1
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Deng Y, Carnevale V, Ditchfield R, Pletneva EV. Applications of the Newly Developed Force-Field Parameters Uncover a Dynamic Nature of Ω-Loop C in the Lys-Ligated Alkaline Form of Cytochrome c. J Phys Chem B 2024; 128:5935-5949. [PMID: 38864552 DOI: 10.1021/acs.jpcb.4c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Lys-ligated cytochromes make up an emerging family of heme proteins. Density functional theory calculations on the amine/imidazole-ligated c-type ferric heme were employed to develop force-field parameters for molecular dynamics (MD) simulations of structural and dynamic features of these proteins. The new force-field parameters were applied to the alkaline form of yeast iso-1 cytochrome c to rationalize discrepancies resulting from distinct experimental conditions in prior structural studies and to provide insights into the mechanisms of the alkaline transition. Our simulations have revealed the dynamic nature of Ω-loop C in the Lys-ligated protein and its unfolding in the Lys-ligated conformer having this loop in the same position as in the native Met-ligated protein. The proximity of Tyr67 or Tyr74 to the Lys ligand of ferric heme iron suggests a possible mechanism of the backward alkaline transition where a proton donor Tyr assists in Lys dissociation. The developed force-field parameters will be useful in structural and dynamic characterization of other native or engineered Lys-ligated heme proteins.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Vincenzo Carnevale
- Institute for Genomics and Evolutionary Medicine, Institute for Computational Molecular Science, and Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Robert Ditchfield
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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2
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Radoń M. Predicting spin states of iron porphyrins with DFT methods including crystal packing effects and thermodynamic corrections. Phys Chem Chem Phys 2024. [PMID: 38899797 DOI: 10.1039/d4cp01327a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Accurate computational treatment of spin states for transition metal complexes, exemplified by iron porphyrins, lies at the heart of quantum bioinorganic chemistry, but at the same time represents a great challenge for approximate density functional theory (DFT) methods, which are predominantly used. Here, the accuracy of DFT methods for spin-state splittings in iron porphyrin is assessed by probing the ability to correctly predict the ground states for six FeIII or FeII complexes experimentally characterized in solid state. For each case, molecular and periodic DFT calculations are employed to quantify the effect of porphyrin side substituents and the crystal packing effect (CPE) on the spin-state splitting. It is proposed to partition the total CPE into additive components, the direct and structural one, the importance of which is shown to significantly vary from case to case. By knowing the substituent effect, the CPE, and the Gibbs free energy thermodynamic correction from calculations, one can employ the experimental ground-state information in order to derive a quantitative constraint on the electronic energy difference for a simplified (porphin) model of the experimentally characterized metalloporphyrin. The constraints derived in such a way-in the form of single or double inequalities-are used to assess the accuracy of dispersion-corrected DFT methods for 6 spin-state splittings of [FeIII(P)(2-MeIm)2]+, [FeIII(P)(2-MeIm)]+, [FeII(P)(THF)2] and [FeII(P)] models (where P is porphin, 2-MeIm is 2-methylimidazole, THF is tetrahydrofuran). These data constitute the new benchmark set of spin states for crystalline iron porphyrins (SSCIP6). The highest accuracy is obtained in the case of double-hybrid functionals (B2PLYP-D3, DSD-PBEB95-D3), whereas hybrid functionals, especially those with reduced admixture of the exact exchange (B3LYP*-D3, TPSSh-D3), are found to considerably overstabilize the intermediate spin state, leading to incorrect ground-state prediction in FeIII porphyrins. The present approach, which can be generalized to other transition metal complexes, is not only useful in method benchmarking, but also sheds light on the interpretations of experimental data for metalloporphyrins, which are important models to understand the electronic properties of heme proteins.
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Affiliation(s)
- Mariusz Radoń
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland.
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3
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Cui Q, Gao Y, Wen Q, Wang T, Ren X, Cheng L, Bai M, Cheng C. Tunable Structured 2D Nanobiocatalysts: Synthesis, Catalytic Properties and New Horizons in Biomedical Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311584. [PMID: 38566551 DOI: 10.1002/smll.202311584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/18/2024] [Indexed: 04/04/2024]
Abstract
2D materials have offered essential contributions to boosting biocatalytic efficiency in diverse biomedical applications due to the intrinsic enzyme-mimetic activity and massive specific surface area for loading metal catalytic centers. Since the difficulty of high-quality synthesis, the varied structure, and the tough choice of efficient surface loading sites with catalytic properties, the artificial building of 2D nanobiocatalysts still faces great challenges. Here, in this review, a timely and comprehensive summarization of the latest progress and future trends in the design and biotherapeutic applications of 2D nanobiocatalysts is provided, which is essential for their development. First, an overview of the synthesis-structure-fundamentals and structure-property relationships of 2D nanobiocatalysts, both metal-free and metal-based is provided. After that, the effective design of the active sites of nanobiocatalysts is discussed. Then, the progress of their applied research in recent years, including biomedical analysis, biomedical therapeutics, pharmacokinetics, and toxicology is systematically highlighted. Finally, future research directions of 2D nanobiocatalysts are prospected. Overall, this review to provide cutting-edge and multidisciplinary guidance for accelerating future developments and biomedical applications of 2D nanobiocatalysts is expected.
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Affiliation(s)
- Qiqi Cui
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Yang Gao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
- Department of Endodontics, State Key Laboratory of Oral Diseases & National Clinical Research, Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qinlong Wen
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Ting Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Xiancheng Ren
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Liang Cheng
- Department of Materials Science and Engineering, Center for Oral Diseases, The Macau University of Science and Technology, Taipa, Macau, China
| | - Mingru Bai
- Department of Endodontics, State Key Laboratory of Oral Diseases & National Clinical Research, Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Chong Cheng
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
- Department of Endodontics, State Key Laboratory of Oral Diseases & National Clinical Research, Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
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4
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Alvarez-Hernandez JL, Salamatian AA, Sopchak AE, Bren KL. Hydrogen evolution catalysis by a cobalt porphyrin peptide: A proposed role for porphyrin propionic acid groups. J Inorg Biochem 2023; 249:112390. [PMID: 37801884 DOI: 10.1016/j.jinorgbio.2023.112390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
Cobalt microperoxidase-11 (CoMP11-Ac) is a cobalt porphyrin-peptide catalyst for hydrogen (H2) evolution from water. Herein, we assess electrocatalytic activity of CoMP11-Ac from pH 1.0-10.0. This catalyst remains intact and active under highly acidic conditions (pH 1.0) that are desirable for maximizing H2 evolution activity. Analysis of electrochemical data indicate that H2 evolution takes place by two pH-dependent mechanisms. At pH < 4.3, a proton transfer mechanism involving the propionic acid groups of the porphyrin is proposed, decreasing the catalytic overpotential by 280 mV.
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Affiliation(s)
| | - Alison A Salamatian
- Department of Chemistry, University of Rochester. Rochester, NY 14627-0216, United States.
| | - Andrew E Sopchak
- Department of Chemistry, University of Rochester. Rochester, NY 14627-0216, United States.
| | - Kara L Bren
- Department of Chemistry, University of Rochester. Rochester, NY 14627-0216, United States.
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5
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Yoo BK, Kruglik SG, Lambry JC, Lamarre I, Raman CS, Nioche P, Negrerie M. The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide. Chem Sci 2023; 14:8408-8420. [PMID: 37564404 PMCID: PMC10411614 DOI: 10.1039/d3sc01685d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O2 for some of them. The signaling pathways where these proteins act as NO or O2 sensors appear various and are fully established for only some species. Here, we investigated the reactivity of H-NOX from bacterial species toward NO with a mechanistic point of view using time-resolved spectroscopy. The present data show that H-NOXs modulate the dynamics of NO as a function of temperature, but in different ranges, changing its affinity by changing the probability of NO rebinding after dissociation in the picosecond time scale. This fundamental mechanism provides a means to adapt the heme structural response to the environment. In one particular H-NOX sensor the heme distortion induced by NO binding is relaxed in an ultrafast manner (∼15 ps) after NO dissociation, contrarily to other H-NOX proteins, providing another sensing mechanism through the H-NOX domain. Overall, our study links molecular dynamics with functional mechanism and adaptation.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Sergei G Kruglik
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS 75005 Paris France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - C S Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore Maryland 21201 USA
| | - Pierre Nioche
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, UMR S1124, Centre Universitaire des Saints-Pères, Université Paris Descartes 75006 Paris France
- Structural and Molecular Analysis Platform, BioMedTech Facilities, INSERM US36-CNRS-UMS2009, Paris Université Paris France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
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6
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Auerbach H, Faus I, Rackwitz S, Wolny JA, Chumakov AI, Knipp M, Walker FA, Schünemann V. Heme protonation affects iron-NO binding in the NO transport protein nitrophorin. J Inorg Biochem 2023; 246:112281. [PMID: 37352657 DOI: 10.1016/j.jinorgbio.2023.112281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/26/2023] [Accepted: 05/30/2023] [Indexed: 06/25/2023]
Abstract
The nitrophorins (NPs) comprise an unusual group of heme proteins with stable ferric heme iron nitric oxide (Fe-NO) complexes. They are found in the salivary glands of the blood-sucking kissing bug Rhodnius prolixus, which uses the NPs to transport the highly reactive signaling molecule NO. Nuclear resonance vibrational spectroscopy (NRVS) of both isoform NP2 and a mutant NP2(Leu132Val) show, after addition of NO, a strong structured vibrational band at around 600 cm-1, which is due to modes with significant Fe-NO bending and stretching contribution. Based on a hybrid calculation method, which uses density functional theory and molecular mechanics, it is demonstrated that protonation of the heme carboxyl groups does influence both the vibrational properties of the Fe-NO entity and its electronic ground state. Moreover, heme protonation causes a significant increase of the gap between the highest occupied and lowest unoccupied molecular orbital by almost one order of magnitude leading to a stabilization of the Fe-NO bond.
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Affiliation(s)
- Hendrik Auerbach
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Isabelle Faus
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Sergej Rackwitz
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Juliusz A Wolny
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | | | - Markus Knipp
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany; Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - F Ann Walker
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721-0041, United States
| | - Volker Schünemann
- Department of Physics, RPTU Kaiserslautern-Landau, 67663 Kaiserslautern, Germany.
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7
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Wu Y, Zhao Y, Liu Y, Niu J, Zhao T, Bai X, Hussain A, Li YY. Insights into heavy metals shock on anammox systems: Cell structure-based mechanisms and new challenges. WATER RESEARCH 2023; 239:120031. [PMID: 37172374 DOI: 10.1016/j.watres.2023.120031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/31/2023] [Accepted: 05/01/2023] [Indexed: 05/14/2023]
Abstract
Anaerobic ammonium oxidation (anammox) as a low-carbon and energy-saving technology, has shown unique advantages in the treatment of high ammonia wastewater. However, wastewater usually contains complex heavy metals (HMs), which pose a potential risk to the stable operation of the anammox system. This review systematically re-evaluates the HMs toxicity level from the inhibition effects and the inhibition recovery process, which can provide a new reference for engineering. From the perspective of anammox cell structure (extracellular, anammoxosome membrane, anammoxosome), the mechanism of HMs effects on cellular substances and metabolism is expounded. Furthermore, the challenges and research gaps for HMs inhibition in anammox research are also discussed. The clarification of material flow, energy flow and community succession under HMs shock will help further reveal the inhibition mechanism. The development of new recovery strategies such as bio-accelerators and bio-augmentation is conductive to breaking through the engineered limitations of HMs on anammox. This review provides a new perspective on the recognition of toxicity and mechanism of HMs in the anammox process, as well as the promotion of engineering applicability.
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Affiliation(s)
- Yichen Wu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yingxin Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Yinuo Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jiaojiao Niu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Tianyang Zhao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Xinhao Bai
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Arif Hussain
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki-Aza, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki-Aza, Sendai, Miyagi 980-8579, Japan.
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8
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Zhang X, Qiu D, Chen J, Zhang Y, Wang J, Chen D, Liu Y, Cheng M, Monchaud D, Mergny JL, Ju H, Zhou J. Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase. J Am Chem Soc 2023; 145:4517-4526. [PMID: 36795970 DOI: 10.1021/jacs.2c11318] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number kcat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.
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Affiliation(s)
- Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
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9
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Olloqui-Sariego JL, Pérez-Mejías G, Márquez I, Guerra-Castellano A, Calvente JJ, De la Rosa MA, Andreu R, Díaz-Moreno I. Electric field-induced functional changes in electrode-immobilized mutant species of human cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148570. [PMID: 35643148 DOI: 10.1016/j.bbabio.2022.148570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/21/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Post-translational modifications and naturally occurring mutations of cytochrome c have been recognized as a regulatory mechanism to control its biology. In this work, we investigate the effect of such in vivo chemical modifications of human cytochrome c on its redox properties in the adsorbed state onto an electrode. In particular, tyrosines 48 and 97 have been replaced by the non-canonical amino acid p-carboxymethyl-L-phenylalanine (pCMF), thus mimicking tyrosine phosphorylation. Additionally, tyrosine 48 has been replaced by a histidine producing the natural Y48H pathogenic mutant. Thermodynamics and kinetics of the interfacial electron transfer of wild-type cytochrome c and herein produced variants, adsorbed electrostatically under different local interfacial electric fields, were determined by means of variable temperature cyclic film voltammetry. It is shown that non-native cytochrome c variants immobilized under a low interfacial electric field display redox thermodynamics and kinetics similar to those of wild-type cytochrome c. However, upon increasing the strength of the electric field, the redox thermodynamics and kinetics of the modified proteins markedly differ from those of the wild-type species. The mutations promote stabilization of the oxidized form and a significant increase in the activation enthalpy values that can be ascribed to a subtle distortion of the heme cofactor and/or difference of the amino acid rearrangements rather than to a coarse protein structural change. Overall, these results point to a combined effect of the single point mutations at positions 48 and 97 and the strength of electrostatic binding on the regulatory mechanism of mitochondrial membrane activity, when acting as a redox shuttle protein.
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Affiliation(s)
- José Luis Olloqui-Sariego
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Inmaculada Márquez
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain; Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Alejandra Guerra-Castellano
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Juan José Calvente
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Rafael Andreu
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain).
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10
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Radical Mediated Rapid In Vitro Formation of c-Type Cytochrome. Biomolecules 2022; 12:biom12101329. [PMID: 36291538 PMCID: PMC9599503 DOI: 10.3390/biom12101329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
A cytochrome c552 mutant from Thermus thermophilus HB8 (rC552 C14A) was reported, where the polypeptide with replaced Cys14 by alanine, overexpressed in the cytosol of E. coli. The apo-form of the C14A mutant (apo-C14A) without the original prosthetic group was obtained by simple chemical treatments that retained compact conformation amenable to reconstitution with heme b and zinc(II)-protoporphyrin(IX), gradually followed by spontaneous formation of a covalent bond between the polypeptide and porphyrin ring in the reconstituted apo-C14A. Further analysis suggested that the residual Cys11 and vinyl group of the porphyrin ring linked through the thiol-ene reaction promoted by light under ambient conditions. In this study, we describe the kinetic improvement of the covalent bond formation in accordance with the mechanism of the photoinduced thiol-ene reaction, which involves a thiyl radical as a reaction intermediate. Adding a radical generator to the reconstituted C14A mutant with either heme-b or zinc(II) porphyrin accelerated the bond-forming reaction, which supported the involvement of a radical species in the reaction. Partial observation of the reconstituted C14A in a dimer form and detection of sulfuryl radical by EPR spectroscopy indicated a thiyl radical on Cys11, a unique cysteinyl residue in rC552 C14A. The covalent bond forming mediated by the radical generator was also adaptable to the reconstituted apo-C14A with manganese(II)-protoporphyrin(IX), which also exhibits light-mediated covalent linkage formation. Therefore, the radical generator extends the versatility of producing c-type-like cytochrome starting from a metallo-protoporphyrin(IX) and the apo-C14A instantaneously.
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11
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Ishizuka T, Grover N, Kingsbury CJ, Kotani H, Senge MO, Kojima T. Nonplanar porphyrins: synthesis, properties, and unique functionalities. Chem Soc Rev 2022; 51:7560-7630. [PMID: 35959748 DOI: 10.1039/d2cs00391k] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Porphyrins are variously substituted tetrapyrrolic macrocycles, with wide-ranging biological and chemical applications derived from metal chelation in the core and the 18π aromatic surface. Under suitable conditions, the porphyrin framework can deform significantly from regular planar shape, owing to steric overload on the porphyrin periphery or steric repulsion in the core, among other structure modulation strategies. Adopting this nonplanar porphyrin architecture allows guest molecules to interact directly with an exposed core, with guest-responsive and photoactive electronic states of the porphyrin allowing energy, information, atom and electron transfer within and between these species. This functionality can be incorporated and tuned by decoration of functional groups and electronic modifications, with individual deformation profiles adapted to specific key sensing and catalysis applications. Nonplanar porphyrins are assisting breakthroughs in molecular recognition, organo- and photoredox catalysis; simultaneously bio-inspired and distinctly synthetic, these molecules offer a new dimension in shape-responsive host-guest chemistry. In this review, we have summarized the synthetic methods and design aspects of nonplanar porphyrin formation, key properties, structure and functionality of the nonplanar aromatic framework, and the scope and utility of this emerging class towards outstanding scientific, industrial and environmental issues.
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Affiliation(s)
- Tomoya Ishizuka
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba and CREST (JST), 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan.
| | - Nitika Grover
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Christopher J Kingsbury
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Hiroaki Kotani
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba and CREST (JST), 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan.
| | - Mathias O Senge
- Institute for Advanced Study (TUM-IAS), Technical University of Munich, Focus Group - Molecular and Interfacial Engineering of Organic Nanosystems, Lichtenbergstrasse 2a, 85748 Garching, Germany.
| | - Takahiko Kojima
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba and CREST (JST), 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan.
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12
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Wang Z, Zhao Z, Li G, Zheng P. Single-Molecule Force Spectroscopy Reveals the Dynamic HgS Coordination Site in the De Novo-Designed Metalloprotein α 3DIV. J Phys Chem Lett 2022; 13:5372-5378. [PMID: 35678420 DOI: 10.1021/acs.jpclett.2c01316] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The de novo-designed metalloprotein α3DIV binds to mercury via three cysteine residues under dynamic conditions. An unusual trigonal three-coordinate HgS3 site is formed in the protein in basic solution, whereas a linear two-coordinate HgS2 site is formed in acidic solution. Furthermore, it is unknown whether the two coordinated cysteines in the HgS2 site are fixed or not, which may lead to more dynamics. However, the signal for HgS2 sites with different cysteines may be similar or may be averaged and indistinguishable. To circumvent this problem, we adopt a single-molecule approach to study one mercury site at a time. Using atomic force microscopy-based single-molecule force spectroscopy, the protein is unfolded, and the HgS site is ruptured. The results confirm the formation of HgS3 and HgS2 sites at different pH values. Moreover, it is found that any two of the three cysteines in the protein bind to mercury in the HgS2 site.
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Affiliation(s)
- Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Zhongxing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P.R. China
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13
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Mischkulnig M, Roetzer-Pejrimovsky T, Lötsch-Gojo D, Kastner N, Bruckner K, Prihoda R, Lang A, Martinez-Moreno M, Furtner J, Berghoff A, Woehrer A, Berger W, Widhalm G, Kiesel B. Heme Biosynthesis Factors and 5-ALA Induced Fluorescence: Analysis of mRNA and Protein Expression in Fluorescing and Non-fluorescing Gliomas. Front Med (Lausanne) 2022; 9:907442. [PMID: 35665365 PMCID: PMC9157484 DOI: 10.3389/fmed.2022.907442] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Objective The intraoperative visualization of adult-type diffuse gliomas with 5-aminolevulinic acid (5-ALA) induced fluorescence is widely used in the neurosurgical field. While visible 5-ALA induced fluorescence is found in the majority of high-grade gliomas, most low-grade gliomas lack visible fluorescence during surgery. Recently, the heme biosynthesis pathway was identified as crucial influencing factor for presence of visible fluorescence since it metabolizes 5-ALA to fluorescing Protoporphyrin IX (PpIX). However, the exact alterations within the heme biosynthesis pathway resulting in visible 5-ALA induced fluorescence in gliomas are still unclear. The aim of the present study was thus to compare the mRNA and protein expression of promising intramitochondrial heme biosynthesis enzymes/transporters in glioma tissue samples of different fluorescence behavior. Methods A total of 19 strongly fluorescing and 21 non-fluorescing tissue samples from neurosurgical adult-type diffuse gliomas (WHO grades II-IV) were included in the current analysis. In these samples, we investigated the mRNA expression by quantitative real time PCR and protein expression using immunohistochemistry of the intramitochondrial heme biosynthesis enzymes Coproporphyrinogen Oxidase (CPOX), Protoporphyrinogen Oxidase (PPOX), Ferrochelatase (FECH), and the transporter ATP-binding Cassette Subfamily B Member 2 (ABCG2). Results Regarding mRNA expression analysis, we found a significantly decreased ABCG2 expression in fluorescing specimens compared to non-fluorescing samples (p = 0.001), whereas no difference in CPOX, PPOX and FECH was present. With respect to protein expression, significantly higher levels of CPOX (p = 0.005), PPOX (p < 0.01) and FECH (p = 0.003) were detected in fluorescing samples. Similar to mRNA expression analysis, the protein expression of ABCG2 (p = 0.001) was significantly lower in fluorescing samples. Conclusion Distinct alterations of the analyzed heme biosynthesis factors were found primarily on protein level. Our data indicate that heme biosynthesis pathway activity in general is enhanced in fluorescing gliomas with upregulation of PpIX generating enzymes and decreased ABCG2 mediated PpIX efflux outweighing the also increased further metabolization of PpIX to heme. Intramitochondrial heme biosynthesis factors thus constitute promising pharmacological targets to optimize intraoperative 5-ALA fluorescence visualization of usually non-fluorescing tumors such as low-grade gliomas.
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Affiliation(s)
- Mario Mischkulnig
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
| | - Thomas Roetzer-Pejrimovsky
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Daniela Lötsch-Gojo
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
| | - Nina Kastner
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Katharina Bruckner
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Romana Prihoda
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Department of Neurosurgery, University Hospital of St. Poelten, Karl Landsteiner University of Health Sciences, St. Poelten, Austria
| | - Alexandra Lang
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
| | | | - Julia Furtner
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
- Department of Radiology and Nuclear Medicine, Medical University of Vienna, Vienna, Austria
| | - Anna Berghoff
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
- Clinical Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Adelheid Woehrer
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Georg Widhalm
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
| | - Barbara Kiesel
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center–Central Nervous System Tumours Unit, Medical University of Vienna, Vienna, Austria
- *Correspondence: Barbara Kiesel,
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14
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Li T, Xi K, Jiang P, Pan Q, Feng Y, Wu H. Mixed Co‐Mn Spinel Oxides Based Electrocatalysts for Amperometric Determination of Hydrogen Peroxide. ChemistrySelect 2022. [DOI: 10.1002/slct.202200631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Tong Li
- School of Chemistry and Chemical Engineering Institute of Clean Energy and Materials Guangzhou Key Laboratory for Clean Energy and Materials Center for Interdisciplinary Health Management Studies Guangzhou University Guangzhou Higher Education Mega Center No. 230 Wai Huan Xi Road 510006 Guangzhou P. R. China
| | - Kaiyin Xi
- School of Chemistry and Chemical Engineering Institute of Clean Energy and Materials Guangzhou Key Laboratory for Clean Energy and Materials Center for Interdisciplinary Health Management Studies Guangzhou University Guangzhou Higher Education Mega Center No. 230 Wai Huan Xi Road 510006 Guangzhou P. R. China
| | - Peng‐Yang Jiang
- School of Chemistry and Chemical Engineering Institute of Clean Energy and Materials Guangzhou Key Laboratory for Clean Energy and Materials Center for Interdisciplinary Health Management Studies Guangzhou University Guangzhou Higher Education Mega Center No. 230 Wai Huan Xi Road 510006 Guangzhou P. R. China
| | - Qiu‐Ren Pan
- School of Chemistry and Chemical Engineering Institute of Clean Energy and Materials Guangzhou Key Laboratory for Clean Energy and Materials Center for Interdisciplinary Health Management Studies Guangzhou University Guangzhou Higher Education Mega Center No. 230 Wai Huan Xi Road 510006 Guangzhou P. R. China
| | - Yunhui Feng
- School of Chemistry and Chemical Engineering Institute of Clean Energy and Materials Guangzhou Key Laboratory for Clean Energy and Materials Center for Interdisciplinary Health Management Studies Guangzhou University Guangzhou Higher Education Mega Center No. 230 Wai Huan Xi Road 510006 Guangzhou P. R. China
| | - Huixiang Wu
- School of Chemistry and Chemical Engineering Institute of Clean Energy and Materials Guangzhou Key Laboratory for Clean Energy and Materials Center for Interdisciplinary Health Management Studies Guangzhou University Guangzhou Higher Education Mega Center No. 230 Wai Huan Xi Road 510006 Guangzhou P. R. China
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15
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Liu Q, Ren W, Zhang S, Huang Y, Chen D, Zeng W, Zhou Z, He L, Guo W, Li J. d‐Orbital Reconstructions Forced by Double Bow‐Shaped Deformations and Second Coordination Sphere Effects of Cu(II) Heme Analogs in HER**. Chemistry 2022; 28:e202103892. [DOI: 10.1002/chem.202103892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Qiuhua Liu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule Ministry of Education and School of Chemistry and Chemical Engineering Institution for Hunan University of Science and Technology Yuhu District Xiangtan 411201 P. R. China
| | - Wanjie Ren
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Yanqi Lake, Huairou District Beijing 101408 P. R. China
| | - Siwei Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule Ministry of Education and School of Chemistry and Chemical Engineering Institution for Hunan University of Science and Technology Yuhu District Xiangtan 411201 P. R. China
| | - Yang Huang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Suzhou Research Institute of LICP Institution for Lanzhou Institute of Chemical Physics (LICP) Chinese Academy of Sciences Lanzhou 730000 P. R. China
| | - Dilong Chen
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule Ministry of Education and School of Chemistry and Chemical Engineering Institution for Hunan University of Science and Technology Yuhu District Xiangtan 411201 P. R. China
| | - Wennan Zeng
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule Ministry of Education and School of Chemistry and Chemical Engineering Institution for Hunan University of Science and Technology Yuhu District Xiangtan 411201 P. R. China
| | - Zaichun Zhou
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule Ministry of Education and School of Chemistry and Chemical Engineering Institution for Hunan University of Science and Technology Yuhu District Xiangtan 411201 P. R. China
| | - Lin He
- State Key Laboratory for Oxo Synthesis and Selective Oxidation Suzhou Research Institute of LICP Institution for Lanzhou Institute of Chemical Physics (LICP) Chinese Academy of Sciences Lanzhou 730000 P. R. China
| | - Wenping Guo
- National Energy Center for Coal to Clean Fuels Synfuels China Company Ltd Huairou District Beijing 101400 P. R. China
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology University of Chinese Academy of Sciences Yanqi Lake, Huairou District Beijing 101408 P. R. China
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16
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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17
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Zhong F, Alden SL, Hughes RP, Pletneva EV. Comparing Properties of Common Bioinorganic Ligands with Switchable Variants of Cytochrome c. Inorg Chem 2021; 61:1207-1227. [PMID: 34699724 DOI: 10.1021/acs.inorgchem.1c02322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand substitution at the metal center is common in catalysis and signal transduction of metalloproteins. Understanding the effects of particular ligands, as well as the polypeptide surrounding, is critical for uncovering mechanisms of these biological processes and exploiting them in the design of bioinspired catalysts and molecular devices. A series of switchable K79G/M80X/F82C (X = Met, His, or Lys) variants of cytochrome (cyt) c was employed to directly compare the stability of differently ligated proteins and activation barriers for Met, His, and Lys replacement at the ferric heme iron. Studies of these variants and their nonswitchable counterparts K79G/M80X have revealed stability trends Met < Lys < His and Lys < His < Met for the protein FeIII-X and FeII-X species, respectively. The differences in the hydrogen-bonding interactions in folded proteins and in solvation of unbound X in the unfolded proteins explain these trends. Calculations of free energy of ligand dissociation in small heme model complexes reveal that the ease of the FeIII-X bond breaking increases in the series amine < imidazole < thioether, mirroring trends in hardness of these ligands. Experimental rate constants for X dissociation in differently ligated cyt c variants are consistent with this sequence, but the differences between Met and His dissociation rates are attenuated because the former process is limited by the heme crevice opening. Analyses of activation parameters and comparisons to those for the Lys-to-Met ligand switch in the alkaline transition suggest that ligand dissociation is entropically driven in all the variants and accompanied by Lys protonation at neutral pH. The described thiolate redox-linked switches have offered a wealth of new information about interactions of different protein-derived ligands with the heme iron in cyt c model proteins, and we anticipate that the strategy of employing these switches could benefit studies of other redox metalloproteins and model complexes.
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Affiliation(s)
- Fangfang Zhong
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Stephanie L Alden
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Russell P Hughes
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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18
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Hniopek J, Bocklitz T, Schmitt M, Popp J. Probing Protein Secondary Structure Influence on Active Centers with Hetero Two-Dimensional Correlation (Resonance) Raman Spectroscopy: A Demonstration on Cytochrome C. APPLIED SPECTROSCOPY 2021; 75:1043-1052. [PMID: 34242104 PMCID: PMC8320570 DOI: 10.1177/00037028211028916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
The functionality of active centers in proteins is governed by the secondary and higher structure of proteins which often lead to structures in the active center that are different from the structures found in protein-free models of the active center. To elucidate this structure-function relationship, it is therefore necessary to investigate both the protein structure and the local structure of the active center. In this work, we investigate the application of hetero (resonance) Raman two-dimensional correlation spectroscopy (2D-COS) to this problem. By employing a combination of near-infrared-Fourier transform-Raman- and vis-resonance Raman spectroscopy, we could show that this combination of techniques is able to directly probe the structure-function relationship of proteins. We were able to correlate the transition of the heme center in cytochrome c from low to high spin with changes in the secondary structure with the above mentioned two spectroscopic in situ techniques and without sample preparation. Thereby, we were able to reveal that the combination of a spectroscopic method to selectively observe the active center with a technique that monitors the whole system offers a promising toolkit to investigate the structure-function relationship of proteins with photoactive centers in general.
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Affiliation(s)
- Julian Hniopek
- Department of Spectroscopy/Imaging, Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Physical Chemistry & Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Bocklitz
- Department of Spectroscopy/Imaging, Leibniz-Institute of Photonic Technologies, Jena, Germany
- Department of Photonic Data Science, Leibniz-Institute of Photonic Technologies, Jena, Germany
| | - Michael Schmitt
- Institute of Physical Chemistry & Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Jürgen Popp
- Department of Spectroscopy/Imaging, Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Physical Chemistry & Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
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19
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Short- and long-term effects of copper on anammox under gradually increased copper concentrations. Biodegradation 2021; 32:273-286. [PMID: 33745118 DOI: 10.1007/s10532-021-09934-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
This study aims to determine both short- and long-term response of enriched anammox culture to Cu. Assessment of short-term inhibition is based both on total applied Cu concentration and potential bioavailable fractions like intracellular, surface-bound, soluble and free Cu ion. The half maximal inhibitory concentration (IC50) values for total applied, soluble, intracellular and cell-associated concentrations were determined as 4.57 mg/L, 1.97 mg/L, 0.71 mg/L, 1.11 mg/L, respectively. Correlation between the surface-bound fraction of Cu and inhibition response was weak, suggesting that Cu sorbed to biomass was not directly responsible for the effects on anammox activity. There was a disparity between the results of short- and long-term experiments in terms of inhibition threshold concentration (i.e. short-term IC50 = 4.57 mg/L vs long-term IC50 = 6.74 mg/L). Candidatus Kuenenia (59.8%) and Candidatus Brocadia (40.2%) were the two main anammox genera within the initial biomass sample. One of the most interesting finding of the study is the demonstration that a complete wash-out of C. Brocadia genus at an applied Cu concentration of 6.5 mg/L. This strongly indicates that C. Brocadia were not able to tolerate high copper concentrations and all nitrogen conversion was carried out by C. Kuenenia during the Cu exposure period.
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20
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Ferousi C, Schmitz RA, Maalcke WJ, Lindhoud S, Versantvoort W, Jetten MSM, Reimann J, Kartal B. Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link. J Biol Chem 2021; 296:100476. [PMID: 33652023 PMCID: PMC8042395 DOI: 10.1016/j.jbc.2021.100476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.
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Affiliation(s)
- Christina Ferousi
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter J Maalcke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Simon Lindhoud
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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21
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Roos G, Harvey JN. Histidine versus Cysteine-Bearing Heme-Dependent Halogen Peroxidases: Parallels and Differences for Cl - Oxidation. J Phys Chem B 2021; 125:74-85. [PMID: 33350832 DOI: 10.1021/acs.jpcb.0c09409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The homodimeric myeloperoxidase (MPO) features a histidine as a proximal ligand and a sulfonium linkage covalently attaching the heme porphyrin ring to the protein. MPO is able to catalyze Cl- oxidation with about the same efficiency as chloroperoxidase at pH 7.0. In this study, we seek to explore the parallels and differences between the histidine and cysteine heme-dependent halogen peroxidases. Transition states, reaction barriers, and relevant thermodynamic properties are calculated on protein models. Together with electronic structure calculations, it gives an overview of the reaction mechanisms and of the factors that determine the selectivity between one- and two-electron paths. Conclusions point to the innate oxidizing nature of MPO with the ester and sulfonium linkages hiking up the reactivity to enable chloride oxidation. The installation of a deprotonated imidazolate as a proximal ligand does not shift the equilibrium from one- to two-electron events without influencing the chemistry of the oxidation reaction.
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Affiliation(s)
- Goedele Roos
- UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, University of Lille, CNRS, UMR 8576, F-59000 Lille, France
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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22
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Ozumchelouei EJ, Hamidian AH, Zhang Y, Yang M. A critical review on the effects of antibiotics on anammox process in wastewater. REV CHEM ENG 2020. [DOI: 10.1515/revce-2020-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Anaerobic ammonium oxidation (anammox) has recently become of significant interest due to its capability for cost-effective nitrogen elimination from wastewater. However, anaerobic ammonia-oxidizing bacteria (AnAOB) are sensitive to environmental changes and toxic substances. In particular, the presence of antibiotics in wastewater, which is considered unfavorable to the anammox process, has become a growing concern. Therefore, it is necessary to evaluate the effects of these inhibitors to acquire information on the applicability of the anammox process. Hence, this review summarizes our knowledge of the effects of commonly detected antibiotics in water matrices, including fluoroquinolone, macrolide, β-lactam, chloramphenicol, tetracycline, sulfonamide, glycopeptide, and aminoglycoside, on the anammox process. According to the literature, the presence of antibiotics in wastewater could partially or completely inhibit anammox reactions, in which antibiotics targeting protein synthesis or DNA replication (excluding aminoglycoside) were the most effective against the AnAOB strains.
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Affiliation(s)
- Elnaz Jafari Ozumchelouei
- School of Chemical Engineering , University College of Engineering, University of Tehran , Tehran , Iran
| | - Amir Hossein Hamidian
- Department of Environmental Science and Engineering, Faculty of Natural Resources , University of Tehran , Karaj , Iran
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Min Yang
- Department of Environmental Science and Engineering, Faculty of Natural Resources , University of Tehran , Karaj , Iran
- State Key Laboratory of Environmental Aquatic Chemistry , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
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Wu H, Xiao K, Ouyang T, Wang Z, Chen Y, Li N, Liu ZQ. Co-Cr mixed spinel oxide nanodots anchored on nitrogen-doped carbon nanotubes as catalytic electrode for hydrogen peroxide sensing. J Colloid Interface Sci 2020; 585:605-613. [PMID: 33139019 DOI: 10.1016/j.jcis.2020.10.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
Hydrogen peroxide (H2O2) is a significant biomarker in physiological processes. Abnormal levels of H2O2 are considered to be closely related to some acute diseases. Therefore, it is important to monitor the H2O2 levels in bio-samples. Herein, we present a novel non-enzymatic electrochemical H2O2 sensor based on the excellent electrocatalytic performance of a composite comprising Zn-Cr-Co ternary spinel metal oxide nanodots (ZnCrCoO4) anchored on the surface of nitrogen-doped carbon nanotubes (NCNTs), denoted as ZnCrCoO4/NCNTs, toward H2O2 reduction. ZnCrCoO4/NCNTs were synthesized using a facile one-pot hydrothermal strategy. The enhanced electrocatalytic performance of ZnCrCoO4 is resulted from the partial substitution of Co in spinel zinc cobaltate (ZnCo2O4) with Cr, which modifies the CoO electronic structure and enhances electroconductivity. The ZnCrCoO4/NCNTs-based H2O2 sensor exhibited a wide quantitative detection range from 1 to 7330 μM with a detection limit of 1 μM. The sensor showed excellent reproducibility and selectivity for H2O2 sensing. In addition, remarkable recoveries were obtained for H2O2-spiked fish serum samples. These results demonstrated that the as-developed sensor has a great potential in monitoring H2O2 levels in practical applications.
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Affiliation(s)
- Huixiang Wu
- School of Chemistry and Chemical Engineering/Institute of Clean Energy and Materials/Guangzhou Key Laboratory for Clean Energy and Materials/Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou Higher Education Mega Center, No. 230 Wai Huan Xi Road, 510006, PR China
| | - Kang Xiao
- School of Chemistry and Chemical Engineering/Institute of Clean Energy and Materials/Guangzhou Key Laboratory for Clean Energy and Materials/Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou Higher Education Mega Center, No. 230 Wai Huan Xi Road, 510006, PR China
| | - Ting Ouyang
- School of Chemistry and Chemical Engineering/Institute of Clean Energy and Materials/Guangzhou Key Laboratory for Clean Energy and Materials/Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou Higher Education Mega Center, No. 230 Wai Huan Xi Road, 510006, PR China
| | - Zhu Wang
- School of Chemistry and Chemical Engineering/Institute of Clean Energy and Materials/Guangzhou Key Laboratory for Clean Energy and Materials/Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou Higher Education Mega Center, No. 230 Wai Huan Xi Road, 510006, PR China
| | - Yibo Chen
- School of Chemistry and Chemical Engineering/Institute of Clean Energy and Materials/Guangzhou Key Laboratory for Clean Energy and Materials/Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou Higher Education Mega Center, No. 230 Wai Huan Xi Road, 510006, PR China
| | - Nan Li
- School of Chemistry and Chemical Engineering/Institute of Clean Energy and Materials/Guangzhou Key Laboratory for Clean Energy and Materials/Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou Higher Education Mega Center, No. 230 Wai Huan Xi Road, 510006, PR China
| | - Zhao-Qing Liu
- School of Chemistry and Chemical Engineering/Institute of Clean Energy and Materials/Guangzhou Key Laboratory for Clean Energy and Materials/Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou Higher Education Mega Center, No. 230 Wai Huan Xi Road, 510006, PR China.
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24
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Layer G. Heme biosynthesis in prokaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118861. [PMID: 32976912 DOI: 10.1016/j.bbamcr.2020.118861] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
The cyclic tetrapyrrole heme is used as a prosthetic group in a broad variety of different proteins in almost all organisms. Often, it is essential for vital biochemical processes such as aerobic and anaerobic respiration as well as photosynthesis. In Nature, heme is made from the common tetrapyrrole precursor 5-aminolevulinic acid, and for a long time it was assumed that heme is biosynthesized by a single, common pathway in all organisms. However, although this is indeed the case in eukaryotes, heme biosynthesis is more diverse in the prokaryotic world, where two additional pathways exist. The final elucidation of the two 'alternative' heme biosynthesis routes operating in some bacteria and archaea was achieved within the last decade. This review summarizes the three different heme biosynthesis pathways with a special emphasis on the two 'new' prokaryotic routes.
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Affiliation(s)
- Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Wissenschaften, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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25
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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26
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Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
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Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
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27
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Chen H, Mao YY, Jin RC. What's the variation in anammox reactor performance after single and joint temperature based shocks? THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136609. [PMID: 31955101 DOI: 10.1016/j.scitotenv.2020.136609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
A laboratory-scale up-flow anaerobic sludge blanket reactor was used to investigate the effects of temperature-based (single and combined with loading) shocks on the performance of anaerobic ammonium oxidation (anammox) reactor. The reactor was tolerant to 15 °C and 25 °C shocks; however, temperature shock of 55 °C led to severe accumulation of effluent NO2--N (>100 mg L-1), which induced substrate inhibition. Although the shock experiments achieved a maximum effluent NO2--N concentration of 205.4 mg L-1 after a hydraulic retention time-substrate concentration shock at 25 °C, the inhibition was still reversible. During the experiments, the content of extracellular polymeric substances (EPS) increased significantly after each shock to protect the anammox bacteria, and the value decreased correspondingly at the end of the recovery phase. The specific anammox activity showed the opposite tendency compared with that of the EPS. The performance of anammox reactor under a series of short-term temperature shocks was investigated, and the results can provide new ideas for future research.
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Affiliation(s)
- Hui Chen
- Department of Environmental Engineering, Taizhou University, Taizhou 318000, China
| | - Yuan-Yuan Mao
- Appraisal Center for Eco-environment & Engineering of Chongqing, Chongqing 400021, China
| | - Ren-Cun Jin
- Laboratory of Environmental Technology, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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28
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Govind C, Paul M, Karunakaran V. Ultrafast Heme Relaxation Dynamics Probing the Unfolded States of Cytochrome c Induced by Liposomes: Effect of Charge of Phospholipids. J Phys Chem B 2020; 124:2769-2777. [DOI: 10.1021/acs.jpcb.9b11957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chinju Govind
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Megha Paul
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Venugopal Karunakaran
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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29
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30
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Lei H, Bowler BE. Naturally Occurring A51V Variant of Human Cytochrome c Destabilizes the Native State and Enhances Peroxidase Activity. J Phys Chem B 2019; 123:8939-8953. [PMID: 31557440 DOI: 10.1021/acs.jpcb.9b05869] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The A51V variant of human cytochrome c is linked to thrombocytopenia 4 (THC4), a condition that causes decreased blood platelet counts. A 1.82 Å structure of the A51V variant shows only minor changes in tertiary structure relative to the wild-type (WT) protein. Guanidine hydrochloride denaturation demonstrates that the global stability of the A51V variant is 1.3 kcal/mol less than that of the WT protein. The midpoint pH, pH1/2, of the alkaline transition of the A51V variant is 1 unit less than that of the WT protein. Stopped-flow pH jump experiments show that the A51V substitution affects the triggering ionization for one of two kinetically distinguishable alkaline conformers and enhances the accessibility of a high-spin heme transient. The pH1/2 for acid unfolding of the A51V variant is 0.7 units higher than for that of the WT protein. Consistent with the greater accessibility of non-native conformers for the A51V variant, the kcat values for its peroxidase activity increase by 6- to 15-fold in the pH range of 5-8 versus those of the WT protein. These data along with previously reported data for the other THC4-linked variants, G41S and Y48H, underscore the role of Ω-loop C (residues 40-57) in modulating the peroxidase activity of cytochrome c early in apoptosis.
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Affiliation(s)
- Haotian Lei
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, Center for Bimolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
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31
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Ferousi C, Lindhoud S, Baymann F, Hester ER, Reimann J, Kartal B. Discovery of a functional, contracted heme-binding motif within a multiheme cytochrome. J Biol Chem 2019; 294:16953-16965. [PMID: 31582564 DOI: 10.1074/jbc.ra119.010568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/02/2019] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria convert nitrite and ammonium via nitric oxide (NO) and hydrazine into dinitrogen gas by using a diverse array of proteins, including numerous c-type cytochromes. Many new catalytic and spectroscopic properties of c-type cytochromes have been unraveled by studies on the biochemical pathways underlying the anammox process. The unique anammox intermediate hydrazine is produced by a multiheme cytochrome c protein, hydrazine synthase, through the comproportionation of ammonium and NO and the input of three electrons. It is unclear how these electrons are delivered to hydrazine synthase. Here, we report the discovery of a functional tetraheme c-type cytochrome from the anammox bacterium Kuenenia stuttgartiensis with a naturally-occurring contracted Cys-Lys-Cys-His (CKCH) heme-binding motif, which is encoded in the hydrazine synthase gene cluster. The purified tetraheme protein (named KsTH) exchanged electrons with hydrazine synthase. Complementary spectroscopic techniques revealed that this protein harbors four low-spin hexa-coordinated hemes with His/Lys (heme 1), His/Cys (heme 2), and two His/His ligations (hemes 3 and 4). A genomic database search revealed that c-type cytochromes with a contracted CXCH heme-binding motif are present throughout the bacterial and archaeal domains in the tree of life, suggesting that this heme recognition site may be employed by many different groups of microorganisms.
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Affiliation(s)
- Christina Ferousi
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Simon Lindhoud
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Frauke Baymann
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, Marseille Cedex 09, France
| | - Eric R Hester
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, IWWR, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
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32
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Ma H, Zhang Y, Xue Y, Zhang Y, Li YY. Relationship of heme c, nitrogen loading capacity and temperature in anammox reactor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:568-577. [PMID: 31096386 DOI: 10.1016/j.scitotenv.2018.12.377] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 06/09/2023]
Abstract
The characteristic carmine red color due to heme proteins is always observed in enriched anammox biomass. Heme c is a very important co-factor participating the main metabolic reactions with catalytic and electron-transfer potential in the anammox bacteria, and is possible for use as an indicator to evaluate anammox performance. Knowledge of the relationship between the heme c concentration and the anammox reactor performance is, however, very limited available information is constrained at an operation temperature of 35 °C. In this study, we report the heme c concentration change along with nitrogen removal rate (NRR) in three anammox expanded granular sludge bed reactors operated at different temperatures (15, 25, 35 °C). The response of specific anammox activity (SAA) to temperature was revealed for biomass originating from three reactors. The results indicate a strong relationship between heme c concentration and NRR at different culture temperatures. The possibility of evaluating the anammox performance by combining heme c quantification and the temperature is revealed.
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Affiliation(s)
- Haiyuan Ma
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yanlong Zhang
- College of the Environment and Ecology, Xiamen University, South Xiang'an Road, Xiang'an District, Xiamen, Fujian 361102, China
| | - Yi Xue
- Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yuanfan Zhang
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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33
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Akram M, Dietl A, Mersdorf U, Prinz S, Maalcke W, Keltjens J, Ferousi C, de Almeida NM, Reimann J, Kartal B, Jetten MSM, Parey K, Barends TRM. A 192-heme electron transfer network in the hydrazine dehydrogenase complex. SCIENCE ADVANCES 2019; 5:eaav4310. [PMID: 31001586 PMCID: PMC6469936 DOI: 10.1126/sciadv.aav4310] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/28/2019] [Indexed: 05/21/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
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Affiliation(s)
- M. Akram
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - A. Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - U. Mersdorf
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - S. Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - W. Maalcke
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - J. Keltjens
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - C. Ferousi
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - N. M. de Almeida
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - J. Reimann
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - B. Kartal
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - M. S. M. Jetten
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - K. Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Corresponding author. (K.P.); (T.R.M.B.)
| | - T. R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Corresponding author. (K.P.); (T.R.M.B.)
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34
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Shen HQ, Wu B, Xie HP, Zhou YG. Preparation of Axially Chiral 2,2′-Biimidazole Ligands through Remote Chirality Delivery and Their Application in Asymmetric Carbene Insertion into N–H of Carbazoles. Org Lett 2019; 21:2712-2717. [DOI: 10.1021/acs.orglett.9b00687] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hong-Qiang Shen
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Bo Wu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Huan-Ping Xie
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
- Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin 300071, People’s Republic of China
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35
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Liu W, Pan H, Liu C, Su C, Liu W, Wang K, Jiang J. Ultrathin Phthalocyanine-Conjugated Polymer Nanosheet-Based Electrochemical Platform for Accurately Detecting H 2O 2 in Real Time. ACS APPLIED MATERIALS & INTERFACES 2019; 11:11466-11473. [PMID: 30821143 DOI: 10.1021/acsami.8b22686] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As a vital biological mediator and a widely used industrial oxidant, the accurate detection of hydrogen peroxide (H2O2) is of significance for both academic purpose and practical applications. Herein, we report a novel approach for the development of a high-performance electrochemical H2O2 sensor constructed by iron phthalocyanine (FePc)-based diyne-linked conjugated polymeric nanosheets (NSs), FePc-CP NSs. The FePc-CP NSs were delaminated from the bulk material via a defect- and disorder-induced synthetic strategy. By the quasi-Langmuir-Shäfer method, the prepared FePc-CP NSs were self-assembled into multilayer films with controllable thickness on electrodes. Owing to the highly exposed active centers on the surfaces, the FePc-CP NS film-modified electrodes exhibited excellent H2O2 determination performance with a wide linear detection range (0.1-1000 μM), a short response time (the response current approached the maximum value within 0.1 s), a low limit of detection (0.017 μM), and excellent sensitivity (97 μA cm-2 mM-1), which are comparable to the best results reported so far for electrochemical H2O2 sensors. In addition, the fabricated electrochemical H2O2 sensor also displayed satisfactory stability, reproducibility, and selectivity. Furthermore, the obtained FePc-CP NS film sensor can be applied in real-time monitoring of H2O2 in commercial orange juice and beer as well as H2O2 secreted from A549 live cells, revealing its application potential toward the accurate detection of H2O2 in real-sample analysis.
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Affiliation(s)
- Wenping Liu
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry , University of Science and Technology Beijing , Beijing 100083 , China
| | - Houhe Pan
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry , University of Science and Technology Beijing , Beijing 100083 , China
| | - Chenxi Liu
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry , University of Science and Technology Beijing , Beijing 100083 , China
| | - Chaorui Su
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry , University of Science and Technology Beijing , Beijing 100083 , China
| | - Wenbo Liu
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry , University of Science and Technology Beijing , Beijing 100083 , China
| | - Kang Wang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry , University of Science and Technology Beijing , Beijing 100083 , China
| | - Jianzhuang Jiang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry , University of Science and Technology Beijing , Beijing 100083 , China
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36
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Dietl A, Maalcke WJ, Ferousi C, Jetten MSM, Kartal B, Barends TRM. A 60-heme reductase complex from an anammox bacterium shows an extended electron transfer pathway. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:333-341. [DOI: 10.1107/s2059798318017473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/10/2018] [Indexed: 11/10/2022]
Abstract
The hydroxylamine oxidoreductase/hydrazine dehydrogenase (HAO/HDH) protein family constitutes an important group of octaheme cytochromes c (OCCs). The majority of these proteins form homotrimers, with their subunits being covalently attached to each other via a rare cross-link between the catalytic heme moiety and a conserved tyrosine residue in an adjacent subunit. This covalent cross-link has been proposed to modulate the active-site heme towards oxidative catalysis by distorting the heme plane. In this study, the crystal structure of a stable complex of an HAO homologue (KsHAOr) with its diheme cytochrome c redox partner (KsDH) from the anammox bacterium Kuenenia stuttgartiensis was determined. KsHAOr lacks the tyrosine cross-link and is therefore tuned to reductive catalysis. The molecular model of the KsHAOr–KsDH complex at 2.6 Å resolution shows a heterododecameric (α6β6) assembly, which was also shown to be the oligomeric state in solution by analytical ultracentrifugation and multi-angle static light scattering. The 60-heme-containing protein complex reveals a unique extended electron transfer pathway and provides deeper insights into catalysis and electron transfer in reductive OCCs.
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37
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Magallanes G, Kärkäs MD, Bosque I, Lee S, Maldonado S, Stephenson CRJ. Selective C–O Bond Cleavage of Lignin Systems and Polymers Enabled by Sequential Palladium-Catalyzed Aerobic Oxidation and Visible-Light Photoredox Catalysis. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04172] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gabriel Magallanes
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Markus D. Kärkäs
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Organic Chemistry, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Irene Bosque
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sudarat Lee
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Stephen Maldonado
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Program in Applied Physics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Corey R. J. Stephenson
- Willard Henry Dow Laboratory, Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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38
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Ultrathin two-dimension metal-organic framework nanosheets/multi-walled carbon nanotube composite films for the electrochemical detection of H2O2. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.01.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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39
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Liu Q, Zhang J, Tang M, Yang Y, Zhang J, Zhou Z. Geometric deconstruction of core and electron activation of a π-system in a series of deformed porphyrins: mimics of heme. Org Biomol Chem 2018; 16:7725-7736. [PMID: 30289139 DOI: 10.1039/c8ob01959b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The predominant distortion of heme is responsible for its electronic activity, catalytic ability and spectral properties. In this work, altogether 12 new X-ray structures of saddled, waved and ruffled porphyrins are reported. Three types of deformed porphyrins as mimics of heme were evaluated and analyzed by geometric deconstruction, spectral comparison, and electrochemical tracking, which shows a unique relationship of deformation fashions and distortion degree to the geometry of the core and electron transfer ability of rings in these enzyme containing porphyrins. These mimics can adjust their core geometry for changing the structures of potential metals; while for rings themselves, they can also regulate the electron activity by switching the HOMO of the large π systems. These deformed porphyrins can be used as ideal mimics for heme. These findings help us to understand the principle and contribution of these deformations to electron transfer in catalytic oxidation and photoreactions. The nonplanar mimics have been synthesized through a modular synthetic approach under Adler-Longo or Lindsey condensation conditions.
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Affiliation(s)
- Qiuhua Liu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Jinjin Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Min Tang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Yan Yang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
| | - Jian Zhang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, USA.
| | - Zaichun Zhou
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education; and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China.
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40
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G-quadruplex Nanowires To Direct the Efficiency and Selectivity of Electrocatalytic CO 2
Reduction. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Influence of heme c attachment on heme conformation and potential. J Biol Inorg Chem 2018; 23:1073-1083. [PMID: 30143872 DOI: 10.1007/s00775-018-1603-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Heme c is characterized by its covalent attachment to a polypeptide. The attachment is typically to a CXXCH motif in which the two Cys form thioether bonds with the heme, "X" can be any amino acid other than Cys, and the His serves as a heme axial ligand. Some cytochromes c, however, contain heme attachment motifs with three or four intervening residues in a CX3CH or CX4CH motif. Here, the impacts of these variations in the heme attachment motif on heme ruffling and electronic structure are investigated by spectroscopically characterizing CX3CH and CX4CH variants of Hydrogenobacter thermophilus cytochrome c552. In addition, a novel CXCH variant is studied. 1H and 13C NMR, EPR, and resonance Raman spectra of the protein variants are analyzed to deduce the extent of ruffling using previously reported relationships between these spectral data and heme ruffling. In addition, the reduction potentials of these protein variants are measured using protein film voltammetry. The CXCH and CX4CH variants are found to have enhanced heme ruffling and lower reduction potentials. Implications of these results for the use of these noncanonical motifs in nature, and for the engineering of novel heme peptide structures, are discussed.
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42
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He L, Sun X, Zhang H, Shao F. G-quadruplex Nanowires To Direct the Efficiency and Selectivity of Electrocatalytic CO2
Reduction. Angew Chem Int Ed Engl 2018; 57:12453-12457. [DOI: 10.1002/anie.201806652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/13/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Lei He
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University, Singapore; 21 Nanyang Link Singapore 637371 Singapore
| | - Xiaofu Sun
- Center for Programmable Materials; School of Materials Science and Engineering; Nanyang Technological University; 50 Nanyang Avenue Singapore 639798 Singapore
| | - Hua Zhang
- Center for Programmable Materials; School of Materials Science and Engineering; Nanyang Technological University; 50 Nanyang Avenue Singapore 639798 Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University, Singapore; 21 Nanyang Link Singapore 637371 Singapore
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43
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Caserta G, Chino M, Firpo V, Zambrano G, Leone L, D'Alonzo D, Nastri F, Maglio O, Pavone V, Lombardi A. Enhancement of Peroxidase Activity in Artificial Mimochrome VI Catalysts through Rational Design. Chembiochem 2018; 19:1823-1826. [PMID: 29898243 DOI: 10.1002/cbic.201800200] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Indexed: 11/09/2022]
Abstract
Rational design provides an attractive strategy to tune and control the reactivity of bioinspired catalysts. Although there has been considerable progress in the design of heme oxidase mimetics with active-site environments of ever-growing complexity and catalytic efficiency, their stability during turnover is still an open challenge. Herein, we show that the simple incorporation of two 2-aminoisobutyric acids into an artificial peptide-based peroxidase results in a new catalyst (FeIII -MC6*a) with higher resistance against oxidative damage and higher catalytic efficiency. The turnover number of this catalyst is twice as high as that of its predecessor. These results point out the protective role exerted by the peptide matrix and pave the way to the synthesis of robust bioinspired catalysts.
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Affiliation(s)
- Giorgio Caserta
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy.,Present address: Department of Chemistry, Technische Universität Berlin, Strasse des 17 Juni 135, 10623, Berlin, Germany
| | - Marco Chino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Vincenzo Firpo
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Gerardo Zambrano
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy.,IBB, National Research Council, via Mezzocannone, 16, 80134, Napoli, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
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44
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Lewis RD, Garcia-Borràs M, Chalkley MJ, Buller AR, Houk KN, Kan SBJ, Arnold FH. Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase. Proc Natl Acad Sci U S A 2018; 115:7308-7313. [PMID: 29946033 PMCID: PMC6048479 DOI: 10.1073/pnas.1807027115] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently, heme proteins have been discovered and engineered by directed evolution to catalyze chemical transformations that are biochemically unprecedented. Many of these nonnatural enzyme-catalyzed reactions are assumed to proceed through a catalytic iron porphyrin carbene (IPC) intermediate, although this intermediate has never been observed in a protein. Using crystallographic, spectroscopic, and computational methods, we have captured and studied a catalytic IPC intermediate in the active site of an enzyme derived from thermostable Rhodothermus marinus (Rma) cytochrome c High-resolution crystal structures and computational methods reveal how directed evolution created an active site for carbene transfer in an electron transfer protein and how the laboratory-evolved enzyme achieves perfect carbene transfer stereoselectivity by holding the catalytic IPC in a single orientation. We also discovered that the IPC in Rma cytochrome c has a singlet ground electronic state and that the protein environment uses geometrical constraints and noncovalent interactions to influence different IPC electronic states. This information helps us to understand the impressive reactivity and selectivity of carbene transfer enzymes and offers insights that will guide and inspire future engineering efforts.
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Affiliation(s)
- Russell D Lewis
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Matthew J Chalkley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Andrew R Buller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;
| | - S B Jennifer Kan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Frances H Arnold
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125;
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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45
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KOZAKAI T, HARASHIMA T, KIGUCHI M, NISHINO T. Measurement of Electron Transfer within a Single Supramolecular Assembly Containing a Biological Molecule. ANAL SCI 2018; 34:521-523. [DOI: 10.2116/analsci.18c010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Takafumi KOZAKAI
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Takanori HARASHIMA
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Manabu KIGUCHI
- Department of Chemistry, School of Science, Tokyo Institute of Technology
| | - Tomoaki NISHINO
- Department of Chemistry, School of Science, Tokyo Institute of Technology
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46
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Sterically induced distortions of nickel(II) porphyrins – Comprehensive investigation by DFT calculations and resonance Raman spectroscopy. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2017.12.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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47
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Affiliation(s)
| | - Marina Gobbo
- Department of Chemical SciencesUniversity of PadovaPadova35131 Italy
- Institute of Biomolecular Chemistry of CNR, Padova UnitPadova35131 Italy
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48
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Chino M, Leone L, Zambrano G, Pirro F, D'Alonzo D, Firpo V, Aref D, Lista L, Maglio O, Nastri F, Lombardi A. Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages. Biopolymers 2018; 109:e23107. [DOI: 10.1002/bip.23107] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/31/2018] [Accepted: 02/05/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Gerardo Zambrano
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Vincenzo Firpo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Diaa Aref
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Liliana Lista
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
- Institute of Biostructures and Bioimages-National Research Council, Via Mezzocannone 16; Napoli 80134 Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
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49
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Kepp KP. Heme isomers substantially affect heme's electronic structure and function. Phys Chem Chem Phys 2018; 19:22355-22362. [PMID: 28805222 DOI: 10.1039/c7cp03285d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as due to similar energy of the isomers but with a sizable (25 kJ mol-1) barrier to interconversion arising from restricted rotation around the conjugated bonds. The four isomers, EE, EZ, ZE, and ZZ, were then investigated as 4-coordinate hemes, as 5-coordinate deoxyhemes, in 6-coordinate O2-adducts of globins and as compound I intermediates typical of heme peroxidases. Substantial differences were observed in electronic properties relevant to heme function: notably, the spin state energy gap of O2-heme adducts, important for fast reversible binding of O2, depends on the isomer state, and O2-binding enthalpies change by up to 16 kJ mol-1; redox potentials change by up to 0.2 V depending on the isomer, and the doublet-quartet energy splitting of compound I, central to "two-state" reactivity, is affected by up to ∼15 kJ mol-1. These effects are consistently seen with three distinct density functionals, i.e. the effects are not method-dependent. Thus, the nature of the isomer state is an important but overlooked feature of heme chemistry and function, and previous and future studies of hemes may be reconsidered in this new context.
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Affiliation(s)
- Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, DK, Denmark.
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50
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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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