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Salehi SM, Pezzella M, Willard A, Meuwly M, Karplus M. Water dynamics around T 0 vs R 4 of hemoglobin from local hydrophobicity analysis. J Chem Phys 2023; 158:025101. [PMID: 36641390 DOI: 10.1063/5.0129990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The local hydration around tetrameric hemoglobin (Hb) in its T0 and R4 conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the α1β2 and α2β1 interfaces, responsible for the quaternary T → R transition, which is encoded in the Monod-Wyman-Changeux model, as well as comparison with earlier computations of the solvent accessible surface area, makes clear that the two quantities measure different aspects of hydration. Local hydrophobicity quantifies the presence and structure of water molecules at the interface, whereas "buried surface" reports on the available space for solvent. For simulations with Hb frozen in its T0 and R4 states, the correlation coefficient between LH and buried surface is 0.36 and 0.44, respectively, but it increases considerably if the 95% confidence interval is used. The LH with Hb frozen and flexible changes little for most residues at the interfaces but is significantly altered for a few select ones: Thr41α, Tyr42α, Tyr140α, Trp37β, Glu101β (for T0) and Thr38α, Tyr42α, Tyr140α (for R4). The number of water molecules at the interface is found to increase by ∼25% for T0 → R4, which is consistent with earlier measurements. Since hydration is found to be essential to protein function, it is clear that hydration also plays an essential role in allostery.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Marco Pezzella
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Adam Willard
- Department of Chemistry MIT, Cambridge, Massachusetts 02139, USA
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Martin Karplus
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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2
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Schay G, Fidy J, Herenyi L. Slow dynamics measured by phosphorescence lifetime reveals global conformational changes in human adult hemoglobin induced by allosteric effectors. PLoS One 2022; 17:e0278417. [PMID: 36454779 PMCID: PMC9714750 DOI: 10.1371/journal.pone.0278417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
The mechanism underlying allostery in hemoglobin (Hb) is still not completely understood. Various models describing the action of allosteric effectors on Hb function have been published in the literature. It has also been reported that some allosteric effectors-such as chloride ions, inositol hexaphosphate, 2,3-diphospho-glycerate and bezafibrate-considerably lower the oxygen affinity of Hb. In this context, an important question is the extent to which these changes influence the conformational dynamics of the protein. Earlier, we elaborated a challenging method based on phosphorescence quenching, which makes characterizing protein-internal dynamics possible in the ms time range. The experimental technique involves phosphorescence lifetime measurements in thermal equilibrium at varied temperatures from 10 K up to 273 K, based on the signal of Zn-protoporphyrin substituted for the heme in the β-subunits of Hb. The thermal activation of protein dynamics was observed by the enhancement of phosphorescence quenching attributed to O2 diffusion. It was shown that the thermal activation of protein matrix dynamics was clearly distinguishable from the dynamic activation of the aqueous solvent, and was therefore highly specific for the protein. In the present work, the same method was used to study the changes in the parameters of the dynamic activation of human HbA induced by binding allosteric effectors. We interpreted the phenomenon as phase transition between two states. The fitting of this model to lifetime data yielded the change of energy and entropy in the activation process and the quenching rate in the dynamically activated state. The fitted parameters were particularly sensitive to the presence of allosteric effectors and could be interpreted in line with results from earlier experimental studies. The results suggest that allosteric effectors are tightly coupled to the dynamics of the whole protein, and thus underline the importance of global dynamics in the regulation of Hb function.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herenyi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- * E-mail:
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3
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Olson JS. Kinetic mechanisms for O 2 binding to myoglobins and hemoglobins. Mol Aspects Med 2021; 84:101024. [PMID: 34544605 DOI: 10.1016/j.mam.2021.101024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 11/29/2022]
Abstract
Antonini and Brunori's 1971 book "Hemoglobin and Myoglobin in Their Reactions with Ligands" was a truly remarkable publication that summarized almost 100 years of research on O2 binding to these globins. Over the ensuing 50 years, ultra-fast laser photolysis techniques, high-resolution and time resolved X-ray crystallography, molecular dynamics simulations, and libraries of recombinant myoglobin (Mb) and hemoglobin (Hb) variants have provided structural interpretations of O2 binding to these proteins. The resultant mechanisms provide quantitative descriptions of the stereochemical factors that govern overall affinity, including proximal and distal steric restrictions that affect iron reactivity and favorable positive electrostatic interactions that preferentially stabilize bound O2. The pathway for O2 uptake and release by Mb and subunits of Hb has been mapped by screening libraries of site-directed mutants in laser photolysis experiments. O2 enters mammalian Mb and the α and β subunits of human HbA through a channel created by upward and outward rotation of the distal His at the E7 helical position, is non-covalently captured in the interior of the distal cavity, and then internally forms a bond with the heme Fe(II) atom. O2 dissociation is governed by disruption of hydrogen bonding interactions with His (E7), breakage of the Fe(II)-O2 bond, and then competition between rebinding and escape through the E7-gate. The structural features that govern the rates of both the individual steps and overall reactions have been determined and provide the framework for: (1) defining the physiological functions of specific globins and their evolution; (2) understanding the clinical features of hemoglobinopathies; and (3) designing safer and more efficient acellular hemoglobin-based oxygen carriers (HBOCs) for transfusion therapy, organ preservation, and other commercially relevant O2 transport and storage processes.
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Affiliation(s)
- John S Olson
- Department of Biosciences, Rice University, Houston, TX, 77005, USA.
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4
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Powell SM, Thomas LM, Richter-Addo GB. The nitrosoamphetamine metabolite is accommodated in the active site of human hemoglobin: Spectroscopy and crystal structure. J Inorg Biochem 2020; 213:111262. [PMID: 33049600 DOI: 10.1016/j.jinorgbio.2020.111262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022]
Abstract
Amphetamine-based (Amph) drugs are metabolized in humans to their hydroxylamine (AmphNHOH) and nitroso (AmphNO) derivatives. The latter metabolites are known to bind to the Fe centers of cytochrome P450 and other heme enzymes to inhibit their activities. Although these AmphNHOH/AmphNO metabolites are present in vivo, their interactions with the blood protein hemoglobin (Hb) and the muscle protein (Mb) have been largely discounted due to a perception that the relatively small heme active sites of Hb and Mb will not be able to accommodate the large AmphNO group. We report the 2.15 Å resolution X-ray crystal structure of the AmphNO adduct of adult human hemoglobin as the Hb [α-FeIII(H2O)][β-FeII(AmphNO)] derivative. We show that the binding of AmphNO to the β subunit is enabled by an E helix movement and stabilization of ligand binding by H-bonding with the distal His63 residue. We also observe an AmphNHOH group in the Xe2 pocket in close proximity to the α heme site in this derivative. Additionally, UV-vis spectroscopy was used to characterize this and related wt and mutant Mb adducts. Importantly, our X-ray crystal structure of this Hb-nitrosoamphetamine complex represents the first crystal structure of a wild-type heme protein adduct of any amphetamine metabolite. Our results provide a framework for further studies of AmphNHOH/AmphNO interactions with Hb and Mb as viable processes that potentially contribute to the overall biological inorganic chemistry of amphetamine drugs.
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Affiliation(s)
- Samantha M Powell
- Price Family Foundation Institute of Structural Biology, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States of America
| | - Leonard M Thomas
- Price Family Foundation Institute of Structural Biology, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States of America
| | - George B Richter-Addo
- Price Family Foundation Institute of Structural Biology, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, United States of America.
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5
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Schay G, Kaposi AD, Smeller L, Szigeti K, Fidy J, Herenyi L. Dissimilar flexibility of α and β subunits of human adult hemoglobin influences the protein dynamics and its alteration induced by allosteric effectors. PLoS One 2018; 13:e0194994. [PMID: 29584765 PMCID: PMC5871000 DOI: 10.1371/journal.pone.0194994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/14/2018] [Indexed: 12/19/2022] Open
Abstract
The general question by what mechanism an "effector" molecule and the hemes of hemoglobin interact over widely separated intramolecular distances to change the oxygen affinity has been extensively investigated, and still has remained of central interest. In the present work we were interested in clarifying the general role of the protein matrix and its dynamics in the regulation of human adult hemoglobin (HbA). We used a spectroscopy approach that yields the compressibility (κ) of the protein matrix around the hemes of the subunits in HbA and studied how the binding of heterotropic allosteric effectors modify this parameter. κ is directly related to the variance of volume fluctuation, therefore it characterizes the molecular dynamics of the protein structure. For the experiments the heme groups either in the α or in the β subunits of HbA were replaced by fluorescent Zn-protoporphyrinIX, and series of fluorescence line narrowed spectra were measured at varied pressures. The evaluation of the spectra yielded the compressibility that showed significant dynamic asymmetry between the subunits: κ of the α subunit was 0.17±0.05/GPa, while for the β subunit it was much higher, 0.36±0.07/GPa. The heterotropic effectors, chloride ions, inositol hexaphosphate and bezafibrate did not cause significant changes in κ of the α subunits, while in the β subunits the effectors lead to a significant reduction down to 0.15±0.04/GPa. We relate our results to structural data, to results of recent functional studies and to those of molecular dynamics simulations, and find good agreements. The observed asymmetry in the flexibility suggests a distinct role of the subunits in the regulation of Hb that results in the observed changes of the oxygen binding capability.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - András D. Kaposi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Krisztián Szigeti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Judit Fidy
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herenyi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- * E-mail:
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6
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Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:59-80. [PMID: 27567484 DOI: 10.1016/bs.apcsb.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the impact of differences in amino acid sequence on the topological features of docking sites and cavities and to the influence of conformational flexibility in facilitating the migration of small ligands through these cavities. Often, tunnels are carved in the interior of globins, and ligand exchange is regulated by gating residues. Understanding the subtle intricacies that relate the differences in sequence with the structural and dynamical features of globins with the ultimate aim of rationalizing the thermodynamics and kinetics of ligand binding continues to be a major challenge in the field. Due to the evolution of computational techniques, significant advances into our understanding of these questions have been made. In this review we focus our attention on the analysis of the ligand migration pathways as well as the function of the structural cavities and tunnels in a series of representative globins, emphasizing the synergy between experimental and theoretical approaches to gain a comprehensive knowledge into the molecular mechanisms of this diverse family of proteins.
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7
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Zhao C, Du W. Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations. J Biol Inorg Chem 2016; 21:251-61. [DOI: 10.1007/s00775-016-1334-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
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8
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Zhao C, Zhang B, Du W. Effects of distal mutation on the dynamic properties of carboxycytoglobin: a molecular dynamics simulation study. J Biol Inorg Chem 2013; 18:947-55. [DOI: 10.1007/s00775-013-1041-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/26/2013] [Indexed: 11/29/2022]
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9
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Takayanagi M, Kurisaki I, Nagaoka M. Oxygen Entry through Multiple Pathways in T-State Human Hemoglobin. J Phys Chem B 2013; 117:6082-91. [DOI: 10.1021/jp401459b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Masayoshi Takayanagi
- Core
Research for Evolutional
Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
| | - Ikuo Kurisaki
- Core
Research for Evolutional
Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Core
Research for Evolutional
Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 332-0012, Japan
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10
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Barbieri M, Roncone R, Gabbini R, Nicolis S, Monzani E, Galliano M, Casella L. Nitrative Stress Causes Nitration, Oxidation, and Subunit Cross Linking in Human Hemoglobin. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Bocahut A, Derrien V, Bernad S, Sebban P, Sacquin-Mora S, Guittet E, Lescop E. Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin. J Biol Inorg Chem 2012; 18:111-22. [PMID: 23135388 PMCID: PMC3535368 DOI: 10.1007/s00775-012-0956-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/21/2012] [Indexed: 11/05/2022]
Abstract
Neuroglobin (Ngb) is a globin present in the brain and retina of mammals. This hexacoordinated hemoprotein binds small diatomic molecules, albeit with lower affinity compared with other globins. Another distinctive feature of most mammalian Ngb is their ability to form an internal disulfide bridge that increases ligand affinity. As often seen for prosthetic heme b containing proteins, human Ngb exhibits heme heterogeneity with two alternative heme orientations within the heme pocket. To date, no details are available on the impact of heme orientation on the binding properties of human Ngb and its interplay with the cysteine oxidation state. In this work, we used 1H NMR spectroscopy to probe the cyanide binding properties of different Ngb species in solution, including wild-type Ngb and the single (C120S) and triple (C46G/C55S/C120S) mutants. We demonstrate that in the disulfide-containing wild-type protein cyanide ligation is fivefold faster for one of the two heme orientations (the A isomer) compared with the other isomer, which is attributed to the lower stability of the distal His64–iron bond and reduced steric hindrance at the bottom of the cavity for heme sliding in the A conformer. We also attribute the slower cyanide reactivity in the absence of a disulfide bridge to the tighter histidine–iron bond. More generally, enhanced internal mobility in the CD loop bearing the disulfide bridge hinders access of the ligand to heme iron by stabilizing the histidine–iron bond. The functional impact of heme disorder and cysteine oxidation state on the properties of the Ngb ligand is discussed.
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Affiliation(s)
- Anthony Bocahut
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris-Sud 11, Bât. 350, 91405 Orsay, France
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12
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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.
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Affiliation(s)
- Mallory D Salter
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005-1892, USA
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13
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Quach P, Gutierrez E, Basha MT, Kalinowski DS, Sharpe PC, Lovejoy DB, Bernhardt PV, Jansson PJ, Richardson DR. Methemoglobin formation by triapine, di-2-pyridylketone-4,4-dimethyl-3-thiosemicarbazone (Dp44mT), and other anticancer thiosemicarbazones: identification of novel thiosemicarbazones and therapeutics that prevent this effect. Mol Pharmacol 2012; 82:105-14. [PMID: 22508546 DOI: 10.1124/mol.112.078964] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Thiosemicarbazones are a group of compounds that have received comprehensive investigation as anticancer agents. The antitumor activity of the thiosemicarbazone, 3-amino-2-pyridinecarboxaldehyde thiosemicarbazone (3-AP; triapine), has been extensively assessed in more than 20 phase I and II clinical trials. These studies have demonstrated that 3-AP induces methemoglobin (metHb) formation and hypoxia in patients, limiting its usefulness. Considering this problem, we assessed the mechanism of metHb formation by 3-AP compared with that of more recently developed thiosemicarbazones, including di-2-pyridylketone-4,4-dimethyl-3-thiosemicarbazone (Dp44mT). This was investigated using intact red blood cells (RBCs), RBC lysates, purified oxyhemoglobin, and a mouse model. The chelation of cellular labile iron with the formation of a redox-active thiosemicarbazone-iron complex was found to be crucial for oxyhemoglobin oxidation. This observation was substantiated using a thiosemicarbazone that cannot ligate iron and also by using the chelator, desferrioxamine, that forms a redox-inactive iron complex. Of significance, cellular copper chelation was not important for metHb generation in contrast to its role in preventing tumor cell proliferation. Administration of Dp44mT to mice catalyzed metHb and cardiac metmyoglobin formation. However, ascorbic acid administered together with the drug in vivo significantly decreased metHb levels, providing a potential therapeutic intervention. Moreover, we demonstrated that the structure of the thiosemicarbazone is of importance in terms of metHb generation, because the DpT analog, di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC), does not induce metHb generation in vivo. Hence, DpC represents a next-generation thiosemicarbazone that possesses markedly superior properties. This investigation is important for developing more effective thiosemicarbazone treatment regimens.
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Affiliation(s)
- Patricia Quach
- Discipline of Pathology, University of Sydney, Sydney, New South Wales, Australia
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14
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Lucas MF, Guallar V. An atomistic view on human hemoglobin carbon monoxide migration processes. Biophys J 2012; 102:887-96. [PMID: 22385860 DOI: 10.1016/j.bpj.2012.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 01/02/2012] [Accepted: 01/11/2012] [Indexed: 10/28/2022] Open
Abstract
A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing the ligand migration processes. First, the methodology was tested on myoglobin's CO migration, and the results were compared with the wealth of theoretical and experimental studies. Then, we explored both hemoglobin tense and relaxed states and identified the differences between the α-and β-subunits. Our results indicate that the proximal site, equivalent to the Xe1 cavity in myoglobin, is never visited. Furthermore, strategically positioned residues alter the diffusion processes within hemoglobin's subunits and suggest that multiple pathways exist, especially diversified in the α-globins. A significant dependency of the ligand dynamics on the tertiary structure is also observed.
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Affiliation(s)
- M Fátima Lucas
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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15
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Lepeshkevich SV, Biziuk SA, Lemeza AM, Dzhagarov BM. The kinetics of molecular oxygen migration in the isolated α chains of human hemoglobin as revealed by molecular dynamics simulations and laser kinetic spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1279-88. [DOI: 10.1016/j.bbapap.2011.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/16/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
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16
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Zhang B, Xu J, Li Y, Du W, Fang W. Molecular dynamics simulation of carboxy and deoxy human cytoglobin in solution. J Inorg Biochem 2011; 105:949-56. [DOI: 10.1016/j.jinorgbio.2011.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 11/30/2022]
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17
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Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Frontier Residues Lining Globin Internal Cavities Present Specific Mechanical Properties. J Am Chem Soc 2011; 133:8753-61. [DOI: 10.1021/ja202587a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anthony Bocahut
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Bernad
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
- Université des Sciences et des Technologies de Hanoi, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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18
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Birukou I, Soman J, Olson JS. Blocking the gate to ligand entry in human hemoglobin. J Biol Chem 2010; 286:10515-29. [PMID: 21193395 DOI: 10.1074/jbc.m110.176271] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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Savino C, Miele AE, Draghi F, Johnson KA, Sciara G, Brunori M, Vallone B. Pattern of cavities in globins: The case of human hemoglobin. Biopolymers 2009; 91:1097-107. [DOI: 10.1002/bip.21201] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Relating the Diffusion of Small Ligands in Human Neuroglobin to Its Structural and Mechanical Properties. J Phys Chem B 2009; 113:16257-67. [DOI: 10.1021/jp906854x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony Bocahut
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Sophie Bernad
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
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Golden SD, Olsen KW. Identification of ligand-binding pathways in truncated hemoglobins using locally enhanced sampling molecular dynamics. Methods Enzymol 2008; 437:459-75. [PMID: 18433642 DOI: 10.1016/s0076-6879(07)37023-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This chapter reviews the use of a locally enhanced sampling molecular dynamics (LESMD) for the study of ligand binding in truncated hemoglobins. The method, however, can be applied to any protein-ligand system. Truncated hemoglobins appear to have a tunnel(s) potentially used by the ligand to bind. These structural features give some indication of how the ligand moves through the protein to bind but do not give the complete picture. The LESMD method has been used to investigate the pathways of ligand binding to group I truncated hemoglobins from the eubacteria Mycobacterium tuberculosis, the ciliated protozoa Paramecium caudatum, and the unicellular alga Chlamydomonas eugametos.
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Affiliation(s)
- Stephen D Golden
- Department of Chemistry, Loyola University Chicago, Chicago, Illinois, USA
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Monzani E, Nicolis S, Roncone R, Barbieri M, Granata A, Casella L. Protein self-modification by heme-generated reactive species. IUBMB Life 2007; 60:41-56. [DOI: 10.1002/iub.10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Mouawad L, Tetreau C, Abdel-Azeim S, Perahia D, Lavalette D. CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations. Protein Sci 2007; 16:781-94. [PMID: 17400927 PMCID: PMC2206643 DOI: 10.1110/ps.062374707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450(cam)(camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450(cam)(cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics.
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Affiliation(s)
- Liliane Mouawad
- Inserm U759, Institut Curie-Recherche, Bâtiment 112, Université Paris-Sud, 91405 Orsay cedex, France.
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Bikiel DE, Boechi L, Capece L, Crespo A, De Biase PM, Di Lella S, González Lebrero MC, Martí MA, Nadra AD, Perissinotti LL, Scherlis DA, Estrin DA. Modeling heme proteins using atomistic simulations. Phys Chem Chem Phys 2006; 8:5611-28. [PMID: 17149482 DOI: 10.1039/b611741b] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme proteins are found in all living organisms, and perform a wide variety of tasks ranging from electron transport, to the oxidation of organic compounds, to the sensing and transport of small molecules. In this work we review the application of classical and quantum-mechanical atomistic simulation tools to the investigation of several relevant issues in heme proteins chemistry: (i) conformational analysis, ligand migration, and solvation effects studied using classical molecular dynamics simulations; (ii) electronic structure and spin state energetics of the active sites explored using quantum-mechanics (QM) methods; (iii) the interaction of heme proteins with small ligands studied through hybrid quantum mechanics-molecular mechanics (QM-MM) techniques; (iv) and finally chemical reactivity and catalysis tackled by a combination of quantum and classical tools.
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Affiliation(s)
- Damián E Bikiel
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires, Argentina
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