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Numoto N, Onoda S, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobiol 2022; 19:1-10. [PMID: 35797404 PMCID: PMC9173864 DOI: 10.2142/biophysico.bppb-v19.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 12/01/2022] Open
Abstract
Ever since the historic discovery of the cooperative oxygenation of its multiple subunits, hemoglobin (Hb) has been among the most exhaustively studied allosteric proteins. However, the lack of structural information on the intermediates between oxygenated and deoxygenated forms prevents our detailed understanding of the molecular mechanism of its allostery. It has been difficult to prepare crystals of intact oxy-deoxy intermediates and to individually identify the oxygen saturation for each subunit. However, our recent crystallographic studies have demonstrated that giant Hbs from annelids are suitable for overcoming these problems and can provide abundant information on oxy-deoxy intermediate structures. Here, we report the crystal structures of oxy-deoxy intermediates of a 400 kDa Hb (V2Hb) from the annelid Lamellibrachia satsuma, following up on a series of previous studies of similar giant Hbs. Four intermediate structures had average oxygen saturations of 78%, 69%, 55%, and 26%, as determined by the occupancy refinement of the bound oxygen based on ambient temperature factors. The structures demonstrate that the cooperative oxygen dissociation is weaker, large ternary and quaternary changes are induced at a later stage of the oxygen dissociation process, and the ternary and quaternary changes are smaller with local perturbations. Nonetheless, the overall structural transition seemed to proceed in the manner of the MWC two-state model. Our crystallographic snapshots of the allosteric transition of V2Hb provide important experimental evidence for a more detailed understanding of the allostery of Hbs by extension of the Monod–Wyman–Changeux (MWC) model.
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Affiliation(s)
- Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University (TMDU)
| | - Seiko Onoda
- Graduate School of Natural Science and Technology, Kanazawa University
| | | | - Hideo Okumura
- Structural Biology Division, Japan Synchrotron Radiation Research Institute
| | - Seiki Baba
- Structural Biology Division, Japan Synchrotron Radiation Research Institute
| | | | - Kunio Miki
- Graduate School of Science, Kyoto University
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU)
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2
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Numoto N, Kawano Y, Okumura H, Baba S, Fukumori Y, Miki K, Ito N. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. IUCRJ 2021; 8:954-962. [PMID: 34804547 PMCID: PMC8562662 DOI: 10.1107/s2052252521009386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Cooperative oxygen binding of hemoglobin (Hb) has been studied for over half a century as a representative example of the allostericity of proteins. The most important problem remaining to be solved is the lack of structural information on the intermediates between the oxygenated and deoxygenated forms. In order to characterize the intermediate structures, it is necessary to obtain intermediate-state crystals, determine their oxygen saturations and then determine the oxygen saturations of each of their constituent subunits, all of which are challenging issues even now. Here, intermediate forms of the 400 kDa giant Hb from the tubeworm Oligobrachia mashikoi are reported. To overcome the above problems without any artificial modifications to the protein or prosthetic groups, intermediate crystals of the giant Hb were prepared from fully oxygenated crystals by a soaking method. The oxygen saturation of the crystals was measured by in situ observation with a microspectrophotometer using thin plate crystals processed by an ultraviolet laser to avoid saturation of absorption. The oxygen saturation of each subunit was determined by occupancy refinement of the bound oxygen based on ambient temperature factors. The obtained structures reveal the detailed relationship between the structural transition and oxygen dissociation. The dimer subassembly of the giant Hb shows strong correlation with the local structural changes at the heme pockets. Although some local ternary-structural changes occur in the early stages of the structural transition, the associated global ternary-structural and quaternary-structural changes might arise at about 50% oxygen saturation. The models based on coarse snapshots of the allosteric transition support the conventional two-state model of Hbs and provide the missing pieces of the intermediate structures that are required for full understanding of the allosteric nature of Hbs in detail.
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Affiliation(s)
- Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hideo Okumura
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Seiki Baba
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yoshihiro Fukumori
- Nano Life Science Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kunio Miki
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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3
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Lee Y, Kim JG, Lee SJ, Muniyappan S, Kim TW, Ki H, Kim H, Jo J, Yun SR, Lee H, Lee KW, Kim SO, Cammarata M, Ihee H. Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering. Nat Commun 2021; 12:3677. [PMID: 34135339 PMCID: PMC8209046 DOI: 10.1038/s41467-021-23947-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion. Femtosecond time-resolved X-ray solution scattering (fs-TRXSS) measurements provide information on the structural dynamics of proteins in solution. Here, the authors present a structure refinement method for the analysis of fs-TRXSS data and use it to characterise the ultrafast structural changes of homodimeric haemoglobin.
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Affiliation(s)
- Yunbeom Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Srinivasan Muniyappan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hanui Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Junbeom Jo
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Kyung Won Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | | | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea. .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
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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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5
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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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6
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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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7
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Chintapalli SV, Anishkin A, Adams SH. Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin. Arch Biochem Biophys 2018; 655:56-66. [PMID: 30092229 DOI: 10.1016/j.abb.2018.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 11/26/2022]
Abstract
Myoglobin, besides its role in oxygen turnover, has gained recognition as a potential regulator of lipid metabolism. Previously, we confirmed the interaction of fatty acids and acylcarnitines with Oxy-Myoglobin, using both molecular dynamic simulations and Isothermal Titration Calorimetry studies. However, those studies were limited to testing only the binding sites derived from homology to fatty acid binding proteins and predictions using automated docking. To explore the entry mechanisms of the lipid ligands into myoglobin, we conducted molecular dynamic simulations of murine Oxy- and Deoxy-Mb structures with palmitate or palmitoylcarnitine starting at different positions near the protein surface. The simulations indicated that both ligands readily (under ∼10-20 ns) enter the Oxy-Mb structure through a dynamic area ("portal region") near heme, known to be the entry point for small molecule gaseous ligands like O2, CO and NO. The entry is not observed with Deoxy-Mb where lipid ligands move away from protein surface, due to a compaction of the entry portal and the heme-containing crevice in the Mb protein upon O2 removal. The results suggest quick spontaneous binding of lipids to Mb driven by hydrophobic interactions, strongly enhanced by oxygenation, and consistent with the emergent role of Mb in lipid metabolism.
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Affiliation(s)
- Sree V Chintapalli
- Arkansas Children's Nutrition Center -and- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, USA.
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, USA
| | - Sean H Adams
- Arkansas Children's Nutrition Center -and- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, USA
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8
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El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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9
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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10
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Nienhaus K, Hahn V, Hüpfel M, Nienhaus GU. Substrate Binding Primes Human Tryptophan 2,3-Dioxygenase for Ligand Binding. J Phys Chem B 2017; 121:7412-7420. [PMID: 28715185 DOI: 10.1021/acs.jpcb.7b03463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human heme enzyme tryptophan 2,3-dioxygenase (hTDO) catalyzes the insertion of dioxygen into its cognate substrate, l-tryptophan (l-Trp). Its active site structure is highly dynamic, and the mechanism of enzyme-substrate-ligand complex formation and the ensuing enzymatic reaction is not yet understood. Here we have studied complex formation in hTDO by using time-resolved optical and infrared spectroscopy with carbon monoxide (CO) as a ligand. We have observed that both substrate-free and substrate-bound hTDO coexist in two discrete conformations with greatly different ligand binding rates. In the fast rebinding hTDO conformation, there is facile ligand access to the heme iron, but it is greatly hindered in the slowly rebinding conformation. Spectroscopic evidence implicates active site solvation as playing a crucial role for the observed kinetic differences. Substrate binding shifts the conformational equilibrium markedly toward the fast species and thus primes the active site for subsequent ligand binding, ensuring that formation of the ternary complex occurs predominantly by first binding l-Trp and then the ligand. Consequently, the efficiency of catalysis is enhanced because O2 binding prior to substrate binding, resulting in nonproductive oxidation of the heme iron, is greatly suppressed.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Vincent Hahn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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11
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Diamantis P, Unke OT, Meuwly M. Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N. PLoS Comput Biol 2017; 13:e1005450. [PMID: 28358830 PMCID: PMC5391117 DOI: 10.1371/journal.pcbi.1005450] [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: 10/06/2016] [Revised: 04/13/2017] [Accepted: 03/13/2017] [Indexed: 11/18/2022] Open
Abstract
In heme proteins, the efficient transport of ligands such as NO or O2 to the binding site is achieved via ligand migration networks. A quantitative assessment of ligand diffusion in these networks is thus essential for a better understanding of the function of these proteins. For this, Xe migration in truncated hemoglobin N (trHbN) of Mycobacterium Tuberculosis was studied using molecular dynamics simulations. Transitions between pockets of the migration network and intra-pocket relaxation occur on similar time scales (10 ps and 20 ps), consistent with low free energy barriers (1-2 kcal/mol). Depending on the pocket from where Xe enters a particular transition, the conformation of the side chains lining the transition region differs which highlights the coupling between ligand and protein degrees of freedom. Furthermore, comparison of transition probabilities shows that Xe migration in trHbN is a non-Markovian process. Memory effects arise due to protein rearrangements and coupled dynamics as Xe moves through it. Binding and transport of ligands in proteins is essential, in particular in globular proteins which often exhibit internal cavities. In truncated Hemoglobin N (trHbN) these cavities are arranged as a network with particular connectivities. The present work supports the notion that ligand diffusion in trHbN is an active process and coupled to the protein dynamics. Furthermore, transition probabilities between neighboring pockets depend on the location from where the ligand entered the transition, which is typical for non-Markovian processes. Hence, ligand migration in trHbN exhibits memory effects due to dynamical coupling between the protein and ligand motion.
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Affiliation(s)
| | - Oliver T. Unke
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
- * E-mail:
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12
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Andrew CR, Petrova ON, Lamarre I, Lambry JC, Rappaport F, Negrerie M. The Dynamics Behind the Affinity: Controlling Heme-Gas Affinity via Geminate Recombination and Heme Propionate Conformation in the NO Carrier Cytochrome c'. ACS Chem Biol 2016; 11:3191-3201. [PMID: 27709886 DOI: 10.1021/acschembio.6b00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) sensors are heme proteins which may also bind CO and O2. Control of heme-gas affinity and their discrimination are achieved by the structural properties and reactivity of the heme and its distal and proximal environments, leading to several energy barriers. In the bacterial NO sensor cytochrome c' from Alcaligenes xylosoxidans (AXCP), the single Leu16Ala distal mutation boosts the affinity for gas ligands by a remarkable 106-108-fold, transforming AXCP from one of the lowest affinity gas binding proteins to one of the highest. Here, we report the dynamics of diatomics after photodissociation from wild type and L16A-AXCP over 12 orders of magnitude in time. For the L16A variant, the picosecond geminate rebinding of both CO and NO appears with an unprecedented 100% yield, and no exit of these ligands from protein to solvent could be observed. Molecular dynamic simulations saliently demonstrate that dissociated CO stays within 4 Å from Fe2+, in contrast to wild-type AXCP. The L16A mutation confers a heme propionate conformation and docking site which traps the diatomics, maximizing the probability of recombination and directly explaining the ultrahigh affinities for CO, NO, and O2. Overall, our results point to a novel mechanism for modulating heme-gas affinities in proteins.
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Affiliation(s)
- Colin R. Andrew
- Department
of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Olga N. Petrova
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Fabrice Rappaport
- Laboratoire
de Physiologie Membranaire et Moléculaire du Chloroplaste, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Michel Negrerie
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
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13
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Trana EN, Nocek JM, Woude JV, Span I, Smith SM, Rosenzweig AC, Hoffman BM. Charge-Disproportionation Symmetry Breaking Creates a Heterodimeric Myoglobin Complex with Enhanced Affinity and Rapid Intracomplex Electron Transfer. J Am Chem Soc 2016; 138:12615-28. [PMID: 27646786 DOI: 10.1021/jacs.6b07672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report rapid photoinitiated intracomplex electron transfer (ET) within a "charge-disproportionated" myoglobin (Mb) dimer with greatly enhanced affinity. Two mutually supportive Brownian Dynamics (BD) interface redesign strategies, one a new "heme-filtering" approach, were employed to "break the symmetry" of a Mb homodimer by pairing Mb constructs with complementary highly positive and highly negative net surface charges, introduced through D/E → K and K → E mutations, respectively. BD simulations using a previously developed positive mutant, Mb(+6) = Mb(D44K/D60K/E85K), led to construction of the complementary negative mutant Mb(-6) = Mb(K45E, K63E, K95E). Simulations predict the pair will form a well-defined complex comprising a tight ensemble of conformations with nearly parallel hemes, at a metal-metal distance ∼18-19 Å. Upon expression and X-ray characterization of the partners, BD predictions were verified through ET photocycle measurements enabled by Zn-deuteroporphyrin substitution, forming the [ZnMb(-6), Fe(3+)Mb(+6)] complex. Triplet ET quenching shows charge disproportionation increases the binding constant by no less than ∼5 orders of magnitude relative to wild-type Mb values. All progress curves for charge separation (CS) and charge recombination (CR) are reproduced by a generalized kinetic model for the interprotein ET photocycle. The intracomplex ET rate constants for both CS and CR are increased by over 5 orders of magnitude, and their viscosity independence is indicative of true interprotein ET, rather than dynamic gating as seen in previous studies. The complex displays an unprecedented timecourse for CR of the CS intermediate I. After a laser flash, I forms through photoinduced CS, accumulates to a maximum concentration, then dies away through CR. However, before completely disappearing, I reappears without another flash and reaches a second maximum before disappearing completely.
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Affiliation(s)
- Ethan N Trana
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Judith M Nocek
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Jon Vander Woude
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Ingrid Span
- Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Stephen M Smith
- Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
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14
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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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15
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Gupta PK, Meuwly M. Ligand and interfacial dynamics in a homodimeric hemoglobin. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:012003. [PMID: 26958581 PMCID: PMC4760971 DOI: 10.1063/1.4940228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/08/2016] [Indexed: 05/18/2023]
Abstract
The structural dynamics of dimeric hemoglobin (HbI) from Scapharca inaequivalvis in different ligand-binding states is studied from atomistic simulations on the μs time scale. The intermediates are between the fully ligand-bound (R) and ligand-free (T) states. Tertiary structural changes, such as rotation of the side chain of Phe97, breaking of the Lys96-heme salt bridge, and the Fe-Fe separation, are characterized and the water dynamics along the R-T transition is analyzed. All these properties for the intermediates are bracketed by those determined experimentally for the fully ligand-bound and ligand-free proteins, respectively. The dynamics of the two monomers is asymmetric on the 100 ns timescale. Several spontaneous rotations of the Phe97 side chain are observed which suggest a typical time scale of 50-100 ns for this process. Ligand migration pathways include regions between the B/G and C/G helices and, if observed, take place in the 100 ns time scale.
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Affiliation(s)
- Prashant Kumar Gupta
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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16
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Trujillo K, Papagiannopoulos T, Olsen KW. Effects of mutations on the molecular dynamics of oxygen escape from the dimeric hemoglobin of Scapharca inaequivalvis. F1000Res 2015; 4:65. [PMID: 25866622 PMCID: PMC4376171 DOI: 10.12688/f1000research.6127.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2015] [Indexed: 12/15/2022] Open
Abstract
Like many hemoglobins, the structure of the dimeric hemoglobin from the clam
Scapharca inaequivalvis is a “closed bottle” since there is no direct tunnel from the oxygen binding site on the heme to the solvent. The proximal histidine faces the dimer interface, which consists of the E and F helicies. This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules. Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the structure would seem to make that pathway less likely. Locally enhanced sampling molecular dynamics are used here to suggest alternative pathways in the wild-type and six mutant proteins. In most cases the point mutations change the selection of exit routes observed in the simulations. Exit via the histidine gate is rarely seem although oxygen molecules do occasionally cross over the interface from one subunit to the other. The results suggest that changes in flexibility and, in some cases, creation of new cavities can explain the effects of the mutations on ligand exit paths.
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Affiliation(s)
- Kevin Trujillo
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Tasso Papagiannopoulos
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
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17
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Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 DOI: 10.12688/f1000research.5836.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2014] [Indexed: 03/23/2024] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
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Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany ; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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18
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Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 PMCID: PMC4304226 DOI: 10.12688/f1000research.5836.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/11/2014] [Indexed: 11/20/2022] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
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Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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19
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Zhao J, Srajer V, Franzen S. Functional consequences of the open distal pocket of dehaloperoxidase-hemoglobin observed by time-resolved X-ray crystallography. Biochemistry 2013; 52:7943-50. [PMID: 24116924 DOI: 10.1021/bi401118q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using time-resolved X-ray crystallography, we contrast a bifunctional dehaloperoxidase-hemoglobin (DHP) with previously studied examples of myoglobin and hemoglobin to understand the functional role of the distal pocket of globins. One key functional difference between DHP and other globins is the requirement that H2O2 enter the distal pocket of oxyferrous DHP to displace O2 from the heme Fe atom and thereby activate the heme for the peroxidase function. The open architecture of DHP permits more than one molecule to simultaneously enter the distal pocket of the protein above the heme to facilitate the unique peroxidase cycle starting from the oxyferrous state. The time-resolved X-ray data show that the distal pocket of DHP lacks a protein valve found in the two other globins that have been studied previously. The photolyzed CO ligand trajectory in DHP does not have a docking site; rather, the CO moves immediately to the Xe-binding site. From there, CO can escape but can also recombine an order of magnitude more rapidly than in other globins. The contrast with DHP dynamics and function more precisely defines the functional role of the multiple conformational states of myoglobin. Taken together with the high reduction potential of DHP, the open distal site helps to explain how a globin can also function as a peroxidase.
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Affiliation(s)
- Junjie Zhao
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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20
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Nienhaus K, Zosel F, Nienhaus GU. Ligand binding to heme proteins: a comparison of cytochrome c variants with globins. J Phys Chem B 2012; 116:12180-8. [PMID: 22978708 DOI: 10.1021/jp306775n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have studied the binding of carbon monoxide (CO) in mutants of Cyt c having its methionine at position 80 replaced by alanine, aspartate, and arginine, so that the sixth coordination is available for ligand binding. We have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy to examine interactions of the heme-bound and photolyzed CO (and also nitric oxide, NO) in the small heme pocket created by the mutations. By using FTIR temperature derivative spectroscopy (TDS) and nanosecond flash photolysis, the enthalpy barrier distributions for CO rebinding were determined. In flash photolysis experiments, the majority of ligands rebind to the heme iron on picosecond time scales so that only the high-barrier tail of the distributions is visible on the nanosecond scale. By continuous wave excitation prior to TDS characterization of the barriers, however, each Cyt c molecule is photoexcited multiple times and complete photodissociation can be achieved, which likely arises from a rotation of the CO within the heme pocket so that the oxygen faces the heme iron. Apparently, reorientation prior to rebinding constitutes an additional and significant contribution to the rebinding barrier. Our experiments reveal that the compact, rigid structure of Cyt c offers no alternative binding sites for photodissociated ligands in the protein matrix. A comparison of ligand binding in these Cyt c mutants and hemoglobins underscores the importance of internal ligand docking sites and ligand migration routes for conveying a ligand binding function to heme proteins.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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21
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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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22
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Drummond ML, Wilson AK, Cundari TR. Carbon Dioxide Migration Pathways in Proteins. J Phys Chem Lett 2012; 3:830-833. [PMID: 26286405 DOI: 10.1021/jz3001085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Some of the most important biological processes, such as carbon fixation, are dependent on protein-gas interactions. The motion of CO2 through the enzyme phosphoenolpyruvate carboxykinase was investigated using extensive all-atom molecular dynamics simulations. Three discrete migration pathways were located, suggesting the protein directs the movement of CO2. The chemical nature of these pathways is discussed, as are their biotechnological ramifications.
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Affiliation(s)
- Michael L Drummond
- Center for Advanced Scientific Computing and Modeling (CASCaM), Department of Chemistry, University of North Texas, Denton, Texas 76203-5070, United States
| | - Angela K Wilson
- Center for Advanced Scientific Computing and Modeling (CASCaM), Department of Chemistry, University of North Texas, Denton, Texas 76203-5070, United States
| | - Thomas R Cundari
- Center for Advanced Scientific Computing and Modeling (CASCaM), Department of Chemistry, University of North Texas, Denton, Texas 76203-5070, United States
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23
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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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24
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Carbon monoxide poisoning is prevented by the energy costs of conformational changes in gas-binding haemproteins. Proc Natl Acad Sci U S A 2011; 108:15780-5. [PMID: 21900609 DOI: 10.1073/pnas.1109051108] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbon monoxide (CO) is a product of haem metabolism and organisms must evolve strategies to prevent endogenous CO poisoning of haemoproteins. We show that energy costs associated with conformational changes play a key role in preventing irreversible CO binding. AxCYTcp is a member of a family of haem proteins that form stable 5c-NO and 6c-CO complexes but do not form O(2) complexes. Structure of the AxCYTcp-CO complex at 1.25 Å resolution shows that CO binds in two conformations moderated by the extent of displacement of the distal residue Leu16 toward the haem 7-propionate. The presence of two CO conformations is confirmed by cryogenic resonance Raman data. The preferred linear Fe-C-O arrangement (170 ± 8°) is accompanied by a flip of the propionate from the distal to proximal face of the haem. In the second conformation, the Fe-C-O unit is bent (158 ± 8°) with no flip of propionate. The energetic cost of the CO-induced Leu-propionate movements is reflected in a 600 mV (57.9 kJ mol(-1)) decrease in haem potential, a value in good agreement with density functional theory calculations. Substitution of Leu by Ala or Gly (structures determined at 1.03 and 1.04 Å resolutions) resulted in a haem site that binds CO in the linear mode only and where no significant change in redox potential is observed. Remarkably, these variants were isolated as ferrous 6c-CO complexes, attributable to the observed eight orders of magnitude increase in affinity for CO, including an approximately 10,000-fold decrease in the rate of dissociation. These new findings have wide implications for preventing CO poisoning of gas-binding haem proteins.
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25
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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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26
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Birukou I, Soman J, Olson JS. Blocking the gate to ligand entry in human hemoglobin. J Biol Chem 2010; 286:10515-29. [PMID: 21193395 DOI: 10.1074/jbc.m110.176271] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.
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Affiliation(s)
- Ivan Birukou
- Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
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27
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Gnanasekaran R, Xu Y, Leitner DM. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin. J Phys Chem B 2010; 114:16989-96. [PMID: 21126033 DOI: 10.1021/jp109173t] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.
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28
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Nienhaus K, Nienhaus GU. Ligand dynamics in heme proteins observed by Fourier transform infrared-temperature derivative spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1030-41. [PMID: 20656073 DOI: 10.1016/j.bbapap.2010.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a powerful tool for the investigation of protein-ligand interactions in heme proteins. Nitric oxide and carbon monoxide are attractive physiologically relevant ligands because their bond stretching vibrations give rise to strong mid-infrared absorption bands that can be measured with exquisite sensitivity and precision using photolysis difference spectroscopy at cryogenic temperatures. These stretching bands are fine-tuned by electrostatic interactions with the environment and, therefore, ligands can be utilized as local probes of structure and dynamics. Bound to the heme iron, the ligand stretching bands are susceptible to changes in the iron-ligand bond and the electric field at the active site. Upon photolysis, the vibrational bands display changes due to ligand relocation to docking sites within the protein, rotational motions of the ligand in these sites and protein conformational changes. Photolysis difference spectra taken over a wide temperature range (3-300K) using specific temperature protocols for sample photodissociation can provide detailed insights into both protein and ligand dynamics. Moreover, temperature-derivative spectroscopy (TDS) has proven to be a particularly powerful technique to study protein-ligand interactions. The FTIR-TDS technique has been extensively applied to studies of carbon monoxide binding to heme proteins, whereas measurements with nitric oxide are still scarce. Here we describe infrared cryo-spectroscopy and present a variety of applications to the study of protein-ligand interactions in heme proteins. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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29
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Knapp JE, Pahl R, Cohen J, Nichols JC, Schulten K, Gibson QH, Srajer V, Royer WE. Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis. Structure 2010; 17:1494-504. [PMID: 19913484 DOI: 10.1016/j.str.2009.09.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 08/25/2009] [Accepted: 09/09/2009] [Indexed: 11/19/2022]
Abstract
As in many other hemoglobins, no direct route for migration of ligands between solvent and active site is evident from crystal structures of Scapharca inaequivalvis dimeric HbI. Xenon (Xe) and organic halide binding experiments, along with computational analysis presented here, reveal protein cavities as potential ligand migration routes. Time-resolved crystallographic experiments show that photodissociated carbon monoxide (CO) docks within 5 ns at the distal pocket B site and at more remote Xe4 and Xe2 cavities. CO rebinding is not affected by the presence of dichloroethane within the major Xe4 protein cavity, demonstrating that this cavity is not on the major exit pathway. The crystal lattice has a substantial influence on ligand migration, suggesting that significant conformational rearrangements may be required for ligand exit. Taken together, these results are consistent with a distal histidine gate as one important ligand entry and exit route, despite its participation in the dimeric interface.
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Affiliation(s)
- James E Knapp
- Department of Biochemistry and Molecular Pharmacology, The University of Massachusetts Medical School, Worcester, MA 01605, USA
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30
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31
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Nickel E, Nienhaus K, Lu C, Yeh SR, Nienhaus GU. Ligand and substrate migration in human indoleamine 2,3-dioxygenase. J Biol Chem 2009; 284:31548-54. [PMID: 19767648 DOI: 10.1074/jbc.m109.039859] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human indoleamine 2,3-dioxygenase (hIDO), a monomeric heme enzyme, catalyzes the oxidative degradation of L-Trp and other indoleamine derivatives. Using Fourier transform infrared and optical absorption spectroscopy, we have investigated the interplay between ferrous hIDO, the ligand analog CO, and the physiological substrate L-Trp. These data provide the long sought evidence for two distinct L-Trp binding sites. Upon photodissociation from the heme iron at T > 200 K, CO escapes into the solvent. Concomitantly, L-Trp exits the active site and, depending on the l-Trp concentration, migrates to a secondary binding site or into the solvent. Although L-Trp is spectroscopically silent at this site, it is still noticeable due to its pronounced effect on the CO association kinetics, which are significantly slower than those of L-Trp-free hIDO. L-Trp returns to its initial site only after CO has rebound to the heme iron.
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Affiliation(s)
- Elena Nickel
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany
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32
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Murray JW, Maghlaoui K, Kargul J, Sugiura M, Barber J. Analysis of xenon binding to photosystem II by X-ray crystallography. PHOTOSYNTHESIS RESEARCH 2008; 98:523-7. [PMID: 18839332 DOI: 10.1007/s11120-008-9366-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 09/09/2008] [Indexed: 05/03/2023]
Abstract
In order to investigate oxygen binding and hydrophobic cavities in photosystem II (PSII), we have introduced xenon under pressure into crystals of PSII isolated from Thermosynechococcus elongatus and used X-ray anomalous diffraction analyses to identify the xenon sites in the complex. Under the conditions employed, 25 Xe-binding sites were identified in each monomer of the dimeric PSII complex. The majority of these were distributed within the membrane spanning portion of the complex with no obvious correlation with the previously proposed oxygen channels. One binding site was located close to the haem of cytochrome b559 in a position analogous to a Xe-binding site of myoglobin. The only Xe-binding site not associated with the intrinsic subunits of PSII was within the hydrophobic core of the PsbO protein.
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Affiliation(s)
- J W Murray
- Division of Molecular Biosciences, Imperial College London, London, UK
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