1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Córdova JA, Palermo JC, Estrin DA, Bari SE, Capece L. Binding mechanism of disulfide species to ferric hemeproteins: The case of metmyoglobin. J Inorg Biochem 2023; 247:112313. [PMID: 37467661 DOI: 10.1016/j.jinorgbio.2023.112313] [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: 05/15/2023] [Revised: 06/15/2023] [Accepted: 07/01/2023] [Indexed: 07/21/2023]
Abstract
The interactions of the heme iron of hemeproteins with sulfide and disulfide compounds are of potential interest as physiological signaling processes. While the interaction with hydrogen sulfide has been described computationally and experimentally, the reaction with disulfide, and specifically the molecular mechanism for ligand binding has not been studied in detail. In this work, we study the association process for disulfane and its conjugate base disulfanide at different pH conditions. Additionally, by means of advanced sampling techniques based on multiple steered molecular dynamics, we provide free energy profiles for ligand migration for both acid/base species, showing a similar behavior to the previously reported for the related H2S/HS¯ pair. Finally, we studied the ligand interchange reaction (H2O/H2S, HS¯ and H2O/HSSH, HSS¯) by means of hybrid quantum mechanics-molecular mechanics calculations. We show that the anionic species are able to displace more efficiently the H2O bound to the iron, and that the H-bond network in the distal cavity can help the neutral species to perform the reaction. Altogether, we provide a molecular explanation for the experimental information and show that the global association process depends on a fine balance between the migration towards the active site and the ligand interchange reaction.
Collapse
Affiliation(s)
- Jonathan Alexis Córdova
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Juan Cruz Palermo
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Darío A Estrin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Sara E Bari
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina..
| | - Luciana Capece
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina..
| |
Collapse
|
3
|
Álvarez L, Suárez SA, González PJ, Brondino CD, Doctorovich F, Martí MA. The Underlying Mechanism of HNO Production by the Myoglobin-Mediated Oxidation of Hydroxylamine. Inorg Chem 2020; 59:7939-7952. [DOI: 10.1021/acs.inorgchem.9b02750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucía Álvarez
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- INQUIMAE-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Sebastián A. Suárez
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- INQUIMAE-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Pablo J. González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral y CONICET, S3000ZAA Santa Fe, Argentina
| | - Carlos D. Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral y CONICET, S3000ZAA Santa Fe, Argentina
| | - Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- INQUIMAE-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Marcelo A. Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- IQUIBICEN-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| |
Collapse
|
4
|
Foglia NO, Bari SE, Estrin DA. In Silico Insight into the Reductive Nitrosylation of Ferric Hemeproteins. Inorg Chem 2020; 59:3631-3641. [DOI: 10.1021/acs.inorgchem.9b03198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nicolás O. Foglia
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica, Buenos Aires, Argentina
| | - Sara E. Bari
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - Darío A. Estrin
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Quı́mica de los Materiales, Medio Ambiente y Energı́a, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Quı́mica Inorgánica, Analı́tica y Quı́mica Fı́sica, Buenos Aires, Argentina
| |
Collapse
|
5
|
Olson JS. Lessons Learned from 50 Years of Hemoglobin Research: Unstirred and Cell-Free Layers, Electrostatics, Baseball Gloves, and Molten Globules. Antioxid Redox Signal 2020; 32:228-246. [PMID: 31530172 PMCID: PMC6948003 DOI: 10.1089/ars.2019.7876] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Significance: Over the past 50 years, the mechanisms for O2 storage and transport have been determined quantitatively on distance scales from millimeters to tenths of nanometers and timescales from seconds to picoseconds. Recent Advances: In this review, I have described four key conclusions from work done by my group and our close colleagues. (i) O2 uptake by mammalian red cells is limited by diffusion through unstirred water layers adjacent to the cell surface and across cell-free layers adjacent to vessel walls. (ii) In most vertebrates, hemoglobins (Hbs) and myoglobins (Mbs), the distal histidine at the E7 helical position donates a strong hydrogen bond to bound O2, which selectively enhances O2 affinity, prevents carbon monoxide poisoning, and markedly slows autoxidation. (iii) O2 binding to mammalian Hbs and Mbs occurs by migration of the ligand through a channel created by upward rotation of the His(E7) side chain, capture in the empty space of the distal pocket, and then coordination with the ferroprotoporphyrin IX (heme) iron atom. (iv) The assembly of Mbs and Hbs occurs by formation of molten globule intermediates, in which the N- and C-terminal helices have almost fully formed secondary structures, but the heme pockets are disordered and followed by high-affinity binding of heme. Critical Issues: These conclusions indicate that there are often compromises between O2 transport function, holoprotein stability, and the efficiency of assembly. Future Directions: However, the biochemical mechanisms underlying these conclusions provide the framework for understanding globin evolution in greater detail and for engineering more efficient and stable globins.
Collapse
Affiliation(s)
- John S Olson
- BioSciences Department, Rice University, Houston, Texas
| |
Collapse
|
6
|
Rodriguez-Mackenzie AD, Arbelo-Lopez HD, Wymore T, Lopez-Garriga J. A reaction pathway to compound 0 intermediates in oxy-myoglobin through interactions with hydrogen sulfide and His64. J Mol Graph Model 2019; 94:107465. [PMID: 31670138 DOI: 10.1016/j.jmgm.2019.107465] [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: 08/09/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022]
Abstract
Myoglobin (Mb) binds oxygen with high affinity as a low spin singlet complex and thus functions as an oxygen storage protein. Yet, hybrid Density Functional Theory/Molecular Mechanical (DFT/MM) calculations of oxy-Mb models predict that the O2 bond is much less resistant to breaking in the presence of hydrogen sulfide (H2S) compared with water. Specifically, a hydrogen atom from H2S can be transferred to the distal oxygen atom through homolytic cleavage of the S-H bond to form the intermediate Compound (Cpd) 0 structure and a thiyl radical. In the presence of a neutral His64 (Nε protonation, His64-ε) and H2S, only a metastable Cpd 0 would be formed as the active site is devoid of any additional proton donor to fully break the O2 bond. In contrast, the calculations predict that the triplet state is significantly favored over the open shell singlet diradical state throughout the entire reaction coordinate in the presence of H2S and a positively charged His64. Furthermore, a positively charged His64 can readily donate a proton to Cpd 0 to fully break the O2 bond resulting in a configuration analogous to reported reaction models of a hemoglobin mutant bound to H2O2 with H2S present. Typically, exotic techniques are required to generate Cpd 0 but under the conditions just described the intermediate is readily detected in UV-Vis spectra at room temperature. The effect is observed as a 2 nm red shift of the Soret band from 414 nm to 416 nm (pH 5.0, His64-εδ) and from 416 nm to 418 nm (pH 6.6, His64-ε).
Collapse
Affiliation(s)
| | - Hector D Arbelo-Lopez
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico
| | - Troy Wymore
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, United States.
| | - Juan Lopez-Garriga
- Department of Chemistry, University of Puerto Rico Mayaguez Campus, Mayaguez, 00680, Puerto Rico.
| |
Collapse
|
7
|
Arrar M, Boubeta FM, Szretter ME, Sued M, Boechi L, Rodriguez D. On the accurate estimation of free energies using the jarzynski equality. J Comput Chem 2018; 40:688-696. [DOI: 10.1002/jcc.25754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/18/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Mehrnoosh Arrar
- Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, CONICET-Facultad de Ciencias Exactas y Naturales, 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
| | - Fernando Martín Boubeta
- Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, CONICET-Facultad de Ciencias Exactas y Naturales, 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
| | - Maria Eugenia Szretter
- Departamento de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina, Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Mariela Sued
- Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| | - Daniela Rodriguez
- Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires; Buenos Aires Argentina
| |
Collapse
|
8
|
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
|
9
|
Yang Y, Liu F, Liu A. Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities. J Biol Chem 2018; 293:10415-10424. [PMID: 29784877 DOI: 10.1074/jbc.ra118.002698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/18/2018] [Indexed: 11/06/2022] Open
Abstract
3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O2 and inserts both oxygen atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O2, even though local O2 concentrations and diffusion rates are relatively low. Here, a close inspection of the HAO structures revealed that substrate- and inhibitor-bound structures exhibit a closed conformation with three hydrophobic loop regions moving toward the catalytic iron center, whereas the ligand-free structure is open. We hypothesized that these loop movements enhance O2 binding to the binary complex of HAO and 3-HAA. We found that the carboxyl end of 3-HAA triggers changes in two loop regions and that the third loop movement appears to be driven by an H-bond interaction between Asn27 and Ile142 Mutational analyses revealed that N27A, I142A, and I142P variants cannot form a closed conformation, and steady-state kinetic assays indicated that these variants have a substantially higher Km for O2 than WT HAO. This observation suggested enhanced hydrophobicity at the iron center resulting from the concerted loop movements after the binding of the primary substrate, which is hydrophilic. Given that O2 is nonpolar, the increased hydrophobicity at the iron center of the binary complex appears to be essential for rapid O2 binding and activation, explaining the reason for the 3-HAA-induced loop movements. Because substrate binding-induced open-to-closed conformational changes are common, the results reported here may help further our understanding of how oxygen is enriched in nonheme iron-dependent dioxygenases.
Collapse
Affiliation(s)
- Yu Yang
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
| | - Fange Liu
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Aimin Liu
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
| |
Collapse
|
10
|
Wang XW, Zhang JZH, He X. Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1709169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xian-wei Wang
- College of Science, Zhejiang University of Technology, Hangzhou 310023, China
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- Zhejiang Provincial Collaborative Innovation Center of High-end Laser Manufacturing Equipment, Hangzhou 310014, China
| | - John Z. H. Zhang
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York 10003, USA
| | - Xiao He
- College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| |
Collapse
|
11
|
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: 98] [Impact Index Per Article: 14.0] [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
|
12
|
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.
Collapse
|
13
|
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
|
14
|
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.
Collapse
|
15
|
Ramírez CL, Petruk A, Bringas M, Estrin DA, Roitberg AE, Marti MA, Capece L. Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions. J Chem Theory Comput 2016; 12:3390-7. [DOI: 10.1021/acs.jctc.6b00278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Claudia L. Ramírez
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
- Dto.
de Química Biologica Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Ariel Petruk
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Mauro Bringas
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Dario A. Estrin
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Adrian E. Roitberg
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Marcelo A. Marti
- Dto.
de Química Biologica Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/IQUIBICEN-CONICET, Buenos Aires, C1428EGA, Argentina
| | - Luciana Capece
- Dto.
de Química Inorgánica, Analítica y Química
Física, Fac. de Ciencias Exactas y Naturales, Univ. de Buenos Aires/INQUIMAE-CONICET, Buenos Aires, C1428EGA, Argentina
| |
Collapse
|
16
|
Shadrina MS, English AM, Peslherbe GH. Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study. J Chem Theory Comput 2016; 12:2038-46. [PMID: 26938707 DOI: 10.1021/acs.jctc.5b01132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independently, while the protein and water molecules experience an average interaction from all copies. Furthermore, gas migration within a protein matrix can be accelerated without altering protein dynamics by increasing the effective temperature of the TLES copies. These features of TLES enable rapid simulations of gas diffusion within a protein matrix at significantly reduced (∼98%) computational cost. However, the results of TLES and standard MD simulations have not been systematically compared, which limits the adoption of the TLES approach. We address this drawback here by benchmarking TLES against standard MD in the simulation of O2 diffusion in myoglobin (Mb) as a case study since this model system has been extensively characterized. We find that 2 ns TLES and 108 ns standard simulations map the same network of diffusion tunnels in Mb and uncover the same docking sites, barriers, and escape portals. We further discuss the influence of simulation time as well as the number of independent simulations on the O2 population density within the diffusion tunnels and on the sampling of Mb's conformational space as revealed by principal component analysis. Overall, our comprehensive benchmarking reveals that TLES is an appropriate and robust tool for the rapid mapping of gas diffusion in proteins when the kinetic data provided by standard MD are not required. Furthermore, TLES provides explicit ligand diffusion pathways, unlike most rapid methods.
Collapse
Affiliation(s)
- Maria S Shadrina
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
| | - Ann M English
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
| | - Gilles H Peslherbe
- Centre for Research in Molecular Modeling (CERMM) and Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke Street West, Montréal, Québec, Canada H4B 1R6
| |
Collapse
|
17
|
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
|
18
|
Shadrina MS, Peslherbe GH, English AM. O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7. Biochemistry 2015; 54:5279-89. [PMID: 26226401 DOI: 10.1021/acs.biochem.5b00369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the release of O2 to the solvent via a transient E7 channel. To reveal the O2 escape routes controlled by HisE7 and to evaluate its role in gating heme access, we compare simulations of O2 diffusion from the distal heme pockets of the T and R states of HbA performed with HisE7 in its open (protonated) and closed (neutral) conformations. Irrespective of HisE7's conformation, we observe the same four or five escape routes leading directly from the α- or β-distal heme pockets to the solvent. Only 21-53% of O2 escapes occur via these routes, with the remainder escaping through routes that encompass multiple internal cavities in HbA. The conformation of the distal HisE7 controls the escape of O2 from the heme by altering the distal pocket architecture in a pH-dependent manner, not by gating the E7 channel. Removal of the HisE7 side chain in the GlyE7 variant exposes the distal pockets to the solvent, and the percentage of O2 escapes to the solvent directly from the α- or β-distal pockets of the mutant increases to 70-88%. In contrast to O2, the dominant water route from the bulk solvent is gated by HisE7 because protonation and opening of this residue dramatically increase the rate of influx of water into the empty distal heme pockets. The occupancy of the distal heme site by a water molecule, which functions as an additional nonprotein barrier to binding of the ligand to the heme, is also controlled by HisE7. Overall, analysis of gas and water diffusion routes in the subunits of HbA and its GlyE7 variant sheds light on the contribution of distal HisE7 in controlling polar and nonpolar ligand movement between the solvent and the hemes.
Collapse
Affiliation(s)
- Maria S Shadrina
- Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University , Montreal, Quebec H4B 1R6, Canada
| | - Gilles H Peslherbe
- Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University , Montreal, Quebec H4B 1R6, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University , Montreal, Quebec H4B 1R6, Canada
| |
Collapse
|
19
|
Di Russo NV, Condurso HL, Li K, Bruner SD, Roitberg AE. Oxygen diffusion pathways in a cofactor-independent dioxygenase. Chem Sci 2015; 6:6341-6348. [PMID: 26508997 PMCID: PMC4618494 DOI: 10.1039/c5sc01638j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A combination of experimental and computational studies reveals the main O2 diffusion pathways, providing insight into how cofactor-independent oxygenases control stereospecificity and prevent oxidative inactivation.
Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O2 diffusion is emerging, where specific channels guide O2 to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O2 reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O2 at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O2 in the absence of cofactors or metals, the way O2 reaches the active site is similar to that reported for other O2-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O2 access that are conserved among very different types of proteins.
Collapse
Affiliation(s)
- Natali V Di Russo
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Heather L Condurso
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Kunhua Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| |
Collapse
|
20
|
Chintapalli SV, Bhardwaj G, Patel R, Shah N, Patterson RL, van Rossum DB, Anishkin A, Adams SH. Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin. PLoS One 2015; 10:e0128496. [PMID: 26030763 PMCID: PMC4451517 DOI: 10.1371/journal.pone.0128496] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 04/27/2015] [Indexed: 11/18/2022] Open
Abstract
The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolites; however, the binding pocket and regulation of the interaction remains to be established. In this study, we employed a computational strategy to elucidate the structural determinants of fatty acids (palmitic & oleic acid) binding to Mb. Sequence analysis and docking simulations with a horse (Equus caballus) structural Mb reference reveals a fatty acid-binding site in the hydrophobic cleft near the heme region in Mb. Both palmitic acid and oleic acid attain a "U" shaped structure similar to their conformation in pockets of other fatty acid-binding proteins. Specifically, we found that the carboxyl head group of palmitic acid coordinates with the amino group of Lys45, whereas the carboxyl group of oleic acid coordinates with both the amino groups of Lys45 and Lys63. The alkyl tails of both fatty acids are supported by surrounding hydrophobic residues Leu29, Leu32, Phe33, Phe43, Phe46, Val67, Val68 and Ile107. In the saturated palmitic acid, the hydrophobic tail moves freely and occasionally penetrates deeper inside the hydrophobic cleft, making additional contacts with Val28, Leu69, Leu72 and Ile111. Our simulations reveal a dynamic and stable binding pocket in which the oxygen molecule and heme group in Mb are required for additional hydrophobic interactions. Taken together, these findings support a mechanism in which Mb acts as a muscle transporter for fatty acid when it is in the oxygenated state and releases fatty acid when Mb converts to deoxygenated state.
Collapse
Affiliation(s)
- Sree V. Chintapalli
- Arkansas Children’s Nutrition Center, and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SVC); (SHA)
| | - Gaurav Bhardwaj
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Reema Patel
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Natasha Shah
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Randen L. Patterson
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- Department of Physiology and Membrane Biology, School of Medicine, University of California Davis, Davis, California, United States of America
| | - Damian B. van Rossum
- Center for Computational Proteomics, The Pennsylvania State University, State College, Pennsylvania, United States of America
- Department of Biology, The Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Sean H. Adams
- Arkansas Children’s Nutrition Center, and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SVC); (SHA)
| |
Collapse
|
21
|
De Sancho D, Kubas A, Wang PH, Blumberger J, Best RB. Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin. J Chem Theory Comput 2015; 11:1919-27. [PMID: 26574395 PMCID: PMC6132223 DOI: 10.1021/ct5011455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pathways by which small molecules (substrates or inhibitors) access active sites are a key aspect of the function of enzymes and other proteins. A key problem in designing or altering such proteins is to identify sites for mutation that will have the desired effect on the substrate transport properties. While specific access channels have been invoked in the past, molecular simulations suggest that multiple routes are possible, complicating the analysis. This complexity, however, can be captured by a Markov State Model (MSM) of the ligand diffusion process. We have developed a sensitivity analysis of the resulting rate matrix, which identifies the locations where mutations should have the largest effect on the diffusive on rate. We apply this method to myoglobin, which is the best characterized example both from experiment and simulation. We validate the approach by translating the sensitivity parameter obtained from this method into the CO binding rates in myoglobin upon mutation, resulting in a semi-quantitative correlation with experiments. The model is further validated against an explicit simulation for one of the experimental mutants.
Collapse
Affiliation(s)
- David De Sancho
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
- CIC nanoGUNE , Tolosa Hiribidea 76, 20018 Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science , Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Adam Kubas
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Po-Hung Wang
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
- Theoretical Molecular Science Laboratory , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| |
Collapse
|
22
|
Arcon JP, Rosi P, Petruk AA, Marti MA, Estrin DA. Molecular Mechanism of Myoglobin Autoxidation: Insights from Computer Simulations. J Phys Chem B 2015; 119:1802-13. [DOI: 10.1021/jp5093948] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. P. Arcon
- Departamento
de Química Inorgánica, Analítica y Química
Física e INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
- Departamento
de Química Biológica, Facultad de Ciencias Exactas y
Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón
2, C1428EHA, Ciudad
de Buenos Aires, Argentina
| | - P. Rosi
- Departamento
de Química Inorgánica, Analítica y Química
Física e INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - A. A. Petruk
- Departamento
de Química Inorgánica, Analítica y Química
Física e INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| | - M. A. Marti
- Departamento
de Química Inorgánica, Analítica y Química
Física e INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
- Departamento
de Química Biológica, Facultad de Ciencias Exactas y
Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón
2, C1428EHA, Ciudad
de Buenos Aires, Argentina
| | - D. A. Estrin
- Departamento
de Química Inorgánica, Analítica y Química
Física e INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA, Ciudad de Buenos Aires, Argentina
| |
Collapse
|
23
|
Boron I, Bustamante JP, Davidge KS, Singh S, Bowman LA, 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] [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
|
24
|
Engineered chimeras reveal the structural basis of hexacoordination in globins: A case study of neuroglobin and myoglobin. Biochim Biophys Acta Gen Subj 2015; 1850:169-77. [DOI: 10.1016/j.bbagen.2014.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/12/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022]
|
25
|
Temelso B, Alser KA, Gauthier A, Palmer AK, Shields GC. Structural Analysis of α-Fetoprotein (AFP)-like Peptides with Anti-Breast-Cancer Properties. J Phys Chem B 2014; 118:4514-26. [DOI: 10.1021/jp500017b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Berhane Temelso
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Katherine A. Alser
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Arianne Gauthier
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Amber Kay Palmer
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - George C. Shields
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| |
Collapse
|
26
|
Abstract
![]()
Myoglobin
(Mb) binds diatomic ligands, like O2, CO,
and NO, in a cavity that is only transiently accessible. Crystallography
and molecular simulations show that the ligands can migrate through
an extensive network of transiently connected cavities but disagree
on the locations and occupancy of internal hydration sites. Here,
we use water 2H and 17O magnetic relaxation
dispersion (MRD) to characterize the internal water molecules in Mb
under physiological conditions. We find that equine carbonmonoxy Mb
contains 4.5 ± 1.0 ordered internal water molecules with a mean
survival time of 5.6 ± 0.5 μs at 25 °C. The likely
locations of these water molecules are the four polar hydration sites,
including one of the xenon-binding cavities, that are fully occupied
in all high-resolution crystal structures of equine Mb. The finding
that water escapes from these sites, located 17–31 Å apart
in the protein, on the same μs time scale suggests a global
exchange mechanism. We propose that this mechanism involves transient
penetration of the protein by H-bonded water chains. Such a mechanism
could play a functional role by eliminating trapped ligands. In addition,
the MRD results indicate that 2 or 3 of the 11 histidine residues
of equine Mb undergo intramolecular hydrogen exchange on a μs
time scale.
Collapse
Affiliation(s)
- Shuji Kaieda
- Department of Biophysical Chemistry, Lund University , P.O. Box 124, SE-22100 Lund, Sweden
| | | |
Collapse
|
27
|
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
|