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Eaton WA. A retrospective on statistical mechanical models for hemoglobin allostery. J Chem Phys 2022; 157:184104. [PMID: 36379793 PMCID: PMC9830738 DOI: 10.1063/5.0127585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Understanding allosteric interactions in proteins has become one of the major research areas in protein science. The original aim of the famous theoretical model of Monod, Wyman, and Changeux (MWC) was to explain the regulation of enzymatic activity in biochemical pathways. However, its first successful quantitative application was to explain cooperative oxygen binding by hemoglobin, often called the "hydrogen molecule of biology." The combination of its original application and the enormous amount of research on hemoglobin has made it the paradigm for studies of allostery, especially for multi-subunit proteins, and for the development of statistical mechanical models to describe how structure determines function. This article is a historical account of the development of statistical mechanical models for hemoglobin to explain both the cooperative binding of oxygen (called homotropic effects by MWC) and how oxygen binding is affected by ligands that bind distant from the heme oxygen binding site (called heterotropic allosteric effects by MWC). This account makes clear the many remaining challenges for describing the relationship of structure to function for hemoglobin in terms of a satisfactory statistical mechanical model.
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Kraka E, Quintano M, La Force HW, Antonio JJ, Freindorf M. The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena. J Phys Chem A 2022; 126:8781-8798. [DOI: 10.1021/acs.jpca.2c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Hunter W. La Force
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Juliana J. Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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Nagatomo S, Nagai M, Kitagawa T. Structural origin of cooperativity in human hemoglobin: a view from different roles of α and β subunits in the α2β2 tetramer. Biophys Rev 2022; 14:483-498. [PMID: 35528033 PMCID: PMC9043147 DOI: 10.1007/s12551-022-00945-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022] Open
Abstract
This mini-review, mainly based on our resonance Raman studies on the structural origin of cooperative O2 binding in human adult hemoglobin (HbA), aims to answering why HbA is a tetramer consisting of two α and two β subunits. Here, we focus on the Fe-His bond, the sole coordination bond connecting heme to a globin. The Fe-His stretching frequencies reflect the O2 affinity and also the magnitude of strain imposed through globin by inter-subunit interactions, which is the origin of cooperativity. Cooperativity was first explained by Monod, Wyman, and Changeux, referred to as the MWC theory, but later explained by the two tertiary states (TTS) theory. Here, we related the higher-order structures of globin observed mainly by vibrational spectroscopy to the MWC theory. It became clear from the recent spectroscopic studies, X-ray crystallographic analysis, and mutagenesis experiments that the Fe-His bonds exhibit different roles between the α and β subunits. The absence of the Fe-His bond in the α subunit in some mutant and artificial Hbs inhibits T to R quaternary structural change upon O2 binding. However, its absence from the β subunit in mutant and artificial Hbs simply enhances the O2 affinity of the α subunit. Accordingly, the inter-subunit interactions between α and β subunits are nonsymmetric but substantial for HbA to perform cooperative O2 binding.
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Affiliation(s)
- Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571 Japan
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-0003 Japan
- School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-0942 Japan
| | - Teizo Kitagawa
- Graduate School of Life Science, Picobiology Institute, University of Hyogo, Kouto, Kamigori, Ako-gun Hyogo, 678-1297 Japan
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5
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Faggiano S, Ronda L, Bruno S, Abbruzzetti S, Viappiani C, Bettati S, Mozzarelli A. From hemoglobin allostery to hemoglobin-based oxygen carriers. Mol Aspects Med 2021; 84:101050. [PMID: 34776270 DOI: 10.1016/j.mam.2021.101050] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 12/18/2022]
Abstract
Hemoglobin (Hb) plays its vital role through structural and functional properties evolutionarily optimized to work within red blood cells, i.e., the tetrameric assembly, well-defined oxygen affinity, positive cooperativity, and heterotropic allosteric regulation by protons, chloride and 2,3-diphosphoglycerate. Outside red blood cells, the Hb tetramer dissociates into dimers, which exhibit high oxygen affinity and neither cooperativity nor allosteric regulation. They are prone to extravasate, thus scavenging endothelial NO and causing hypertension, and cause nephrotoxicity. In addition, they are more prone to autoxidation, generating radicals. The need to overcome the adverse effects associated with cell-free Hb has always been a major hurdle in the development of substitutes of allogeneic blood transfusions for all clinical situations where blood is unavailable or cannot be used due to, for example, religious objections. This class of therapeutics, indicated as hemoglobin-based oxygen carriers (HBOCs), is formed by genetically and/or chemically modified Hbs. Many efforts were devoted to the exploitation of the wealth of biochemical and biophysical information available on Hb structure, function, and dynamics to design safe HBOCs, overcoming the negative effects of free plasma Hb. Unfortunately, so far, no HBOC has been approved by FDA and EMA, except for compassionate use. However, the unmet clinical needs that triggered intensive investigations more than fifty years ago are still awaiting an answer. Recently, HBOCs "repositioning" has led to their successful application in organ perfusion fluids.
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Affiliation(s)
- Serena Faggiano
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy
| | - Luca Ronda
- Institute of Biophysics, National Research Council, Pisa, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Stefano Bettati
- Institute of Biophysics, National Research Council, Pisa, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy
| | - Andrea Mozzarelli
- Department of Food and Drug, University of Parma, Parma, Italy; Institute of Biophysics, National Research Council, Pisa, Italy.
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Maity D, Pal D. Molecular Dynamics of Hemoglobin Reveals Structural Alterations and Explains the Interactions Driving Sickle Cell Fibrillation. J Phys Chem B 2021; 125:9921-9933. [PMID: 34459602 DOI: 10.1021/acs.jpcb.1c01684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In sickle cell anemia, deoxyhemoglobin deforms RBCs by forming fibrils inside that disintegrate on oxygenation. We studied 100 ns long all-atom molecular dynamics (MD) for sickle and normal hemoglobin fibril models to understand this process, complemented by multiple 1 μs MD for a single tetramer of sickle and normal hemoglobin in deoxy and oxy states. We find that the presence of hydrophobic residues without a bulky side chain at β-6 in hemoglobin is the reason for the stability of the fibrils. Moreover, the free energy landscapes from MD of hemoglobin starting in the tensed (T) state capture the putative transition from T to relaxed (R) state, associated with oxygen binding. The three conformational wells in the landscapes are characterized by the quaternary changes where one αβ dimer rotates with respect to the other. The conformational changes from the oxygenation of sickle hemoglobin hinder the intermolecular contacts necessary for fibril formation.
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Affiliation(s)
- Dibyajyoti Maity
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, Karnataka, India
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Eaton WA. Impact of hemoglobin biophysical studies on molecular pathogenesis and drug therapy for sickle cell disease. Mol Aspects Med 2021; 84:100971. [PMID: 34274158 DOI: 10.1016/j.mam.2021.100971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/26/2021] [Indexed: 01/20/2023]
Abstract
Basic research on hemoglobin has been essential for understanding the origin and treatment of many hematological disorders due to abnormal hemoglobins. The most important of the hemoglobinopathies is sickle cell disease - Linus Pauling's "molecular disease" that gave birth to molecular medicine. In this review, I will describe the contributions of basic biophysical research on normal and sickle cell hemoglobin (HbS) to understanding the molecular pathogenesis of the disease and providing the conceptual basis for the various approaches to drug therapy that target HbS polymerization. Most prominent among these are the experimental results on the solubility of HbS as a function of oxygen saturation explained by the allosteric model of Monod, Wyman, and Changeux and the Gill-Wyman thermodynamic linkage relation between solubility and oxygen binding, the solubility of mixtures of HbS with normal or fetal hemoglobin explained by Minton's thermodynamic model, and the highly unusual kinetics of HbS polymerization explained by a novel double nucleation mechanism that also accounts for the aggregation kinetics of the Alzheimer's peptide. The HbS polymerization kinetics are of great importance to understanding the pathophysiology and clinical course, as well as guiding drug development for treating this common and severe disease. The article focuses primarily on experimental and theoretical results from my lab, so it is not a comprehensive review of the subject.
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Affiliation(s)
- William A Eaton
- Laboratory of Chemical Physics, 5/104, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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Lepeshkevich SV, Sazanovich IV, Parkhats MV, Gilevich SN, Dzhagarov BM. Towards understanding non-equivalence of α and β subunits within human hemoglobin in conformational relaxation and molecular oxygen rebinding. Chem Sci 2021; 12:7033-7047. [PMID: 34123331 PMCID: PMC8153241 DOI: 10.1039/d1sc00712b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Picosecond to millisecond laser time-resolved transient absorption spectroscopy was used to study molecular oxygen (O2) rebinding and conformational relaxation following O2 photodissociation in the α and β subunits within human hemoglobin in the quaternary R-like structure. Oxy-cyanomet valency hybrids, α2(Fe2+-O2)β2(Fe3+-CN) and α2(Fe3+-CN)β2(Fe2+-O2), were used as models for oxygenated R-state hemoglobin. An extended kinetic model for geminate O2 rebinding in the ferrous hemoglobin subunits, ligand migration between the primary and secondary docking site(s), and nonexponential tertiary relaxation within the R quaternary structure, was introduced and discussed. Significant functional non-equivalence of the α and β subunits in both the geminate O2 rebinding and concomitant structural relaxation was revealed. For the β subunits, the rate constant for the geminate O2 rebinding to the unrelaxed tertiary structure and the tertiary transition rate were found to be greater than the corresponding values for the α subunits. The conformational relaxation following the O2 photodissociation in the α and β subunits was found to decrease the rate constant for the geminate O2 rebinding, this effect being more than one order of magnitude greater for the β subunits than for the α subunits. Evidence was provided for the modulation of the O2 rebinding to the individual α and β subunits within human hemoglobin in the R-state structure by the intrinsic heme reactivity through a change in proximal constraints upon the relaxation of the tertiary structure on a picosecond to microsecond time scale. Our results demonstrate that, for native R-state oxyhemoglobin, O2 rebinding properties and spectral changes following the O2 photodissociation can be adequately described as the sum of those for the α and β subunits within the valency hybrids. The isolated β chains (hemoglobin H) show similar behavior to the β subunits within the valency hybrids and can be used as a model for the β subunits within the R-state oxyhemoglobin. At the same time, the isolated α chains behave differently to the α subunits within the valency hybrids.
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Affiliation(s)
- Sergei V Lepeshkevich
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Harwell Campus OX11 0QX UK
| | - Marina V Parkhats
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Syargey N Gilevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus 5 Academician V. F. Kuprevich Street Minsk 220141 Belarus
| | - Boris M Dzhagarov
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
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Morita Y, Saito A, Yamaguchi J, Komatsu T. Haemoglobin(βK120C)-albumin trimer as an artificial O 2 carrier with sufficient haemoglobin allostery. RSC Chem Biol 2020; 1:128-136. [PMID: 34458753 PMCID: PMC8341959 DOI: 10.1039/d0cb00056f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/25/2020] [Indexed: 11/21/2022] Open
Abstract
The allosteric O2 release of haemoglobin (Hb) allows for efficient O2 delivery from the lungs to the tissues. However, allostery is weakened in Hb-based O2 carriers because the chemical modifications of the Lys- and Cys-β93 residues prevent the quaternary transition of Hb. In this paper, we describe the synthesis and O2 binding properties of a recombinant Hb [rHb(βK120C)]–albumin heterotrimer that maintains sufficient Hb allostery. The rHb(βK120C) core, with two additional cysteine residues at the symmetrical positions on its protein surface, was expressed using yeast cells. The mutations did not influence either the O2 binding characteristics or the quaternary transition of Hb. Maleimide-activated human serum albumins (HSAs) were coupled with rHb(βK120C) at the two Cys-β120 positions, yielding the rHb(βK120C)–HSA2 trimer, in which the Cys-β93 residues were unreacted. Molecular dynamics simulation demonstrated that the HSA moiety does not interact with the amino acid residues around the haem pockets and the α1β2 surfaces of the rHb(βK120C) core, the alteration of which retards Hb allostery. Circular dichroism spectroscopy demonstrated that the quaternary transition between the relaxed (R) state and the tense (T) state of the Hb core occurred upon both the association and dissociation of O2. In phosphate-buffered saline solution (pH 7.4) at 37 °C, the rHb(βK120C)–HSA2 trimer exhibited a sigmoidal O2 equilibrium curve with the O2 affinity and cooperativity identical to those of native Hb (p50 = 12 Torr, n = 2.4). Moreover, we observed an equal Bohr effect and 2,3-diphosphoglycerate response in the rHb(βK120C)–HSA2 trimer compared with naked Hb. Recombinant haemoglobin [rHb(βK120C)] was coupled with two human serum albumins (HSAs), yielding a rHb(βK120C)–HSA2 heterotrimer, which shows a sigmoidal O2 equilibrium curve and sufficient Hb allostery identical to those of native Hb.![]()
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Affiliation(s)
- Yoshitsugu Morita
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Asuka Saito
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Jun Yamaguchi
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Teruyuki Komatsu
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
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10
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Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
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Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
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11
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Ascenzi P, De Simone G, Tundo GR, Coletta M. Kinetics of cyanide and carbon monoxide dissociation from ferrous human haptoglobin:hemoglobin(II) complexes. J Biol Inorg Chem 2020; 25:351-360. [DOI: 10.1007/s00775-020-01766-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/12/2020] [Indexed: 12/17/2022]
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12
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Shibayama N. Allosteric transitions in hemoglobin revisited. Biochim Biophys Acta Gen Subj 2020; 1864:129335. [DOI: 10.1016/j.bbagen.2019.03.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 12/19/2022]
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13
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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14
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More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function. Catalysts 2019. [DOI: 10.3390/catal9121024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
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El Hage K, Hédin F, Gupta PK, Meuwly M, Karplus M. Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size. eLife 2018; 7:35560. [PMID: 29998846 PMCID: PMC6042964 DOI: 10.7554/elife.35560] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/18/2018] [Indexed: 12/25/2022] Open
Abstract
Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T[Formula: see text]) and liganded (R[Formula: see text]) tetramers are stable in solution, the published MD simulations of T[Formula: see text] undergo a rapid quaternary transition to an R-like structure. We show that T[Formula: see text] is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T[Formula: see text] tetramer, to be manifested. Even in the largest box, T[Formula: see text] is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Florent Hédin
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Prashant K Gupta
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States.,Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
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16
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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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Nagai M, Mizusawa N, Kitagawa T, Nagatomo S. A role of heme side-chains of human hemoglobin in its function revealed by circular dichroism and resonance Raman spectroscopy. Biophys Rev 2017; 10:271-284. [PMID: 29260461 DOI: 10.1007/s12551-017-0364-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/19/2017] [Indexed: 11/26/2022] Open
Abstract
Structural changes of heme side-chains of human adult hemoglobin (Hb A) upon ligand (O2 or CO) dissociation have been studied by circular dichroism (CD) and resonance Raman (RR) spectroscopies. We point out the occurrence of appreciable deformation of heme side-chains like vinyl and propionate groups prior to the out-of-plane displacement of heme iron. Referring to the recent fine resolved crystal structure of Hb A, the deformations of heme side-chains take place only in the β subunits. However, these changes are not observed in the isolated β chain (β4 homotetramer) and, therefore, are associated with the α-β inter-subunit interactions. For the communications between α and β subunits in Hb A regarding signals of ligand dissociation, possible routes are proposed on the basis of the time-resolved absorption, CD, MCD (magnetic CD), and RR spectroscopies. Our finding of the movements of heme side-chains would serve as one of the clues to solve the cooperative O2 binding mechanism of Hb A.
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Affiliation(s)
- Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-0003, Japan.
- School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-0942, Japan.
| | - Naoki Mizusawa
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, 184-0003, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, 678-1297, Japan
| | - Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8571, Japan
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18
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Mot AC, Bischin C, Damian G, Attia AAA, Gal E, Dina N, Leopold N, Silaghi-Dumitrescu R. Fe(III) - Sulfide interaction in globins: Characterization and quest for a putative Fe(IV)-sulfide species. J Inorg Biochem 2017; 179:32-39. [PMID: 29156293 DOI: 10.1016/j.jinorgbio.2017.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 10/16/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023]
Abstract
The present study reports findings regarding the contrast between H2S interaction with bovine hemoglobin (Hb) and horse heart myoglobin (Mb), in terms of binding and dissociation kinetics, affinities, and mechanism. At pH9.5, oxidation of ferric-sulfide adducts in presence of no free sulfide, using hexachloroiridate as oxidant is examined using stopped-flow UV-vis, EPR, vibrational spectroscopy and mass spectrometry. Oxidation of the ferric-sulfide adduct in such conditions occurs with a putative unstable Fe(IV)-sulfide adduct as intermediate that finally leads to a paramagnetic ferric species with distinct EPR features. As detected by MS spectrometry, this final species appears to be a truncated form of globin at a distinct Tyr. In case of Hb, only β-chain is truncated at Tyr144.
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Affiliation(s)
- Augustin C Mot
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania.
| | - Cristina Bischin
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Grigore Damian
- Faculty of Physics, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Amr A A Attia
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Emese Gal
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Nicoleta Dina
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Radu Silaghi-Dumitrescu
- Faculty of Chemistry and Chemical Engineering, Babes-Bolyai University, Cluj-Napoca, Romania.
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19
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Nagatomo S, Saito K, Yamamoto K, Ogura T, Kitagawa T, Nagai M. Heterogeneity between Two α Subunits of α2β2 Human Hemoglobin and O2 Binding Properties: Raman, 1H Nuclear Magnetic Resonance, and Terahertz Spectra. Biochemistry 2017; 56:6125-6136. [DOI: 10.1021/acs.biochem.7b00733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shigenori Nagatomo
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Kazuya Saito
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Kohji Yamamoto
- Research
Center for Development of Far-Infrared Region, University of Fukui, Fukui, Fukui 910-8507, Japan
| | - Takashi Ogura
- Picobiology
Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading
Program Center, Sayo, Sayo-gun, Hyogo 679-5148, Japan
| | - Teizo Kitagawa
- Picobiology
Institute, Graduate School of Life Science, University of Hyogo, Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
| | - Masako Nagai
- Research
Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
- School
of
Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-0942, Japan
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20
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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21
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Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations. Sci Rep 2017; 7:10926. [PMID: 28883619 PMCID: PMC5589765 DOI: 10.1038/s41598-017-11259-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 11/30/2022] Open
Abstract
Human hemoglobin (Hb) is a benchmark protein of structural biology that shaped our view of allosterism over 60 years ago, with the introduction of the MWC model based on Perutz structures of the oxy(R) and deoxy(T) states and the more recent Tertiary Two-State model that proposed the existence of individual subunit states -“r” and “t”-, whose structure is yet unknown. Cooperative oxygen binding is essential for Hb function, and despite decades of research there are still open questions related to how tertiary and quaternary changes regulate oxygen affinity. In the present work, we have determined the free energy profiles of oxygen migration and for HisE7 gate opening, with QM/MM calculations of the oxygen binding energy in order to address the influence of tertiary differences in the control of oxygen affinity. Our results show that in the α subunit the low to high affinity transition is achieved by a proximal effect that mostly affects oxygen dissociation and is the driving force of the allosteric transition, while in the β subunit the affinity change results from a complex interplay of proximal and distal effects, including an increase in the HE7 gate opening, that as shown by free energy profiles promotes oxygen uptake.
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22
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Krafft C, Schmitt M, Schie IW, Cialla-May D, Matthäus C, Bocklitz T, Popp J. Markerfreie molekulare Bildgebung biologischer Zellen und Gewebe durch lineare und nichtlineare Raman-spektroskopische Ansätze. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201607604] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christoph Krafft
- Leibniz-Institut für Photonische Technologien; Albert-Einstein-Straße 9 07745 Jena Deutschland
| | - Michael Schmitt
- Institut für Physikalische Chemie und Abbe Center of Photonics; Friedrich-Schiller-Universität Jena; Helmholtzweg 4 07743 Jena Deutschland
| | - Iwan W. Schie
- Leibniz-Institut für Photonische Technologien; Albert-Einstein-Straße 9 07745 Jena Deutschland
| | - Dana Cialla-May
- Leibniz-Institut für Photonische Technologien; Albert-Einstein-Straße 9 07745 Jena Deutschland
- Institut für Physikalische Chemie und Abbe Center of Photonics; Friedrich-Schiller-Universität Jena; Helmholtzweg 4 07743 Jena Deutschland
| | - Christian Matthäus
- Leibniz-Institut für Photonische Technologien; Albert-Einstein-Straße 9 07745 Jena Deutschland
- Institut für Physikalische Chemie und Abbe Center of Photonics; Friedrich-Schiller-Universität Jena; Helmholtzweg 4 07743 Jena Deutschland
| | - Thomas Bocklitz
- Leibniz-Institut für Photonische Technologien; Albert-Einstein-Straße 9 07745 Jena Deutschland
- Institut für Physikalische Chemie und Abbe Center of Photonics; Friedrich-Schiller-Universität Jena; Helmholtzweg 4 07743 Jena Deutschland
| | - Jürgen Popp
- Leibniz-Institut für Photonische Technologien; Albert-Einstein-Straße 9 07745 Jena Deutschland
- Institut für Physikalische Chemie und Abbe Center of Photonics; Friedrich-Schiller-Universität Jena; Helmholtzweg 4 07743 Jena Deutschland
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23
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Krafft C, Schmitt M, Schie IW, Cialla-May D, Matthäus C, Bocklitz T, Popp J. Label-Free Molecular Imaging of Biological Cells and Tissues by Linear and Nonlinear Raman Spectroscopic Approaches. Angew Chem Int Ed Engl 2017; 56:4392-4430. [PMID: 27862751 DOI: 10.1002/anie.201607604] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/04/2016] [Indexed: 12/20/2022]
Abstract
Raman spectroscopy is an emerging technique in bioanalysis and imaging of biomaterials owing to its unique capability of generating spectroscopic fingerprints. Imaging cells and tissues by Raman microspectroscopy represents a nondestructive and label-free approach. All components of cells or tissues contribute to the Raman signals, giving rise to complex spectral signatures. Resonance Raman scattering and surface-enhanced Raman scattering can be used to enhance the signals and reduce the spectral complexity. Raman-active labels can be introduced to increase specificity and multimodality. In addition, nonlinear coherent Raman scattering methods offer higher sensitivities, which enable the rapid imaging of larger sampling areas. Finally, fiber-based imaging techniques pave the way towards in vivo applications of Raman spectroscopy. This Review summarizes the basic principles behind medical Raman imaging and its progress since 2012.
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Affiliation(s)
- Christoph Krafft
- Leibniz-Institut für Photonische Technologien, Albert-Einstein-Strasse 9, 07745, Jena, Germany
| | - Michael Schmitt
- Institut für Physikalische Chemie und Abbe Center für Photonics, Friedrich Schiller Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Iwan W Schie
- Leibniz-Institut für Photonische Technologien, Albert-Einstein-Strasse 9, 07745, Jena, Germany
| | - Dana Cialla-May
- Leibniz-Institut für Photonische Technologien, Albert-Einstein-Strasse 9, 07745, Jena, Germany.,Institut für Physikalische Chemie und Abbe Center für Photonics, Friedrich Schiller Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Christian Matthäus
- Leibniz-Institut für Photonische Technologien, Albert-Einstein-Strasse 9, 07745, Jena, Germany.,Institut für Physikalische Chemie und Abbe Center für Photonics, Friedrich Schiller Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Thomas Bocklitz
- Leibniz-Institut für Photonische Technologien, Albert-Einstein-Strasse 9, 07745, Jena, Germany.,Institut für Physikalische Chemie und Abbe Center für Photonics, Friedrich Schiller Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Jürgen Popp
- Leibniz-Institut für Photonische Technologien, Albert-Einstein-Strasse 9, 07745, Jena, Germany.,Institut für Physikalische Chemie und Abbe Center für Photonics, Friedrich Schiller Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
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24
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Nagatomo S, Okumura M, Saito K, Ogura T, Kitagawa T, Nagai M. Interrelationship among Fe-His Bond Strengths, Oxygen Affinities, and Intersubunit Hydrogen Bonding Changes upon Ligand Binding in the β Subunit of Human Hemoglobin: The Alkaline Bohr Effect. Biochemistry 2017; 56:1261-1273. [PMID: 28199095 DOI: 10.1021/acs.biochem.6b01118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Regulation of the oxygen affinity of human adult hemoglobin (Hb A) at high pH, known as the alkaline Bohr effect, is essential for its physiological function. In this study, structural mechanisms of the alkaline Bohr effect and pH-dependent O2 affinity changes were investigated via 1H nuclear magnetic resonance and visible and UV resonance Raman spectra of mutant Hbs, Hb M Iwate (αH87Y) and Hb M Boston (αH58Y). It was found that even though the binding of O2 to the α subunits is forbidden in the mutant Hbs, the O2 affinity was higher at alkaline pH than at neutral pH, and concomitantly, the Fe-His stretching frequency of the β subunits was shifted to higher values. Thus, it was confirmed for the β subunits that the stronger the Fe-His bond, the higher the O2 affinity. It was found in this study that the quaternary structure of α(Fe3+)β(Fe2+-CO) of the mutant Hb is closer to T than to the ordinary R at neutral pH. The retained Aspβ94-Hisβ146 hydrogen bond makes the extent of proton release smaller upon ligand binding from Hisβ146, known as one of residues contributing to the alkaline Bohr effect. For these T structures, the Aspα94-Trpβ37 hydrogen bond in the hinge region and the Tyrα42-Aspβ99 hydrogen bond in the switch region of the α1-β2 interface are maintained but elongated at alkaline pH. Thus, a decrease in tension in the Fe-His bond of the β subunits at alkaline pH causes a substantial increase in the change in global structure upon binding of CO to the β subunit.
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Affiliation(s)
- Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8571, Japan
| | - Miki Okumura
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8571, Japan
| | - Kazuya Saito
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8571, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo , 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo , 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University , Koganei, Tokyo 184-0003, Japan.,School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University , Kanazawa, Ishikawa 920-0942, Japan
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25
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Lal J, Maccarini M, Fouquet P, Ho NT, Ho C, Makowski L. Modulation of hemoglobin dynamics by an allosteric effector. Protein Sci 2017; 26:505-514. [PMID: 27977887 PMCID: PMC5326564 DOI: 10.1002/pro.3099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 12/03/2016] [Accepted: 12/07/2016] [Indexed: 11/24/2022]
Abstract
Hemoglobin (Hb) is an extensively studied paradigm of proteins that alter their function in response to allosteric effectors. Models of its action have been used as prototypes for structure‐function relationships in many proteins, and models for the molecular basis of its function have been deeply studied and extensively argued. Recent reports suggest that dynamics may play an important role in its function. Relatively little is known about the slow, correlated motions of hemoglobin subunits in various structural states because experimental and computational strategies for their characterization are challenging. Allosteric effectors such as inositol hexaphosphate (IHP) bind to both deoxy‐Hb and HbCO, albeit at different sites, leading to a lowered oxygen affinity. The manner in which these effectors impact oxygen binding is unclear and may involve changes in structure, dynamics or both. Here we use neutron spin echo measurements accompanied by wide‐angle X‐ray scattering to show that binding of IHP to HbCO results in an increase in the rate of coordinated motions of Hb subunits relative to one another with little if any change in large scale structure. This increase of large‐scale dynamics seems to be coupled with a decrease in the average magnitude of higher frequency modes of individual residues. These observations indicate that enhanced dynamic motions contribute to the functional changes induced by IHP and suggest that they may be responsible for the lowered oxygen affinity triggered by these effectors.
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Affiliation(s)
- Jyotsana Lal
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Marco Maccarini
- Institut Laue-Langevin, CS 20156, 38042 Grenoble Cedex 9, France
| | - Peter Fouquet
- Institut Laue-Langevin, CS 20156, 38042 Grenoble Cedex 9, France
| | - Nancy T Ho
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213
| | - Chien Ho
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213
| | - Lee Makowski
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439.,Department of Bioengineering, Northeastern University, Boston, Massachusetts, 02115
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26
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Esquerra RM, Bibi BM, Tipgunlakant P, Birukou I, Soman J, Olson JS, Kliger DS, Goldbeck RA. Role of Heme Pocket Water in Allosteric Regulation of Ligand Reactivity in Human Hemoglobin. Biochemistry 2016; 55:4005-17. [PMID: 27355904 PMCID: PMC4978812 DOI: 10.1021/acs.biochem.6b00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water molecules can enter the heme pockets of unliganded myoglobins and hemoglobins, hydrogen bond with the distal histidine, and introduce steric barriers to ligand binding. The spectrokinetics of photodissociated CO complexes of human hemoglobin and its isolated α and β chains were analyzed for the effect of heme hydration on ligand rebinding. A strong coupling was observed between heme hydration and quaternary state. This coupling may contribute significantly to the 20-60-fold difference between the R- and T-state bimolecular CO binding rate constants and thus to the modulation of ligand reactivity that is the hallmark of hemoglobin allostery. Heme hydration proceeded over the course of several kinetic phases in the tetramer, including the R to T quaternary transition. An initial 150 ns hydration phase increased the R-state distal pocket water occupancy, nw(R), to a level similar to that of the isolated α (∼60%) and β (∼10%) chains, resulting in a modest barrier to ligand binding. A subsequent phase, concurrent with the first step of the R → T transition, further increased the level of heme hydration, increasing the barrier. The final phase, concurrent with the final step of the allosteric transition, brought the water occupancy of the T-state tetramer, nw(T), even higher and close to full occupancy in both the α and β subunits (∼90%). This hydration level could present an even larger barrier to ligand binding and contribute significantly to the lower iron reactivity of the T state toward CO.
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Affiliation(s)
- Raymond M. Esquerra
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Bushra M. Bibi
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Pooncharas Tipgunlakant
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Ivan Birukou
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - Jayashree Soman
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - John S. Olson
- Department of Biochemistry and Cell Biology and W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
| | - David S. Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Robert A. Goldbeck
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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27
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Yang C, Choi J, Ihee H. The time scale of the quaternary structural changes in hemoglobin revealed using the transient grating technique. Phys Chem Chem Phys 2015; 17:22571-5. [PMID: 26272458 DOI: 10.1039/c5cp03059e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quaternary structural transition between the R and T states of human hemoglobin was investigated using the transient grating technique. The results presented herein reveal that the quaternary structural change accompanied by the R-T transition occurs within a few microseconds.
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Affiliation(s)
- Cheolhee Yang
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea.
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28
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Nagatomo S, Nagai Y, Aki Y, Sakurai H, Imai K, Mizusawa N, Ogura T, Kitagawa T, Nagai M. An Origin of Cooperative Oxygen Binding of Human Adult Hemoglobin: Different Roles of the α and β Subunits in the α2β2 Tetramer. PLoS One 2015; 10:e0135080. [PMID: 26244770 PMCID: PMC4526547 DOI: 10.1371/journal.pone.0135080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 07/17/2015] [Indexed: 02/02/2023] Open
Abstract
Human hemoglobin (Hb), which is an α2β2 tetramer and binds four O2 molecules, changes its O2-affinity from low to high as an increase of bound O2, that is characterized by 'cooperativity'. This property is indispensable for its function of O2 transfer from a lung to tissues and is accounted for in terms of T/R quaternary structure change, assuming the presence of a strain on the Fe-histidine (His) bond in the T state caused by the formation of hydrogen bonds at the subunit interfaces. However, the difference between the α and β subunits has been neglected. To investigate the different roles of the Fe-His(F8) bonds in the α and β subunits, we investigated cavity mutant Hbs in which the Fe-His(F8) in either α or β subunits was replaced by Fe-imidazole and F8-glycine. Thus, in cavity mutant Hbs, the movement of Fe upon O2-binding is detached from the movement of the F-helix, which is supposed to play a role of communication. Recombinant Hb (rHb)(αH87G), in which only the Fe-His in the α subunits is replaced by Fe-imidazole, showed a biphasic O2-binding with no cooperativity, indicating the coexistence of two independent hemes with different O2-affinities. In contrast, rHb(βH92G), in which only the Fe-His in the β subunits is replaced by Fe-imidazole, gave a simple high-affinity O2-binding curve with no cooperativity. Resonance Raman, 1H NMR, and near-UV circular dichroism measurements revealed that the quaternary structure change did not occur upon O2-binding to rHb(αH87G), but it did partially occur with O2-binding to rHb(βH92G). The quaternary structure of rHb(αH87G) appears to be frozen in T while its tertiary structure is changeable. Thus, the absence of the Fe-His bond in the α subunit inhibits the T to R quaternary structure change upon O2-binding, but its absence in the β subunit simply enhances the O2-affinity of α subunit.
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Affiliation(s)
- Shigenori Nagatomo
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (SN); (TK); (MN)
| | - Yukifumi Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Yayoi Aki
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Hiroshi Sakurai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Kiyohiro Imai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Naoki Mizusawa
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Takashi Ogura
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
| | - Teizo Kitagawa
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
- * E-mail: (SN); (TK); (MN)
| | - Masako Nagai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan,3 School of Health Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan,4 Department of Frontier Biosciences, Hosei University, Koganei, Tokyo, Japan,5 Picobiology Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Sayo, Sayo-gun, Hyogo, Japan
- * E-mail: (SN); (TK); (MN)
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Experiments on Hemoglobin in Single Crystals and Silica Gels Distinguish among Allosteric Models. Biophys J 2015; 109:1264-72. [PMID: 26038112 DOI: 10.1016/j.bpj.2015.04.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/24/2015] [Indexed: 01/14/2023] Open
Abstract
Trapping quaternary structures of hemoglobin in single crystals or by encapsulation in silica gels has provided a demanding set of data to test statistical mechanical models of allostery. In this work, we compare the results of those experiments with predictions of the four major allosteric models for hemoglobin: the quaternary two-state model of Monod, Wyman, and Changeux; the tertiary two-state model of Henry et al., which is the simplest extension of the Monod-Wyman-Changeux model to include pre-equilibria of tertiary as well as quaternary conformations; the structure-based model of Szabo and Karplus; and the modification of the latter model by Lee and Karplus. We show that only the tertiary two-state model can provide a near quantitative explanation of the single-crystal and gel experimental results.
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30
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Ronda L, Bruno S, Bettati S, Storici P, Mozzarelli A. From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci 2015; 2:12. [PMID: 25988179 PMCID: PMC4428442 DOI: 10.3389/fmolb.2015.00012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/31/2015] [Indexed: 11/23/2022] Open
Abstract
The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms.
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Affiliation(s)
- Luca Ronda
- Department of Neurosciences, University of Parma Parma, Italy
| | - Stefano Bruno
- Department of Pharmacy, University of Parma Parma, Italy
| | - Stefano Bettati
- Department of Neurosciences, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy
| | | | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma Parma, Italy ; National Institute of Biostructures and Biosystems Rome, Italy ; Institute of Biophysics, Consiglio Nazionale delle Ricerche Pisa, Italy
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31
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Affiliation(s)
- Yue Yuan
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
| | - Ming F. Tam
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
| | - Virgil Simplaceanu
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
| | - Chien Ho
- Department of Biological Sciences Carnegie Mellon University Pittsburgh, PA 15213
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32
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Experimental basis for a new allosteric model for multisubunit proteins. Proc Natl Acad Sci U S A 2014; 111:12758-63. [PMID: 25139985 DOI: 10.1073/pnas.1413566111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Monod, Wyman, and Changeux (MWC) explained allostery in multisubunit proteins with a widely applied theoretical model in which binding of small molecules, so-called allosteric effectors, affects reactivity by altering the equilibrium between more reactive (R) and less reactive (T) quaternary structures. In their model, each quaternary structure has a single reactivity. Here, we use silica gels to trap protein conformations and a new kind of laser photolysis experiment to show that hemoglobin, the paradigm of allostery, exhibits two ligand binding phases with the same fast and slow rates in both R and T quaternary structures. Allosteric effectors change the fraction of each phase but not the rates. These surprising results are readily explained by the simplest possible extension of the MWC model to include a preequilibrium between two tertiary conformations that have the same functional properties within each quaternary structure. They also have important implications for the long-standing question of a structural explanation for the difference in hemoglobin oxygen affinity of the two quaternary structures.
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