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Barbosa HJ, Quevedo YS, Torres AM, Veloza GAG, Carranza Martínez JC, Urrea-Montes DA, Robello-Porto C, Vallejo GA. Comparative proteomic analysis of the hemolymph and salivary glands of Rhodnius prolixus and R. colombiensis reveals candidates associated with differential lytic activity against Trypanosoma cruzi Dm28c and T. cruzi Y. PLoS Negl Trop Dis 2024; 18:e0011452. [PMID: 38568999 PMCID: PMC10990223 DOI: 10.1371/journal.pntd.0011452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Immune response of triatomines plays an important role in the success or failure of transmission of T. cruzi. Studies on parasite-vector interaction have shown the presence of trypanolytic factors and have been observed to be differentially expressed among triatomines, which affects the transmission of some T. cruzi strains or DTUs (Discrete Typing Units). METHODOLOGY/PRINCIPAL FINDINGS Trypanolytic factors were detected in the hemolymph and saliva of R. prolixus against epimastigotes and trypomastigotes of the Y strain (T. cruzi II). To identify the components of the immune response that could be involved in this lytic activity, a comparative proteomic analysis was carried out, detecting 120 proteins in the hemolymph of R. prolixus and 107 in R. colombiensis. In salivary glands, 1103 proteins were detected in R. prolixus and 853 in R. colombiensis. A higher relative abundance of lysozyme, prolixin, nitrophorins, and serpin as immune response proteins was detected in the hemolymph of R. prolixus. Among the R. prolixus salivary proteins, a higher relative abundance of nitrophorins, lipocalins, and triabins was detected. The higher relative abundance of these immune factors in R. prolixus supports their participation in the lytic activity on Y strain (T. cruzi II), but not on Dm28c (T. cruzi I), which is resistant to lysis by hemolymph and salivary proteins of R. prolixus due to mechanisms of evading oxidative stress caused by immune factors. CONCLUSIONS/SIGNIFICANCE The lysis resistance observed in the Dm28c strain would be occurring at the DTU I level. T. cruzi I is the DTU with the greatest geographic distribution, from the south of the United States to central Chile and Argentina, a distribution that could be related to resistance to oxidative stress from vectors. Likewise, we can say that lysis against strain Y could occur at the level of DTU II and could be a determinant of the vector inability of these species to transmit T. cruzi II. Future proteomic and transcriptomic studies on vectors and the interactions of the intestinal microbiota with parasites will help to confirm the determinants of successful or failed vector transmission of T. cruzi DTUs in different parts of the Western Hemisphere.
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Affiliation(s)
- Hamilton J. Barbosa
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Yazmin Suárez Quevedo
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Arlid Meneses Torres
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Gustavo A. Gaitán Veloza
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Julio C. Carranza Martínez
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Daniel A. Urrea-Montes
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Carlos Robello-Porto
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Gustavo A. Vallejo
- Laboratorio de Investigaciones en Parasitología Tropical (LIPT), Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
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2
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Nitrosylation of ferric zebrafish nitrobindin: A spectroscopic, kinetic, and thermodynamic study. J Inorg Biochem 2022; 237:111996. [PMID: 36150290 DOI: 10.1016/j.jinorgbio.2022.111996] [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: 07/06/2022] [Revised: 08/30/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023]
Abstract
Nitrobindins (Nbs) are all-β-barrel heme-proteins present in all the living kingdoms. Nbs inactivate reactive nitrogen species by sequestering NO, converting NO to HNO2, and isomerizing peroxynitrite to NO3- and NO2-. Here, the spectroscopic characterization of ferric Danio rerio Nb (Dr-Nb(III)) and NO scavenging through the reductive nitrosylation of the metal center are reported, both processes being relevant for the regulation of blood flow in fishes through poorly oxygenated tissues, such as retina. Both UV-Vis and resonance Raman spectroscopies indicate that Dr-Nb(III) is a mixture of a six-coordinated aquo- and a five-coordinated species, whose relative abundancies depend on pH. At pH ≤ 7.0, Dr-Nb(III) binds reversibly NO, whereas at pH ≥ 7.8 NO induces the conversion of Dr-Nb(III) to Dr-Nb(II)-NO. The conversion of Dr-Nb(III) to Dr-Nb(II)-NO is a monophasic process, suggesting that the formation of the transient Dr-Nb(III)-NO species is lost in the mixing time of the rapid-mixing stopped-flow apparatus (∼ 1.5 ms). The pseudo-first-order rate constant for the reductive nitrosylation of Dr-Nb(III) is not linearly dependent on the NO concentration but tends to level off. Values of the rate-limiting constant (i.e., klim) increase linearly with the OH- concentration, indicating that the conversion of Dr-Nb(III) to Dr-Nb(II)-NO is limited by the OH--based catalysis. From the dependence of klim on [OH-], the value of the second-order rate constant kOH- was obtained (5.2 × 103 M-1 s-1). Reductive nitrosylation of Dr-Nb(III) leads to the inactivation of two NO molecules: one being converted to HNO2, and the other being tightly bound to the heme-Fe(II) atom.
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3
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De Simone G, Fattibene P, Sebastiani F, Smulevich G, Coletta M, Ascenzi P. Dissociation of the proximal His-Fe bond upon NO binding to ferrous zebrafish nitrobindin. J Inorg Biochem 2022; 236:111962. [PMID: 36075159 DOI: 10.1016/j.jinorgbio.2022.111962] [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: 06/22/2022] [Revised: 07/22/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Nitrobindins (Nbs) are all-β-barrel heme-proteins present in prokaryotes and eukaryotes. Although the physiological role(s) of Nbs are still unclear, it has been postulated that they are involved in the NO/O2 metabolism, which is particularly relevant in fishes for the oxygen supply. Here, the reactivity of ferrous Danio rerio Nb (Dr-Nb(II)) towards NO has been investigated from the spectroscopic and kinetic viewpoints and compared with those of Mycobacterium tuberculosis Nb, Arabidopsis thaliana Nb, Homo sapiens Nb, and Equus ferus caballus myoglobin. Between pH 5.5 and 9.1 at 22.0 °C, Dr-Nb(II) nitrosylation is a monophasic process; values of the second-order rate constant for Dr-Nb(II) nitrosylation and of the first-order rate constant for Dr-Nb(II)-NO denitrosylation are pH-independent ranging between 1.6 × 106 M-1 s-1 and 2.3 × 106 M-1 s-1 and between 5.3 × 10-2 s-1 and 8.2 × 10-2 s-1, respectively. Interestingly, both UV-Vis and EPR spectroscopies indicate that the heme-Fe(II) atom of Dr-Nb(II)-NO is five-coordinated. Kinetics of Dr-Nb(II) nitrosylation may reflect the ligand accessibility to the metal center, which is likely impaired by the crowded network of water molecules which shields the heme pocket from the bulk solvent. On the other hand, kinetics of Dr-Nb(II)-NO denitrosylation may reflect an easy pathway for the ligand escape into the outer solvent.
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Affiliation(s)
| | - Paola Fattibene
- Servizio Grandi Strumentazioni e Core Facilities, Istituto Superiore di Sanità, Roma, Italy
| | | | | | | | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, 00146 Roma, Italy.
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4
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Huang S, Deng WH, Liao RZ, He C. Repurposing a Nitric Oxide Transport Hemoprotein Nitrophorin 2 for Olefin Cyclopropanation. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shunzhi Huang
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
| | - Wen-Hao Deng
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Rong-Zhen Liao
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
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5
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Portlock TJ, Tyson JY, Dantu SC, Rehman S, White RC, McIntire IE, Sewell L, Richardson K, Shaw R, Pandini A, Cianciotto NP, Garnett JA. Structure, Dynamics and Cellular Insight Into Novel Substrates of the Legionella pneumophila Type II Secretion System. Front Mol Biosci 2020; 7:112. [PMID: 32656228 PMCID: PMC7325957 DOI: 10.3389/fmolb.2020.00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Legionella pneumophila is a Gram-negative bacterium that is able to replicate within a broad range of aquatic protozoan hosts. L. pneumophila is also an opportunistic human pathogen that can infect macrophages and epithelia in the lung and lead to Legionnaires’ disease. The type II secretion system is a key virulence factor of L. pneumophila and is used to promote bacterial growth at low temperatures, regulate biofilm formation, modulate host responses to infection, facilitate bacterial penetration of mucin gels and is necessary for intracellular growth during the initial stages of infection. The L. pneumophila type II secretion system exports at least 25 substrates out of the bacterium and several of these, including NttA to NttG, contain unique amino acid sequences that are generally not observed outside of the Legionella genus. NttA, NttC, and NttD are required for infection of several amoebal species but it is unclear what influence other novel substrates have within their host. In this study, we show that NttE is required for optimal infection of Acanthamoeba castellanii and Vermamoeba vermiformis amoeba and is essential for the typical colony morphology of L. pneumophila. In addition, we report the atomic structures of NttA, NttC, and NttE and through a combined biophysical and biochemical hypothesis driven approach we propose novel functions for these substrates during infection. This work lays the foundation for future studies into the mechanistic understanding of novel type II substrate functions and how these relate to L. pneumophila ecology and disease.
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Affiliation(s)
- Theo J Portlock
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom.,Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Jessica Y Tyson
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Sarath C Dantu
- Department of Computer Science, Brunel University London, Uxbridge, United Kingdom
| | - Saima Rehman
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom
| | - Richard C White
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Ian E McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lee Sewell
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom
| | - Katherine Richardson
- Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Rosie Shaw
- Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Alessandro Pandini
- Department of Computer Science, Brunel University London, Uxbridge, United Kingdom
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom.,Department of Chemistry and Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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6
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Hubbard CD, Chatterjee D, Oszajca M, Polaczek J, Impert O, Chrzanowska M, Katafias A, Puchta R, van Eldik R. Inorganic reaction mechanisms. A personal journey. Dalton Trans 2020; 49:4599-4659. [PMID: 32162632 DOI: 10.1039/c9dt04620h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This review covers highlights of the work performed in the van Eldik group on inorganic reaction mechanisms over the past two decades in the form of a personal journey. Topics that are covered include, from NO to HNO chemistry, peroxide activation in model porphyrin and enzymatic systems, the wonder-world of RuIII(edta) chemistry, redox chemistry of Ru(iii) complexes, Ru(ii) polypyridyl complexes and their application, relevant physicochemical properties and reaction mechanisms in ionic liquids, and mechanistic insight from computational chemistry. In each of these sections, typical examples of mechanistic studies are presented in reference to related work reported in the literature.
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Affiliation(s)
- Colin D Hubbard
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Egerlandstr. 1, 91058 Erlangen, Germany.
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Ozone-assisted catalytic oxidation of aqueous nitrite ions on HZSM-5 zeolites. Sci Rep 2019; 9:14322. [PMID: 31586086 PMCID: PMC6778124 DOI: 10.1038/s41598-019-50662-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/17/2019] [Indexed: 12/05/2022] Open
Abstract
Simultaneous removal of NOx and SO2 during the wet absorption process has made it possible for nitrogen resource utilization. However, nitrites formation at high ratio in absorption solution would limit its application. In this study, the catalytic oxidation behaviors of aqueous nitrite ions assisted by ozone on HZSM-5 zeolites with different SiO2/Al2O3 ratios have been investigated. The experimental results revealed that the oxidation and disproportionation reactions of nitrite ions took place competitively, both of which were accelerated under acidic condition. Moreover, the introduction of HZSM-5 zeolites and ozone would significantly improve the nitrite oxidation rate, where the zeolites with high SiO2/Al2O3 ratios were found to be more effective owing to the enhanced adsorption of nitrite ions and ozone. Based on the results under different operating conditions (such as O3 concentration, HZSM-5 dosage, pH values and presence of radical scavengers etc.), the reaction mechanism was then proposed. The disproportionation reaction of nitrite ions mainly occurred in the bulk solution. And the catalytic oxidation of nitrite ions over zeolites proceeded via a non-radical surface reaction between the adsorbed nitrite ions and ozone/oxygen molecular.
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8
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De Simone G, Ascenzi P, di Masi A, Polticelli F. Nitrophorins and nitrobindins: structure and function. Biomol Concepts 2018; 8:105-118. [PMID: 28574374 DOI: 10.1515/bmc-2017-0013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/03/2017] [Indexed: 12/23/2022] Open
Abstract
Classical all α-helical globins are present in all living organisms and are ordered in three lineages: (i) flavohemoglobins and single domain globins, (ii) protoglobins and globin coupled sensors and (iii) truncated hemoglobins, displaying the 3/3 or the 2/2 all α-helical fold. However, over the last two decades, all β-barrel and mixed α-helical-β-barrel heme-proteins displaying heme-based functional properties (e.g. ligand binding, transport and sensing) closely similar to those of all α-helical globins have been reported. Monomeric nitrophorins (NPs) and α1-microglobulin (α1-m), belonging to the lipocalin superfamily and nitrobindins (Nbs) represent prototypical heme-proteins displaying the all β-barrel and mixed α-helical-β-barrel folds. NPs are confined to the Reduviidae and Cimicidae families of Heteroptera, whereas α1-m and Nbs constitute heme-protein families spanning bacteria to Homo sapiens. The structural organization and the reactivity of the stable ferric solvent-exposed heme-Fe atom suggest that NPs and Nbs are devoted to NO transport, storage and sensing, whereas Hs-α1-m participates in heme metabolism. Here, the structural and functional properties of NPs and Nbs are reviewed in parallel with those of sperm whale myoglobin, which is generally taken as the prototype of monomeric globins.
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9
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Oliveira DS, Brito NF, Nogueira FCS, Moreira MF, Leal WS, Soares MR, Melo ACA. Proteomic analysis of the kissing bug Rhodnius prolixus antenna. JOURNAL OF INSECT PHYSIOLOGY 2017; 100:108-118. [PMID: 28606853 DOI: 10.1016/j.jinsphys.2017.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/07/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Reception of odorants is essential in insects' life since the chemical signals in the environment (=semiochemicals) convey information about availability of hosts for a blood meal, mates for reproduction, sites for oviposition and other relevant information for fitness in the environment. Once they reach the antennae, these semiochemicals bind to odorant-binding proteins and are transported through the sensillar lymph until reach the odorant receptors. Such perireceptor events, particularly the interactions with transport proteins, are the liaison between the external environment and the entire neuroethological system and, therefore, a potential target to disrupt insect chemical communication. In this study, a proteomic profile of female and male antennae of Rhodnius prolixus, a vector of Chagas disease, was obtained in an attempt to unravel the entire repertoire of olfactory proteins involved in perireceptor events. Using shotgun proteomics and two-dimensional gel electrophoresis approaches followed by nano liquid chromatography coupled with tandem LTQ Velos Orbitrap mass spectrometry, we have identified 581 unique proteins. Putative olfactory proteins, including 17 odorant binding proteins, 6 chemosensory proteins, 2 odorant receptors, 3 transient receptor channels and 1 gustatory receptor were identified. Proteins involved in general cellular functions such as generation of precursor metabolites, energy generation and catabolism were expressed at high levels. Additionally, proteins that take part in signal transduction, ion binding, and stress response, kinase and oxidoreductase activity were frequent in antennae from both sexes. This proteome strategy unraveled for the first time the complex nature of perireceptor and other olfactory events that occur in R. prolixus antennae, including evidence for phosphorylation of odorant-binding and chemosensory proteins. These findings not only increase our understanding of the olfactory process in triatomine species, but also identify potential molecular targets to be explored for population control of such insect vectors.
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Affiliation(s)
- Daniele S Oliveira
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Nathalia F Brito
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Fabio C S Nogueira
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Monica F Moreira
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909 Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil
| | - Walter S Leal
- University of California-Davis, Department of Molecular and Cellular Biology, 95616 Davis, CA, USA
| | - Marcia R Soares
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Ana C A Melo
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909 Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil.
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
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11
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017; 56:5904-5908. [PMID: 28440962 DOI: 10.1002/anie.201702472] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 01/21/2023]
Abstract
The structure and function of naturally occurring proteins are governed by a large number of amino acids (≥100). The design of miniature proteins with desired structures and functions not only substantiates our knowledge about proteins but can also contribute to the development of novel applications. Excellent progress has been made towards the design of helical proteins with diverse functions. However, the development of functional β-sheet proteins remains challenging. Herein, we describe the construction and characterization of four-stranded β-sheet miniproteins made up of about 19 amino acids that bind heme inside a hydrophobic binding pocket or "heme cage" by bis-histidine coordination in an aqueous environment. The designed miniproteins bound to heme with high affinity comparable to that of native heme proteins. Atomic-resolution structures confirmed the presence of a four-stranded β-sheet fold. The heme-protein complexes also exhibited high stability against thermal and chaotrope-induced unfolding.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
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12
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He C, Ogata H, Lubitz W. Elucidation of the heme active site electronic structure affecting the unprecedented nitrite dismutase activity of the ferriheme b proteins, the nitrophorins. Chem Sci 2016; 7:5332-5340. [PMID: 30155185 PMCID: PMC6020753 DOI: 10.1039/c6sc01019a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/23/2016] [Indexed: 12/14/2022] Open
Abstract
Nitrophorins (NPs) catalyze the nitrite dismutation reaction that is unprecedented in ferriheme proteins. Despite progress in studying the reaction mechanism, fundamental issues regarding the correlation of the structural features with the nitrite dismutase activity of NPs remain elusive. On the other hand, it has been shown that the nitrite complexes of NPs are unique among those of the ferriheme proteins since some of their electron paramagnetic resonance (EPR) spectra show significant highly anisotropic low spin (HALS) signals with large gmax values over 3.2. The origin of HALS signals in ferriheme proteins or models is not well understood, especially in cases where axial ligands other than histidine are present. In this study several mutations were introduced in NP4. The related nitrite coordination and dismutation reaction were investigated. As a result, the EPR spectra of the NP-nitrite complexes were found to be tightly correlated with the extent of heme ruffling and protonation state of the proximal His ligand-dictated by an extended H-bonding network at the heme active site. Furthermore, it is established that the two factors are essential in determining the nitrite dismutase activity of NPs. These results may provide a valuable guide for identifying or designing novel heme proteins with similar activity.
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Affiliation(s)
- Chunmao He
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
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Abstract
If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.
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Affiliation(s)
- Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche “Alessandro Rossi Fanelli” and Istituto Pasteur — Fondazione Cenci, Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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14
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D'Souza A, Mahajan M, Bhattacharjya S. Designed multi-stranded heme binding β-sheet peptides in membrane. Chem Sci 2016; 7:2563-2571. [PMID: 28660027 PMCID: PMC5477022 DOI: 10.1039/c5sc04108b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/14/2015] [Indexed: 01/20/2023] Open
Abstract
Designed peptides demonstrating well-defined structures and functioning in membrane environment are of significant interest in developing novel proteins for membrane active biological processes including enzymes, electron transfer, ion channels and energy conversion. Heme proteins' ability to carry out multiple functions in nature has inspired the design of several helical heme binding peptides and proteins soluble in water and also recently in membrane. Naturally occurring β-sheet proteins are both water and membrane soluble, and are known to bind heme, however, designed heme binding β-sheet proteins are yet to be reported, plausibly because of the complex folding and difficulty in introducing heme binding sites in the β-sheet structures. Here, we describe the design, NMR structures and biochemical functional characterization of four stranded and six stranded membrane soluble β-sheet peptides that bind heme and di-heme, respectively. The designed peptides contain either DP-G or DP-DA residues for the nucleation of β-turns intended to stabilize multi-stranded β-sheet topologies and ligate heme with bis-His coordination between adjacent antiparallel β-strands. Furthermore, we have optimized a high affinity heme binding pocket, Kd ∼ nM range, in the adjacent β-strands by utilizing a series of four stranded β-sheet peptides employing β- and ω-amino acids. We find that there is a progressive increase in cofactor binding affinity in the designed peptides with the alkyl chain length of ω-amino acids. Notably, the six stranded β-sheet peptide binds two molecules of heme in a cooperative fashion. The designed peptides perform peroxidase activity with varying ability and efficiently carried out electron transfer with membrane associated protein cytochrome c. The current study demonstrates the designing of functional β-sheet proteins in a membrane environment and expands the repertoire of heme protein design.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences , 60 Nanyang Drive , 637551 , Singapore .
| | - Mukesh Mahajan
- School of Biological Sciences , 60 Nanyang Drive , 637551 , Singapore .
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15
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He C, Kulkarni SS, Thuaud F, Bode JW. Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α-Ketoacid-Hydroxylamine (KAHA) Ligation. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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He C, Kulkarni SS, Thuaud F, Bode JW. Chemical Synthesis of the 20 kDa Heme Protein Nitrophorin 4 by α‐Ketoacid‐Hydroxylamine (KAHA) Ligation. Angew Chem Int Ed Engl 2015; 54:12996-3001. [DOI: 10.1002/anie.201505379] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Chunmao He
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
| | - Sameer S. Kulkarni
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
| | - Frédéric Thuaud
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
- Laboratorium für Organische Chemie, ETH Zurich, 8093 Zurich (Switzerland) http://www.bode.ethz.ch/
| | - Jeffrey W. Bode
- Institute of Transformative Bio‐Molecules (WPI‐ITbM), Nagoya University, Chikusa, Nagoya 464‐8602 (Japan)
- Laboratorium für Organische Chemie, ETH Zurich, 8093 Zurich (Switzerland) http://www.bode.ethz.ch/
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17
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Tang K, Knipp M, Liu BB, Cox N, Stabel R, He Q, Zhou M, Scheer H, Zhao KH, Gärtner W. Redox-dependent Ligand Switching in a Sensory Heme-binding GAF Domain of the Cyanobacterium Nostoc sp. PCC7120. J Biol Chem 2015; 290:19067-80. [PMID: 26063806 DOI: 10.1074/jbc.m115.654087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 11/06/2022] Open
Abstract
The genome of the cyanobacterium Nostoc sp. PCC7120 carries three genes (all4978, all7016, and alr7522) encoding putative heme-binding GAF (cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA) proteins that were annotated as transcriptional regulators. They are composed of an N-terminal cofactor domain and a C-terminal helix-turn-helix motif. All4978 showed the highest affinity for protoheme binding. The heme binding capability of All7016 was moderate, and Alr7522 did not bind heme at all. The "as isolated" form of All4978, identified by Soret band (λmax = 427 nm), was assigned by electronic absorption, EPR, and resonance Raman spectroscopy as a hexa-coordinated low spin Fe(III) heme with a distal cysteine ligand (absorption of δ-band around 360 nm). The protoheme cofactor is noncovalently incorporated. Reduction of the heme could be accomplished by chemically using sodium dithionite and electrospectrochemically; this latter method yielded remarkably low midpoint potentials of -445 and -453 mV (following Soret and α-band absorption changes, respectively). The reduced form of the heme (Fe(II) state) binds both NO and CO. Cysteine coordination of the as isolated Fe(III) protein is unambiguous, but interestingly, the reduced heme instead displays spectral features indicative of histidine coordination. Cys-His ligand switches have been reported as putative signaling mechanisms in other heme-binding proteins; however, these novel cyanobacterial proteins are the first where such a ligand-switch mechanism has been observed in a GAF domain. DNA binding of the helix-turn-helix domain was investigated using a DNA sequence motif from its own promoter region. Formation of a protein-DNA complex preferentially formed in ferric state of the protein.
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Affiliation(s)
- Kun Tang
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China, the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Markus Knipp
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany, Resolv, Faculty for Chemistry and Biochemistry, Ruhr University Bochum, D-44780 Bochum, Germany, and
| | - Bing-Bing Liu
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Nicholas Cox
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Robert Stabel
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany
| | - Qi He
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Zhou
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hugo Scheer
- the Department of Biologie I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, D-80638 München, Germany
| | - Kai-Hong Zhao
- From the State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China,
| | - Wolfgang Gärtner
- the Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany,
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18
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He C, Howes BD, Smulevich G, Rumpel S, Reijerse EJ, Lubitz W, Cox N, Knipp M. Nitrite Dismutase Reaction Mechanism: Kinetic and Spectroscopic Investigation of the Interaction between Nitrophorin and Nitrite. J Am Chem Soc 2015; 137:4141-50. [DOI: 10.1021/ja512938u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chunmao He
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Barry D. Howes
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino(Fi), Italy
| | - Giulietta Smulevich
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino(Fi), Italy
| | - Sigrun Rumpel
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward J. Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Markus Knipp
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Faculty
of Chemistry and Biochemistry, Ruhr University, Universitätsstrasse 150, D-44780 Bochum, Germany
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19
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Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ. Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7. F1000Res 2015; 4:45. [PMID: 26167269 PMCID: PMC4482215 DOI: 10.12688/f1000research.6060.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 11/20/2022] Open
Abstract
Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.
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Affiliation(s)
- Markus Knipp
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Hideaki Ogata
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, 45470, Germany
| | - Giancarlo Soavi
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, Milano, 20133, Italy
| | - Alessandro Allegri
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Bioscienze, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Stefano Bruno
- Dipartimento di Farmacia, Università di Parma, Parma, 43124, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, 43124, Italy ; NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, 56127, Italy
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
| | - F Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia and Institute of Biomedicine, Universitat de Barcelona, Santa Coloma de Gramenet, E-08921, Spain
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20
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Kim-Shapiro DB, Gladwin MT. Mechanisms of nitrite bioactivation. Nitric Oxide 2014; 38:58-68. [PMID: 24315961 PMCID: PMC3999231 DOI: 10.1016/j.niox.2013.11.002] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/19/2013] [Accepted: 11/21/2013] [Indexed: 12/18/2022]
Abstract
It is now accepted that the anion nitrite, once considered an inert oxidation product of nitric oxide (NO), contributes to hypoxic vasodilation, physiological blood pressure control, and redox signaling. As such, its application in therapeutics is being actively tested in pre-clinical models and in human phase I-II clinical trials. Major pathways for nitrite bioactivation involve its reduction to NO by members of the hemoglobin or molybdopterin family of proteins, or catalyzed dysproportionation. These conversions occur preferentially under hypoxic and acidic conditions. A number of enzymatic systems reduce nitrite to NO and their activity and importance are defined by oxygen tension, specific organ system and allosteric and redox effectors. In this work, we review different proposed mechanisms of nitrite bioactivation, focusing on analysis of kinetics and experimental evidence for the relevance of each mechanism under different conditions.
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Affiliation(s)
- Daniel B Kim-Shapiro
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, United States; Translational Science Center, Wake Forest University, Winston-Salem, NC 27109, United States.
| | - Mark T Gladwin
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, United States; Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States.
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21
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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22
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Risse C, Taing JJ, Knipp M. Preparation of nitrophorin 7(Δ1-3) from Rhodnius prolixus without start-methionine using recombinant expression in Escherichia coli. Anal Biochem 2014; 451:28-30. [PMID: 24463016 DOI: 10.1016/j.ab.2014.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/04/2014] [Accepted: 01/13/2014] [Indexed: 11/16/2022]
Abstract
The heterologous recombinant expression of proteins in Escherichia coli without start-methionine is a common problem. The nitrophorin 7 heme properties and function strongly depend on the accurate N-terminal amino acid sequence. Leading protein expression into the periplasm by fusion with the leader peptide pelB yields functional protein; however, the folded protein sticks to the cell debris. Therefore, the periplasmic fraction was dissolved in guanidinium chloride and folded by a drop-in method. Separation from impurities including residual pelB-nitrophorin 7 required establishing an unconventional chromatographic technique using calcium-loaded Chelating Sepharose as cation exchanger and elution by a linear CaCl2 gradient.
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Affiliation(s)
- Carmen Risse
- Max-Planck-Institut für Chemische Energiekonversion, D-45470 Mülheim an der Ruhr, Germany
| | - Johanna J Taing
- Max-Planck-Institut für Chemische Energiekonversion, D-45470 Mülheim an der Ruhr, Germany
| | - Markus Knipp
- Max-Planck-Institut für Chemische Energiekonversion, D-45470 Mülheim an der Ruhr, Germany; Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, D-44801 Bochum, Germany.
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23
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Varghese S, Yang F, Pacheco V, Wrede K, Medvedev A, Ogata H, Knipp M, Heise H. Expression, purification, and solid-state NMR characterization of the membrane binding heme protein nitrophorin 7 in two electronic spin states. Biochemistry 2013; 52:7031-40. [PMID: 24033104 DOI: 10.1021/bi401020t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nitrophorins (NPs) comprise a group of NO transporting ferriheme b proteins found in the saliva of the blood sucking insect Rhodnius prolixus . In contrast to other nitrophorins (NP1-4), the recently identified membrane binding isoform NP7 tends to form oligomers and precipitates at higher concentrations in solution. Hence, solid-state NMR (ssNMR) was employed as an alternative method to gain structural insights on the precipitated protein. We report the expression and purification of (13)C,(15)N isotopically labeled protein together with the first ssNMR characterization of NP7. Because the size of NP7 (21 kDa) still provides a challenge for ssNMR, the samples were reverse labeled with Lys and Val to reduce the number of crosspeaks in two-dimensional spectra. The two electronic spin states with S = 1/2 and S = 0 at the ferriheme iron were generated by the complexation with imidazole and NO, respectively. ssNMR spectra of both forms are well resolved, which allows for sequential resonance assignments of 22 residues. Importantly, the ssNMR spectra demonstrate that aggregation does not affect the protein fold. Comparison of the spectra of the two electronic spin states allows the determination of paramagnetically shifted cross peaks due to pseudocontact shifts, which assists the assignment of residues close to the heme center.
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Affiliation(s)
- Sabu Varghese
- ICS-6 Institute of Complex Systems-Structural Biochemistry, Forschungszentrum Jülich , D-2425 Jülich, Germany
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24
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Complexes of ferriheme nitrophorin 4 with low-molecular weight thiol(ate)s occurring in blood plasma. J Inorg Biochem 2013; 122:38-48. [DOI: 10.1016/j.jinorgbio.2013.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/14/2013] [Accepted: 01/14/2013] [Indexed: 11/17/2022]
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25
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Nalepa AI, Taing JJ, Savitsky A, Knipp M. Preparation of cysteine-34-nitroxide spin labeled human α₁-microglobulin. Protein Expr Purif 2012. [PMID: 23201281 DOI: 10.1016/j.pep.2012.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
α(1)-Microglobulin (α(1)m) is a protein of yet unresolved function occurring in blood plasma and urine. It consists of a lipocaline type of fold with two cysteine residues forming a disulfide bridge and the third cysteine-34 remaining a free, somewhat reactive thiol. A number of investigations point to an interaction with heme and we have recently reported, that heme binding triggers the formation of a stable α(1)m trimer upon modification of cysteine-34 with 2-iodoacetamide, i.e., [α(1)m(heme)(2)](3) [J.F. Siebel, R.L. Kosinsky, B. Åkerström, M. Knipp, Insertion of heme b into the structure of the Cys34-carbamidomethylated human lipocalin α(1)-microglobulin-formation of a [(heme)(2)(α(1)-microglobulin)](3) complex, ChemBioChem 13 (2012) 879-887]. For further structural and functional investigations, an improved purification protocol for α(1)m was sought, in particular yielding an untagged amino acid sequence. The method reported herein improves the speed and the yield of the protein production even when an expression plasmid without tag was applied. Furthermore, for the purpose of future structural studies using electron paramagnetic resonance (EPR) techniques, in accordance to the modification with 2-iodoacetamide (α(1)m(AM)), the protein was modified with 3-(2-iodoacetamido)-2,2,5,5-tetramethyl-1-pyrrolidinyloxy (3-(2-iodoacetamido)-PROXYL) yielding the nitroxide spin labeled α(1)m(N-O). The extinction coefficient of the protein was calibrated using magnetic circular dichroism (MCD) spectroscopy of tryptophan (ε(280nm)=40,625M(-1)cm(-1)). The parallel quantification by absorbance spectroscopy (protein) and cw-EPR spectroscopy (radical spin) determined the degree of spin labeling to 90%. Characterization of the protein by circular dichroism (CD) spectroscopy and matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) upon tryptic digestion further demonstrated the similar fold of α(1)m(AM) and α(1)m(N-O), but also established the modification of cystein-34 as well as the formation of the cysteine-72-cysteine-169 disulfide bond.
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Affiliation(s)
- Anna I Nalepa
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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26
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Siebel JF, Kosinsky RL, Åkerström B, Knipp M. Insertion of heme b into the structure of the Cys34-carbamidomethylated human lipocalin α(1)-microglobulin: formation of a [(heme)(2) (α(1)-Microglobulin)](3) complex. Chembiochem 2012; 13:879-87. [PMID: 22492620 DOI: 10.1002/cbic.201100808] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
α(1)-Microglobulin (α(1)m) is a 26 kDa plasma and tissue protein belonging to the lipocalin protein family. Previous investigations indicate that the protein interacts with heme and suggest that it has a function in heme metabolism. However, detailed characterizations of the α(1)m-heme interactions are lacking. Here, we report for the first time the preparation and analysis of a stable α(1)m-heme complex upon carbamidomethylation of the reactive Cys34 by using recombinantly expressed human α(1)m. Analytical size-exclusion chromatography coupled with a diode-array absorbance spectrophotometry demonstrates that at first an α(1)m-heme monomer is formed. Subsequently, a second heme triggers oligomerization that leads to trimerization. The resulting (α(1)m[heme](2))(3) complex was characterized by resonance Raman and EPR spectroscopy, which support the presence of two ferrihemes, thus indicating an unusual spin-state admixed ground state with S=(3)/(2), (5)/(2).
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Affiliation(s)
- Judith F Siebel
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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27
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He C, Ogata H, Knipp M. Insertion of an H-Bonding Residue into the Distal Pocket of the Ferriheme Protein Nitrophorin 4: Effect on NitriteIron Coordination and Nitrite Disproportionation. Chem Biodivers 2012; 9:1761-75. [DOI: 10.1002/cbdv.201100401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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28
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Abbruzzetti S, He C, Ogata H, Bruno S, Viappiani C, Knipp M. Heterogeneous kinetics of the carbon monoxide association and dissociation reaction to nitrophorin 4 and 7 coincide with structural heterogeneity of the gate-loop. J Am Chem Soc 2012; 134:9986-98. [PMID: 22594621 DOI: 10.1021/ja2121662] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
NO is an important signaling molecule in human tissue. However, the mechanisms by which this molecule is controlled and directed are currently little understood. Nitrophorins (NPs) comprise a group of ferriheme proteins originating from blood-sucking insects that are tailored to protect and deliver NO via coordination to and release from the heme iron. Therefore, the kinetics of the association and dissociation reactions were studied in this work using the ferroheme-CO complexes of NP4, NP4(D30N), and NP7 as isoelectronic models for the ferriheme-NO complexes. The kinetic measurements performed by nanosecond laser-flash-photolysis and stopped-flow are accompanied by resonance Raman and FT-IR spectroscopy to characterize the carbonyl species. Careful analysis of the CO rebinding kinetics reveals that in NP4 and, to a larger extent, NP7 internal gas binding cavities are located, which temporarily trap photodissociated ligands. Moreover, changes in the free energy barriers throughout the rebinding and release pathway upon increase of the pH are surprisingly small in case of NP4. Also in case of NP4, a heterogeneous kinetic trace is obtained at pH 7.5, which corresponds to the presence of two carbonyl species in the heme cavity that are seen in vibrational spectroscopy and that are due to the change of the distal heme pocket polarity. Quantification of the two species from FT-IR spectra allowed the fitting of the kinetic traces as two processes, corresponding to the previously reported open and closed conformation of the A-B and G-H loops. With the use of the A-B loop mutant NP4(D30N), it was confirmed that the kinetic heterogeneity is controlled by pH through the disruption of the H-bond between the Asp30 side chain and the Leu130 backbone carbonyl. Overall, this first study on the slow phase of the dynamics of diatomic gas molecule interaction with NPs comprises an important experimental contribution for the understanding of the dynamics involved in the binding/release processes of NO/CO in NPs.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica, Università degli Studi di Parma, viale delle Scienze 7A, I-43124, Parma, Italy
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29
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Knipp M, Soares RP, Pereira MH. Identification of the native N-terminus of the membrane attaching ferriheme protein nitrophorin 7 from Rhodnius prolixus. Anal Biochem 2012; 424:79-81. [DOI: 10.1016/j.ab.2012.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/06/2012] [Accepted: 02/08/2012] [Indexed: 11/28/2022]
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30
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Knipp M, Taing JJ, He C, Viappiani C. A caged cyanide. Photochem Photobiol Sci 2012; 11:620-2. [PMID: 22406687 DOI: 10.1039/c2pp05359d] [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
A photoactivatable caged cyanide, 1-(2-nitrophenyl)ethyl (NPE) cyanide, was synthesized, which upon irradiation in the near UV releases cyanide. It is demonstrated that the compound can be used to induce formation of the Fe(III)-CN(-) complex in the heme protein nitrophorin 4 from Rhodnius prolixus.
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Affiliation(s)
- Markus Knipp
- Max-Planck-Institut für Bioanorganische Chemie, Stifstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
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He C, Fuchs MR, Ogata H, Knipp M. Guanidin-Ferrohäm-Koordination in der Proteinmutante Nitrophorin 4(L130R). Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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He C, Fuchs MR, Ogata H, Knipp M. Guanidine-ferroheme coordination in the mutant protein nitrophorin 4(L130R). Angew Chem Int Ed Engl 2012; 51:4470-3. [PMID: 22334402 DOI: 10.1002/anie.201108691] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Chunmao He
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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Ogata H, Knipp M. Crystallization and preliminary X-ray crystallographic analysis of the membrane-binding haemprotein nitrophorin 7 from Rhodnius prolixus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:37-40. [PMID: 22232167 PMCID: PMC3253830 DOI: 10.1107/s1744309111044708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 10/25/2011] [Indexed: 11/10/2022]
Abstract
Nitrophorins (nitric oxide transport proteins) are haemproteins originating from the blood-feeding insect Rhodnius prolixus. They consist of an eight-stranded β-barrel, which classifies them into the lipocalin family. Nitrophorin 7 (NP7) and the E27V mutant protein NP7(E27V) were crystallized at 277 K using the vapour-diffusion method with PEG as the precipitating agent. Data sets for wild-type NP7 and NP7(E27V) were collected to 1.80 Å resolution from single crystals at 100 K using synchrotron radiation. The crystals belonged to space group P2(1), with unit-cell parameters a = 38, b = 67, c = 39 Å, β = 117°. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (V(M)) of 2.11 Å(3) Da(-1); the solvent content was estimated to be 41.8%.
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Affiliation(s)
- Hideaki Ogata
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
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Reduction of the lipocalin type heme containing protein nitrophorin — Sensitivity of the fold-stabilizing cysteine disulfides toward routine heme-iron reduction. J Inorg Biochem 2011; 105:1405-12. [DOI: 10.1016/j.jinorgbio.2011.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 11/23/2022]
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He C, Neya S, Knipp M. Breaking the Proximal FeII–NHis Bond in Heme Proteins through Local Structural Tension: Lessons from the Heme b Proteins Nitrophorin 4, Nitrophorin 7, and Related Site-Directed Mutant Proteins. Biochemistry 2011; 50:8559-75. [DOI: 10.1021/bi201073t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Chunmao He
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470
Mülheim an der Ruhr, Germany
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Image-Yayoi,
Chiba 263-8522, Japan
| | - Markus Knipp
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470
Mülheim an der Ruhr, Germany
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