1
|
de Armiño DJA, Di Lella S, Montepietra D, Delcanale P, Bruno S, Giordano D, Verde C, Estrin DA, Viappiani C, Abbruzzetti S. Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Protein Sci 2024; 33:e5064. [PMID: 38864722 PMCID: PMC11168075 DOI: 10.1002/pro.5064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024]
Abstract
Due to the low temperature, the Antarctic marine environment is challenging for protein functioning. Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologs, resulting in enhanced reaction rates at low temperatures. The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) genome is one of the few examples of coexistence of multiple hemoglobin genes encoding, among others, two constitutively transcribed 2/2 hemoglobins (2/2Hbs), also named truncated Hbs (TrHbs), belonging to the Group II (or O), annotated as PSHAa0030 and PSHAa2217. In this work, we describe the ligand binding kinetics and their interrelationship with the dynamical properties of globin Ph-2/2HbO-2217 by combining experimental and computational approaches and implementing a new computational method to retrieve information from molecular dynamic trajectories. We show that our approach allows us to identify docking sites within the protein matrix that are potentially able to transiently accommodate ligands and migration pathways connecting them. Consistently with ligand rebinding studies, our modeling suggests that the distal heme pocket is connected to the solvent through a low energy barrier, while inner cavities play only a minor role in modulating rebinding kinetics.
Collapse
Affiliation(s)
- Diego Javier Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Santiago Di Lella
- Departamento de Química Biológica and IQUIBICEN‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Daniele Montepietra
- Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Nanoscience Institute—CNR‐NANOModenaItaly
| | - Pietro Delcanale
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
| | - Stefano Bruno
- Department of Food and Drug SciencesUniversity of ParmaParmaItaly
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNRNaplesItaly
- Department of Ecosustainable Marine BiotechnologyStazione Zoologica Anton DohrnNaplesItaly
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNRNaplesItaly
- Department of Ecosustainable Marine BiotechnologyStazione Zoologica Anton DohrnNaplesItaly
| | - Dario A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, and INQUIMAE‐CONICET, Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires, Ciudad UniversitariaBuenos AiresArgentina
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer SciencesUniversity of ParmaParmaItaly
| |
Collapse
|
2
|
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.
Collapse
Affiliation(s)
- Marco Nardini
- Department of Biosciences, University of Milano, Milano, Italy
| | | | | |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Myxococcus xanthus truncated globin HbO: in silico analysis and functional characterization. Mol Biol Rep 2019; 46:2101-2110. [PMID: 30729391 DOI: 10.1007/s11033-019-04662-5] [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: 09/23/2018] [Accepted: 01/29/2019] [Indexed: 10/27/2022]
Abstract
Truncated globins are 20-40 amino acids shorter than full length globins. Till date, globins have been characterized predominantly from bacteria involved in pathogenicity, nitrogen fixation and photosynthesis, where they are implicated in bacterial virulence within the host, protection of nitrogenase from oxygen inactivation and prevention of oxidative damage to the photosynthetic machinery respectively. Myxococcus xanthus, the model myxobacterium, is an obligate aerobe with a multicellular stage in its life cycle where cells encounter oxygen limitation. This work was undertaken to investigate the potential role of the truncated globin in M. xanthus. To examine the role of globins in this unique group of bacteria, the gene coding for a putative truncated globin (HbO) was identified in the genome of M. xanthus DK 1622. The sequence analysis by bioinformatics approaches revealed that HbO from M. xanthus (Mx-HbO) likely adopts a 2-on-2 alpha helical fold of the truncated globins. The gene coding for Mx-HbO was cloned and its expression in E. coli imparted reddish tinge to the cells. The spectral analysis confirmed it to be a functional globin. The expression of Mx-HbO in the heterologous host improved its growth, resulting in the attainment of higher cell density in culture. The transcript of Mx-hbO was induced threefold in the host cells when grown under low aeration condition as compared to the cells grown under high aeration condition. In M. xanthus, an obligate aerobe, where cell growth accompanies swarming, there is a higher density of cells in the middle of the swarm. Our results suggest that Mx-HbO is a functional globin and could facilitate the growth of cells facing oxygen deprivation, the condition prevailing in the middle of the swarm.
Collapse
|
5
|
Boubeta FM, Boechi L, Estrin D, Patrizi B, Di Donato M, Iagatti A, Giordano D, Verde C, Bruno S, Abbruzzetti S, Viappiani C. Cold-Adaptation Signatures in the Ligand Rebinding Kinetics to the Truncated Hemoglobin of the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125. J Phys Chem B 2018; 122:11649-11661. [PMID: 30230844 DOI: 10.1021/acs.jpcb.8b07682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cold-adapted organisms have evolved proteins endowed with higher flexibility and lower stability in comparison to their thermophilic homologues, resulting in enhanced reaction rates at low temperatures. In this context, protein-bound water molecules were suggested to play a major role, and their weaker interactions at protein active sites have been associated with cold adaptation. In this work, we tested this hypothesis on truncated hemoglobins (a family of microbial heme-proteins of yet-unclear function) applying molecular dynamics simulations and ligand-rebinding kinetics on a protein from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 in comparison with its thermophilic Thermobifida fusca homologue. The CO rebinding kinetics of the former highlight several geminate phases, with an unusually long-lived geminate intermediate. An articulated tunnel with at least two distinct docking sites was identified by analysis of molecular dynamics simulations and was suggested to be at the origin of the unusual geminate rebinding phase. Water molecules are present in the distal pocket, but their stabilization by TrpG8, TyrB10, and HisCD1 is much weaker than in thermophilic Thermobifida fusca truncated hemoglobin, resulting in a faster geminate rebinding. Our results support the hypothesis that weaker water-molecule interactions at the reaction site are associated with cold adaptation.
Collapse
Affiliation(s)
- Fernando M Boubeta
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Leonardo Boechi
- Instituto de Calculo, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , C1428EGA Buenos Aires , Argentina
| | - Dario Estrin
- Instituto de Quimica Fisica de los Materiales, Medio Ambiente y Energia (INQUIMAE), CONICET, and Universidad de Buenos Aires , C1428EHA Buenos Aires , Argentina
| | - Barbara Patrizi
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Mariangela Di Donato
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy.,INO-CNR, Istituto Nazionale di Ottica, Consiglio Nazionale delle Ricerche , Largo Fermi 6 , 50125 Florence , Italy
| | - Alessandro Iagatti
- European Laboratory for Non Linear Spectroscopy (LENS), Università di Firenze , Via Nello Carrara 1 , 50019 Sesto Fiorentino, Florence , Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR , Via Pietro Castellino 111 , I-80131 Naples , Italy.,Stazione Zoologica Anton Dohrn , Villa Comunale , 80121 Naples , Italy
| | - Stefano Bruno
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , Parco Area delle Scienze 23A , 43124 , Parma , Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche , Università di Parma , Parco Area delle Scienze 7A , 43124 , Parma , Italy
| |
Collapse
|
6
|
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
| |
Collapse
|
7
|
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.
Collapse
Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
| |
Collapse
|
8
|
Carabet LA, Guertin M, Lagüe P, Lamoureux G. Mechanism of the Nitric Oxide Dioxygenase Reaction of Mycobacterium tuberculosis Hemoglobin N. J Phys Chem B 2017; 121:8706-8718. [DOI: 10.1021/acs.jpcb.7b06494] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lavinia A. Carabet
- Department of Chemistry
and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montréal, Québec, Canada H4B 1R6
| | | | | | - Guillaume Lamoureux
- Department of Chemistry
and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montréal, Québec, Canada H4B 1R6
| |
Collapse
|
9
|
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
| |
Collapse
|
10
|
Esquerra RM, Bibi BM, Tipgunlakant P, Birukou I, Soman J, Olson JS, Kliger DS, Goldbeck RA. Role of Heme Pocket Water in Allosteric Regulation of Ligand Reactivity in Human Hemoglobin. Biochemistry 2016; 55:4005-17. [PMID: 27355904 PMCID: PMC4978812 DOI: 10.1021/acs.biochem.6b00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water molecules can enter the heme pockets of unliganded myoglobins and hemoglobins, hydrogen bond with the distal histidine, and introduce steric barriers to ligand binding. The spectrokinetics of photodissociated CO complexes of human hemoglobin and its isolated α and β chains were analyzed for the effect of heme hydration on ligand rebinding. A strong coupling was observed between heme hydration and quaternary state. This coupling may contribute significantly to the 20-60-fold difference between the R- and T-state bimolecular CO binding rate constants and thus to the modulation of ligand reactivity that is the hallmark of hemoglobin allostery. Heme hydration proceeded over the course of several kinetic phases in the tetramer, including the R to T quaternary transition. An initial 150 ns hydration phase increased the R-state distal pocket water occupancy, nw(R), to a level similar to that of the isolated α (∼60%) and β (∼10%) chains, resulting in a modest barrier to ligand binding. A subsequent phase, concurrent with the first step of the R → T transition, further increased the level of heme hydration, increasing the barrier. The final phase, concurrent with the final step of the allosteric transition, brought the water occupancy of the T-state tetramer, nw(T), even higher and close to full occupancy in both the α and β subunits (∼90%). This hydration level could present an even larger barrier to ligand binding and contribute significantly to the lower iron reactivity of the T state toward CO.
Collapse
Affiliation(s)
- Raymond M. Esquerra
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Bushra M. Bibi
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Pooncharas Tipgunlakant
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Ivan Birukou
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - Jayashree Soman
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - John S. Olson
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - David S. Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Robert A. Goldbeck
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| |
Collapse
|
11
|
Navati MS, Chung W, Friedman JM. Trehalose-Based Glassy Matrices as an Effective Tool to Trap Short-Lived Intermediates in the Nitric Oxide Dioxygenation (NOD) Reaction of Hemoglobin. J Phys Chem B 2016; 120:4529-39. [DOI: 10.1021/acs.jpcb.5b12778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahantesh S. Navati
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Will Chung
- Joel Friedman
Laboratory, Herricks High School, Shelter Rock Road, New Hyde Park, New York 11040, United States
| | - Joel M. Friedman
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Koebke KJ, Waletzko MT, Pacheco AA. Direct Monitoring of the Reaction between Photochemically Generated Nitric Oxide and Mycobacterium tuberculosis Truncated Hemoglobin N Wild Type and Variant Forms: An Assessment of Computational Mechanistic Predictions. Biochemistry 2016; 55:686-96. [DOI: 10.1021/acs.biochem.5b01145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Michael T. Waletzko
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - A. Andrew Pacheco
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin 53211, United States
| |
Collapse
|
15
|
Bustamante JP, Radusky L, Boechi L, Estrin DA, ten Have A, Martí MA. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family. PLoS Comput Biol 2016; 12:e1004701. [PMID: 26788940 PMCID: PMC4720485 DOI: 10.1371/journal.pcbi.1004701] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022] Open
Abstract
Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends.
Collapse
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
| | - Leandro Radusky
- 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
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, 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, Buenos Aires, Argentina
| | - Arjen ten Have
- Instituto de Investigación Biológica, CONICET, Universidad Nacional de Mar del Plata. Buenos Aires, Argentina
| | - Marcelo A. Martí
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
16
|
Pesce A, Bustamante JP, Bidon-Chanal A, Boechi L, Estrin DA, Luque FJ, Sebilo A, Guertin M, Bolognesi M, Ascenzi P, Nardini M. The N-terminal pre-A region of Mycobacterium tuberculosis 2/2HbN promotes NO-dioxygenase activity. FEBS J 2015; 283:305-22. [PMID: 26499089 DOI: 10.1111/febs.13571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/09/2015] [Accepted: 08/16/2015] [Indexed: 01/24/2023]
Abstract
UNLABELLED A unique defense mechanisms by which Mycobacterium tuberculosis protects itself from nitrosative stress is based on the O2 -dependent NO-dioxygenase (NOD) activity of truncated hemoglobin 2/2HbN (Mt2/2HbN). The NOD activity largely depends on the efficiency of ligand migration to the heme cavity through a two-tunnel (long and short) system; recently, it was also correlated with the presence at the Mt2/2HbN N-terminus of a short pre-A region, not conserved in most 2/2HbNs, whose deletion results in a drastic reduction of NO scavenging. In the present study, we report the crystal structure of Mt2/2HbN-ΔpreA, lacking the pre-A region, at a resolution of 1.53 Å. We show that removal of the pre-A region results in long range effects on the protein C-terminus, promoting the assembly of a stable dimer, both in the crystals and in solution. In the Mt2/2HbN-ΔpreA dimer, access of heme ligands to the short tunnel is hindered. Molecular dynamics simulations show that the long tunnel branch is the only accessible pathway for O2 -ligand migration to/from the heme, and that the gating residue Phe(62)E15 partly restricts the diameter of the tunnel. Accordingly, kinetic measurements indicate that the kon value for peroxynitrite isomerization by Mt2/2HbN-ΔpreA-Fe(III) is four-fold lower relative to the full-length protein, and that NO scavenging by Mt2/2HbN-ΔpreA-Fe(II)-O2 is reduced by 35-fold. Therefore, we speculate that Mt2/2HbN evolved to host the pre-A region as a mechanism for preventing dimerization, thus reinforcing the survival of the microorganism against the reactive nitrosative stress in macrophages. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank under accession number 5AB8.
Collapse
Affiliation(s)
| | - Juan P Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Argentina
| | - Francisco Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, University of Barcelona, Santa Coloma de Gramenet, Spain
| | - Anne Sebilo
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Michel Guertin
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Italy.,CNR-IBF and CIMAINA, University of Milan, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, Roma Tre University, Rome, Italy.,National Institute of Biostructures and Biosystems, Rome, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milan, Italy
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Ascenzi P, di Masi A, Tundo GR, Pesce A, Visca P, Coletta M. Nitrosylation mechanisms of Mycobacterium tuberculosis and Campylobacter jejuni truncated hemoglobins N, O, and P. PLoS One 2014; 9:e102811. [PMID: 25051055 PMCID: PMC4106858 DOI: 10.1371/journal.pone.0102811] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/23/2014] [Indexed: 01/19/2023] Open
Abstract
Truncated hemoglobins (trHbs) are widely distributed in bacteria and plants and have been found in some unicellular eukaryotes. Phylogenetic analysis based on protein sequences shows that trHbs branch into three groups, designated N (or I), O (or II), and P (or III). Most trHbs are involved in the O2/NO chemistry and/or oxidation/reduction function, permitting the survival of the microorganism in the host. Here, a detailed comparative analysis of kinetics and/or thermodynamics of (i) ferrous Mycobacterium tubertulosis trHbs N and O (Mt-trHbN and Mt-trHbO, respectively), and Campylobacter jejuni trHb (Cj-trHbP) nitrosylation, (ii) nitrite-mediated nitrosylation of ferrous Mt-trHbN, Mt-trHbO, and Cj-trHbP, and (iii) NO-based reductive nitrosylation of ferric Mt-trHbN, Mt-trHbO, and Cj-trHbP is reported. Ferrous and ferric Mt-trHbN and Cj-trHbP display a very high reactivity towards NO; however, the conversion of nitrite to NO is facilitated primarily by ferrous Mt-trHbN. Values of kinetic and/or thermodynamic parameters reflect specific trHb structural features, such as the ligand diffusion pathways to/from the heme, the heme distal pocket structure and polarity, and the ligand stabilization mechanisms. In particular, the high reactivity of Mt-trHbN and Cj-trHbP reflects the great ligand accessibility to the heme center by two protein matrix tunnels and the E7-path, respectively, and the penta-coordination of the heme-Fe atom. In contrast, the heme-Fe atom of Mt-trHbO the ligand accessibility to the heme center of Mt-trHbO needs large conformational readjustments, thus limiting the heme-based reactivity. These results agree with different roles of Mt-trHbN, Mt-trHbO, and Cj-trHbP in vivo.
Collapse
Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
- * E-mail:
| | - Alessandra di Masi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
- Department of Sciences, University Roma Tre, Roma, Italy
| | - Grazia R. Tundo
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | | | - Paolo Visca
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| |
Collapse
|
20
|
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.
Collapse
|
21
|
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.
Collapse
|
22
|
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.
Collapse
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
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Khoshtariya DE, Dolidze TD, Shushanyan M, van Eldik R. Long-range electron transfer with myoglobin immobilized at Au/mixed-SAM junctions: mechanistic impact of the strong protein confinement. J Phys Chem B 2014; 118:692-706. [PMID: 24369906 DOI: 10.1021/jp4101569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Horse muscle myoglobin (Mb) was tightly immobilized at Au-deposited ~15-Å-thick mixed-type (1:1) alkanethiol SAMs, HS-(CH₂)₁₁-COOH/HS-(CH₂)₁₁-OH, and placed in contact with buffered H₂O or D₂O solutions. Fast-scan cyclic voltammetry (CV) and a Marcus-equation-based analysis were applied to determine unimolecular standard rate constants and reorganization free energies for electron transfer (ET), under variable-temperature (15-55 °C) and -pressure (0.01-150 MPa) conditions. The CV signal was surprisingly stable and reproducible even after multiple temperature and pressure cycles. The data analysis revealed the following values: standard rate constant, 33 s⁻¹ (25 °C, 0.01 MPa, H₂O); reorganization free energy, 0.5 ± 0.1 eV (throughout); activation enthalpy, 12 ± 3 kJ mol⁻¹; activation volume, -3.1 ± 0.2 cm³ mol⁻¹; and pH-dependent solvent kinetic isotope effect (k(H)⁰/k(D)⁰), 0.7-1.4. Furthermore, the values for the rate constant and reorganization free energy are very similar to those previously found for cytochrome c electrostatically immobilized at the monocomponent Au/HS-(CH₂)₁₁-COOH junction. In vivo, Mb apparently forms a natural electrostatic complex with cytochrome b₅ (cyt-b₅) through the "dynamic" (loose) docking pattern, allowing for a slow ET that is intrinsically coupled to the water's removal from the "defective" heme iron (altogether shaping the biological repair mechanism for Mb's "met" form). In contrary, our experiments rather mimic the case of a "simple" (tight) docking of the redesigned (mutant) Mb with cyt-b₅ (Nocek et al. J. Am. Chem. Soc. 2010, 132, 6165-6175). According to our analysis, in this configuration, Mb's distal pocket (linked to the "ligand channel") seems to be arrested within the restricted configuration, allowing the rate-determining reversible ET process to be coupled only to the inner-sphere reorganization (minimal elongation/shortening of an Fe-OH₂ bond) rather than the pronounced detachment (rebinding) of water and, hence, to be much faster.
Collapse
Affiliation(s)
- Dimitri E Khoshtariya
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg , 91058 Erlangen, Germany
| | | | | | | |
Collapse
|
24
|
Ramos-Alvarez C, Yoo BK, Pietri R, Lamarre I, Martin JL, Lopez-Garriga J, Negrerie M. Reactivity and dynamics of H2S, NO, and O2 interacting with hemoglobins from Lucina pectinata. Biochemistry 2013; 52:7007-21. [PMID: 24040745 DOI: 10.1021/bi400745a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hemoglobin HbI from the clam Lucina pectinata is involved in H2S transport, whereas homologous heme protein HbII/III is involved in O2 metabolism. Despite similar tertiary structures, HbI and HbII/III exhibit very different reactivity toward heme ligands H2S, O2, and NO. To investigate this reactivity at the heme level, we measured the dynamics of ligand interaction by time-resolved absorption spectroscopy in the picosecond to nanosecond time range. We demonstrated that H2S can be photodissociated from both ferric and ferrous HbI. H2S geminately rebinds to ferric and ferrous out-of-plane iron with time constants (τgem) of 12 and 165 ps, respectively, with very different proportions of photodissociated H2S exiting the protein (24% in ferric and 80% in ferrous HbI). The Gln(E7)His mutation considerably changes H2S dynamics in ferric HbI, indicating the role of Gln(E7) in controling H2S reactivity. In ferric HbI, the rate of diffusion of H2S from the solvent into the heme pocket (kentry) is 0.30 μM(-1) s(-1). For the HbII/III-O2 complex, we observed mainly a six-coordinate vibrationally excited heme-O2 complex with O2 still bound to the iron. This explains the low yield of O2 photodissociation and low koff from HbII/III, compared with those of HbI and Mb. Both isoforms behave very differently with regard to NO and O2 dynamics. Whereas the amplitude of geminate rebinding of O2 to HbI (38.5%) is similar to that of myoglobin (34.5%) in spite of different distal heme sites, it appears to be much larger for HbII/III (77%). The distal Tyr(B10) side chain present in HbII/III increases the energy barrier for ligand escape and participates in the stabilization of bound O2 and NO.
Collapse
Affiliation(s)
- Cacimar Ramos-Alvarez
- Department of Chemistry, University of Puerto Rico , Mayagüez Campus, Mayagüez 00680, Puerto Rico
| | | | | | | | | | | | | |
Collapse
|
25
|
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.
Collapse
|
26
|
Salter MD, Blouin GC, Soman J, Singleton EW, Dewilde S, Moens L, Pesce A, Nardini M, Bolognesi M, Olson JS. Determination of ligand pathways in globins: apolar tunnels versus polar gates. J Biol Chem 2012; 287:33163-78. [PMID: 22859299 DOI: 10.1074/jbc.m112.392258] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although molecular dynamics simulations suggest multiple interior pathways for O(2) entry into and exit from globins, most experiments indicate well defined single pathways. In 2001, we highlighted the effects of large-to-small amino acid replacements on rates for ligand entry and exit onto the three-dimensional structure of sperm whale myoglobin. The resultant map argued strongly for ligand movement through a short channel from the heme iron to solvent that is gated by the distal histidine (His-64(E7)) near the solvent edge of the porphyrin ring. In this work, we have applied the same mutagenesis mapping strategy to the neuronal mini-hemoglobin from Cerebratulus lacteus (CerHb), which has a large internal tunnel from the heme iron to the C-terminal ends of the E and H helices, a direction that is 180° opposite to the E7 channel. Detailed comparisons of the new CerHb map with expanded results for Mb show unambiguously that the dominant (>90%) ligand pathway in CerHb is through the internal tunnel, and the major (>75%) ligand pathway in Mb is through the E7 gate. These results demonstrate that: 1) mutagenesis mapping can identify internal pathways when they exist; 2) molecular dynamics simulations need to be refined to address discrepancies with experimental observations; and 3) alternative pathways have evolved in globins to meet specific physiological demands.
Collapse
Affiliation(s)
- Mallory D Salter
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Mañez PA, Lu C, Boechi L, Martí MA, Shepherd M, Wilson JL, Poole RK, Luque FJ, Yeh SR, Estrin DA. Role of the distal hydrogen-bonding network in regulating oxygen affinity in the truncated hemoglobin III from Campylobacter jejuni. Biochemistry 2011; 50:3946-56. [PMID: 21476539 PMCID: PMC4535342 DOI: 10.1021/bi101137n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxygen affinity in heme-containing proteins is determined by a number of factors, such as the nature and conformation of the distal residues that stabilize the heme bound-oxygen via hydrogen-bonding interactions. The truncated hemoglobin III from Campylobacter jejuni (Ctb) contains three potential hydrogen-bond donors in the distal site: TyrB10, TrpG8, and HisE7. Previous studies suggested that Ctb exhibits an extremely slow oxygen dissociation rate due to an interlaced hydrogen-bonding network involving the three distal residues. Here we have studied the structural and kinetic properties of the G8(WF) mutant of Ctb and employed state-of-the-art computer simulation methods to investigate the properties of the O(2) adduct of the G8(WF) mutant, with respect to those of the wild-type protein and the previously studied E7(HL) and/or B10(YF) mutants. Our data indicate that the unique oxygen binding properties of Ctb are determined by the interplay of hydrogen-bonding interactions between the heme-bound ligand and the surrounding TyrB10, TrpG8, and HisE7 residues.
Collapse
Affiliation(s)
- Pau Arroyo Mañez
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Changyuan Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Fisica, 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 Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Mark Shepherd
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Jayne Louise Wilson
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - F. Javier Luque
- Department de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| |
Collapse
|
28
|
A hydrogen-bonding network formed by the B10–E7–E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification. J Biol Inorg Chem 2011; 16:599-609. [DOI: 10.1007/s00775-011-0761-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
|
29
|
Kuwada T, Hasegawa T, Takagi T, Sato I, Shishikura F. pH-dependent structural changes in haemoglobin component V from the midge larvaPropsilocerus akamusi(Orthocladiinae, Diptera). ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:258-67. [DOI: 10.1107/s0907444909055760] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 12/30/2009] [Indexed: 11/10/2022]
Abstract
Haemoglobin component V (Hb V) from the midge larvaPropsilocerus akamusiexhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb V retains its functional properties by adapting to the structural changes caused by amino-acid replacements.
Collapse
|