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Ciaccio C, Coletta A, Coletta M. Role of hemoglobin structural-functional relationships in oxygen transport. Mol Aspects Med 2021; 84:101022. [PMID: 34509280 DOI: 10.1016/j.mam.2021.101022] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
The molecular mechanism of O2 binding to hemoglobin (Hb) has been critically reviewed on the basis of the information built up in the last decades. It allows to describe in detail from the kinetic and thermodynamic viewpoint the process of O2 uptake in the lungs and release to the tissues, casting some light on the physiological and pathological aspects of this process. The relevance of structural-functional relationships for O2 binding is particularly outlined in the case of poorly vascularized tissues, such as retina, briefly discussing of strategies employed for optimization of oxygen supply to this type of tissues.
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Affiliation(s)
- Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy
| | | | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy; IRCCS Fondazione Bietti, Rome, Italy.
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2
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Choi M, Kim JG, Muniyappan S, Kim H, Kim TW, Lee Y, Lee SJ, Kim SO, Ihee H. Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics. Chem Sci 2021; 12:8207-8217. [PMID: 34194711 PMCID: PMC8208487 DOI: 10.1039/d1sc01207j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
A salt bridge, one of the representative structural factors established by non-covalent interactions, plays a crucial role in stabilizing the structure and regulating the protein function, but its role in dynamic processes has been elusive. Here, to scrutinize the structural and functional roles of the salt bridge in the process of performing the protein function, we investigated the effects of salt bridges on the allosteric structural transition of homodimeric hemoglobin (HbI) by applying time-resolved X-ray solution scattering (TRXSS) to the K30D mutant, in which the interfacial salt bridges of the wild type (WT) are abolished. The TRXSS data of K30D are consistent with the kinetic model that requires one monomer intermediate in addition to three structurally distinct dimer intermediates (I1, I2, and I3) observed in WT and other mutants. The kinetic and structural analyses show that K30D has an accelerated biphasic transition from I2 to I3 by more than nine times compared to WT and lacks significant structural changes in the transition from R-like I2 to T-like I3 observed in WT, unveiling that the loss of the salt bridges interrupts the R-T allosteric transition of HbI. Besides, the correlation between the bimolecular CO recombination rates in K30D, WT, and other mutants reveals that the bimolecular CO recombination is abnormally decelerated in K30D, indicating that the salt bridges also affect the cooperative ligand binding in HbI. These comparisons of the structural dynamics and kinetics of K30D and WT show that the interfacial salt bridges not only assist the physical connection of two subunits but also play a critical role in the global structural signal transduction of one subunit to the other subunit via a series of well-organized structural transitions.
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Affiliation(s)
- Minseo Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Jong Goo Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Srinivasan Muniyappan
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Hanui Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Tae Wu Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Seong Ok Kim
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
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3
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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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Kim H, Kim JG, Muniyappan S, Kim TW, Lee SJ, Ihee H. Effect of Occluded Ligand Migration on the Kinetics and Structural Dynamics of Homodimeric Hemoglobin. J Phys Chem B 2020; 124:1550-1556. [PMID: 32027135 DOI: 10.1021/acs.jpcb.9b11749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules such as molecular oxygen, nitric oxide, and carbon monoxide play important roles in life, and many proteins require the transport of small molecules to and from the bulk solvent for their function. Ligand migration within a protein molecule is expected to be closely related to the overall structural changes of the protein, but the detailed and quantitative connection remains elusive. For example, despite numerous studies, how occluded ligand migration affects the kinetics and structural dynamics of the R-T transition remains unclear. To shed light on this issue, we chose homodimeric hemoglobin (HbI) with the I114F mutation (I114F), which is known to interfere with ligand migration between the primary and secondary docking sites, and studied its kinetics and structural dynamics using time-resolved X-ray solution scattering. The kinetic analysis shows that I114F has three structurally distinct intermediates (I1, I2, and I3) as in the wild type (WT), but its geminate CO recombination occurs directly from I1 without the path via I2 observed in WT. Moreover, the structural transitions, which involve ligand migration (the transitions from I1 to I2 and from I3 to the initial state), are decelerated compared to WT. The structural analysis revealed that I114F involves generally smaller structural changes in all three intermediates compared to WT.
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Affiliation(s)
- Hanui Kim
- Department of Chemistry and KI for the BioCentury , KAIST , Daejeon 305-701 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 305-701 , Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury , KAIST , Daejeon 305-701 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 305-701 , Republic of Korea
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury , KAIST , Daejeon 305-701 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 305-701 , Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury , KAIST , Daejeon 305-701 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 305-701 , Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry and KI for the BioCentury , KAIST , Daejeon 305-701 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 305-701 , Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury , KAIST , Daejeon 305-701 , Republic of Korea.,Center for Nanomaterials and Chemical Reactions , Institute for Basic Science (IBS) , Daejeon 305-701 , Republic of Korea
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Abstract
Human hemoglobin is the textbook example of the stereochemistry of an allosteric protein and of the exquisite control that a protein can exert over ligand binding. However, the fundamental basis by which the protein facilitates the ligand movement remains unknown. In this study, we used cryogenic X-ray crystallography and a high-repetition pulsed laser irradiation technique to elucidate the atomic details of ligand migration processes in hemoglobin after photolysis of the bound CO. Our data clarify the distinct CO migration pathways in the individual subunits of hemoglobin and unravel the functional roles of the internal cavities and neighboring amino acid residues in ligand exit and entry. Our results also demonstrate the high gas permeability and porosity of hemoglobin, facilitating O2 delivery. Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and β subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), β15Trp(A12), and β71Phe(E15). We also observe electron density evidence for the distal histidine [α58/β63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in β subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or β subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.
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Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prangé T, Brunori M, Colloc’h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCRJ 2019; 6:832-842. [PMID: 31576217 PMCID: PMC6760443 DOI: 10.1107/s2052252519008157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Life and Environmental Sciences, New York–Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli–IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Avella
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy
| | - Cécile Exertier
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thierry Prangé
- CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France
| | - Maurizio Brunori
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nathalie Colloc’h
- ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France
| | - Beatrice Vallone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Yang C, Choi M, Kim JG, Kim H, Muniyappan S, Nozawa S, Adachi SI, Henning R, Kosheleva I, Ihee H. Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering. Int J Mol Sci 2018; 19:ijms19113633. [PMID: 30453670 PMCID: PMC6274816 DOI: 10.3390/ijms19113633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 01/30/2023] Open
Abstract
The quaternary transition between the relaxed (R) and tense (T) states of heme-binding proteins is a textbook example for the allosteric structural transition. Homodimeric hemoglobin (HbI) from Scapharca inaequivalvis is a useful model system for investigating the allosteric behavior because of the relatively simple quaternary structure. To understand the cooperative transition of HbI, wild-type and mutants of HbI have been studied by using time-resolved X-ray solution scattering (TRXSS), which is sensitive to the conformational changes. Herein, we review the structural dynamics of HbI investigated by TRXSS and compare the results of TRXSS with those of other techniques.
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Affiliation(s)
- Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Minseo Choi
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Hanui Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA.
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA.
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Center for Nanomaterials and Chemical Reactions, Institute of Basic Science (IBS), Daejeon 34141, Korea.
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Okamoto T, Ohmichi E, Saito Y, Sakurai T, Ohta H. Pressure Effect on Zero-Field Splitting Parameter of Hemin: Model Case of Hemoproteins under Pressure. J Phys Chem B 2018; 122:6880-6887. [PMID: 29902002 DOI: 10.1021/acs.jpcb.8b03128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We experimentally studied the pressure dependence of the zero-field splitting (ZFS) parameter of hemin (iron(III) protoporphyrin IX chloride), which is a model complex of hemoproteins, via high-frequency and high-field electron paramagnetic resonance (HFEPR) under pressure. Owing to the large ZFS, the pressure effect on the electronic structure of iron-porphyrin complexes has not yet been explored using EPR. Therefore, we systematically studied this effect using our newly developed sub-terahertz EPR spectroscopy system in the frequency range of 80-515 GHz, under magnetic fields up to 10 T and pressure up to 2 GPa. We observed a systematic shift of the resonance fields of hemin upon pressure application, from which the axial component of the ZFS parameter was found to increase from D = 6.9 to 7.9 cm-1 at 2 GPa. In contrast to the previous methods used to study proteins under pressure, which mainly focused on conformational changes, our HFEPR technique can obtain more microscopic insights into the electronic structures of metal ions under pressure. In this sense, our technique provides novel opportunities to study the pressure effects on biofunctional active centers of versatile metalloproteins.
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9
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Size and Shape Controlled Crystallization of Hemoglobin for Advanced Crystallography. CRYSTALS 2017. [DOI: 10.3390/cryst7090282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
While high-throughput screening for protein crystallization conditions have rapidly evolved in the last few decades, it is also becoming increasingly necessary for the control of crystal size and shape as increasing diversity of protein crystallographic experiments. For example, X-ray crystallography (XRC) combined with photoexcitation and/or spectrophotometry requires optically thin but well diffracting crystals. By contrast, large-volume crystals are needed for weak signal experiments, such as neutron crystallography (NC) or recently developed X-ray fluorescent holography (XFH). In this article, we present, using hemoglobin as an example protein, some techniques for obtaining the crystals of controlled size, shape, and adequate quality. Furthermore, we describe a few case studies of applications of the optimized hemoglobin crystals for implementing the above mentioned crystallographic experiments, providing some hints and tips for the further progress of advanced protein crystallography.
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Inoguchi N, Mizuno N, Baba S, Kumasaka T, Natarajan C, Storz JF, Moriyama H. Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice. PLoS One 2017; 12:e0174921. [PMID: 28362841 PMCID: PMC5376325 DOI: 10.1371/journal.pone.0174921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/17/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant. RESULTS Highland hemoglobin yielded at least two crystal types, in which the longest axes were 507 and 230 Å. Using the smaller unit cell crystal, the structure was solved at 2.2 Å resolution. The asymmetric unit contained two tetrameric hemoglobin molecules. CONCLUSIONS The analyses revealed that αPro50 in the highland hemoglobin variant promoted a stable interaction between αHis45 and heme that was not seen in the αHis50 lowland variant. The αPro50 mutation also altered the nature of atomic contacts at the α1β2/α2β1 intersubunit interfaces. These results demonstrate how affinity-altering changes in intersubunit interactions can be produced by mutations at structurally remote sites.
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Affiliation(s)
- Noriko Inoguchi
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Nobuhiro Mizuno
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Takashi Kumasaka
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Sayo, Japan
| | - Chandrasekhar Natarajan
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
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11
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Lepeshkevich SV, Gilevich SN, Parkhats MV, Dzhagarov BM. Molecular oxygen migration through the xenon docking sites of human hemoglobin in the R-state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1110-1121. [DOI: 10.1016/j.bbapap.2016.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 11/25/2022]
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12
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Kim JG, Muniyappan S, Oang KY, Kim TW, Yang C, Kim KH, Kim J, Ihee H. Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:023610. [PMID: 27158635 PMCID: PMC4833754 DOI: 10.1063/1.4947071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/06/2016] [Indexed: 05/30/2023]
Abstract
Homodimeric hemoglobin (HbI) consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3) and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find that the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI.
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Affiliation(s)
| | | | | | | | | | | | - Jeongho Kim
- Department of Chemistry, Inha University , Incheon 402-751, South Korea
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13
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Shadrina MS, Peslherbe GH, English AM. Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin’s Gas Diffusion Tunnels. Biochemistry 2015; 54:5268-78. [DOI: 10.1021/acs.biochem.5b00368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria S. Shadrina
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Gilles H. Peslherbe
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Ann M. English
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
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14
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Shadrina MS, Peslherbe GH, English AM. O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7. Biochemistry 2015; 54:5279-89. [PMID: 26226401 DOI: 10.1021/acs.biochem.5b00369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the release of O2 to the solvent via a transient E7 channel. To reveal the O2 escape routes controlled by HisE7 and to evaluate its role in gating heme access, we compare simulations of O2 diffusion from the distal heme pockets of the T and R states of HbA performed with HisE7 in its open (protonated) and closed (neutral) conformations. Irrespective of HisE7's conformation, we observe the same four or five escape routes leading directly from the α- or β-distal heme pockets to the solvent. Only 21-53% of O2 escapes occur via these routes, with the remainder escaping through routes that encompass multiple internal cavities in HbA. The conformation of the distal HisE7 controls the escape of O2 from the heme by altering the distal pocket architecture in a pH-dependent manner, not by gating the E7 channel. Removal of the HisE7 side chain in the GlyE7 variant exposes the distal pockets to the solvent, and the percentage of O2 escapes to the solvent directly from the α- or β-distal pockets of the mutant increases to 70-88%. In contrast to O2, the dominant water route from the bulk solvent is gated by HisE7 because protonation and opening of this residue dramatically increase the rate of influx of water into the empty distal heme pockets. The occupancy of the distal heme site by a water molecule, which functions as an additional nonprotein barrier to binding of the ligand to the heme, is also controlled by HisE7. Overall, analysis of gas and water diffusion routes in the subunits of HbA and its GlyE7 variant sheds light on the contribution of distal HisE7 in controlling polar and nonpolar ligand movement between the solvent and the hemes.
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Affiliation(s)
- Maria S Shadrina
- Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University , Montreal, Quebec H4B 1R6, Canada
| | - Gilles H Peslherbe
- Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University , Montreal, Quebec H4B 1R6, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University , Montreal, Quebec H4B 1R6, Canada
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15
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Ohgo Y, Takahashi M, Neya S, Nakamura M, Takahashi K, Namatame Y, Konaka H, Mori H, Hashizume D. A less common spin-crossover process observed in the six-coordinated model heme complexes. Polyhedron 2013. [DOI: 10.1016/j.poly.2013.02.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Ren Z. Reverse engineering the cooperative machinery of human hemoglobin. PLoS One 2013; 8:e77363. [PMID: 24312167 PMCID: PMC3842276 DOI: 10.1371/journal.pone.0077363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/30/2013] [Indexed: 11/25/2022] Open
Abstract
Hemoglobin transports molecular oxygen from the lungs to all human tissues for cellular respiration. Its α2β2 tetrameric assembly undergoes cooperative binding and releasing of oxygen for superior efficiency and responsiveness. Over past decades, hundreds of hemoglobin structures were determined under a wide range of conditions for investigation of molecular mechanism of cooperativity. Based on a joint analysis of hemoglobin structures in the Protein Data Bank (Ren, companion article), here I present a reverse engineering approach to elucidate how two subunits within each dimer reciprocate identical motions that achieves intradimer cooperativity, how ligand-induced structural signals from two subunits are integrated to drive quaternary rotation, and how the structural environment at the oxygen binding sites alter their binding affinity. This mechanical model reveals the intricate design that achieves the cooperative mechanism and has previously been masked by inconsistent structural fluctuations. A number of competing theories on hemoglobin cooperativity and broader protein allostery are reconciled and unified.
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Affiliation(s)
- Zhong Ren
- Center for Advanced Radiation Sources, The University of Chicago, Argonne, Illinois, United States of America
- Renz Research, Inc., Westmont, Illinois, United States of America
- * E-mail:
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17
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Reaction trajectory revealed by a joint analysis of protein data bank. PLoS One 2013; 8:e77141. [PMID: 24244274 PMCID: PMC3823880 DOI: 10.1371/journal.pone.0077141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/29/2013] [Indexed: 11/19/2022] Open
Abstract
Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article), and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.
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18
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Schotte F, Cho HS, Soman J, Wulff M, Olson JS, Anfinrud PA. Real-time tracking of CO migration and binding in the α and β subunits of human hemoglobin via 150-ps time-resolved Laue crystallography. Chem Phys 2013; 422:98-106. [PMID: 24839343 DOI: 10.1016/j.chemphys.2012.12.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed the method of picosecond Laue crystallography and used this capability to probe ligand dynamics in tetrameric R-state hemoglobin (Hb). Time-resolved, 2 Å-resolution electron density maps of photolyzed HbCO reveal the time-dependent population of CO in the binding (A) and primary docking (B) sites of both α and β subunits from 100 ps to 10 μs. The proximity of the B site in the β subunit is about 0.25 Å closer to its A binding site, and its kBA rebinding rate (~300 μs-1) is six times faster, suggesting distal control of the rebinding dynamics. Geminate rebinding in the β subunit exhibits both prompt and delayed geminate phases. We developed a microscopic model to quantitatively explain the observed kinetics, with three states for the α subunit and four states for the β subunit. This model provides a consistent framework for interpreting rebinding kinetics reported in prior studies of both HbCO and HbO2.
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Affiliation(s)
- Friedrich Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Jayashree Soman
- Department of Biochemistry and Cell Biology, and W.M. Keck Center for Computational Biology, Rice University, Houston, TX 77251-1892, USA
| | - Michael Wulff
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France
| | - John S Olson
- Department of Biochemistry and Cell Biology, and W.M. Keck Center for Computational Biology, Rice University, Houston, TX 77251-1892, USA
| | - Philip A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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19
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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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20
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Inoguchi N, Oshlo JR, Natarajan C, Weber RE, Fago A, Storz JF, Moriyama H. Deer mouse hemoglobin exhibits a lowered oxygen affinity owing to mobility of the E helix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:393-8. [PMID: 23545644 PMCID: PMC3614163 DOI: 10.1107/s1744309113005708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 02/27/2013] [Indexed: 11/10/2022]
Abstract
The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was expressed in Escherichia coli and was purified by ion-exchange chromatography. Recombinant hemoglobin was crystallized by the hanging-drop vapor-diffusion method using polyethylene glycol as a precipitant. The obtained orthorhombic crystal contained two subunits in the asymmetric unit. The refined structure was interpreted as the aquo-met form. Structural comparisons were performed among hemoglobins from deer mouse, house mouse and human. In contrast to human hemoglobin, deer mouse hemoglobin lacks the hydrogen bond between α1Trp14 in the A helix and α1Thr67 in the E helix owing to the Thr67Ala substitution. In addition, deer mouse hemoglobin has a unique hydrogen bond at the α1β1 interface between residues α1Cys34 and β1Ser128.
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Affiliation(s)
- Noriko Inoguchi
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jake R. Oshlo
- Nebraska Wesleyan University, Lincoln, Nebraska, USA
| | | | - Roy E. Weber
- Zoophysiology, Department of Biological Sciences, Aarhus University, Aarhus, Denmark
| | - Angela Fago
- Zoophysiology, Department of Biological Sciences, Aarhus University, Aarhus, Denmark
| | - Jay F. Storz
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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21
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Tekpinar M, Zheng W. Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin. Proteins 2012; 81:240-52. [PMID: 22987685 DOI: 10.1002/prot.24180] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/27/2012] [Accepted: 09/10/2012] [Indexed: 11/08/2022]
Abstract
Hemoglobin (Hb), an oxygen-binding protein composed of four subunits (α1, α2, β1, and β2), is a well-known example of allosteric proteins that are capable of cooperative ligand binding. Despite decades of studies, the structural basis of its cooperativity remains controversial. In this study, we have integrated coarse-grained (CG) modeling, all-atom simulation, and structural data from X-ray crystallography and wide-angle X-ray scattering (WAXS), aiming to probe dynamic properties of the two structural states of Hb (T and R state) and the transitions between them. First, by analyzing the WAXS data of unliganded and liganded Hb, we have found that the structural ensemble of T or R state is dominated by one crystal structure of Hb with small contributions from other crystal structures of Hb. Second, we have used normal mode analysis to identify two distinct quaternary rotations between the α1β1 and α2β2 dimer, which drive the transitions between T and R state. We have also identified the hot-spot residues whose mutations are predicted to greatly change these quaternary motions. Third, we have generated a CG transition pathway between T and R state, which predicts a clear order of quaternary and tertiary changes involving α and β subunits in Hb. Fourth, we have used the accelerated molecular dynamics to perform an all-atom simulation starting from the T state of Hb, and we have observed a transition toward the R state of Hb. Further analysis of crystal structural data and the all-atom simulation trajectory has corroborated the order of quaternary and tertiary changes predicted by CG modeling.
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Affiliation(s)
- Mustafa Tekpinar
- Physics Department, University at Buffalo, Buffalo, New York 14260, USA
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22
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Sugishima M, Moffat K, Noguchi M. Discrimination between CO and O(2) in heme oxygenase: comparison of static structures and dynamic conformation changes following CO photolysis. Biochemistry 2012; 51:8554-62. [PMID: 23043644 DOI: 10.1021/bi301175x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Heme oxygenase (HO) catalyzes heme degradation, one of its products being carbon monoxide (CO). It is well known that CO has a higher affinity for heme iron than does molecular oxygen (O(2)); therefore, CO is potentially toxic. Because O(2) is required for the HO reaction, HO must discriminate effectively between CO and O(2) and thus escape product inhibition. Previously, we demonstrated large conformational changes in the heme-HO-1 complex upon CO binding that arise from steric hindrance between CO bound to the heme iron and Gly-139. However, we have not yet identified those changes that are specific to CO binding and do not occur upon O(2) binding. Here we determine the crystal structure of the O(2)-bound form at 1.8 Å resolution and reveal the structural changes that are specific to CO binding. Moreover, difference Fourier maps comparing the structures before and after CO photolysis at <160 K clearly show structural changes such as movement of the distal F-helix upon CO photolysis. No such changes are observed upon O(2) photolysis, consistent with the structures of the ligand-free, O(2)-bound, and CO-bound forms. Protein motions even at cryogenic temperatures imply that the CO-bound heme-HO-1 complex is severely constrained (as in ligand binding to the T-state of hemoglobin), indicating that CO binding to the heme-HO-1 complex is specifically inhibited by steric hindrance. The difference Fourier maps also suggest new routes for CO migration.
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Affiliation(s)
- Masakazu Sugishima
- Department of Medical Biochemistry, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011, Japan.
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23
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Shadrina MS, English AM, Peslherbe GH. Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O2 Pathways and Escape Routes in T-state Deoxyhemoglobin. J Am Chem Soc 2012; 134:11177-84. [DOI: 10.1021/ja300903c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria S. Shadrina
- Department
of Chemistry and Biochemistry and Centre
for Research in Molecular Modeling, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
| | - Ann M. English
- Department
of Chemistry and Biochemistry and Centre
for Research in Molecular Modeling, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
| | - Gilles H. Peslherbe
- Department
of Chemistry and Biochemistry and Centre
for Research in Molecular Modeling, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, Canada H4B 1R6
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24
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Kim S, Lim M. Protein Conformation-Controlled Rebinding Barrier of NO and Its Binding Trajectories in Myoglobin and Hemoglobin at Room Temperature. J Phys Chem B 2012; 116:5819-30. [DOI: 10.1021/jp300176q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Seongheun Kim
- Department of Chemistry and Chemistry Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute for
Functional Materials, Pusan National University, Busan 609-735, Korea
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25
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Kim K, Muniyappan S, Oang KY, Kim JG, Nozawa S, Sato T, Koshihara SY, Henning R, Kosheleva I, Ki H, Kim Y, Kim TW, Kim J, Adachi SI, Ihee H. Direct observation of cooperative protein structural dynamics of homodimeric hemoglobin from 100 ps to 10 ms with pump-probe X-ray solution scattering. J Am Chem Soc 2012; 134:7001-8. [PMID: 22494177 PMCID: PMC3337689 DOI: 10.1021/ja210856v] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Indexed: 01/11/2023]
Abstract
Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps to 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I(1), I(2), and I(3)) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I(1) intermediate is generated within 100 ps and transforms to the R-like I(2) intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I(3) intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I(3) intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.
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Affiliation(s)
- Kyung
Hwan Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Srinivasan Muniyappan
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Key Young Oang
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Jong Goo Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Shunsuke Nozawa
- Photon Factory,
Institute of
Materials Structure Science, High Energy Accelerator
Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki
305-0801, Japan
| | - Tokushi Sato
- Photon Factory,
Institute of
Materials Structure Science, High Energy Accelerator
Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki
305-0801, Japan
| | - Shin-ya Koshihara
- Department
of Chemistry and Materials
Science, Tokyo Institute of Technology and
CREST, Japan Science and Technology Agency (JST), Meguro-ku, Tokyo 152-8551, Japan
| | - Robert Henning
- Center for Advanced Radiation
Sources, The University of Chicago, Chicago,
Illinois 60637, United States
| | - Irina Kosheleva
- Center for Advanced Radiation
Sources, The University of Chicago, Chicago,
Illinois 60637, United States
| | - Hosung Ki
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Youngmin Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Tae Wu Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Jeongho Kim
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
| | - Shin-ichi Adachi
- Photon Factory,
Institute of
Materials Structure Science, High Energy Accelerator
Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki
305-0801, Japan
- PRESTO, Japan Science
and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi,
Saitama 332-0012, Japan
| | - Hyotcherl Ihee
- Center for Time-Resolved Diffraction,
Department of Chemistry, Graduate School of Nanoscience & Technology
(WCU), KAIST, Daejeon, 305-701, Republic
of Korea
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26
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Jones EM, Balakrishnan G, Spiro TG. Heme reactivity is uncoupled from quaternary structure in gel-encapsulated hemoglobin: a resonance Raman spectroscopic study. J Am Chem Soc 2012; 134:3461-71. [PMID: 22263778 PMCID: PMC3307588 DOI: 10.1021/ja210126j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Encapsulation of hemoglobin (Hb) in silica gel preserves structure and function but greatly slows protein motion, thereby providing access to intermediates along the allosteric pathway that are inaccessible in solution. Resonance Raman (RR) spectroscopy with visible and ultraviolet laser excitation provides probes of heme reactivity and of key tertiary and quaternary contacts. These probes were monitored in gels after deoxygenation of oxyHb and after CO binding to deoxyHb, which initiate conformational change in the R-T and T-R directions, respectively. The spectra establish that quaternary structure change in the gel takes a week or more but that the evolution of heme reactivity, as monitored by the Fe-histidine stretching vibration, ν(FeHis), is completed within two days, and is therefore uncoupled from the quaternary structure. Within each quaternary structure, the evolving ν(FeHis) frequencies span the full range of values between those previously associated with the high- and low-affinity end states, R and T. This result supports the tertiary two-state (TTS) model, in which the Hb subunits can adopt high- and low-affinity tertiary structures, r and t, within each quaternary state. The spectra also reveal different tertiary pathways, involving the breaking and reformation of E and F interhelical contacts in the R-T direction but not the T-R direction. In the latter, tertiary motions are restricted by the T quaternary contacts.
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Affiliation(s)
- Eric M. Jones
- Department of Chemistry, University of Washington, Box 351700, Seattle Washington 98195-1700 USA
| | - Gurusamy Balakrishnan
- Department of Chemistry, University of Washington, Box 351700, Seattle Washington 98195-1700 USA
| | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle Washington 98195-1700 USA
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27
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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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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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Birukou I, Maillett DH, Birukova A, Olson JS. Modulating distal cavities in the α and β subunits of human HbA reveals the primary ligand migration pathway. Biochemistry 2011; 50:7361-74. [PMID: 21793487 DOI: 10.1021/bi200923k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The free volume in the active site of human HbA plays a crucial role in governing the bimolecular rates of O(2), CO, and NO binding, the fraction of geminate ligand recombination, and the rate of NO dioxygenation by the oxygenated complex. We have decreased the size of the distal pocket by mutating Leu(B10), Val(E11), and Leu(G8) to Phe and Trp and that of other more internal cavities by filling them with Xe at high gas pressures. Increasing the size of the B10 side chain reduces bimolecular rates of ligand binding nearly 5000-fold and inhibits CO geminate recombination due to both reduction of the capture volume in the distal pocket and direct steric hindrance of Fe-ligand bond formation. Phe and Trp(E11) mutations also cause a decrease in distal pocket volume but, at the same time, increase access to the Fe atom because of the loss of the γ2 CH(3) group of the native Val(E11) side chain. The net result of these E11 substitutions is a dramatic increase in the rate of geminate recombination because dissociated CO is sequestered close to the Fe atom and can rapidly rebind without steric resistance. However, the bimolecular rate constants for binding of ligand to the Phe and Trp(E11) mutants are decreased 5-30-fold, because of a smaller capture volume. Geminate and bimolecular kinetic parameters for Phe and Trp(G8) mutants are similar to those for the native HbA subunits because the aromatic rings at this position cause little change in distal pocket volume and because ligands do not move past this position into the globin interior of wild-type HbA subunits. The latter conclusion is verified by the observation that Xe binding to the α and β Hb subunits has little effect on either geminate or bimolecular ligand rebinding. All of these experimental results argue strongly against alternative ligand migration pathways that involve movements through the protein interior in HbA. Instead, ligands appear to enter through the His(E7) gate and are captured directly in the distal cavity.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and WM Keck Center for Computational Biology, Rice University, Houston, Texas 77005, United States
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Kuwada T, Hasegawa T, Takagi T, Sato I, Shishikura F. pH-dependent structural changes in haemoglobin component V from the midge larvaPropsilocerus akamusi(Orthocladiinae, Diptera). ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:258-67. [DOI: 10.1107/s0907444909055760] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 12/30/2009] [Indexed: 11/10/2022]
Abstract
Haemoglobin component V (Hb V) from the midge larvaPropsilocerus akamusiexhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb V retains its functional properties by adapting to the structural changes caused by amino-acid replacements.
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Tomita A, Sato T, Nozawa S, Koshihara SY, Adachi SI. Tracking ligand-migration pathways of carbonmonoxy myoglobin in crystals at cryogenic temperatures. Acta Crystallogr A 2010; 66:220-8. [DOI: 10.1107/s0108767309050752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 11/25/2009] [Indexed: 05/26/2023] Open
Abstract
In order to explore the ligand-migration dynamics in myoglobin induced by photodissociation, cryogenic X-ray crystallographic investigations of carbonmonoxy myoglobin crystals illuminated by continuous wave and pulsed lasers at 1–15 kHz repetition rate have been carried out. Here it is shown that this novel method, extended pulsed-laser pumping of carbonmonoxy myoglobin, promotes ligand migration in the protein matrix by crossing the glass transition temperature repeatedly, and enables the visualization of the migration pathway of the photodissociated ligands in native Mb at cryogenic temperatures. It has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino-acid residues around the cavity which result in the expansion of the cavity. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand-migration channel arising by induced fit.
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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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Ding L, Shen L, Chen XB, Fang WH. Solvent Effects on Photoreactivity of Valerophenone: A Combined QM and MM Study. J Org Chem 2009; 74:8956-62. [DOI: 10.1021/jo902080z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Lina Ding
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lin Shen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xue-Bo Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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Fournier F, Guo R, Gardner EM, Donaldson PM, Loeffeld C, Gould IR, Willison KR, Klug DR. Biological and biomedical applications of two-dimensional vibrational spectroscopy: proteomics, imaging, and structural analysis. Acc Chem Res 2009; 42:1322-31. [PMID: 19548660 DOI: 10.1021/ar900074p] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump-probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron-vibration-vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we also show how post-translational modifications in peptides (tyrosine phosphorylation) can be detected by EVV 2DIR spectroscopy. The feasibility of EVV 2DIR spectroscopy for tissue imaging is also evaluated. Preliminary results were obtained on a mouse kidney histological section that was stained with hematoxylin (a small organic molecule). We obtained images by setting the IR frequencies to a specific cross-peak (the strongest for hematoxylin was obtained from its analysis in isolation; a general CH(3) cross-peak for proteins was also used) and then spatially mapping as a function of the beam position relative to the sample. Protein and hematoxylin distribution in the tissue were measured and show differential contrast, which can be entirely explained by the different tissue structures and their functions. The possibility of triply resonant EVV 2DIR spectroscopy was investigated on the retinal chromophore at the centre of the photosynthetic protein bacteriorhodopsin (bR). By putting the visible third beam in resonance with an electronic transition, we were able to enhance the signal and increase the sensitivity of the method by several orders of magnitude. This increase in sensitivity is of great importance for biological applications, in which the number of proteins, metabolites, or drug molecules to be detected is low (typically pico- to femtomoles). Finally, we present theoretical investigations for using EVV 2DIR spectroscopy as a structural analysis tool for inter- and intramolecular interaction geometries.
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Affiliation(s)
- Frederic Fournier
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Rui Guo
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Elizabeth M. Gardner
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Paul M. Donaldson
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Christian Loeffeld
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Ian R. Gould
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Keith R. Willison
- Institute of Cancer Research, Chester Beatty Laboratories, Cancer Research U.K., Centre of Cellular and Molecular Biology, London SW3 6JB, U.K
| | - David R. Klug
- Department of Chemistry and Chemical Biology Centre, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
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Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin. Proc Natl Acad Sci U S A 2009; 106:2612-6. [PMID: 19204297 DOI: 10.1073/pnas.0807774106] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.
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Vitagliano L, Vergara A, Bonomi G, Merlino A, Verde C, Prisco GD, Howes BD, Smulevich G, Mazzarella L. Spectroscopic and Crystallographic Characterization of a Tetrameric Hemoglobin Oxidation Reveals Structural Features of the Functional Intermediate Relaxed/Tense State. J Am Chem Soc 2008; 130:10527-35. [DOI: 10.1021/ja803363p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Alessandro Vergara
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Giovanna Bonomi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Antonello Merlino
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Cinzia Verde
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Guido di Prisco
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Barry D. Howes
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Giulietta Smulevich
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
| | - Lelio Mazzarella
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy, Department of Chemistry, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy, Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy, and Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy
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Fang WH. Ab initio determination of dark structures in radiationless transitions for aromatic carbonyl compounds. Acc Chem Res 2008; 41:452-7. [PMID: 18251513 DOI: 10.1021/ar700205f] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Mechanistic photodissociation of a polyatomic molecule has long been regarded as an intellectually challenging area of chemical physics, the results of which are relevant to atmospheric chemistry, biological systems, and many application fields. Carbonyl compounds play a unique role in the development of our understanding of the spectroscopy, photochemistry, and photophysics of polyatomic molecules and their photodissociation has been the subject of numerous studies over many decades. Upon irradiation, a molecule can undergo internal conversion (IC) and intersystem crossing (ISC) processes, besides photochemical and other photophysical processes. Transient intermediates formed in the IC and ISC radiationless processes, which are termed "dark", are not amenable to detection by conventional light absorption or emission. However, these dark intermediates play critical roles in IC and ISC processes and thus are essential to understanding mechanistic photochemistry of a polyatomic molecule. We have applied the multiconfiguration complete active space self-consistent field (CASSCF) method to determine the dark transient structures involved in radiationless processes for acetophenone and the related aromatic carbonyl compounds. The electronic and geometric structures predicted for the dark states are in a good agreement with those determined by ultrafast electron diffraction experiments. Intersection structure of different electronic states provides a very efficient "funnel" for the IC or ISC process. However, experimental determination of the intersection structure involved in radiationless transitions of a polyatomic molecule is impossible at present. We have discovered a minimum energy crossing point among the three potential energy surfaces (S1, T1, and T2) that appears to be common to a wide variety of aromatic carbonyl compounds with a constant structure. This new type of crossing point holds the key to understanding much about radiationless processes after photoexcitation of aromatic carbonyl compounds. The importance of ab initio determination of transient structures in the photodissociation dynamics has been demonstrated for the case of the aromatic carbonyl compounds. In addition, the detailed knowledge of mechanistic photochemistry for aromatic carbonyl compounds forms the basis for further investigating photodissociation dynamics of a polyatomic molecule.
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Affiliation(s)
- Wei-Hai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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Ciaccio C, Coletta A, De Sanctis G, Marini S, Coletta M. Cooperativity and allostery in haemoglobin function. IUBMB Life 2008; 60:112-23. [DOI: 10.1002/iub.6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics. Biophys J 2007; 94:2737-51. [PMID: 18096633 DOI: 10.1529/biophysj.107.114942] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent functional studies reported on human adult hemoglobin (HbA) show that heterotropic effector-linked tertiary structural changes are primarily responsible for modulating the oxygen affinity of hemoglobin. We present the results of 6-ns molecular dynamics simulations performed to gain insights into the dynamical and structural details of these effector-linked tertiary changes. All-atom simulations were carried out on a series of models generated for T- and R-state HbA, and for 2,3-diphosphoglycerate-bound models. Cross-correlation analyses identify both intra- and intersubunit correlated motions that are perturbed by the presence of the effector. Principal components analysis was used to decompose the covariance matrix extracted from the simulations and reconstruct the trajectories along the principal coordinates representative of functionally important collective motions. It is found that HbA in both quaternary states exists as ensembles of tertiary conformations that introduce dynamic heterogeneity in the protein. 2,3-Diphosphoglycerate induces significant perturbations in the fluctuations of both HbA states that translate into the protein visiting different tertiary conformations within each quaternary state. The analysis reveals that the presence of the effector affects the most important components of HbA motions and that heterotropic effectors modify the overall dynamics of the quaternary equilibrium via tertiary changes occurring in regions where conserved functionally significant residues are located, namely in the loop regions between helices C and E, E and F, and F and G, and in concerted helix motions. The changes are not apparent when comparing the available x-ray crystal structures in the presence and absence of effector, but are striking when comparing the respective dynamic tertiary conformations of the R and T tetramers.
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Abstract
Understanding the molecular mechanism of hemoglobin cooperativity remains an enduring challenge. Protein forces that control ligand affinity are not directly accessible by experiment. We demonstrate that computational quantum mechanics/molecular mechanics methods can provide reasonable values of ligand binding energies in Hb, and of their dependence on allostery. About 40% of the binding energy differences between the relaxed state and tense state quaternary structures result from strain induced in the heme and its ligands, especially in one of the pyrrole rings. The proximal histidine also contributes significantly, in particular, in the alpha-chains. The remaining energy difference resides in protein contacts, involving residues responsible for locking the quaternary changes. In the alpha-chains, the most important contacts involve the FG corner, at the "hinge" region of the alpha(1)beta(2) quaternary interface. The energy differences are spread more evenly among the beta-chain residues, suggesting greater flexibility for the beta- than for the alpha-chains along the quaternary transition. Despite this chain differentiation, the chains contribute equally to the relaxed substitute state energy difference. Thus, nature has evolved a symmetric response to the quaternary structure change, which is a requirement for maximum cooperativity, via different mechanisms for the two kinds of chains.
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41
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Kong Q, Wulff M, Lee JH, Bratos S, Ihee H. Photochemical Reaction Pathways of Carbon Tetrabromide in Solution Probed by Picosecond X-ray Diffraction. J Am Chem Soc 2007; 129:13584-91. [DOI: 10.1021/ja073503e] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Qingyu Kong
- Contribution from the European Synchrotron Radiation Facility, Grenoble Cedex 38043, BP 220, France, National Creative Research Initiative Center for Time-Resolved Diffraction, Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea, and Laboratoire de Physique, Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 Place Jussieu, Paris Cedex 75252, France
| | - Michael Wulff
- Contribution from the European Synchrotron Radiation Facility, Grenoble Cedex 38043, BP 220, France, National Creative Research Initiative Center for Time-Resolved Diffraction, Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea, and Laboratoire de Physique, Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 Place Jussieu, Paris Cedex 75252, France
| | - Jae Hyuk Lee
- Contribution from the European Synchrotron Radiation Facility, Grenoble Cedex 38043, BP 220, France, National Creative Research Initiative Center for Time-Resolved Diffraction, Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea, and Laboratoire de Physique, Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 Place Jussieu, Paris Cedex 75252, France
| | - Savo Bratos
- Contribution from the European Synchrotron Radiation Facility, Grenoble Cedex 38043, BP 220, France, National Creative Research Initiative Center for Time-Resolved Diffraction, Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea, and Laboratoire de Physique, Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 Place Jussieu, Paris Cedex 75252, France
| | - Hyotcherl Ihee
- Contribution from the European Synchrotron Radiation Facility, Grenoble Cedex 38043, BP 220, France, National Creative Research Initiative Center for Time-Resolved Diffraction, Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea, and Laboratoire de Physique, Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 Place Jussieu, Paris Cedex 75252, France
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Tung CH, Huang JW, Yang JM. Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol 2007; 8:R31. [PMID: 17335583 PMCID: PMC1868941 DOI: 10.1186/gb-2007-8-3-r31] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/05/2007] [Accepted: 03/03/2007] [Indexed: 11/23/2022] Open
Abstract
3D BLAST, a novel protein structure database search tool, is a useful tool for analysing novel structures, capable of returning a list of aligned structures ordered according to E-values. We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (κ, α) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity.
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Affiliation(s)
- Chi-Hua Tung
- Institute of Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan
| | - Jhang-Wei Huang
- Institute of Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan
| | - Jinn-Moon Yang
- Institute of Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan
- Core Facility for Structural Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, Taiwan
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Knapp JE, Pahl R, Šrajer V, Royer WE. Allosteric action in real time: time-resolved crystallographic studies of a cooperative dimeric hemoglobin. Proc Natl Acad Sci U S A 2006; 103:7649-54. [PMID: 16684887 PMCID: PMC1472499 DOI: 10.1073/pnas.0509411103] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Indexed: 11/18/2022] Open
Abstract
Protein allostery provides mechanisms for regulation of biological function at the molecular level. We present here an investigation of global, ligand-induced allosteric transition in a protein by time-resolved x-ray diffraction. The study provides a view of structural changes in single crystals of Scapharca dimeric hemoglobin as they proceed in real time, from 5 ns to 80 micros after ligand photodissociation. A tertiary intermediate structure forms rapidly (<5 ns) as the protein responds to the presence of an unliganded heme within each R-state protein subunit, with key structural changes observed in the heme groups, neighboring residues, and interface water molecules. This intermediate lays a foundation for the concerted tertiary and quaternary structural changes that occur on a microsecond time scale and are associated with the transition to a low-affinity T-state structure. Reversal of these changes shows a considerable lag as a T-like structure persists well after ligand rebinding, suggesting a slow T-to-R transition.
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Affiliation(s)
- James E. Knapp
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | | | - Vukica Šrajer
- Consortium for Advanced Radiation Sources and
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - William E. Royer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655; and
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Bourgeois D, Royant A. Advances in kinetic protein crystallography. Curr Opin Struct Biol 2006; 15:538-47. [PMID: 16129597 DOI: 10.1016/j.sbi.2005.08.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 07/09/2005] [Accepted: 08/18/2005] [Indexed: 10/25/2022]
Abstract
Many proteins function in the crystalline state, making crystallography a tool that can address mechanism, as well as structure. By initiating biological turnover in the crystal, transient structural species form, which may be filmed by Laue diffraction or captured by freeze-trapping methods. Laue diffraction has now reached an unprecedented level of sophistication and has found a 'niche of excellence' in the study of cyclic, ultra-fast, light-triggered reactions. Trapping methods, on the other hand, are more generally applicable, but require care to avoid artifacts. New strategies have been developed and difficulties such as radiation damage have received particular attention. Complementary methods--mainly UV/visible single-crystal spectroscopy--have proven essential to design, interpret and validate kinetic crystallography experiments.
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Affiliation(s)
- Dominique Bourgeois
- LCCP, UMR 5075, IBS, 41 avenue Jules Horowitz, 38027 Grenoble Cedex 1, France.
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Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K. Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi. Proc Natl Acad Sci U S A 2005; 102:14521-6. [PMID: 16204001 PMCID: PMC1253539 DOI: 10.1073/pnas.0501541102] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Accepted: 08/25/2005] [Indexed: 11/18/2022] Open
Abstract
Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.
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Affiliation(s)
- Nobutaka Numoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Lepeshkevich SV, Konovalova NV, Stepuro II, Dzhagarov BM. Kinetic studies of oxygenation of α- and β-subunits within pyridoxal 5′-phosphate derivatives of human hemoglobin. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.10.091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Sugishima M, Sakamoto H, Noguchi M, Fukuyama K. CO-trapping site in heme oxygenase revealed by photolysis of its co-bound heme complex: mechanism of escaping from product inhibition. J Mol Biol 2004; 341:7-13. [PMID: 15312758 DOI: 10.1016/j.jmb.2004.05.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 05/12/2004] [Accepted: 05/23/2004] [Indexed: 11/12/2022]
Abstract
Heme oxygenase (HO) catalyzes physiological heme degradation using O(2) and reducing equivalents to produce biliverdin, iron, and CO. Notably, the HO reaction proceeds without product inhibition by CO, which is generated in the conversion reaction of alpha-hydroxyheme to verdoheme, although CO is known to be a potent inhibitor of HO and other heme proteins. In order to probe how endogenous CO is released from the reaction site, we collected X-ray diffraction data from a crystal of the CO-bound form of the ferrous heme-HO complex in the dark and under illumination by a red laser at approximately 35 K. The difference Fourier map indicates that the CO ligand is partially photodissociated from the heme and that the photolyzed CO is trapped in a hydrophobic cavity adjacent to the heme pocket. This hydrophobic cavity was occupied also by xenon, which is similar to CO in terms of size and properties. Taking account of the affinity of CO for the ferrous verdoheme-HO complex being much weaker than that for the ferrous heme complex, the CO derived from alpha-hydroxyheme would be trapped preferentially in the hydrophobic cavity but not coordinated to the iron of verdoheme. This structural device would ensure the smooth progression of the subsequent reaction, from verdoheme to biliverdin, which requires O(2) binding to verdoheme.
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Affiliation(s)
- Masakazu Sugishima
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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48
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Brunori M, Bourgeois D, Vallone B. The structural dynamics of myoglobin. J Struct Biol 2004; 147:223-34. [PMID: 15450292 DOI: 10.1016/j.jsb.2004.04.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 03/15/2004] [Indexed: 10/26/2022]
Abstract
Conformational fluctuations in proteins were initially invoked to explain the observation that diffusion of small ligands through the matrix is a global phenomenon. Small globular proteins contain internal cavities that play a role not only in matrix dynamics but also in controlling function, tracing a pathway for the diffusion of the ligand to and from the active site. This is the main point addressed in this Review, which presents pertinent information obtained on myoglobin (Mb). Mb, a simple globular heme protein which binds reversibly oxygen and other ligands. The bond between the heme Fe(II) and gaseous ligands can be photodissociated by a laser pulse, generating a non-equilibrium population of protein structures that relaxes on a picosecond to millisecond time range. This process is associated with migration of the ligand to internal cavities of the protein, which are known to bind xenon. Some of the results obtained by laser photolysis, molecular dynamics simulations, and X-ray diffraction of intermediate states of wild-type and mutant myoglobins are summarized. The extended relaxation of the globin moiety directly observed by Laue crystallography reflects re-equilibration among conformational substates known to play an essential role in controlling protein function.
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Affiliation(s)
- M Brunori
- Departimento di Scienze Biochimiche and Istituto Pasteur-Fondazione Cenci Bolognetti, Università di Roma "La Sapienza," Rome, Italy.
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Kwon SJ, Petri R, DeBoer AL, Schmidt-Dannert C. A High-Throughput Screen for Porphyrin Metal Chelatases: Application to the Directed Evolution of Ferrochelatases for Metalloporphyrin Biosynthesis. Chembiochem 2004; 5:1069-74. [PMID: 15300829 DOI: 10.1002/cbic.200400051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Porphyrins are of particular interest in a variety of applications ranging from biocatalysis and chemical synthesis to biosensor and electronic technologies as well as cancer treatment. Recently, we have developed a versatile system for the high-level production of porphyrins in engineered E. coli cells with the aim of diversifying substitution patterns and accessing porphyrin systems not readily available through chemical synthesis. However, this approach failed to produce significant amounts of the metalloporphyrin in vivo from overproduced protoporphyrin due to insufficient metal insertion. Therefore, we systematically assessed the activity of the B. subtilis ferrochelatase in vivo and in vitro. A true high-throughput-screening approach based on catalytic in vivo ferrochelatase activity was developed by using fluorescence-activated cell sorting (FACS). This assay was used to screen a library of 2.4 x 10(6) ferrochelatase mutants expressed in protoporphyrin-overproducing recombinant E. coli cells. Several selected protein variants were purified, and their improved catalytic activity was confirmed in vitro. In addition to ferrochelatase activity, metal transport into E. coli was identified as another limitation for in vivo heme overproduction. Overexpression of the metal transporter zupT as part of the assembled pathway increased the overall metalloporphyrin production twofold. This report represents the most exhaustive in vitro evolution study of a ferrochelatase and demonstrates the effectiveness of our novel high-throughput-screening system for directed evolution of ferrochelatases based on their catalytic activity.
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Affiliation(s)
- Seok Joon Kwon
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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