209312k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Enrica Droghetti
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandra Bonamore
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Natascia Sciamanna
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alessandro Feis
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Alberto Boffi
- Institute Pasteur, Fondazione Cenci Bolognetti, Department of Biochemical Sciences and CNR, Institute of Molecular Biology and Pathology, University of Rome “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
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Forti F, Boechi L, Bikiel D, Martí MA, Nardini M, Bolognesi M, Viappiani C, Estrin D, Luque FJ. Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly. J Phys Chem B 2011; 115:13771-80. [DOI: 10.1021/jp208562b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Flavio Forti
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Diagonal 643, E-08028, Barcelona, Spain
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Damian Bikiel
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marco Nardini
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, I-20131 Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, I-20131 Milano, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Italy
| | - Darío Estrin
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Diagonal 643, E-08028, Barcelona, Spain
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34
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Birukou I, Maillett DH, Birukova A, Olson JS. Modulating distal cavities in the α and β subunits of human HbA reveals the primary ligand migration pathway. Biochemistry 2011; 50:7361-74. [PMID: 21793487 DOI: 10.1021/bi200923k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The free volume in the active site of human HbA plays a crucial role in governing the bimolecular rates of O(2), CO, and NO binding, the fraction of geminate ligand recombination, and the rate of NO dioxygenation by the oxygenated complex. We have decreased the size of the distal pocket by mutating Leu(B10), Val(E11), and Leu(G8) to Phe and Trp and that of other more internal cavities by filling them with Xe at high gas pressures. Increasing the size of the B10 side chain reduces bimolecular rates of ligand binding nearly 5000-fold and inhibits CO geminate recombination due to both reduction of the capture volume in the distal pocket and direct steric hindrance of Fe-ligand bond formation. Phe and Trp(E11) mutations also cause a decrease in distal pocket volume but, at the same time, increase access to the Fe atom because of the loss of the γ2 CH(3) group of the native Val(E11) side chain. The net result of these E11 substitutions is a dramatic increase in the rate of geminate recombination because dissociated CO is sequestered close to the Fe atom and can rapidly rebind without steric resistance. However, the bimolecular rate constants for binding of ligand to the Phe and Trp(E11) mutants are decreased 5-30-fold, because of a smaller capture volume. Geminate and bimolecular kinetic parameters for Phe and Trp(G8) mutants are similar to those for the native HbA subunits because the aromatic rings at this position cause little change in distal pocket volume and because ligands do not move past this position into the globin interior of wild-type HbA subunits. The latter conclusion is verified by the observation that Xe binding to the α and β Hb subunits has little effect on either geminate or bimolecular ligand rebinding. All of these experimental results argue strongly against alternative ligand migration pathways that involve movements through the protein interior in HbA. Instead, ligands appear to enter through the His(E7) gate and are captured directly in the distal cavity.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and WM Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
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35
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Forti F, Boechi L, Estrin DA, Marti MA. Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins. J Comput Chem 2011; 32:2219-31. [DOI: 10.1002/jcc.21805] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 01/18/2011] [Accepted: 03/06/2011] [Indexed: 12/30/2022]
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36
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Heroux MS, Mohan AD, Olsen KW. Ligand migration in the truncated hemoglobin of Mycobacterium tuberculosis. IUBMB Life 2011; 63:214-20. [DOI: 10.1002/iub.438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Boechi L, Martì MA, Vergara A, Sica F, Mazzarella L, Estrin DA, Merlino A. Protonation of histidine 55 affects the oxygen access to heme in the alpha chain of the hemoglobin from the Antarctic fish Trematomus bernacchii. IUBMB Life 2011; 63:175-82. [DOI: 10.1002/iub.436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Birukou I, Soman J, Olson JS. Blocking the gate to ligand entry in human hemoglobin. J Biol Chem 2010; 286:10515-29. [PMID: 21193395 DOI: 10.1074/jbc.m110.176271] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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39
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Exploring the molecular basis of human manganese superoxide dismutase inactivation mediated by tyrosine 34 nitration. Arch Biochem Biophys 2010; 507:304-9. [PMID: 21167124 DOI: 10.1016/j.abb.2010.12.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/17/2010] [Accepted: 12/09/2010] [Indexed: 11/23/2022]
Abstract
Manganese Superoxide Dismutase (MnSOD) is an essential mitochondrial antioxidant enzyme that protects organisms against oxidative damage, dismutating superoxide radical (O₂(.)⁻) into H₂O₂ and O₂. The active site of the protein presents a Mn ion in a distorted trigonal-bipyramidal environment, coordinated by H26, H74, H163, D159 and one ⁻OH ion or H₂O molecule. The catalytic cycle of the enzyme is a "ping-pong" mechanism involving Mn³+/Mn²+. It is known that nitration of Y34 is responsible for enzyme inactivation, and that this protein oxidative modification is found in tissues undergoing inflammatory and degenerative processes. However, the molecular basis about MnSOD tyrosine nitration affects the protein catalytic function is mostly unknown. In this work we strongly suggest, using computer simulation tools, that Y34 nitration affects protein function by restricting ligand access to the active site. In particular, deprotonation of 3-nitrotyrosine increases drastically the energetic barrier for ligand entry due to the absence of the proton. Our results for the WT and selected mutant proteins confirm that the phenolic moiety of Y34 plays a key role in assisting superoxide migration.
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40
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Droghetti E, Nicoletti FP, Bonamore A, Boechi L, Arroyo Mañez P, Estrin DA, Boffi A, Smulevich G, Feis A. Heme pocket structural properties of a bacterial truncated hemoglobin from Thermobifida fusca. Biochemistry 2010; 49:10394-402. [PMID: 21049911 DOI: 10.1021/bi101452k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An acidic surface variant (ASV) of the "truncated" hemoglobin from Thermobifida fusca was designed with the aim of creating a versatile globin scaffold endowed with thermostability and a high level of recombinant expression in its soluble form while keeping the active site unmodified. This engineered protein was obtained by mutating the surface-exposed residues Phe107 and Arg91 to Glu. Molecular dynamics simulations showed that the mutated residues remain solvent-exposed, not affecting the overall protein structure. Thus, the ASV was used in a combinatorial mutagenesis of the distal heme pocket residues in which one, two, or three of the conserved polar residues [TyrB10(54), TyrCD1(67), and TrpG8(119)] were substituted with Phe. Mutants were characterized by infrared and resonance Raman spectroscopy and compared with the wild-type protein. Similar Fe-proximal His stretching frequencies suggest that none of the mutations alters the proximal side of the heme cavity. Two conformers were observed in the spectra of the CO complexes of both wild-type and ASV protein: form 1 with ν(FeC) and ν(CO) at 509 and 1938 cm(-1) and form 2 with ν(FeC) and ν(CO) at 518 and 1920 cm(-1), respectively. Molecular dynamics simulations were performed for the wild-type and ASV forms, as well as for the TyrB10 mutant. The spectroscopic and computational results demonstrate that CO interacts with TrpG8 in form 1 and interacts with both TrpG8 and TyrCD1 in form 2. TyrB10 does not directly interact with the bound CO.
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Affiliation(s)
- Enrica Droghetti
- Dipartimento di Chimica Ugo Schiff, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
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41
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Howes BD, Giordano D, Boechi L, Russo R, Mucciacciaro S, Ciaccio C, Sinibaldi F, Fittipaldi M, Martí MA, Estrin DA, di Prisco G, Coletta M, Verde C, Smulevich G. The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125. J Biol Inorg Chem 2010; 16:299-311. [PMID: 21076847 DOI: 10.1007/s00775-010-0726-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 10/11/2010] [Indexed: 11/25/2022]
Abstract
The genome of the cold-adapted bacterium Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct monomeric hemoglobins exhibiting a 2/2 α-helical fold. In the present work, one of these hemoglobins is studied by resonance Raman, electronic absorption and electronic paramagnetic resonance spectroscopies, kinetic measurements, and different bioinformatic approaches. It is the first cold-adapted bacterial hemoglobin to be characterized. The results indicate that this protein belongs to the 2/2 hemoglobin family, Group II, characterized by the presence of a tryptophanyl residue on the bottom of the heme distal pocket in position G8 and two tyrosyl residues (TyrCD1 and TyrB10). However, unlike other bacterial hemoglobins, the ferric state, in addition to the aquo hexacoordinated high-spin form, shows multiple hexacoordinated low-spin forms, where either TyrCD1 or TyrB10 can likely coordinate the iron. This is the first example in which both TyrCD1 and TyrB10 are proposed to be the residues that are alternatively involved in heme hexacoordination by endogenous ligands.
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Affiliation(s)
- Barry D Howes
- Dipartimento di Chimica, Università di Firenze, 50019, Sesto Fiorentino (FI), Italy
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42
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Arroyo-Mañez P, Bikiel DE, Boechi L, Capece L, Di Lella S, Estrin DA, Martí MA, Moreno DM, Nadra AD, Petruk AA. Protein dynamics and ligand migration interplay as studied by computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1054-64. [PMID: 20797453 DOI: 10.1016/j.bbapap.2010.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/12/2010] [Accepted: 08/13/2010] [Indexed: 10/19/2022]
Abstract
Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Pau Arroyo-Mañez
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
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43
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Bikiel DE, Forti F, Boechi L, Nardini M, Luque FJ, Martí MA, Estrin DA. Role of Heme Distortion on Oxygen Affinity in Heme Proteins: The Protoglobin Case. J Phys Chem B 2010; 114:8536-43. [DOI: 10.1021/jp102135p] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Damián E. Bikiel
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain, Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Milano, Italy, and Departamento de Química
| | - Flavio Forti
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain, Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Milano, Italy, and Departamento de Química
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain, Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Milano, Italy, and Departamento de Química
| | - Marco Nardini
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain, Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Milano, Italy, and Departamento de Química
| | - F. Javier Luque
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain, Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Milano, Italy, and Departamento de Química
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain, Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Milano, Italy, and Departamento de Química
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina, Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain, Department of Biomolecular Sciences and Biotechnology, CNR-INFM, University of Milano, Milano, Italy, and Departamento de Química
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Capece L, Lewis-Ballester A, Batabyal D, Di Russo N, Yeh SR, Estrin DA, Marti MA. The first step of the dioxygenation reaction carried out by tryptophan dioxygenase and indoleamine 2,3-dioxygenase as revealed by quantum mechanical/molecular mechanical studies. J Biol Inorg Chem 2010; 15:811-23. [PMID: 20361220 DOI: 10.1007/s00775-010-0646-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
Abstract
Tryptophan dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) are two heme-containing enzymes which catalyze the conversion of L: -tryptophan to N-formylkynurenine (NFK). In mammals, TDO is mostly expressed in liver and is involved in controlling homeostatic serum tryptophan concentrations, whereas IDO is ubiquitous and is involved in modulating immune responses. Previous studies suggested that the first step of the dioxygenase reaction involves the deprotonation of the indoleamine group of the substrate by an evolutionarily conserved distal histidine residue in TDO and the heme-bound dioxygen in IDO. Here, we used classical molecular dynamics and hybrid quantum mechanical/molecular mechanical methods to evaluate the base-catalyzed mechanism. Our data suggest that the deprotonation of the indoleamine group of the substrate by either histidine in TDO or heme-bound dioxygen in IDO is not energetically favorable. Instead, the dioxygenase reaction can be initiated by a direct attack of heme-bound dioxygen on the C(2)=C(3) bond of the indole ring, leading to a protein-stabilized 2,3-alkylperoxide transition state and a ferryl epoxide intermediate, which subsequently recombine to generate NFK. The novel sequential two-step oxygen addition mechanism is fully supported by our recent resonance Raman data that allowed identification of the ferryl intermediate (Lewis-Ballester et al. in Proc Natl Acad Sci USA 106:17371-17376, 2009). The results reveal the subtle differences between the TDO and IDO reactions and highlight the importance of protein matrix in modulating stereoelectronic factors for oxygen activation and the stabilization of both transition and intermediate states.
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Affiliation(s)
- Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Buenos Aires, Argentina
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45
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Boechi L, Mañez PA, Luque FJ, Marti MA, Estrin DA. Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis
case. Proteins 2009; 78:962-70. [DOI: 10.1002/prot.22620] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Xu L, Liu X, Zhao W, Wang X. Locally Enhanced Sampling Study of Dioxygen Diffusion Pathways in Homoprotocatechuate 2,3-Dioxygenase. J Phys Chem B 2009; 113:13596-603. [DOI: 10.1021/jp902597t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liang Xu
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Xin Liu
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Weijie Zhao
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
| | - Xicheng Wang
- Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, and Department of Chemistry, Dalian University of Technology, Dalian 116023, China, and School of Chemical Engineering, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
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47
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Guallar V, Lu C, Borrelli K, Egawa T, Yeh SR. Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan. J Biol Chem 2008; 284:3106-3116. [PMID: 19019831 DOI: 10.1074/jbc.m806183200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Resonance Raman studies show that the heme-bound CO in trHbO, a truncated-II hemoglobin from Mycobacterium tuberculosis, is exposed to an environment with a positive electrostatic potential. The mutation of Trp(G8), an absolutely conserved residue in group II and III truncated hemoglobins, to Phe introduces two new Fe-CO conformers, both of which exhibit reduced electrostatic potentials. Computer simulations reveal that the structural perturbation is a result of the increased flexibility of the Tyr(CD1) and Leu(E11) side chains due to the reduction of the size of the G8 residue. Laser flash photolysis studies show that the G8 mutation induces 1) the presence of two new geminate recombination phases, one with a rate faster than the time resolution of our instrument and the other with a rate 13-fold slower than that of the wild type protein, and 2) the reduction of the total geminate recombination yield from 86 to 62% and the increase in the bimolecular recombination rate by a factor of 530. Computer simulations uncover that the photodissociated ligand migrates between three distal temporary docking sites before it subsequently rebinds to the heme iron or ultimately escapes into the solvent via a hydrophobic tunnel. The calculated energy profiles associated with the ligand migration processes are in good agreement with the experimental observations. The results highlight the importance of the Trp(G8) in regulating ligand migration in trHbO, underscoring its pivotal role in the structural and functional properties of the group II and III truncated hemoglobins.
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Affiliation(s)
- Victor Guallar
- Catalan Institution for Research and Advanced Studies, Life Science Program, Barcelona Supercomputing Center, Edificio Nexus II, Barcelona 08028, Spain.
| | - Changyuan Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Kenneth Borrelli
- Catalan Institution for Research and Advanced Studies, Life Science Program, Barcelona Supercomputing Center, Edificio Nexus II, Barcelona 08028, Spain
| | - Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461.
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