1
|
Xiong J, Reed C, Lavina B, Hu MY, Zhao J, Alp EE, Agapie T, Guo Y. 57Fe nuclear resonance vibrational spectroscopic studies of tetranuclear iron clusters bearing terminal iron(iii)-oxido/hydroxido moieties. Chem Sci 2024:d4sc03396e. [PMID: 39296996 PMCID: PMC11403573 DOI: 10.1039/d4sc03396e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 09/08/2024] [Indexed: 09/21/2024] Open
Abstract
57Fe nuclear resonance vibrational spectroscopy (NRVS) has been applied to study a series of tetranuclear iron ([Fe4]) clusters based on a multidentate ligand platform (L3-) anchored by a 1,3,5-triarylbenzene linker and pyrazolate or (tertbutylamino)pyrazolate ligand (PzNH t Bu-). These clusters bear a terminal Fe(iii)-O/OH moiety at the apical position and three additional iron centers forming the basal positions. The three basal irons are connected with the apical iron center via a μ4-oxido ligand. Detailed vibrational analysis via density functional theory calculations revealed that strong NRVS spectral features below 400 cm-1 can be used as an oxidation state marker for the overall [Fe4] cluster core. The terminal Fe(iii)-O/OH stretching frequencies, which were observed in the range of 500-700 cm-1, can be strongly modulated (energy shifts of 20-40 cm-1 were observed) upon redox events at the three remote basal iron centers of the [Fe4] cluster without the change of the terminal Fe(iii) oxidation state and its coordination environment. Therefore, the current study provides a quantitative vibrational analysis of how the remote iron centers within the same iron cluster exert exquisite control of the chemical reactivities and thermodynamic properties of the specific iron site that is responsible for small molecule activation.
Collapse
Affiliation(s)
- Jin Xiong
- Department of Chemistry, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Christopher Reed
- Division of Chemistry and Chemical Engineering, California Institute of Technology CA 91125 USA
| | - Barbara Lavina
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
- Center for Advanced Radiation Source, University of Chicago Chicago Illinois 60439 USA
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Esen E Alp
- Advanced Photon Source, Argonne National Laboratory Argonne Illinois 60439 USA
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology CA 91125 USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University Pittsburgh PA 15213 USA
| |
Collapse
|
2
|
Verde C, Giordano D, Bruno S. NO and Heme Proteins: Cross-Talk between Heme and Cysteine Residues. Antioxidants (Basel) 2023; 12:antiox12020321. [PMID: 36829880 PMCID: PMC9952723 DOI: 10.3390/antiox12020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Heme proteins are a diverse group that includes several unrelated families. Their biological function is mainly associated with the reactivity of the heme group, which-among several other reactions-can bind to and react with nitric oxide (NO) and other nitrogen compounds for their production, scavenging, and transport. The S-nitrosylation of cysteine residues, which also results from the reaction with NO and other nitrogen compounds, is a post-translational modification regulating protein activity, with direct effects on a variety of signaling pathways. Heme proteins are unique in exhibiting this dual reactivity toward NO, with reported examples of cross-reactivity between the heme and cysteine residues within the same protein. In this work, we review the literature on this interplay, with particular emphasis on heme proteins in which heme-dependent nitrosylation has been reported and those for which both heme nitrosylation and S-nitrosylation have been associated with biological functions.
Collapse
Affiliation(s)
- Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
- Biopharmanet-TEC, University of Parma, 43124 Parma, Italy
- Correspondence:
| |
Collapse
|
3
|
Zurakowski JA, Austen BJ, Drover MW. Exterior decorating: Lewis acid secondary coordination spheres for cooperative reactivity. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
4
|
Muraki N, Takeda K, Nam D, Muraki M, Aono S. Structural Characterization of Y29F Mutant of Thermoglobin from a Hyperthermophilic Bacterium Aquifex aeolicus. CHEM LETT 2021. [DOI: 10.1246/cl.200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Norifumi Muraki
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| | - Kouta Takeda
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Dayeon Nam
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Megumi Muraki
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shigetoshi Aono
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
5
|
Gong W, Liu Y, Zhao Y, Wang S, Han Z, Li C. Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models. J Chem Inf Model 2021; 61:921-937. [PMID: 33496590 DOI: 10.1021/acs.jcim.0c01178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dynamical properties of proteins play an essential role in their function exertion. The elastic network model (ENM) is an effective and efficient tool in characterizing the intrinsic dynamical properties encoded in biomacromolecule structures. The Gaussian network model (GNM) and anisotropic network model (ANM) are the two often-used ENM models. Here, we introduce an equally weighted multiscale ENM (equally weighted mENM) based on the original mENM (denoted as mENM), in which fitting weights of Kirchhoff/Hessian matrixes in mENM are removed since they neglect the details of pairwise interactions. Then, we perform its comparison with the mENM, traditional ENM, and parameter-free ENM (pfENM) in reproducing dynamical properties for the six representative proteins whose molecular dynamics (MD) trajectories are available in http://mmb.pcb.ub.es/MoDEL/. In the results, for B-factor prediction, mENM performs best, while the equally weighted mENM performs also well, better than the traditional ENM and pfENM models. As to the dynamical cross-correlation map calculation, mENM performs worst, while the results produced from the equally weighted mENM and pfENM models are close to those from MD trajectories with the latter a little better than the former. Furthermore, encouragingly, the equally weighted mANM displays the best performance in capturing the functional motional modes, followed by pfANM and traditional ANM models, while the mANM fails in all the cases. This work is helpful for strengthening the understanding of the elastic network model and provides a valuable guide for researchers to utilize the model to explore protein dynamics.
Collapse
Affiliation(s)
- Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.,Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing University of Technology, Beijing 100124, China
| | - Yang Liu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.,Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing University of Technology, Beijing 100124, China
| | - Yanpeng Zhao
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.,Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing University of Technology, Beijing 100124, China
| | - Shihao Wang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.,Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.,Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.,Beijing International Science and Technology Cooperation Base for Intelligent Physiological Measurement and Clinical Transformation, Beijing University of Technology, Beijing 100124, China
| |
Collapse
|
6
|
Latham RD, Torrado M, Atto B, Walshe JL, Wilson R, Guss JM, Mackay JP, Tristram S, Gell DA. A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae. Mol Microbiol 2019; 113:381-398. [PMID: 31742788 DOI: 10.1111/mmi.14426] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 01/02/2023]
Abstract
Commensal bacteria serve as an important line of defense against colonisation by opportunisitic pathogens, but the underlying molecular mechanisms remain poorly explored. Here, we show that strains of a commensal bacterium, Haemophilus haemolyticus, make hemophilin, a heme-binding protein that inhibits growth of the opportunistic pathogen, non-typeable Haemophilus influenzae (NTHi) in culture. We purified the NTHi-inhibitory protein from H. haemolyticus and identified the hemophilin gene using proteomics and a gene knockout. An x-ray crystal structure of recombinant hemophilin shows that the protein does not belong to any of the known heme-binding protein folds, suggesting that it evolved independently. Biochemical characterisation shows that heme can be captured in the ferrous or ferric state, and with a variety of small heme-ligands bound, suggesting that hemophilin could function under a range of physiological conditions. Hemophilin knockout bacteria show a limited capacity to utilise free heme for growth. Our data suggest that hemophilin is a hemophore and that inhibition of NTHi occurs by heme starvation, raising the possibility that competition from hemophilin-producing H. haemolyticus could antagonise NTHi colonisation in the respiratory tract.
Collapse
Affiliation(s)
- Roger D Latham
- School of Medicine, University of Tasmania, Hobart, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Australia
| | - J Mitchell Guss
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Australia
| | - David A Gell
- School of Medicine, University of Tasmania, Hobart, Australia
| |
Collapse
|
7
|
Crystal structure of a neoagarobiose-producing GH16 family β-agarase from Persicobacter sp. CCB-QB2. Appl Microbiol Biotechnol 2019; 104:633-641. [PMID: 31784792 DOI: 10.1007/s00253-019-10237-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/02/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
PdAgaC from the marine bacterium Persicobacter sp. CCB-QB2 is a β-agarase belonging to the glycoside hydrolase family 16 (GH16). It is one of only a handful of endo-acting GH16 β-agarases able to degrade agar completely to produce neoagarobiose (NA2). The crystal structure of PdAgaC's catalytic domain, which has one of the highest Vmax value at 2.9 × 103 U/mg, was determined in order to understand its unique mechanism. The catalytic domain is made up of a typical β-jelly roll fold with two additional insertions, and a well-conserved but wider substrate-binding cleft with some minor changes. Among the unique differences, two unconserved residues, Asn226 and Arg286, may potentially contribute additional hydrogen bonds to subsites -1 and +2, respectively, while a third, His185 from one of the additional insertions, may further contribute another bond to subsite +2. These additional hydrogen bonds may probably have enhanced PdAgaC's affinity for short agaro-oligosaccharides such as neoagarotetraose (NA4), rendering it capable of binding NA4 strongly enough for rapid degradation into NA2.
Collapse
|
8
|
Weitz AC, Hill EA, Oswald VF, Bominaar EL, Borovik AS, Hendrich MP, Guo Y. Probing Hydrogen Bonding Interactions to Iron-Oxido/Hydroxido Units by 57 Fe Nuclear Resonance Vibrational Spectroscopy. Angew Chem Int Ed Engl 2018; 57:16010-16014. [PMID: 30353620 PMCID: PMC6263813 DOI: 10.1002/anie.201810227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Indexed: 11/11/2022]
Abstract
Hydrogen bonds (H-bonds) have been shown to modulate the chemical reactivities of iron centers in iron-containing dioxygen-activating enzymes and model complexes. However, few examples are available that investigate how systematic changes in intramolecular H-bonds within the secondary coordination sphere influence specific properties of iron intermediates, such as iron-oxido/hydroxido species. Here, we used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the Fe-O/OH vibrations in a series of FeIII -hydroxido and FeIV/III -oxido complexes with varying H-bonding networks but having similar trigonal bipyramidal primary coordination spheres. The data show that even subtle changes in the H-bonds to the Fe-O/OH units result in significant changes in their vibrational frequencies, thus demonstrating the utility of NRVS in studying the effect of the secondary coordination sphere to the reactivities of iron complexes.
Collapse
Affiliation(s)
- Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Ethan A Hill
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Victoria F Oswald
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Andrew S Borovik
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| |
Collapse
|
9
|
Weitz AC, Hill EA, Oswald VF, Bominaar EL, Borovik AS, Hendrich MP, Guo Y. Probing Hydrogen Bonding Interactions to Iron‐Oxido/Hydroxido Units by
57
Fe Nuclear Resonance Vibrational Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrew C. Weitz
- Department of Chemistry Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Ethan A. Hill
- Department of Chemistry University of California Irvine CA 92697 USA
| | | | - Emile L. Bominaar
- Department of Chemistry Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Andrew S. Borovik
- Department of Chemistry University of California Irvine CA 92697 USA
| | | | - Yisong Guo
- Department of Chemistry Carnegie Mellon University Pittsburgh PA 15213 USA
| |
Collapse
|
10
|
Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Chem Rev 2018; 118:10840-11022. [PMID: 30372042 PMCID: PMC6360144 DOI: 10.1021/acs.chemrev.8b00074] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.
Collapse
Affiliation(s)
- Suzanne M. Adam
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gayan B. Wijeratne
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Patrick J. Rogler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Daniel E. Diaz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J. Liu
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
11
|
Nishiura T, Chiba Y, Nakazawa J, Hikichi S. Tuning the O2 Binding Affinity of Cobalt(II) Centers by Changing the Structural and Electronic Properties of the Distal Substituents on Azole-Based Chelating Ligands. Inorg Chem 2018; 57:14218-14229. [DOI: 10.1021/acs.inorgchem.8b02241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Toshiki Nishiura
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yosuke Chiba
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Jun Nakazawa
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Shiro Hikichi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| |
Collapse
|
12
|
Bhadra M, Lee JYC, Cowley RE, Kim S, Siegler MA, Solomon EI, Karlin KD. Intramolecular Hydrogen Bonding Enhances Stability and Reactivity of Mononuclear Cupric Superoxide Complexes. J Am Chem Soc 2018; 140:9042-9045. [PMID: 29957998 PMCID: PMC6217813 DOI: 10.1021/jacs.8b04671] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
[(L)CuII(O2•-)]+ (i.e., cupric-superoxo) complexes, as the first and/or key reactive intermediates in (bio)chemical Cu-oxidative processes, including in the monooxygenases PHM and DβM, have been systematically stabilized by intramolecular hydrogen bonding within a TMPA ligand-based framework. Also, gradual strengthening of ligand-derived H-bonding dramatically enhances the [(L)CuII(O2•-)]+ reactivity toward hydrogen-atom abstraction (HAA) of phenolic O-H bonds. Spectroscopic properties of the superoxo complexes and their azido analogues, [(L)CuII(N3-)]+, also systematically change as a function of ligand H-bonding capability.
Collapse
Affiliation(s)
- Mayukh Bhadra
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jung Yoon C. Lee
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ryan E. Cowley
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sunghee Kim
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Maxime A. Siegler
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Kenneth D. Karlin
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
13
|
Greer-Phillips SE, Sukomon N, Chua TK, Johnson MS, Crane BR, Watts KJ. THE AER2 RECEPTOR FROM VIBRIO CHOLERAE IS A DUAL PAS-HEME OXYGEN SENSOR. Mol Microbiol 2018; 109:209-224. [PMID: 29719085 DOI: 10.1111/mmi.13978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/28/2018] [Accepted: 04/29/2018] [Indexed: 12/16/2022]
Abstract
The diarrheal pathogen Vibrio cholerae navigates complex environments using three chemosensory systems and 44-45 chemoreceptors. Chemosensory cluster II modulates chemotaxis, whereas clusters I and III have unknown functions. Ligands have been identified for only five V. cholerae chemoreceptors. Here we report that the cluster III receptor, VcAer2, binds and responds to O2 . VcAer2 is an ortholog of Pseudomonas aeruginosa Aer2 (PaAer2), but differs in that VcAer2 has two, rather than one, N-terminal PAS domain. We have determined that both PAS1 and PAS2 form homodimers and bind penta-coordinate b-type heme via an Eη-His residue. Heme binding to PAS1 required the entire PAS core, but receptor function also required the N-terminal cap. PAS2 functioned as an O2 -sensor [Kd(O2) , 19 μM], utilizing the same Iβ Trp (W276) as PaAer2 to stabilize O2 . The crystal structure of PAS2-W276L was similar to that of PaAer2-PAS, but resided in an active conformation mimicking the ligand-bound state, consistent with its signal-on phenotype. PAS1 also bound O2 [Kd(O2), 12 μM], although O2 binding was stabilized by either a Trp or Tyr residue. Moreover, PAS1 appeared to function as a signal modulator, regulating O2 -mediated signaling from PAS2, and resulting in activation of the cluster III chemosensory pathway. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Suzanne E Greer-Phillips
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Nattakan Sukomon
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Mark S Johnson
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Kylie J Watts
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA, 92350, USA
| |
Collapse
|
14
|
Elrod LT, Kim E. Lewis Acid Assisted Nitrate Reduction with Biomimetic Molybdenum Oxotransferase Complex. Inorg Chem 2018; 57:2594-2602. [PMID: 29443517 DOI: 10.1021/acs.inorgchem.7b02956] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reduction of nitrate (NO3-) to nitrite (NO2-) is of significant biological and environmental importance. While MoIV(O) and MoVI(O)2 complexes that mimic the active site structure of nitrate reducing enzymes are prevalent, few of these model complexes can reduce nitrate to nitrite through oxygen atom transfer (OAT) chemistry. We present a novel strategy to induce nitrate reduction chemistry of a previously known catalyst MoIV(O)(SN)2 (2), where SN = bis(4- tert-butylphenyl)-2-pyridylmethanethiolate, that is otherwise incapable of achieving OAT with nitrate. Addition of nitrate with the Lewis acid Sc(OTf)3 (OTf = trifluoromethanesulfonate) to 2 results in an immediate and clean conversion of 2 to MoVI(O)2(SN)2 (1). The Lewis acid additive further reacts with the OAT product, nitrite, to form N2O and O2. This work highlights the ability of Sc3+ additives to expand the reactivity scope of an existing MoIV(O) complex together with which Sc3+ can convert nitrate to stable gaseous molecules.
Collapse
Affiliation(s)
- Lee Taylor Elrod
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Eunsuk Kim
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| |
Collapse
|
15
|
Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
Collapse
Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
| |
Collapse
|
16
|
“Scorpionate-like” complexes that are held together by hydrogen bonds: Crystallographic and spectroscopic studies of (3-NH(t-butyl)-5-methyl-pyrazole) MX2 (M = Zn, Ni, Co, Mn; n= 3, 4; X = Cl, Br). Polyhedron 2016. [DOI: 10.1016/j.poly.2015.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Cook SA, Hill EA, Borovik AS. Lessons from Nature: A Bio-Inspired Approach to Molecular Design. Biochemistry 2015; 54:4167-80. [PMID: 26079379 DOI: 10.1021/acs.biochem.5b00249] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloproteins contain actives sites with intricate structures that perform specific functions with high selectivity and efficiency. The complexity of these systems complicates the study of their function and the understanding of the properties that give rise to their reactivity. One approach that has contributed to the current level of understanding of their biological function is the study of synthetic constructs that mimic one or more aspects of the native metalloproteins. These systems allow individual contributions to the structure and function to be analyzed and also permit spectroscopic characterization of the metal cofactors without complications from the protein environment. This Current Topic is a review of synthetic constructs as probes for understanding the biological activation of small molecules. These topics are developed from the perspective of seminal molecular design breakthroughs from the past that provide the foundation for the systems used today.
Collapse
Affiliation(s)
- Sarah A Cook
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - Ethan A Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| | - A S Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, California 92697, United States
| |
Collapse
|
18
|
González-Fernández J, Daschner A, Nieuwenhuizen NE, Lopata AL, Frutos CD, Valls A, Cuéllar C. Haemoglobin, a new major allergen of Anisakis simplex. Int J Parasitol 2015; 45:399-407. [PMID: 25683373 DOI: 10.1016/j.ijpara.2015.01.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 01/01/2023]
Abstract
Gastro-allergic anisakiasis and Anisakis sensitisation associated chronic urticaria are diseases which differ in their IgE and IgG4 responses against both crude extract and specific allergens. Anisakis and Ascaris are closely related nematodes that usually cause problems with specificity in immunodiagnostics. In this study we measured IgE and IgG4 antibodies against Anisakis simplex sensu lato (s. l.) and Ascaris suum haemoglobins in sera of 21 gastro-allergic anisakiasis and 23 chronic urticaria patients. We used a capture ELISA with the anti-Anisakis haemoglobin monoclonal antibody 4E8g, which also recognises Ascaris haemoglobin. In addition, we determined specific IgE and IgG4 to both nematodes by indirect ELISA and immunoblotting. Anti-A. simplex s. l. haemoglobin IgE and IgG4 levels were higher in gastro-allergic anisakiasis than in chronic urticaria patients (P=0.002 and 0.026, respectively). Surprisingly, no patient had detectable IgE levels against A. suum haemoglobin. Finally, we carried out an in silico study of the B-cell epitopes of both haemoglobin molecules. Five epitopes were predicted in Anisakis pegreffii and four in A. suum haemoglobin. The epitope propensity values of Anisakis haemoglobin in the equivalent IgE binding region of the allergenic haemoglobin Chi t 1 from Chironomus thummi, were higher those of the Ascaris haemoglobin. In conclusion, we describe A. simplex haemoglobin as a new major allergen (Ani s 13), being recognised by a large number (64.3%) of sensitised patients and up to 80.9% in patients with gastro-allergic anisakiasis. The presence of a specific epitope and the different values of epitope propensity between Anisakis and Ascaris haemoglobin could explain the lack of cross-reactivity between the two molecules. The absence of IgE reactivity to Ascaris haemoglobin in Anisakis patients makes Anisakis haemoglobin (Ani s 13) a potential candidate for developing more specific diagnosis tools.
Collapse
Affiliation(s)
- Juan González-Fernández
- Departamento de Parasitología, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain.
| | - Alvaro Daschner
- Servicio de Alergia, Instituto de Investigación Sanitaria-Hospital Universitario de La Princesa, 28006 Madrid, Spain
| | - Natalie E Nieuwenhuizen
- Department of Immunology, Max Planck Institut für Infektionsbiologie, Chariteplatz 1, 10117 Berlin, Germany
| | - Andreas L Lopata
- Department of Molecular and Cell Biology, Centre for Biodiscovery and Molecular Development of Therapeutics, James Cook University, 4811, Australia
| | - Consolación De Frutos
- Servicio de Alergia, Instituto de Investigación Sanitaria-Hospital Universitario de La Princesa, 28006 Madrid, Spain
| | - Ana Valls
- Servicio de Alergia, Instituto de Investigación Sanitaria-Hospital Universitario de La Princesa, 28006 Madrid, Spain
| | - Carmen Cuéllar
- Departamento de Parasitología, Facultad de Farmacia, Universidad Complutense, 28040 Madrid, Spain
| |
Collapse
|
19
|
Gerlach DL, Bhagan S, Cruce AA, Burks DB, Nieto I, Truong HT, Kelley SP, Herbst-Gervasoni CJ, Jernigan KL, Bowman MK, Pan S, Zeller M, Papish ET. Studies of the Pathways Open to Copper Water Oxidation Catalysts Containing Proximal Hydroxy Groups During Basic Electrocatalysis. Inorg Chem 2014; 53:12689-98. [DOI: 10.1021/ic501018a] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Deidra L. Gerlach
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Salome Bhagan
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Alex A. Cruce
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Dalton B. Burks
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Ismael Nieto
- Department
of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Hai T. Truong
- Department
of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Steven P. Kelley
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Corey J. Herbst-Gervasoni
- Department
of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Katherine L. Jernigan
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Michael K. Bowman
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Shanlin Pan
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Matthias Zeller
- Department
of Chemistry, Youngstown State University, One University Plaza, Youngstown, Ohio 44555, United States
| | - Elizabeth T. Papish
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| |
Collapse
|
20
|
Martínková M, Kitanishi K, Shimizu T. Heme-based globin-coupled oxygen sensors: linking oxygen binding to functional regulation of diguanylate cyclase, histidine kinase, and methyl-accepting chemotaxis. J Biol Chem 2013; 288:27702-11. [PMID: 23928310 DOI: 10.1074/jbc.r113.473249] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
An emerging class of novel heme-based oxygen sensors containing a globin fold binds and senses environmental O2 via a heme iron complex. Structure-function relationships of oxygen sensors containing a heme-bound globin fold are different from those containing heme-bound PAS and GAF folds. It is thus worth reconsidering from an evolutionary perspective how heme-bound proteins with a globin fold similar to that of hemoglobin and myoglobin could act as O2 sensors. Here, we summarize the molecular mechanisms of heme-based oxygen sensors containing a globin fold in an effort to shed light on the O2-sensing properties and O2-stimulated catalytic enhancement observed for these proteins.
Collapse
Affiliation(s)
- Markéta Martínková
- From the Department of Biochemistry, Faculty of Science, Charles University in Prague, 128 43 Prague 2, Czech Republic
| | | | | |
Collapse
|
21
|
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.
Collapse
|
22
|
Ramos-Santana BJ, López-Garriga J. Tyrosine B10 triggers a heme propionate hydrogen bonding network loop with glutamine E7 moiety. Biochem Biophys Res Commun 2012; 424:771-6. [PMID: 22809503 PMCID: PMC3422640 DOI: 10.1016/j.bbrc.2012.07.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 07/08/2012] [Indexed: 11/27/2022]
Abstract
Propionates, as peripheral groups of the heme active center in hemeproteins have been described to contribute in the modulation of heme reactivity and ligand selection. These electronic characteristics prompted the question of whether the presence of hydrogen bonding networks between propionates and distal amino acids present in the heme ligand moiety can modulate physiological relevant events, like ligand binding association and dissociation activities. Here, the role of these networks was evaluated by NMR spectroscopy using the hemoglobin I PheB10Tyr mutant from Lucina pectinata as model for TyrB10 and GlnE7 hemeproteins. (1)H-NMR results for the rHbICN PheB10Tyr derivative showed chemical shifts of TyrB10 OHη at 31.00ppm, GlnE7N(ε1)H/N(ε2)H at 10.66ppm/-3.27ppm, and PheE11 C(δ)H at 11.75ppm, indicating the presence of a crowded, collapsed, and constrained distal pocket. Strong dipolar contacts and inter-residues crosspeaks between GlnE7/6-propionate group, GlnE7/TyrB10 and TyrB10/CN suggest that this hydrogen bonding network loop between GlnE7, TyrB10, 6-propionate group, and the heme ligand contribute significantly to the modulation of the heme iron electron density as well as the ligand stabilization mechanism. Therefore, the network loop presented here support the fact that the electron withdrawing character of the hydrogen bonding is controlled by the interaction of the propionates and the nearby electronic environments contributing to the modulation of the heme electron density state. Thus, we hypothesize that in hemeproteins with similar electrostatic environment the flexibility of the heme-6-propionate promotes a hydrogen bonding network loop between the 6-propionate, the heme ligand and nearby amino acids, tailoring in this way the electron density in the heme-ligand moiety.
Collapse
Affiliation(s)
- Brenda J. Ramos-Santana
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, PO BOX 9019, Mayagüez, Puerto Rico 00681-9019
| | - Juan López-Garriga
- Department of Chemistry, University of Puerto Rico, Mayagüez Campus, PO BOX 9019, Mayagüez, Puerto Rico 00681-9019
| |
Collapse
|
23
|
Sickerman NS, Park YJ, Ng GKY, Bates JE, Hilkert M, Ziller JW, Furche F, Borovik AS. Synthesis, structure, and physical properties for a series of trigonal bipyramidal M(II)-Cl complexes with intramolecular hydrogen bonds. Dalton Trans 2012; 41:4358-64. [PMID: 22334366 PMCID: PMC3777263 DOI: 10.1039/c2dt12244h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A series of transition metal chloro complexes with the tetradentate tripodal tris(2-amino-oxazoline)amine ligand (TAO) have been synthesized and characterized. X-Ray structural analyses of these compounds demonstrate the formation of the mononuclear complexes [M(II)(TAO)(Cl)](+), where M(II) = Cr, Mn, Fe, Co, Ni, Cu and Zn. These complexes exhibit distorted trigonal-bipyramidal geometry, coordinating the metal through an apical tertiary amine, three equatorial imino nitrogen atoms, and an axial chloride anion. All the complexes possess an intramolecular hydrogen-bonding (H-bonding) network within the cavity occupied by the metal-bound chloride ion. The metal-chloride bond distances are atypically long, which is attributed to the effects of the H-bonding network. Nuclear magnetic resonance (NMR) spectroscopy of the Zn complex suggests that the solid-state structures are representative of that observed in solution, and that the H-bonding interactions persist as well. Additionally, density functional theory (DFT) calculations were carried out to probe the electronic structures of the complexes.
Collapse
Affiliation(s)
- Nathaniel S Sickerman
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Teh AH, Saito JA, Baharuddin A, Tuckerman JR, Newhouse JS, Kanbe M, Newhouse EI, Rahim RA, Favier F, Didierjean C, Sousa EH, Stott MB, Dunfield PF, Gonzalez G, Gilles-Gonzalez MA, Najimudin N, Alam M. Hell's Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin. FEBS Lett 2011; 585:3250-8. [DOI: 10.1016/j.febslet.2011.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 08/17/2011] [Accepted: 09/01/2011] [Indexed: 11/27/2022]
|
25
|
Teixeira KN, Oliveira JS, Souza KN, de Moura J, Brito CA, Vidigal TH, Santos AM, Santoro MM. Comparison of the biochemical and molecular properties of myoglobins from three Biomphalaria species. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
26
|
Tilleman L, Germani F, De Henau S, Geuens E, Hoogewijs D, Braeckman BP, Vanfleteren JR, Moens L, Dewilde S. Globins in Caenorhabditis elegans. IUBMB Life 2011; 63:166-74. [PMID: 21445847 DOI: 10.1002/iub.443] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Extensive in silico search of the genome of Caenorhabditis elegans revealed the presence of 33 genes coding for globins that are all transcribed. These globins are very diverse in gene and protein structure and are localized in a variety of cells, mostly neurons. The large number of C. elegans globin genes is assumed to be the result of multiple evolutionary duplication and radiation events. Processes of subfunctionalization and diversification probably led to their cell-specific expression patterns and fixation into the genome. To date, four globins (GLB-1, GLB-5, GLB-6, and GLB-26) have been partially characterized physicochemically, and the crystallographic structure of two of them (GLB-1 and GLB-6) was solved. In this article, a three-dimensional model was designed for the other two globins (GLB-5 and GLB-26), and overlays of the globins were constructed to highlight the structural diversity among them. It is clear that although they all share the globin fold, small variations in the three-dimensional structure have major implications on their ligand-binding properties and possibly their function. We also review here all the information available so far on the globin family of C. elegans and suggest potential functions.
Collapse
Affiliation(s)
- Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
A hydrogen-bonding network formed by the B10–E7–E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification. J Biol Inorg Chem 2011; 16:599-609. [DOI: 10.1007/s00775-011-0761-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
|
28
|
Shook RL, Borovik A. Role of the secondary coordination sphere in metal-mediated dioxygen activation. Inorg Chem 2010; 49:3646-60. [PMID: 20380466 PMCID: PMC3417154 DOI: 10.1021/ic901550k] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alfred Werner proposed nearly 100 years ago that the secondary coordination sphere has a role in determining the physical properties of transition-metal complexes. We now know that the secondary coordination sphere impacts nearly all aspects of transition-metal chemistry, including the reactivity and selectivity in metal-mediated processes. These features are highlighted in the binding and activation of dioxygen by transition-metal complexes. There are clear connections between control of the secondary coordination sphere and the ability of metal complexes to (1) reversibly bind dioxygen or (2) bind and activate dioxygen to form highly reactive metal-oxo complexes. In this Forum Article, several biological and synthetic examples are presented and discussed in terms of structure-function relationships. Particular emphasis is given to systems with defined noncovalent interactions, such as intramolecular H-bonds involving dioxygen-derived ligands. To further illustrate these effects, the homolytic cleavage of C-H bonds by metal-oxo complexes with basic oxo ligands is described.
Collapse
Affiliation(s)
- Ryan L. Shook
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697-2025
| | - A.S. Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697-2025
| |
Collapse
|
29
|
Geuens E, Hoogewijs D, Nardini M, Vinck E, Pesce A, Kiger L, Fago A, Tilleman L, De Henau S, Marden MC, Weber RE, Van Doorslaer S, Vanfleteren J, Moens L, Bolognesi M, Dewilde S. Globin-like proteins in Caenorhabditis elegans: in vivo localization, ligand binding and structural properties. BMC BIOCHEMISTRY 2010; 11:17. [PMID: 20361867 PMCID: PMC2867796 DOI: 10.1186/1471-2091-11-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 04/02/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND The genome of the nematode Caenorhabditis elegans contains more than 30 putative globin genes that all are transcribed. Although their translated amino acid sequences fit the globin fold, a variety of amino-acid substitutions and extensions generate a wide structural diversity among the putative globins. No information is available on the physicochemical properties and the in vivo expression. RESULTS We expressed the globins in a bacterial system, characterized the purified proteins by optical and resonance Raman spectroscopy, measured the kinetics and equilibria of O2 binding and determined the crystal structure of GLB-1* (CysGH2 --> Ser mutant). Furthermore, we studied the expression patterns of glb-1 (ZK637.13) and glb-26 (T22C1.2) in the worms using green fluorescent protein technology and measured alterations of their transcript abundances under hypoxic conditions.GLB-1* displays the classical three-over-three alpha-helical sandwich of vertebrate globins, assembled in a homodimer associated through facing E- and F-helices. Within the heme pocket the dioxygen molecule is stabilized by a hydrogen bonded network including TyrB10 and GlnE7.GLB-1 exhibits high ligand affinity, which is, however, lower than in other globins with the same distal TyrB10-GlnE7 amino-acid pair. In the absence of external ligands, the heme ferrous iron of GLB-26 is strongly hexacoordinated with HisE7, which could explain its extremely low affinity for CO. This globin oxidizes instantly to the ferric form in the presence of oxygen and is therefore incapable of reversible oxygen binding. CONCLUSION The presented data indicate that GLB-1 and GLB-26 belong to two functionally-different globin classes.
Collapse
Affiliation(s)
- Eva Geuens
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Projecto-Garcia J, Zorn N, Jollivet D, Schaeffer SW, Lallier FH, Hourdez S. Origin and evolution of the unique tetra-domain hemoglobin from the hydrothermal vent scale worm Branchipolynoe. Mol Biol Evol 2010; 27:143-52. [PMID: 19755665 DOI: 10.1093/molbev/msp218] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hemoglobin is the most common respiratory pigment in annelids. It can be intra or extracellular, and this latter type can form large multimeric complexes. The hydrothermal vent scale worms Branchipolynoe symmytilida and Branchipolynoe seepensis express an extracellular tetra-domain hemoglobin (Hb) that is unique in annelids. We sequenced the gene for the single-domain and tetra-domain globins in these two species. The single-domain gene codes for a mature protein of 137 amino acids, and the tetra-domain gene codes for a mature protein of 552 amino acids. The single-domain gene has a typical three exon/two intron structure, with introns located at their typical positions (B12.2 and G7.0). This structure is repeated four times in the tetra-domain gene, with no bridge introns or linker sequences between domains. The phylogenetic position of Branchipolynoe globins among known annelid globins revealed that, although extracellular, they cluster within the annelid intracellular globins clade, suggesting that the extracellular state of these Hbs is the result of convergent evolution. The tetra-domain structure likely resulted from two tandem duplications, domain 1 giving rise to domain 2 and after this the two-domain gene duplicated to produce domains 3 and 4. The high O(2) affinity of Branchipolynoe extracellular globins may be explained by the two key residues (B10Y and E7Q) in the heme pocket in each of the domains of the single and tetra-domain globins, which have been shown to be essential in the oxygen-avid Hb from the nematode Ascaris suum. This peculiar globin evolutionary path seems to be very different from other annelid extracellular globins and is most likely the product of evolutionary tinkering associated with the strong selective pressure to adapt to chronic hypoxia that characterizes hydrothermal vents.
Collapse
Affiliation(s)
- J Projecto-Garcia
- Equipe GAME, CNRS UMR 7144, Places Georges Teissier, Roscoff Cedex, France
| | | | | | | | | | | |
Collapse
|
31
|
Kuwada T, Hasegawa T, Takagi T, Sato I, Shishikura F. pH-dependent structural changes in haemoglobin component V from the midge larvaPropsilocerus akamusi(Orthocladiinae, Diptera). ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:258-67. [DOI: 10.1107/s0907444909055760] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 12/30/2009] [Indexed: 11/10/2022]
Abstract
Haemoglobin component V (Hb V) from the midge larvaPropsilocerus akamusiexhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb V retains its functional properties by adapting to the structural changes caused by amino-acid replacements.
Collapse
|
32
|
Mishra S, Meuwly M. Atomistic Simulation of NO Dioxygenation in Group I Truncated Hemoglobin. J Am Chem Soc 2010; 132:2968-82. [DOI: 10.1021/ja9078144] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland
| |
Collapse
|
33
|
Mowat CG, Gazur B, Campbell LP, Chapman SK. Flavin-containing heme enzymes. Arch Biochem Biophys 2010; 493:37-52. [DOI: 10.1016/j.abb.2009.10.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 10/13/2009] [Accepted: 10/13/2009] [Indexed: 11/25/2022]
|
34
|
Tran R, Boon EM, Marletta MA, Mathies RA. Resonance Raman spectra of an O2-binding H-NOX domain reveal heme relaxation upon mutation. Biochemistry 2009; 48:8568-77. [PMID: 19653642 DOI: 10.1021/bi900563g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Resonance Raman spectra were measured for the wild type Heme-Nitric oxide/OXygen binding domain from Thermoanaerobacter tengcongensis (Tt H-NOX WT) and three other Tt H-NOX proteins containing mutations at key conserved residues to determine the heme conformation in solution. The most dramatic changes in heme conformation occurred in the O2-bound forms, and the single Tt H-NOX P115A mutation was sufficient to generate a significant relaxation of the chromophore. Clear evidence of heme relaxation in the Tt H-NOX I5L, P115A, and I5L/P115A mutants in solution is demonstrated by the observation of reduced resonance Raman intensities for several out-of-plane low frequency modes (e.g., gamma11, gamma12, gamma13, and gamma15) in the 400-750 cm(-1) region known to be sensitive to ruffling and saddling deformations, as well as increased vibrational frequencies for the core heme skeletal stretching modes, nu3, nu2, and nu10. In addition, all three mutants exhibited some degree of heme conformational heterogeneity based on several broad skeletal markers (e.g., nu10) in the high frequency region. These results are comparable to those observed by Olea et al. for Tt H-NOX P115A in crystal form, where four different heme structures were determined from a single unit cell. On the basis of the resonance Raman spectra, it is clear that the actual heme conformation for Tt H-NOX P115A in solution is considerably more relaxed than that of the WT protein, with increased flexibility within the protein pocket, allowing for rapid sampling of alternate conformations.
Collapse
Affiliation(s)
- Rosalie Tran
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | |
Collapse
|
35
|
Hunt PW, McNally J, Barris W, Blaxter ML. Duplication and divergence: the evolution of nematode globins. J Nematol 2009; 41:35-51. [PMID: 22661776 PMCID: PMC3365290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Indexed: 06/01/2023] Open
Abstract
In common with many other groups, nematodes express globins with unknown functions. Nematode globin-like genes can be divided into class 1 globins, similar to vertebrate myoglobins, and a wide range of additional classes. Here we show that class 1 nematode globins possess a huge amount of diversity in gene sequence and structure. There is evidence for multiple events of gene duplication, intron insertion and loss between species, and for allelic variation effecting both synonymous and non-synonymous sites within species. We have also examined gene expression patterns in class I globins from a variety of species. The results show variation in the degree of gene expression, but the tissue specificity and temporal specificity of expression may be more conserved in the phylum. Because the structure-function relationships for the binding and transport of oxygen by globins are well understood, the consequences of genetic variation causing amino acid changes are explored. The gene family shows great promise for discovering unique insights into both structure-function relationships of globins and their physiologial roles.
Collapse
Affiliation(s)
- P W Hunt
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JT, United Kingdom. CSIRO, Locked Mail Bag 1, Armidale, NSW 2350, Australia. CSIRO, 306 Carmody Road, St Lucia QLD 4067, Australia
| | | | | | | |
Collapse
|
36
|
Wajcman H, Kiger L, Marden MC. Structure and function evolution in the superfamily of globins. C R Biol 2008; 332:273-82. [PMID: 19281958 DOI: 10.1016/j.crvi.2008.07.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 07/30/2008] [Indexed: 11/16/2022]
Abstract
The superfamily of globins has emerged some 4000 Myr from a common ancestor, which was among the basic protein components required for life. Globins are present in the three kingdoms of life. From a structure point of view, these molecules are defined by the presence of a characteristic protein fold, rich in alpha-helix, surrounding a heme group. Depending on the species or organs, they may be physiologically active as monomers, tetramers or large size polymers. Their function varies from the classical reversible binding of oxygen for transport and storage to cytoprotection against reactive oxygen species, NO scavenging, signaling in oxygen dependent metabolic pathways, or possibly other specific properties involving ligand or electron transfer. All these aspects are discussed in this review.
Collapse
Affiliation(s)
- Henri Wajcman
- INSERM U841, Equipe 11, CHU Henri-Mondor, 94010 Créteil, France.
| | | | | |
Collapse
|
37
|
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).
Collapse
Affiliation(s)
- José A Gavira
- Laboratorio de Estudios Cristalográficos, CSIC, P.T. Ciencias de la Salud, Granada, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Abstract
Recent advances in computational biology have made it possible to map the complete network and energy profile of gas migration pathways inside proteins. Although networks of O(2) pathways have already been characterized for a small number of proteins, the general properties and locations of these pathways have not been previously compared between proteins. In this study, maps of the O(2) pathways inside 12 monomeric globins were computed. It is found that, despite the conserved tertiary structure fold of the studied globins, the shape and topology of O(2) pathway networks exhibit a large variability between different globins, except when two globins are nearly identical. The locations of the O(2) pathways are, however, found to be correlated with the location of large hydrophobic residues, and a similar correlation is observed in two unrelated protein families: monomeric globins and copper-containing amine oxidases. The results have implications for the evolution of gas pathways in proteins and for protein engineering applications involving modifications of these pathways.
Collapse
Affiliation(s)
- Jordi Cohen
- Beckman Institute, University of Illinois, Urbana, Illinois, USA
| | | |
Collapse
|
39
|
de Guzman JV, Yu HS, Jeong HJ, Hong YC, Kim J, Kong HH, Chung DI. Molecular characterization of two myoglobins of Paragonimus westermani. J Parasitol 2007; 93:97-103. [PMID: 17436948 DOI: 10.1645/ge-846r3.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Myoglobins (Mbs), globin proteins, are present in high concentrations in trematodes. In Paragonimus westermani, 2 cDNAs were found to encode Mbs. The first clone, Pwmyo1, codes a total of 149 amino acids with a calculated mass of 16.6 kDa. The second, Pwmyo2, encodes a 146-amino acid protein with a calculated mass of 16.2 kDa. The predicted secondary structures showed the presence of 8 helices, which is the basic characteristic of Mbs. Sequence alignment revealed a high homology with the other trematode Mbs. The 2 clones contained the characteristic tyrosyl residues at helical positions B10 and distal E7, which are substitutions that have been previously shown to contribute to the high oxygen affinity of Mbs. Polyclonal antibodies against the recombinant Mbs were raised with no cross-reactivity observed. Immunolocalization revealed the proteins to be distributed generally throughout the parenchymal tissues, but absent from the tegument and reproductive organs. The cell mass of the eggs of the worm stained positive to Pwmyo2 but not Pwmyo1, suggesting the stage-specific expression of these Mbs.
Collapse
Affiliation(s)
- Jefferson V de Guzman
- Department of Parasitology, Kyungpook National University School of Medicine, Daegu 700-422, Korea
| | | | | | | | | | | | | |
Collapse
|
40
|
Upadhyay AK, Hooper AB, Hendrich MP. NO reductase activity of the tetraheme cytochrome C554 of Nitrosomonas europaea. J Am Chem Soc 2006; 128:4330-7. [PMID: 16569009 PMCID: PMC2806813 DOI: 10.1021/ja055183+] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tetraheme cytochrome c(554) (cyt c(554)) from Nitrosomonas europaea is believed to function as an electron-transfer protein from hydroxylamine oxidoreductase (HAO). We show here that cyt c(554) also has significant NO reductase activity. The protein contains one high-spin and three low-spin c-type hemes. HAO catalyzed reduction of the cyt c(554), ligand binding, intermolecular electron transfer, and kinetics of NO reduction by cyt c(554) have been investigated. We detect the formation of a NO-bound ferrous heme species in cyt c(554) by EPR and Mössbauer spectroscopies during the HAO catalyzed oxidation of hydroxylamine, indicating that N-oxide intermediates produced from HAO readily bind to cyt c(554). In the half-reduced state of cyt c(554), we detect a spin interaction between the [FeNO](7) state of heme 2 and the low-spin ferric state of heme 4. We find that ferrous cyt c(554) will reduce NO at a rate greater than 16 s(-1), which is comparable to rates of other known NO reductases. Carbon monoxide or nitrite are shown not to bind to the reduced protein, and previous results indicate the reactions with O(2) are slow and that a variety of ligands will not bind in the oxidized state. Thus, the enzymatic site is highly selective for NO. The NO reductase activity of cyt c(554) may be important during ammonia oxidation in N. europaea at low oxygen concentrations to detoxify NO produced by reduction of nitrite or incomplete oxidation of hydroxylamine.
Collapse
Affiliation(s)
- Anup K. Upadhyay
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Alan B. Hooper
- Department of Biochemistry, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| |
Collapse
|
41
|
Miranda JL. Conservation and diversity of ancient hemoglobins in Bacteria. Biochem Biophys Res Commun 2006; 343:924-7. [PMID: 16574075 DOI: 10.1016/j.bbrc.2006.03.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 03/04/2006] [Indexed: 11/20/2022]
Abstract
A group of single-domain proteins in Bacteria similar to thermoglobin, an oxygen-avid hemoglobin representative of the ancestral form, reveals the primordial structure, function, and evolvability of the family. Conserved residues at specific positions function to bind ligand or participate in hydrophobic packing of the protein core during protein folding. A potential hydrogen bond network consisting of a tyrosine and glutamine residue in the distal ligand-binding site of most hemoglobins suggests that the ancestral protein bound oxygen avidly. Two divergent hemoglobins with mutations at generally conserved positions contain non-canonical ligand-binding sites, illustrating plasticity of the fold. One binds heme in a manner similar to cytochromes and may represent an evolutionary link to the precursor of the hemoglobin fold. Conservation suggests specific biochemical properties of the ancestral protein; diversity suggests an evolvability of this group of hemoglobins tolerant of mutations that perturb conserved biochemical properties for adaptation to novel functions.
Collapse
Affiliation(s)
- Jj L Miranda
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
42
|
Walker FA. The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography. J Biol Inorg Chem 2006; 11:391-7. [PMID: 16586113 DOI: 10.1007/s00775-006-0095-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2006] [Accepted: 02/22/2006] [Indexed: 12/16/2022]
Abstract
The 1H NMR chemical shifts of the heme methyl groups of the ferriheme complex of metneuroglobin (Du et al. in J. Am. Chem. Soc. 125:8080-8081, 2003) predict orientations of the axial histidine ligands (Shokhirev and Walker in J. Biol. Inorg. Chem. 3:581-594, 1998) that are not consistent with the X-ray data (Vallone et al. in Proteins Struct. Funct. Bioinf. 56:85-94, 2004), and the EPR spectrum (Vinck et al. in J. Am. Chem. Soc. 126:4516-4517, 2004) is only marginally consistent with these data. The reasons for these inconsistencies appear to be rooted in the high degree of aqueous solution exposure of the heme group and the fact that there are no strong hydrogen-bond acceptors for the histidine imidazole N-H protons provided by the protein. Similar inconsistencies may exist for other water-soluble heme proteins, and 1H NMR spectroscopy provides a simple means to verify whether the solution structure of the heme center is the same as or different from that in the crystalline state.
Collapse
Affiliation(s)
- F Ann Walker
- Department of Chemistry, The University of Arizona, PO Box 210041, Tucson, AZ 85721-0041, USA.
| |
Collapse
|
43
|
Marti MA, Crespo A, Capece L, Boechi L, Bikiel DE, Scherlis DA, Estrin DA. Dioxygen affinity in heme proteins investigated by computer simulation. J Inorg Biochem 2006; 100:761-70. [PMID: 16442625 DOI: 10.1016/j.jinorgbio.2005.12.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 12/13/2005] [Indexed: 11/24/2022]
Abstract
We present an investigation of the molecular basis of the modulation of oxygen affinity in heme proteins using computer simulation. QM-MM calculations are applied to explore distal and proximal effects on O(2) binding to the heme, while classical molecular dynamics simulations are employed to investigate ligand migration across the polypeptide to the active site. Trends in binding energies and in the kinetic constants are illustrated through a number of selected examples highlighting the virtues and the limitations of the applied methodologies. These examples cover a wide range of O(2)-affinities, and include: the truncated-N and truncated-O hemoglobins from Mycobacterium tuberculosis, the mammalian muscular O(2) storage protein: myoglobin, the hemoglobin from the parasitic nematode Ascaris lumbricoides, the oxygen transporter in the root of leguminous plants: leghemoglobin, the Cerebratulus lacteus nerve tissue hemoglobin, and the Alcaligenes xyloxidans cytochrome c'.
Collapse
Affiliation(s)
- Marcelo A Marti
- Departamento de Química Inorgánica, Analítica y Química Física/Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires, C1428EHA, Argentina
| | | | | | | | | | | | | |
Collapse
|
44
|
Das TK, Dewilde S, Friedman JM, Moens L, Rousseau DL. Multiple active site conformers in the carbon monoxide complexes of trematode hemoglobins. J Biol Chem 2006; 281:11471-9. [PMID: 16481317 DOI: 10.1074/jbc.m512054200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sequence alignment of hemoglobins of the trematodes Paramphistomum epiclitum and Gastrothylax crumenifer with myoglobin suggests the presence of an unusual active site structure in which two tyrosine residues occupy the E7 and B10 helical positions. In the crystal structure of P. epiclitum hemoglobin, such an E7-B10 tyrosine pair at the putative helical positions has been observed, although the E7 Tyr is displaced toward CD region of the polypeptide. Resonance Raman data on both P. epiclitum and G. crumenifer hemoglobins show that interactions of heme-bound ligands with neighboring amino acid residues are unusual. Multiple conformers in the CO complex, termed the C, O, and N conformers, are observed. The conformers are separated by a large difference (approximately 60 cm(-1)) in the frequencies of their Fe-CO stretching modes. In the C conformer the Fe-CO stretching frequency is very high, 539 and 535 cm(-1), for the P. epiclitum and G. crumenifer hemoglobins, respectively. The Fe-CO stretching of the N conformer appears at an unusually low frequency, 479 and 476 cm(-1), respectively, for the two globins. A population of an O conformer is seen in both hemoglobins, at 496 and 492 cm(-1), respectively. The C conformer is stabilized by a strong polar interaction of the CO with the distal B10 tyrosine residue. The O conformer is similar to the ones typically seen in mutant myoglobins in which there are no strong interactions between the CO and residues in the distal pocket. The N conformer possesses an unusual configuration in which a negatively charged group, assigned as the oxygen atom of the B10 Tyr side chain, interacts with the CO. In this conformer, the B10 Tyr assumes an alternative conformation consistent with one of the conformers seen the crystal structure. Implications of the multiple configurations on the ligand kinetics are discussed.
Collapse
Affiliation(s)
- Tapan K Das
- Pfizer Global Biologics, Chesterfield, Missouri 63017, USA
| | | | | | | | | |
Collapse
|
45
|
Simcock DC, Brown S, Neale JD, Przemeck SMC, Simpson HV. L3 and adult Ostertagia (Teladorsagia) circumcincta exhibit cyanide sensitive oxygen uptake. Exp Parasitol 2006; 112:1-7. [PMID: 16198342 DOI: 10.1016/j.exppara.2005.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 08/16/2005] [Accepted: 08/17/2005] [Indexed: 11/21/2022]
Abstract
Oxygen consumption by L3 and adult Ostertagia (Teladorsagia) circumcincta was examined in vitro to determine whether oxygen can be utilised in metabolism. The oxygen concentration in the abomasal fluid of sheep infected with O. circumcincta was also measured. Rates of consumption (in nmol O2/h/1000 worms) were 13+/-1 in sheathed L3, 34+/-6 in ex-sheathed L3, and 1944+/-495 in adult worms. Constant rates of consumption were maintained until media oxygen concentration dropped to between 10 and 20 microM. Consumption was inhibited 95% by cyanide in L3 and 74% in adults. Oxygen concentration in abomasal fluid varied between 10 and 30 microM in both infected and uninfected animals. During infection, oxygen concentration decreased slightly with increased abomasal pH, though the correlation between the two was poor (r=-0.30). In conclusion, O. circumcincta can consume oxygen and oxygen concentration at the infection site is sufficient to support at least some aerobic metabolism.
Collapse
Affiliation(s)
- D C Simcock
- Laboratory for Biochemical Parasitology, Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand.
| | | | | | | | | |
Collapse
|
46
|
Miranda JJL, Maillett DH, Soman J, Olson JS. Thermoglobin, Oxygen-avid Hemoglobin in a Bacterial Hyperthermophile. J Biol Chem 2005; 280:36754-61. [PMID: 16135523 DOI: 10.1074/jbc.m505918200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hemoglobin family of proteins, ubiquitous in all domains of life, evolved from an ancestral protein of primordial function to extant hemoglobins that perform a myriad of functions with diverged biochemical properties. Study of homologs in bacterial hyperthermophiles may shed light on both mechanisms of adaptation to extreme conditions and the nature of the ancestral protein. A hemoglobin was identified in Aquifex aeolicus, cloned, recombinantly expressed, purified, and characterized. This hemoglobin is monomeric, resistant to thermal and chemical denaturation, pentacoordinate in the ferrous deoxygenated state, and oxygen-avid. The oxygen equilibrium dissociation constant is approximately 1 nm at room temperature, due in part to a hydrogen bond between the bound ligand and a tyrosine residue in the distal pocket. These biochemical properties of A. aeolicus thermoglobin, AaTgb, may have been shared by the ancestral hemoglobin, thus suggesting possible primordial functions and providing a starting point for consequent evolution of the hemoglobin family.
Collapse
Affiliation(s)
- J J L Miranda
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | | | | | | |
Collapse
|
47
|
Holmes JB, Tsai J. Characterizing conserved structural contacts by pair-wise relative contacts and relative packing groups. J Mol Biol 2005; 354:706-21. [PMID: 16269154 DOI: 10.1016/j.jmb.2005.09.081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 09/06/2005] [Accepted: 09/26/2005] [Indexed: 10/25/2022]
Abstract
To adequately deal with the inherent complexity of interactions between protein side-chains, we develop and describe here a novel method for characterizing protein packing within a fold family. Instead of approaching side-chain interactions absolutely from one residue to another, we instead consider the relative interactions of contacting residue pairs. The basic element, the pair-wise relative contact, is constructed from a sequence alignment and contact analysis of a set of structures and consists of a cluster of similarly oriented, interacting, side-chain pairs. To demonstrate this construct's usefulness in analyzing protein structure, we used the pair-wise relative contacts to analyze two sets of protein structures as defined by SCOP: the diverse globin-like superfamily (126 structures) and the more uniform heme binding globin family (a 94 structure subset of the globin-like superfamily). The superfamily structure set produced 1266 unique pair-wise relative contacts, whereas the family structure subset gave 1001 unique pair-wise relative contacts. For both sets, we show that these constructs can be used to accurately and automatically differentiate between fold classes. Furthermore, these pair-wise relative contacts correlate well with sequence identity and thus provide a direct relationship between changes in sequence and changes in structure. To capture the complexity of protein packing, these pair-wise relative contacts can be superimposed around a single residue to create a multi-body construct called a relative packing group. Construction of convex hulls around the individual packing groups provides a measure of the variation in packing around a residue and defines an approximate volume of space occupied by the groups interacting with a residue. We find that these relative packing groups are useful in understanding the structural quality of sequence or structure alignments. Moreover, they provide context to calculate a value for structural randomness, which is important in properly assessing the quality of a structural alignment. The results of this study provide the framework for future analysis for correlating sequence changes to specific structure changes.
Collapse
Affiliation(s)
- J Bradley Holmes
- Laboratory of Molecular Genetics NICHD-NIH, Bethesda, MD 20952, USA
| | | |
Collapse
|
48
|
Gow AJ, Payson AP, Bonaventura J. Invertebrate hemoglobins and nitric oxide: how heme pocket structure controls reactivity. J Inorg Biochem 2005; 99:903-11. [PMID: 15811507 DOI: 10.1016/j.jinorgbio.2004.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2004] [Revised: 11/29/2004] [Accepted: 12/06/2004] [Indexed: 11/20/2022]
Abstract
Hemoglobins (Hbs), generally defined as 5 or 6 coordinate heme proteins whose primary function is oxygen transport, are now recognized to occur in virtually all phyla of living organisms. Historically, study of their function focused on oxygen as a reversibly bound ligand of the ferrous form of the protein. Other diatomic ligands like carbon monoxide and nitric oxide were considered "non-physiological" but useful probes of structure-function relationships in Hbs. This investigatory landscape changed dramatically in the 1980s when nitric oxide was discovered to activate a heme protein, cyclic guanylate cyclase. Later, its activation was likened to Perutz' description of Hb's allosteric properties being triggered by a ligand-dependent "out-of-plane/into-plane" movement of the heme iron. In 1996, a functional role for nitric oxide in human and mammalian Hbs was demonstrated and since that time, the interest in NO as a physiologically relevant Hb ligand has greatly increased. Concomitantly, non-oxygen binding properties of Hbs have challenged the view that Hbs arose for their oxygen storage and transport properties. In this focused review we discuss some invertebrate Hbs' functionally significant reactions with nitric oxide and how strategic positioning of a few residues in the heme pocket plays an large role in the interplay of diatomic ligands to ferrous and ferric heme iron in these proteins.
Collapse
Affiliation(s)
- Andrew J Gow
- Stokes Research Institute, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | |
Collapse
|
49
|
Flores JF, Fisher CR, Carney SL, Green BN, Freytag JK, Schaeffer SW, Royer WE. Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin. Proc Natl Acad Sci U S A 2005; 102:2713-8. [PMID: 15710902 PMCID: PMC549462 DOI: 10.1073/pnas.0407455102] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Key to the remarkable ability of vestimentiferan tubeworms to thrive in the harsh conditions of hydrothermal vents are hemoglobins that permit the sequestration and delivery of hydrogen sulfide and oxygen to chemoautotrophic bacteria. Here, we demonstrate that zinc ions, not free cysteine residues, bind sulfide in vestimentiferan hemoglobins. The crystal structure of the C1 hemoglobin from the hydrothermal vent tubeworm Riftia pachyptila has been determined to 3.15 A and revealed the unexpected presence of 12 tightly bound Zn(2+) ions near the threefold axes of this D(3) symmetric hollow sphere. Chelation experiments on R. pachyptila whole-coelomic fluid and purified hemoglobins reveal a role for Zn(2+) ions in sulfide binding. Free cysteine residues, previously proposed as sulfide-binding sites in vestimentiferan hemoglobins, are found buried in surprisingly hydrophobic pockets below the surface of the R. pachyptila C1 molecule, suggesting that access of these residues to environmental sulfide is restricted. Attempts to reduce the sulfide-binding capacities of R. pachyptila hemoglobins by addition of a thiol inhibitor were also unsuccessful. These findings challenge the currently accepted paradigm of annelid hemoglobin evolution and adaptation to reducing environments.
Collapse
Affiliation(s)
- Jason F Flores
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | | | | | | | | | | | | |
Collapse
|
50
|
Imai K, Asakawa N, Tsuji T, Sonoyama M, Mitaku S. Secondary structure breakers and hairpin structures in myoglobin and hemoglobin. CHEM-BIO INFORMATICS JOURNAL 2005. [DOI: 10.1273/cbij.5.65] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kenichiro Imai
- Nagoya University, School of Engineering, Department of Applied Physics
| | - Naoyuki Asakawa
- Nagoya University, School of Engineering, Department of Applied Physics
| | - Toshiyuki Tsuji
- Nagoya University, School of Engineering, Department of Applied Physics
| | - Masashi Sonoyama
- Nagoya University, School of Engineering, Department of Applied Physics
| | - Shigeki Mitaku
- Nagoya University, School of Engineering, Department of Applied Physics
| |
Collapse
|