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Siddika MA, Oi H, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Structural Expansion of Catalytic RNA Nanostructures through Oligomerization of a Cyclic Trimer of Engineered Ribozymes. Molecules 2023; 28:6465. [PMID: 37764241 PMCID: PMC10535472 DOI: 10.3390/molecules28186465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The multimolecular assembly of three-dimensionally structured proteins forms their quaternary structures, some of which have high geometric symmetry. The size and complexity of protein quaternary structures often increase in a hierarchical manner, with simpler, smaller structures serving as units for larger quaternary structures. In this study, we exploited oligomerization of a ribozyme cyclic trimer to achieve larger ribozyme-based RNA assembly. By installing kissing loop (KL) interacting units to one-, two-, or three-unit RNA molecules in the ribozyme trimer, we constructed dimers, open-chain oligomers, and branched oligomers of ribozyme trimer units. One type of open-chain oligomer preferentially formed a closed tetramer containing 12 component RNAs to provide 12 ribozyme units. We also observed large assembly of ribozyme trimers, which reached 1000 nm in size.
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Affiliation(s)
- Mst. Ayesha Siddika
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Toyama, Japan (S.M.)
| | - Hiroki Oi
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Toyama, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8501, Kyoto, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Kyoto, Japan; (H.S.); (M.E.)
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Kyoto, Japan; (H.S.); (M.E.)
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita 564-8680, Osaka, Japan
| | - Shigeyoshi Matsumura
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Toyama, Japan (S.M.)
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Toyama, Japan
| | - Yoshiya Ikawa
- Graduate School of Innovative Life Science, University of Toyama, Toyama 930-8555, Toyama, Japan (S.M.)
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Toyama, Japan
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2
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Pesce A, Barmpidi K, Dewilde S, Estarellas C, Moens L, Bolognesi M, Luque FJ, Nardini M. Structural and dynamic characterization of the hexa-coordinated globin from Spisula solidissima. J Inorg Biochem 2023; 246:112289. [PMID: 37354606 DOI: 10.1016/j.jinorgbio.2023.112289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023]
Abstract
High energy consumption in the nervous system requires a continuous supply of O2. This role is assisted by proteins from the globin super-family in the nerve cells of invertebrates, where 'nerve hemoglobins' (nHbs) are mainly present at mM concentrations and exhibit oxygen affinities comparable to those of vertebrate myoglobins. To gain insight into the structural bases of this function, we report the crystal structure of nHb from the Atlantic surf clam Spisula solidissima (SsHb), previously suggested to display a bis-histidyl hexa-coordinated heme in the deoxy state, high O2 affinity, and ligand binding cooperativity when assayed in situ. The crystallized protein forms a dimer through packing of a 4-helix bundle involving helices E and F of each subunit. The SsHb 'classic' globin fold displays bis-histidyl (His71(E7) and His103(F8)) hexa-coordination of the heme-Fe atom, with structural and dynamics variations found in the inter-helix hinge regions. Molecular Dynamics simulations of both monomeric and dimeric species in the bis-histidyl hexa-coordinated, deoxy penta-coordinated, and O2-bound hexa-coordinated states reveal distinct structural rearrangements at the interface between subunits in the dimer; these would affect the magnitude of the conformational fluctuations observed between monomer and dimer, and the topology of cavities within the protein matrix and at the interface. These results point to a distal site opening mechanism allowing access of the exogenous ligand to the heme and cast hypotheses on the dimer interface structural and dynamic properties that may support ligand binding cooperativity in dimeric SsHb.
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Affiliation(s)
- Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, I-16146 Genova, Italy
| | - Katerina Barmpidi
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Institut de Biomedicina (IBUB) and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Institut de Biomedicina (IBUB) and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milan, Italy
| | - Francisco Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Institut de Biomedicina (IBUB) and Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona, Campus de l'Alimentació de Torribera, Santa Coloma de Gramenet, Spain
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milan, Italy.
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3
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Maiti BK. Cross‐talk Between (Hydrogen)Sulfite and Metalloproteins: Impact on Human Health. Chemistry 2022; 28:e202104342. [DOI: 10.1002/chem.202104342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Indexed: 12/28/2022]
Affiliation(s)
- Biplab K Maiti
- Department of Chemistry National Institute of Technology Sikkim, Ravangla Campus Barfung Block, Ravangla Sub Division South Sikkim 737139 India
- Department of Chemistry Cluster University of Jammu Canal Road Jammu 180001
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4
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Nascimento ED, Abrantes-Coutinho VE, Oliveira TMBF, Santiago PS, Carvalho FAO. Biorecognition of hydrogen peroxide using a novel electrochemical platform designed with Glossoscolex paulistus giant hemoglobin. Anal Bioanal Chem 2022; 414:3729-3739. [PMID: 35338376 DOI: 10.1007/s00216-022-04020-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022]
Abstract
The giant extracellular hemoglobin of the annelid Glossoscolex paulistus (HbGp; 3.6 MDa) is a valuable and underexplored supramolecular hemoprotein system for the biorecognition of reactive oxygen species. In this work, an efficient and simple electrochemical platform was designed for analyzing H2O2, using HbGp covalently immobilized on Nafion®-modified glassy carbon electrode, named as HbGp/Nafion/GCE. Voltammetric and spectroscopic studies revealed the importance of prior modification of the electrodic support with the conducting polymer to obtain satisfactory hemoglobin electroactivity, as well as a biocompatible microenvironment for its immobilization. In terms of biological activity, it was observed a greater reactivity of the biomolecule in acidic medium, enabling the detection of the analyte by a quasi-reversible mechanism, whose kinetics was limited by analyte diffusion. In the presence of H2O2, the native structure of hemoglobin (oxy-HbGp (Fe2+)) oxidizes to ferryl-HbGp (Fe4+) and this redox reaction can be monitored on HbGp/Nafion/GCE with a detection limit of 8.5 × 10‒7 mol L-1. In addition to high sensitivity, the electrochemical biosensor also provided reproducible, consistent, and accurate measurements. The electroanalytical method showed an appropriate performance to quantify different levels of H2O2 in milk samples, proving the potential of HbGp/Nafion/GCE for this purpose.
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Affiliation(s)
- Evair D Nascimento
- Departamento de Química, Universidade Federal de São Carlos, Rod. Washington Luís km 235, São Carlos, SP, 13565-905, Brazil.,Universidade Federal Do Sul E Sudeste Do Pará, Folha 17, Quadra 04, Lote Especial, Marabá, PA, 68505-080, Brazil
| | - Vanessa E Abrantes-Coutinho
- Centro de Ciência E Tecnologia, Universidade Federal Do Cariri, Avenida Tenente Raimundo Rocha, 1639, Cidade Universitária, Juazeiro Do Norte, CE, 63048-080, Brazil
| | - Thiago M B F Oliveira
- Centro de Ciência E Tecnologia, Universidade Federal Do Cariri, Avenida Tenente Raimundo Rocha, 1639, Cidade Universitária, Juazeiro Do Norte, CE, 63048-080, Brazil
| | - Patrícia S Santiago
- Universidade Estadual Paulista, Instituto Avançado de Estudos Do Mar, Campus de Registro, Av. Nelson Brihi Badur, 430 - Vila Tupy, Registro, SP, 11900-000, Brazil
| | - Francisco A O Carvalho
- Universidade Federal Do Sul E Sudeste Do Pará, Folha 17, Quadra 04, Lote Especial, Marabá, PA, 68505-080, Brazil.
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Yu K, Hidaka K, Sugiyama H, Endo M, Matsumura S, Ikawa Y. A hexameric ribozyme nanostructure formed by double-decker assembly of a pair of triangular ribozyme trimers. Chembiochem 2022; 23:e202100573. [PMID: 35088928 DOI: 10.1002/cbic.202100573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/29/2021] [Indexed: 11/12/2022]
Abstract
The modular architecture of naturally occurring ribozymes makes them a promising class of structural platforms to design and assemble three-dimensional (3D) RNA nanostructures, into which the catalytic ability of the platform ribozyme can be installed. We have constructed and analyzed RNA nanostructures with polygonal-shaped (closed) ribozyme oligomers by assembling unit RNAs derived from the Tetrahymena group I intron with a typical modular architecture. In this study, we dimerized ribozyme trimers with a triangular shape by introducing three pillar units. The resulting double-decker nanostructures containing six ribozyme units were characterized biochemically and their structures were observed by atomic force microscopy. The double-decker hexamers exhibited higher catalytic activity than the parent ribozyme trimers.
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Affiliation(s)
- Kai Yu
- University of Toyama: Toyama Daigaku, Department of Chemistry, JAPAN
| | - Kumi Hidaka
- Kyoto University: Kyoto Daigaku, Department of Chemistry, JAPAN
| | | | | | | | - Yoshiya Ikawa
- University of Toyama, Chemistry, Gofuku 3190, 930-8555, Toyama, JAPAN
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6
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Bellelli A, Tame JRH. Hemoglobin allostery and pharmacology. Mol Aspects Med 2021; 84:101037. [PMID: 34600771 DOI: 10.1016/j.mam.2021.101037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
The oxygen demands of the human body require the constant circulation of blood carrying an enormous concentration of hemoglobin (Hb). Oxygen transport depends not only on the amount of Hb, but also on the control over the affinity of the protein for the gas, which can be optimized for the environmental conditions by changes in the concentration of effectors (hydrogen ions, chloride, CO2, and DPG) inside the red cell. Some pathological conditions affecting Hb may benefit from pharmacological interventions to increase or decrease its affinity for oxygen, or otherwise modify its properties, or alter its biosynthesis. Examples of such conditions include sickle cell anemia, thalassemias and inherited hemoglobinopathies. Effective and safe drugs such as voxelotor, bezafibrate and efaproxiral are available that significantly increase or decrease Hb oxygen affinity. Some medical conditions not directly affecting the blood or its oxygen carrying capacity may also be relieved by the manipulation of Hb. For example, the standard treatment of acute cyanide poisoning requires the oxidation of a fraction of the Hb in the bloodstream so that it efficiently scavenges cyanide. Tumors are often extremely hypoxic and therefore strongly resistant to radiotherapy; the sensitivity of cancerous tissue to X-rays may be increased by improved oxygenation through drugs binding Hb. This review attempts to provide a systematic exploration of the pharmacology of Hb, its molecular basis, and its intended and possible uses.
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Affiliation(s)
- Andrea Bellelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
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Kumar S, Kumar K, Yadav R, Kukutla P, Devunuri N, Deenadayalu N, Venkatesu P. Understanding the close encounter of heme proteins with carboxylated multiwalled carbon nanotubes: a case study of contradictory stability trend for hemoglobin and myoglobin. Phys Chem Chem Phys 2021; 23:19740-19751. [PMID: 34525143 DOI: 10.1039/d1cp02167b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Carbon nanotubes (CNTs) are one of the unique and promising nanomaterials that possess plenty of applications, such as biosensors, advanced drug delivery systems and biotechnology. CNTs bind rapidly with proteins, which result in the formation of a protein coating layer known as a "protein corona" around the surface of the nanomaterial. This hinders their applications as a drug carrier and influences the properties of biological macromolecules. The present work focuses on studying the thermal stability and molecular level interactions of two heme proteins, hemoglobin (Hb) and myoglobin (Mb), in the presence of carboxylated functionalized multi-walled CNTs (CA-MWCNTs). Through the current study, the following steps have been taken to distinguish the biocompatibility of the hydrophilic surface CA-MWCNTs for heme proteins via a series of spectroscopic techniques and differential scanning calorimetry (DSC). UV-Visible and steady-state fluorescence spectroscopy were used to reveal changes in the aromatic amino acid residues of heme proteins upon the addition of CA-MWCNTs. Circular dichroism spectroscopy (CD) shows the alteration in the native structure of proteins in the presence of the nanomaterial. A tremendous increase in the size of the protein CA-MWCNTs system is observed in dynamic light scattering (DLS), which clearly manifests the protein corona formation. Unexpectedly, both proteins interact differently with CA-MWCNTs, which is observed in CD spectroscopy and DSC. In the presence of CA-MWCNTs, an increase in the transition temperature (Tm) was observed for Hb, while the Tm value decreases for Mb. Different interactions with proteins at the molecular scale may be the reason for this unexpected behavior. Henceforth, the present results can help in the design of the next-generation drug carrier nanomaterials with the idea of the heme protein corona formation prior to development.
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Affiliation(s)
- Sumit Kumar
- Department of Chemistry, University of Delhi, Delhi-110 007, India.
| | - Krishan Kumar
- Department of Chemistry, University of Delhi, Delhi-110 007, India.
| | - Ritu Yadav
- Department of Chemistry, University of Delhi, Delhi-110 007, India.
| | - Prasanna Kukutla
- Department of Chemistry, University of Delhi, Delhi-110 007, India. .,Vignan's Foundation for Science, Technology and Research (VFSTR) Deemed to be University, Vadlamudi, Guntur-522 213, Andhra Pradesh, India
| | - Nagaraju Devunuri
- Vignan's Foundation for Science, Technology and Research (VFSTR) Deemed to be University, Vadlamudi, Guntur-522 213, Andhra Pradesh, India
| | - Nirmala Deenadayalu
- Department of Chemistry, Durban University of Technology, Durban-4000, South Africa
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8
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Cooperativity and Allostery in RNA Systems. Methods Mol Biol 2020; 2253:255-271. [PMID: 33315228 DOI: 10.1007/978-1-0716-1154-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Allostery is among the most basic biological principles employed by biological macromolecules to achieve a biologically active state in response to chemical cues. Although initially used to describe the impact of small molecules on the conformation and activity of protein enzymes, the definition of this term has been significantly broadened to describe long-range conformational change of macromolecules in response to small or large effectors. Such a broad definition could be applied to RNA molecules, which do not typically serve as protein-free cellular enzymes but fold and form macromolecular assemblies with the help of various ligand molecules, including ions and proteins. Ligand-induced allosteric changes in RNA molecules are often accompanied by cooperative interactions between RNA and its ligand, thus streamlining the folding and assembly pathways. This chapter provides an overview of the interplay between cooperativity and allostery in RNA systems and outlines methods to study these two biological principles.
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Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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Reid KM, Yamato T, Leitner DM. Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin. J Phys Chem B 2020; 124:1148-1159. [DOI: 10.1021/acs.jpcb.9b11413] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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11
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Svejdal RR, Dickinson ER, Sticker D, Kutter JP, Rand KD. Thiol-ene Microfluidic Chip for Performing Hydrogen/Deuterium Exchange of Proteins at Subsecond Time Scales. Anal Chem 2018; 91:1309-1317. [DOI: 10.1021/acs.analchem.8b03050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rasmus R. Svejdal
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Eleanor R. Dickinson
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Drago Sticker
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jörg P. Kutter
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kasper D. Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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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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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation. J Inorg Biochem 2018; 181:65-73. [DOI: 10.1016/j.jinorgbio.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 12/11/2017] [Accepted: 01/07/2018] [Indexed: 11/18/2022]
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15
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Functional diversification of sea lamprey globins in evolution and development. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:283-291. [PMID: 29155105 DOI: 10.1016/j.bbapap.2017.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/06/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022]
Abstract
Agnathans have a globin repertoire that markedly differs from that of jawed (gnathostome) vertebrates. The sea lamprey (Petromyzon marinus) harbors at least 18 hemoglobin, two myoglobin, two globin X, and one cytoglobin genes. However, agnathan hemoglobins and myoglobins are not orthologous to their cognates in jawed vertebrates. Thus, blood-based O2 transport and muscle-based O2 storage proteins emerged twice in vertebrates from a tissue-globin ancestor. Notably, the sea lamprey displays three switches in hemoglobin expression in its life cycle, analogous to hemoglobin switching in vertebrates. To study the functional changes associated with the evolution and ontogenesis of distinct globin types, we determined O2 binding equilibria, type of quaternary assembly, and nitrite reductase enzymatic activities of one adult (aHb5a) and one embryonic/larval hemoglobin (aHb6), myoglobin (aMb1) and cytoglobin (Cygb) of the sea lamprey. We found clear functional differentiation among globin types expressed at different developmental stages and in different tissues. Cygb and aMb1 have high O2 affinity and nitrite reductase activity, while the two hemoglobins display low O2 affinity and nitrite reductase activity. Cygb and aHb6 but not aHb5a show cooperative O2 binding, correlating with increased stability of dimers, as shown by gel filtration and molecular modeling. The high O2-affinity and the lack of cooperativity confirm the identity of the sea lamprey aMb1 as O2 storage protein of the muscle. The dimeric structure and O2-binding properties of sea lamprey and mammalian Cygb were very similar, suggesting a conservation of function since their divergence around 500million years ago.
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16
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Evolution of Single-Domain Globins in Hydrothermal Vent Scale-Worms. J Mol Evol 2017; 85:172-187. [PMID: 29094190 DOI: 10.1007/s00239-017-9815-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/23/2017] [Indexed: 10/18/2022]
Abstract
Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins, in contrast with their shallow-water relatives that only possess intracellular globins in their nervous system (neuroglobins). We sequenced the gene encoding the single-domain (SD) globin from nine species of polynoids found in various vent and deep-sea reduced microhabitats (and associated constraints) to determine if the Polynoidae SD globins have been the targets of diversifying selection. Although extracellular, all the SD globins (and multi-domain ones) form a monophyletic clade that clusters within the intracellular globin group of other annelids, indicating that these hemoglobins have evolved from an intracellular myoglobin-like form. Positive selection could not be detected at the major ecological changes that the colonization of the deep-sea and hydrothermal vents represents. This suggests that no major structural modification was necessary to allow the globins to function under these conditions. The mere expression of these globins extracellularly may have been sufficiently advantageous for the polynoids living in hypoxic hydrothermal vents. Among hydrothermal vent species, positively selected amino acids were only detected in the phylogenetic lineage leading to the two mussel-commensal species (Branchipolynoe). In this lineage, the multiplicity of hemoglobins could have lessened the selective pressure on the SD hemoglobin, allowing the acquisition of novel functions by positive Darwinian selection. Conversely, the colonization of hotter environments (species of Branchinotogluma) does not seem to have required additional modifications.
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17
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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: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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18
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Srinivasu BY, Bose B, Mitra G, Kurpad AV, Mandal AK. Adsorption Induced Changes of Human Hemoglobin on Ferric Pyrophosphate Nanoparticle Surface Probed by Isotope Exchange Mass Spectrometry: An Implication on Structure-Function Correlation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8032-8042. [PMID: 28727441 DOI: 10.1021/acs.langmuir.7b01905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In general, proteins in the biological system interact with nanoparticles (NPs) via adsorption on the particle surface. Understanding the adsorption at the molecular level is crucial to explore NP-protein interactions. The increasing concerns about the risk to human health on NP exposure have been explored through the discovery of a handful protein biomarkers and biochemical analysis. However, detailed information on structural perturbation and associated functional changes of proteins on interaction with NPs is limited. Erythrocytes (red blood cells) are devoid of defense mechanism of protecting NP penetration through endocytosis. Therefore, it is important to investigate the interaction of erythrocyte proteins with NPs. Hemoglobin, the most abundant protein of human erythrocyte, is a tetrameric molecule consisting of α- and β-globin chains in duplicate. In the present study, we have used hemoglobin as a model system to investigate NP-protein interaction with ferric pyrophosphate NPs [NP-Fe4(P2O7)3]. We report the formation of a bioconjugate of hemoglobin upon adsorption to NP-Fe4(P2O7)3 surface. Analysis of the bioconjugate indicated that Fe3+ ion of NP-Fe4(P2O7)3 contributed in the bioconjugate formation. Using hydrogen/deuterium exchange based mass spectrometry, it was observed that the amino termini of α- and β-globin chains of hemoglobin were involved in the adsorption on NP surface whereas the carboxy termini of both chains became more flexible in its conformation compared to the respective regions of the normal hemoglobin. Circular dichroism spectra of desorbed hemoglobin indicated an adsorption induced localized structural change in the protein molecule. The formation of bioconjugate led to functional alteration of hemoglobin, as probed by oxygen binding assay. Thus, we hypothesize that the large amount of energy released upon adsorption of hemoglobin to NP surface might be the fundamental cause of structural perturbation of human hemoglobin and subsequent formation of the bioconjugate with an altered function.
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Affiliation(s)
- Bindu Y Srinivasu
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences , 100 ft road, Koramangala, Bangalore 560034, India
| | - Beena Bose
- Department of Physiology, St John's Medical College, and Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences , 100 ft road, Koramangala, Bangalore 560034, India
| | - Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences , 100 ft road, Koramangala, Bangalore 560034, India
| | - Anura V Kurpad
- Department of Physiology, St John's Medical College, and Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences , 100 ft road, Koramangala, Bangalore 560034, India
| | - Amit K Mandal
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences , 100 ft road, Koramangala, Bangalore 560034, India
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19
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Srivastava A, Tracka MB, Uddin S, Casas-Finet J, Livesay DR, Jacobs DJ. Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations. Biophys J 2017; 110:1933-42. [PMID: 27166802 DOI: 10.1016/j.bpj.2016.03.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/25/2016] [Accepted: 03/28/2016] [Indexed: 11/28/2022] Open
Abstract
A mechanical perturbation method that locally restricts conformational entropy along the protein backbone is used to identify putative allosteric sites in a series of antibody fragments. The method is based on a distance constraint model that integrates mechanical and thermodynamic viewpoints of protein structure wherein mechanical clamps that mimic substrate or cosolute binding are introduced. Across a set of six single chain-Fv fragments of the anti-lymphotoxin-β receptor antibody, statistically significant responses are obtained by averaging over 10 representative structures sampled from a molecular dynamics simulation. As expected, the introduced clamps locally rigidify the protein, but long-ranged increases in both rigidity and flexibility are also frequently observed. Expanding our analysis to every molecular dynamics frame demonstrates that the allosteric responses are modulated by fluctuations within the hydrogen-bond network where the native ensemble is comprised of conformations that both are, and are not, affected by the perturbation in question. Population shifts induced by the mutations alter the allosteric response by adjusting which hydrogen-bond networks are the most probable. These effects are compared using response maps that track changes across each single chain-Fv fragment, thus providing valuable insight into how sensitive allosteric mechanisms are to mutations.
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Affiliation(s)
- Amit Srivastava
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina
| | | | - Shahid Uddin
- Formulation Sciences, MedImmune Ltd., Cambridge, UK
| | - Jose Casas-Finet
- Analytical Biochemistry Department, MedImmune LLC, Gaithersburg, Maryland
| | - Dennis R Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina.
| | - Donald J Jacobs
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina.
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20
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Glossoscolex paulistus hemoglobin with fluorescein isothiocyanate: Steady-state and time-resolved fluorescence. Int J Biol Macromol 2017; 98:777-785. [DOI: 10.1016/j.ijbiomac.2017.02.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 11/20/2022]
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21
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Sheu SY, Liu YC, Yang DY. Interfacial water effect on cooperativity and signal communication in Scapharca dimeric hemoglobin. Phys Chem Chem Phys 2017; 19:7380-7389. [DOI: 10.1039/c7cp00280g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cooperativity is important in controlling the biological functions of allosteric proteins.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences
- National Yang-Ming University
- Taipei 112
- Taiwan
- Institute of Biomedical Informatics
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics
- National Yang-Ming University
- Taipei 112
- Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
- Taiwan
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22
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Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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23
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Ka D, Lee H, Jung YD, Kim K, Seok C, Suh N, Bae E. Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System. Structure 2015; 24:70-79. [PMID: 26671707 DOI: 10.1016/j.str.2015.10.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/25/2015] [Accepted: 10/20/2015] [Indexed: 11/27/2022]
Abstract
CRISPRs and Cas proteins constitute an RNA-guided microbial immune system against invading nucleic acids. Cas1 is a universal Cas protein found in all three types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition during CRISPR-mediated adaptive immunity. Here, we report the crystal structure of Streptococcus pyogenes Cas1 (SpCas1) in a type II CRISPR-Cas system and characterize its interaction with S. pyogenes Csn2 (SpCsn2). The SpCas1 structure reveals a unique conformational state distinct from type I Cas1 structures, resulting in a more extensive dimerization interface, a more globular overall structure, and a disruption of potential metal-binding sites for catalysis. We demonstrate that SpCas1 directly interacts with SpCsn2, and identify the binding interface and key residues for Cas complex formation. These results provide structural information for a type II Cas1 protein, and lay a foundation for studying multiprotein Cas complexes functioning in type II CRISPR-Cas systems.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Hasup Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Yi-Deun Jung
- Stem Cell Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea
| | - Kyunggon Kim
- Clinical Proteomics Core Lab, Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea; Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Nayoung Suh
- Stem Cell Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea; Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea; Center for Food and Bioconvergence, Seoul National University, Seoul 151-921, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
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24
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Projecto-Garcia J, Jollivet D, Mary J, Lallier FH, Schaeffer SW, Hourdez S. Selective forces acting during multi-domain protein evolution: the case of multi-domain globins. SPRINGERPLUS 2015; 4:354. [PMID: 26191481 PMCID: PMC4503718 DOI: 10.1186/s40064-015-1124-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 06/29/2015] [Indexed: 11/10/2022]
Abstract
Multi-domain proteins form the majority of proteins in eukaryotes. During their formation by tandem duplication or gene fusion, new interactions between domains may arise as a result of the structurally-forced proximity of domains. The proper function of the formed proteins likely required the molecular adjustment of these stress zones by specific amino acid replacements, which should be detectable by the molecular signature of selection that governed their changes. We used multi-domain globins from three different invertebrate lineages to investigate the selective forces that acted throughout the evolution of these molecules. In the youngest of these molecules [Branchipolynoe scaleworm; original duplication ca. 60 million years (Ma)], we were able to detect some amino acids under positive selection corresponding to the initial duplication event. In older lineages (didomain globin from bivalve mollusks and nematodes), there was no evidence of amino acid positions under positive selection, possibly the result of accumulated non-adaptative mutations since the original duplication event (165 and 245 Ma, respectively). Some amino acids under positive selection were sometimes detected in later branches, either after speciation events, or after the initial duplication event. In Branchipolynoe, the position of the amino acids under positive selection on a 3D model suggests some of them are located at the interface between two domains; while others are locate in the heme pocket.
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Affiliation(s)
- Joana Projecto-Garcia
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - Didier Jollivet
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - Jean Mary
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - François H Lallier
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - Stephen W Schaeffer
- />Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802 USA
| | - Stéphane Hourdez
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
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25
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Peselis A, Gao A, Serganov A. Cooperativity, allostery and synergism in ligand binding to riboswitches. Biochimie 2015; 117:100-9. [PMID: 26143008 DOI: 10.1016/j.biochi.2015.06.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/29/2015] [Indexed: 01/04/2023]
Abstract
Recent progress in identification and characterization of novel types of non-coding RNAs has proven that RNAs carry out a variety of cellular functions ranging from scaffolding to gene expression control. In both prokaryotic and eukaryotic cells, several classes of non-coding RNAs control expression of dozens of genes in response to specific cues. One of the most interesting and outstanding questions in the RNA field is whether regulatory RNAs are capable of employing basic biological concepts, such as allostery and cooperativity, previously attributed to the function of proteins. Aside from regulatory RNAs that form complementary base pairing with their nucleic acid targets, several RNA classes modulate gene expression via molecular mechanisms which can be paralleled to protein-mediated regulation. Among these RNAs are riboswitches, metabolite-sensing non-coding regulatory elements that adopt intrinsic three-dimensional structures and specifically bind various small molecule ligands. These characteristics of riboswitches make them well-suited for complex regulatory responses observed in allosteric and cooperative protein systems. Here we present an overview of the biochemical, genetic, and structural studies of riboswitches with a major focus on complex regulatory mechanisms and biological principles utilized by riboswitches for such genetic modulation.
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Affiliation(s)
- Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Ang Gao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.
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26
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Brown JR, Livesay DR. Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes. PLoS One 2015; 10:e0125832. [PMID: 26018804 PMCID: PMC4446314 DOI: 10.1371/journal.pone.0125832] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 03/26/2015] [Indexed: 11/24/2022] Open
Abstract
β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme.
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Affiliation(s)
- Jenna R. Brown
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28262, United States of America
| | - Dennis R. Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28262, United States of America
- * E-mail:
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27
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Structural basis for cooperative oxygen binding and bracelet-assisted assembly of Lumbricus terrestris hemoglobin. Sci Rep 2015; 5:9494. [PMID: 25897633 PMCID: PMC5383013 DOI: 10.1038/srep09494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 03/04/2015] [Indexed: 11/25/2022] Open
Abstract
The iron-containing hemoglobins (Hbs) are essential proteins to serve as oxygen transporters in the blood. Among various kinds of Hbs, the earthworm Hbs are the champions in carrying oxygen due to not only their large size but also the unusually high cooperativity of ligand binding. However, the cooperative oxygen binding mechanisms are still mostly unknown. Here we report the cryo-electron microscopy structure of Lumbricus terrestris Hb in its native, oxygenated state at 9.1 Å resolution, showing remarkable differences from the carbon monoxide-binding X-ray structure. Our structural analysis first indicates that the cooperative ligand binding of L. terrestris Hb requires tertiary and quaternary transitions in the heme pocket and a global subunit movement facilitated by intra-ring and inter-ring contacts. Moreover, the additional sinusoidal bracelet provides the confirmation for the long-standing debate about the additional electron densities absent in the X-ray crystal structure.
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28
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Numoto N, Nakagawa T, Ohara R, Hasegawa T, Kita A, Yoshida T, Maruyama T, Imai K, Fukumori Y, Miki K. The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1823-31. [PMID: 25004960 DOI: 10.1107/s1399004714008475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 04/14/2014] [Indexed: 11/10/2022]
Abstract
The quaternary structures of invertebrate haemoglobins (Hbs) are quite different from those of vertebrate Hbs. The extracellular giant Hbs of molecular masses of about 400 and 3600 kDa are composed of a dome-shaped dodecameric subassembly which consists of four individual globin subunits. Several crystal structures of 400 kDa Hbs from annelids have been reported, including structures in oxygenated and partially unliganded states, but the structure of the fully deoxygenated state has not been reported. In the present study, crystal structures of V2Hb from the tube worm Lamellibrachia satsuma have been determined in both the fully oxygenated and deoxygenated states. A glycosylation site and novel metal-binding sites for divalent cations were clearly observed with no intersubunit interactions in V2Hb. A comparison of the oxygenated and the deoxygenated forms of V2Hb reveals that the ternary- and quaternary-structural changes occur in a manner that maintains the molecular D3 symmetry. These structures suggest that the mechanisms of quaternary-structural changes between the oxy and deoxy states for the giant Hbs are identical across species.
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Affiliation(s)
- Nobutaka Numoto
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Taro Nakagawa
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Ryota Ohara
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Tomoyo Hasegawa
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kita
- Research Reactor Institute, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Takao Yoshida
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Kiyohiro Imai
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-0003, Japan
| | - Yoshihiro Fukumori
- Department of Life Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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29
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Agbo JK, Gnanasekaran R, Leitner DM. Communication Maps: Exploring Energy Transport through Proteins and Water. Isr J Chem 2014. [DOI: 10.1002/ijch.201300139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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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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31
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Hong J, Zhao YX, Xiao BL, Moosavi-Movahedi AA, Ghourchian H, Sheibani N. Direct electrochemistry of hemoglobin immobilized on a functionalized multi-walled carbon nanotubes and gold nanoparticles nanocomplex-modified glassy carbon electrode. SENSORS 2013; 13:8595-611. [PMID: 23881129 PMCID: PMC3758613 DOI: 10.3390/s130708595] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/17/2013] [Accepted: 06/30/2013] [Indexed: 12/02/2022]
Abstract
Direct electron transfer of hemoglobin (Hb) was realized by immobilizing Hb on a carboxyl functionalized multi-walled carbon nanotubes (FMWCNTs) and gold nanoparticles (AuNPs) nanocomplex-modified glassy carbon electrode. The ultraviolet-visible absorption spectrometry (UV-Vis), transmission electron microscopy (TEM) and Fourier transform infrared (FTIR) methods were utilized for additional characterization of the AuNPs and FMWCNTs. The cyclic voltammogram of the modified electrode has a pair of well-defined quasi-reversible redox peaks with a formal potential of −0.270 ± 0.002 V (vs. Ag/AgCl) at a scan rate of 0.05 V/s. The heterogeneous electron transfer constant (ks) was evaluated to be 4.0 ± 0.2 s−1. The average surface concentration of electro-active Hb on the surface of the modified glassy carbon electrode was calculated to be 6.8 ± 0.3 × 10−10 mol cm−2. The cathodic peak current of the modified electrode increased linearly with increasing concentration of hydrogen peroxide (from 0.05 nM to 1 nM) with a detection limit of 0.05 ± 0.01 nM. The apparent Michaelis-Menten constant (Kmapp) was calculated to be 0.85 ± 0.1 nM. Thus, the modified electrode could be applied as a third generation biosensor with high sensitivity, long-term stability and low detection limit.
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Affiliation(s)
- Jun Hong
- School of Life Sciences, Henan University, JinMing Road, Kaifeng 475000, China; E-Mails: (Y.-X.Z.); (B.-L.X.)
- Authors to whom correspondence should be addressed; E-Mails: (J.H.); (A.A.M.-M.); Tel.: +86-137-8116-1597 (J.H.); Fax: +86-378-388-6258 (J.H.); Tel.: +98-21-640-3957 (A.A.M.-M.); Fax: +98-21-640-4680 (A.A.M.-M.)
| | - Ying-Xue Zhao
- School of Life Sciences, Henan University, JinMing Road, Kaifeng 475000, China; E-Mails: (Y.-X.Z.); (B.-L.X.)
| | - Bao-Lin Xiao
- School of Life Sciences, Henan University, JinMing Road, Kaifeng 475000, China; E-Mails: (Y.-X.Z.); (B.-L.X.)
| | - Ali Akbar Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Enquelab Avenue, P.O. Box 13145-1384, Tehran, Iran; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (J.H.); (A.A.M.-M.); Tel.: +86-137-8116-1597 (J.H.); Fax: +86-378-388-6258 (J.H.); Tel.: +98-21-640-3957 (A.A.M.-M.); Fax: +98-21-640-4680 (A.A.M.-M.)
| | - Hedayatollah Ghourchian
- Institute of Biochemistry and Biophysics, University of Tehran, Enquelab Avenue, P.O. Box 13145-1384, Tehran, Iran; E-Mail:
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, 600 Highland Avenue, K6/456 CSC, Madison, WI 53792-4673, USA; E-Mail:
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Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1860-72. [PMID: 23523886 DOI: 10.1016/j.bbapap.2013.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/07/2013] [Accepted: 03/08/2013] [Indexed: 12/16/2022]
Abstract
In the last decade, protein allostery has experienced a major resurgence, boosted by the extension of the concept to systems of increasing complexity and by its exploitation for the development of drugs. Expansion of the field into new directions has not diminished the key role of hemoglobin as a test molecule for theory and experimental validation of allosteric models. Indeed, the diffusion of hemoglobins in all kingdoms of life and the variety of functions and of quaternary assemblies based on a common tertiary fold indicate that this superfamily of proteins is ideally suited for investigating the physical and molecular basis of allostery and firmly maintains its role as a main player in the field. This review is an attempt to briefly recollect common and different strategies adopted by metazoan hemoglobins, from monomeric molecules to giant complexes, exploiting homotropic and heterotropic allostery to increase their functional dynamic range. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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33
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Ronda L, Bettati S, Henry ER, Kashav T, Sanders JM, Royer WE, Mozzarelli A. Tertiary and quaternary allostery in tetrameric hemoglobin from Scapharca inaequivalvis. Biochemistry 2013; 52:2108-17. [PMID: 23458680 DOI: 10.1021/bi301620x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.
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Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma , Parco Area delle Scienze, 23/A, 43124 Parma, Italy
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34
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Livesay DR, Kreth KE, Fodor AA. A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms. Methods Mol Biol 2012; 796:385-398. [PMID: 22052502 DOI: 10.1007/978-1-61779-334-9_21] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The notion of using the evolutionary history encoded within multiple sequence alignments to predict allosteric mechanisms is appealing. In this approach, correlated mutations are expected to reflect coordinated changes that maintain intramolecular coupling between residue pairs. Despite much early fanfare, the general suitability of correlated mutations to predict allosteric couplings has not yet been established. Lack of progress along these lines has been hindered by several algorithmic limitations including phylogenetic artifacts within alignments masking true covariance and the computational intractability of consideration of more than two correlated residues at a time. Recent progress in algorithm development, however, has been substantial with a new generation of correlated mutation algorithms that have made fundamental progress toward solving these difficult problems. Despite these encouraging results, there remains little evidence to suggest that the evolutionary constraints acting on allosteric couplings are sufficient to be recovered from multiple sequence alignments. In this review, we argue that due to the exquisite sensitivity of protein dynamics, and hence that of allosteric mechanisms, the latter vary widely within protein families. If it turns out to be generally true that even very similar homologs display a wide divergence of allosteric mechanisms, then even a perfect correlated mutation algorithm could not be reliably used as a general mechanism for discovery of allosteric pathways.
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Affiliation(s)
- Dennis R Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
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35
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Feng Q, Liu K, Fu J, Zhang Y, Zheng Z, Wang C, Du Y, Ye W. Direct electrochemistry of hemoglobin based on nano-composite film of gold nanopaticles and poly (diallyldimethylammonium chloride) functionalized graphene. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2011.11.048] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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36
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Manning JM, Popowicz AM, Padovan JC, Chait BT, Manning LR. Intrinsic regulation of hemoglobin expression by variable subunit interface strengths. FEBS J 2011; 279:361-9. [PMID: 22129306 DOI: 10.1111/j.1742-4658.2011.08437.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The expression of the six types of human Hb subunits over time is currently considered to be regulated mainly by transcription factors that bind to upstream control regions of the gene (the 'extrinsic' component of regulation). Here, we describe how subunit pairing and further assembly to tetramers in the liganded state is influenced by the affinity of subunits for one another (the 'intrinsic' component of regulation). The adult Hb dimers have the strongest subunit interfaces and the embryonic Hbs the weakest, with fetal Hbs being of intermediate strength, corresponding to the temporal order of their expression. These variable subunit binding strengths and the attenuating effects of acetylation contribute to the differences with which these Hb types form functional O(2) -binding tetramers consistent with gene switching.
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Affiliation(s)
- James M Manning
- Department of Biology, Northeastern University, Boston, MA 02115, USA.
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37
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Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures. Proc Natl Acad Sci U S A 2011; 109:107-12. [PMID: 22171006 DOI: 10.1073/pnas.1109213108] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we present a meta-analysis of a large collection of static structures of a protein in the Protein Data Bank in order to extract the progression of structural events during protein function. We apply this strategy to the homodimeric hemoglobin HbI from Scapharca inaequivalvis. We derive a simple dynamic model describing how binding of the first ligand in one of the two chemically identical subunits facilitates a second binding event in the other partner subunit. The results of our ultrafast time-resolved crystallographic studies support this model. We demonstrate that HbI functions like a homodimeric mechanical device, such as pliers or scissors. Ligand-induced motion originating in one subunit is transmitted to the other via conserved pivot points, where the E and F' helices from two partner subunits are "bolted" together to form a stable dimer interface permitting slight relative rotation but preventing sliding.
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38
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Butler EB, Xiong Y, Wang J, Strobel SA. Structural basis of cooperative ligand binding by the glycine riboswitch. ACTA ACUST UNITED AC 2011; 18:293-8. [PMID: 21439473 DOI: 10.1016/j.chembiol.2011.01.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/15/2011] [Accepted: 01/31/2011] [Indexed: 10/18/2022]
Abstract
The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 Å crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.
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Affiliation(s)
- Ethan B Butler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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39
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Armenta-Medina D, Pérez-Rueda E, Segovia L. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches. Proteins 2011; 79:1662-71. [PMID: 21365689 DOI: 10.1002/prot.22995] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 12/03/2010] [Accepted: 12/07/2010] [Indexed: 02/02/2023]
Abstract
Based on integrative computational hybrid approaches that combined statistical coupling analysis (SCA), molecular dynamics (MD), and normal mode analysis (NMA), evolutionarily coupled residues involved in functionally relevant motion in the adenylate kinase protein family were identified. The hybrids identified four top-ranking site pairs that belong to a conserved hydrogen bond network that is involved in the enzyme's flexibility. A second group of top-ranking site pairs was identified in critical regions for functional dynamics, such as those related to enzymatic turnover. The high consistency of the results obtained by SCA with NMA (SCA.NMA) and by SCA.MD hybrid analyses suggests that suitable replacement of the matrix of cross-correlation analysis of atomic fluctuations (derived by using NMA) with those based on MD contributes to the identification of such sites by means of a fast computational calculation. The analysis presented here strongly supports the hypothesis that evolutionary forces, such as coevolution at the sequence level, have promoted functional dynamic properties of the adenylate kinase protein family. Finally, these hybrid approaches can be used to identify, at the residue level, protein motion coordination patterns not previously observed, such as in hinge regions.
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Affiliation(s)
- Dagoberto Armenta-Medina
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
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40
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Alontaga AY, Fenton AW. Effector analogues detect varied allosteric roles for conserved protein-effector interactions in pyruvate kinase isozymes. Biochemistry 2011; 50:1934-9. [PMID: 21261284 DOI: 10.1021/bi200052e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding site for allosteric inhibitor (amino acid) is highly conserved between human liver pyruvate kinase (hL-PYK) and the rabbit muscle isozyme (rM(1)-PYK). To detail similarities/differences in the allosteric function of these two homologues, we quantified the binding of 45 amino acid analogues to hL-PYK and their allosteric impact on affinity for the substrate, phosphoenolpyruvate (PEP). This complements a similar study previously completed for rM(1)-PYK. In hL-PYK, the minimum chemical requirements for effector binding are the same as those identified for rM(1)-PYK (i.e., the l-2-aminopropanaldehyde substructure of the effector is primarily responsible for binding). However, different regions of the effector determine the magnitude of the allosteric response in hL-PYK vs rM(1)-PYK. This finding is inconsistent with the idea that allosteric pathways are conserved between homologues of a protein family.
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Affiliation(s)
- Aileen Y Alontaga
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, United States
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41
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Erion TV, Strobel SA. Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch. RNA (NEW YORK, N.Y.) 2011; 17:74-84. [PMID: 21098652 PMCID: PMC3004068 DOI: 10.1261/rna.2271511] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/27/2010] [Indexed: 05/21/2023]
Abstract
The glycine riboswitch has a tandem dual aptamer configuration, where each aptamer is a separate ligand-binding domain, but the aptamers function together to bind glycine cooperatively. We sought to understand the molecular basis of glycine riboswitch cooperativity by comparing sites of tertiary contacts in a series of cooperative and noncooperative glycine riboswitch mutants using hydroxyl radical footprinting, in-line probing, and native gel-shift studies. The results illustrate the importance of a direct or indirect interaction between the P3b hairpin of aptamer 2 and the P1 helix of aptamer 1 in cooperative glycine binding. Furthermore, our data support a model in which glycine binding is sequential; where the binding of glycine to the second aptamer allows tertiary interactions to be made that facilitate binding of a second glycine molecule to the first aptamer. These results provide insight into cooperative ligand binding in RNA macromolecules.
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Affiliation(s)
- Thanh V Erion
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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42
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Wang X, Zhao W, Lin X, Su B, Liu J. Observation of symmetric denaturation of hemoglobin subunits by electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1306-1311. [PMID: 20963788 DOI: 10.1002/jms.1843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 09/01/2010] [Indexed: 05/30/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has been used to characterize the denaturation of porcine hemoglobin (Hb) induced by solvent changes. This work provides evidence for the symmetric nature of Hb denaturation and demonstrates that heme losses from α- and β-monomers occur in parallel, in response to the addition of acid and organic co-solvents in solution. When subject to one of the following solution conditions (pH 3.2-4.0 or 15-30% acetonitrile-water or 30-45% methanol-water solution), α- and β-globins undergo symmetric dissociation to release the heme groups, which is detected by ESI-MS. Circular dichroism (CD) and fluorescence spectroscopy (FS) data show that the acid-induced and organic solvent-induced heme release, as observed in the mass spectra, can probably be ascribed to different aspects of the conformational changes taking place in the protein. The acidity of the solvent has a significant effect on the secondary structure, whereas organic content level in solution (15-30% acetonitrile or 30-45% methanol) tends to destroy the tertiary structure of Hb globins, both leading to release of the heme from each subunit.
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Affiliation(s)
- Xian Wang
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei 430074, People's Republic of China.
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43
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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: 55] [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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44
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Mottonen JM, Xu M, Jacobs DJ, Livesay DR. Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. Proteins 2009; 75:610-27. [PMID: 19004018 DOI: 10.1002/prot.22273] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We compare various predicted mechanical and thermodynamic properties of nine oxidized thioredoxins (TRX) using a Distance Constraint Model (DCM). The DCM is based on a nonadditive free energy decomposition scheme, where entropic contributions are determined from rigidity and flexibility of structure based on distance constraints. We perform averages over an ensemble of constraint topologies to calculate several thermodynamic and mechanical response functions that together yield quantitative stability/flexibility relationships (QSFR). Applied to the TRX protein family, QSFR metrics display a rich variety of similarities and differences. In particular, backbone flexibility is well conserved across the family, whereas cooperativity correlation describing mechanical and thermodynamic couplings between the residue pairs exhibit distinctive features that readily standout. The diversity in predicted QSFR metrics that describe cooperativity correlation between pairs of residues is largely explained by a global flexibility order parameter describing the amount of intrinsic flexibility within the protein. A free energy landscape is calculated as a function of the flexibility order parameter, and key values are determined where the native-state, transition-state, and unfolded-state are located. Another key value identifies a mechanical transition where the global nature of the protein changes from flexible to rigid. The key values of the flexibility order parameter help characterize how mechanical and thermodynamic response is linked. Variation in QSFR metrics and key characteristics of global flexibility are related to the native state X-ray crystal structure primarily through the hydrogen bond network. Furthermore, comparison of three TRX redox pairs reveals differences in thermodynamic response (i.e., relative melting point) and mechanical properties (i.e., backbone flexibility and cooperativity correlation) that are consistent with experimental data on thermal stabilities and NMR dynamical profiles. The results taken together demonstrate that small-scale structural variations are amplified into discernible global differences by propagating mechanical couplings through the H-bond network.
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Affiliation(s)
- James M Mottonen
- Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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45
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Serganov A, Patel DJ. Amino acid recognition and gene regulation by riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1789:592-611. [PMID: 19619684 PMCID: PMC3744886 DOI: 10.1016/j.bbagrm.2009.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 07/08/2009] [Accepted: 07/09/2009] [Indexed: 01/06/2023]
Abstract
Riboswitches specifically control expression of genes predominantly involved in biosynthesis, catabolism and transport of various cellular metabolites in organisms from all three kingdoms of life. Among many classes of identified riboswitches, two riboswitches respond to amino acids lysine and glycine to date. Though these riboswitches recognize small compounds, they both belong to the largest riboswitches and have unique structural and functional characteristics. In this review, we attempt to characterize molecular recognition principles employed by amino acid-responsive riboswitches to selectively bind their cognate ligands and to effectively perform a gene regulation function. We summarize up-to-date biochemical and genetic data available for the lysine and glycine riboswitches and correlate these results with recent high-resolution structural information obtained for the lysine riboswitch. We also discuss the contribution of lysine riboswitches to antibiotic resistance and outline potential applications of riboswitches in biotechnology and medicine.
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Affiliation(s)
- Alexander Serganov
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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46
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Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K. Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin. Biochemistry 2008; 47:11231-8. [PMID: 18834142 DOI: 10.1021/bi8012609] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxygen binding properties of extracellular giant hemoglobins (Hbs) in some annelids exhibit features significantly different from those of vertebrate tetrameric Hbs. Annelid giant Hbs show cooperative oxygen binding properties in the presence of inorganic cations, while the cooperativities of vertebrate Hbs are enhanced by small organic anions or chloride ions. To elucidate the structural basis for the cation-mediated cooperative mechanisms of these giant Hbs, we determined the crystal structures of Ca2+- and Mg2+-bound Hbs from Oligobrachia mashikoi at 1.6 and 1.7 A resolution, respectively. Both of the metal-bound structures were determined in the oxygenated state. Four Ca2+-binding sites and one Mg2+-binding site were identified in each tetramer subassembly. These cations are considered to stabilize the oxygenated form and increase affinity and cooperativity for oxygen binding, as almost all of the Ca2+ and Mg2+ cations were bound at the interface regions, forming either direct or hydrogen bond-mediated interactions with the neighboring subunits. A comparison of the structures of the oxygenated form and the partially unliganded form provides structural insight into proton-coupled cooperativity (Bohr effect) and ligand-induced transitions. Two histidine residues are assumed to be primarily associated with the Bohr effect. With regard to the ligand-induced cooperativity, a novel quaternary rotation mechanism is proposed to exist at the interface region of the dimer subassembly. Interactions among conserved residues Arg E10, His F3, Gln F7, and Val E11, together with the bending motion of the heme molecules, appear to be essential for quaternary rearrangement.
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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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47
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Livesay DR, Huynh DH, Dallakyan S, Jacobs DJ. Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. Chem Cent J 2008; 2:17. [PMID: 18700034 PMCID: PMC2533333 DOI: 10.1186/1752-153x-2-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 08/12/2008] [Indexed: 11/23/2022] Open
Abstract
Background Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo) and closed (ligated) conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding. Results We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network. Conclusion Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.
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Affiliation(s)
- Dennis R Livesay
- Department of Computer Science and Bioinformatics Research Center, University of North Carolina at Charlotte, Charlotte, NC, USA.
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Li J, Ai YJ, Xie ZZ, Fang WH. How CO Binds to Hexacoordinated Heme in Neuroglobin Protein. J Phys Chem B 2008; 112:8715-23. [DOI: 10.1021/jp711919f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Li
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yue-Jie Ai
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Zhi-Zhong Xie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Wei-Hai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K. Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins. Proteins 2008; 73:113-25. [DOI: 10.1002/prot.22040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gavira JA, Camara-Artigas A, De Jesús-Bonilla W, López-Garriga J, Lewis A, Pietri R, Yeh SR, Cadilla CL, García-Ruiz JM. Structure and ligand selection of hemoglobin II from Lucina pectinata. J Biol Chem 2008; 283:9414-23. [PMID: 18203714 PMCID: PMC2431033 DOI: 10.1074/jbc.m705026200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 01/10/2008] [Indexed: 11/06/2022] Open
Abstract
Lucina pectinata ctenidia harbor three heme proteins: sulfide-reactive hemoglobin I (HbI(Lp)) and the oxygen transporting hemoglobins II and III (HbII(Lp) and HbIII(Lp)) that remain unaffected by the presence of H(2)S. The mechanisms used by these three proteins for their function, including ligand control, remain unknown. The crystal structure of oxygen-bound HbII(Lp) shows a dimeric oxyHbII(Lp) where oxygen is tightly anchored to the heme through hydrogen bonds with Tyr(30)(B10) and Gln(65)(E7). The heme group is buried farther within HbII(Lp) than in HbI(Lp). The proximal His(97)(F8) is hydrogen bonded to a water molecule, which interacts electrostatically with a propionate group, resulting in a Fe-His vibration at 211 cm(-1). The combined effects of the HbII(Lp) small heme pocket, the hydrogen bonding network, the His(97) trans-effect, and the orientation of the oxygen molecule confer stability to the oxy-HbII(Lp) complex. Oxidation of HbI(Lp) Phe(B10) --> Tyr and HbII(Lp) only occurs when the pH is decreased from pH 7.5 to 5.0. Structural and resonance Raman spectroscopy studies suggest that HbII(Lp) oxygen binding and transport to the host bacteria may be regulated by the dynamic displacements of the Gln(65)(E7) and Tyr(30)(B10) pair toward the heme to protect it from changes in the heme oxidation state from Fe(II) to Fe(III).
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Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, CSIC, P.T. Ciencias de la Salud, Granada, Spain
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