1
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Li L, Liu Z, Meng D, Liu Y, Liu T, Jiang C, Yin H. Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation. mSystems 2023; 8:e0072023. [PMID: 37768051 PMCID: PMC10654088 DOI: 10.1128/msystems.00720-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Tianbo Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Chengying Jiang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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2
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Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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3
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Shojapour M, Fatemi F, Farahmand S, Shasaltaneh MD. Investigation of Cyc 1 protein structure stability after H53I mutation using computational approaches to improve redox potential. J Mol Graph Model 2021; 105:107864. [PMID: 33647753 DOI: 10.1016/j.jmgm.2021.107864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 10/22/2022]
Abstract
Acidithiobacillus ferrooxidans (Af) is an acidophilic bacterium that grows in rigid surroundings and gets its own energy from the oxidation of Fe2+ to Fe3+. These bacteria are involved in the bioleaching process. Cyc1 is a periplasmic protein with a crucial role in electron transportation in the respiratory chain. His53 of the Cyc1 protein, involved in electron transfer to CoxB, was selected for mutation and bioinformatics studies. His53 was substituted by Ile using PyMol software. Molecular dynamics simulations were performed for wild and mutant types of Cyc1 protein. The conformational changes of mutated protein were studied by analyzing RMSD, RMSF, SASA, Rg, H Bond, and DSSP. The results of the RMSF analysis indicated an increase in the flexibility of the ligand in the mutant. Finally, active site instability leads to an increase in the value of E0 at the mutation point and improving electron transfer. On the other, His53 in Cyc1 is interconnected to Glu126 in CoxB through the water molecule (W76) and hydrogen bonding. In the H53I mutation, there was a decrease in the distance between H2O 2030, 2033, and isoleucine 53, and subsequently, the distance to the water molecule 76 between the two proteins was reduced and strengthens the hydrogen bond between Cyc1 and CoxB, finally improves electron transfer and the bioleaching process.
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Affiliation(s)
- Mahnaz Shojapour
- Department of Biology, Faculty of Sciences, Payame Noor University, Tehran, Iran.
| | - Faezeh Fatemi
- Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Somayeh Farahmand
- Department of Biology, Faculty of Sciences, Payame Noor University, Tehran, Iran
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4
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Jafarpour R, Fatemi F, Eidi A, Mehrnejad F. Effect of the Met148Leu mutation on the structure and dynamics of the rusticyanin protein from Acidithiobacillus sp. FJ2. J Biomol Struct Dyn 2020; 39:4122-4132. [PMID: 32462978 DOI: 10.1080/07391102.2020.1775119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rusticyanin protein, a blue monomeric copper protein type-1, is one of the main components in the iron-electron transfer chain of the Acidithiobacillus ferrooxidans, and is the product of the rus gene expression. Herein, first the bacterial DNA of Acidithiobacillus sp. FJ2 was extracted. Then, the rus gene sequence and the sequence amino acid rusticyanin protein were determined. The Met148Leu mutation increased the oxidase activity of the rusticyanin protein, thereby enhancing the efficiency of the bioleaching process by bacteria Acidithiobacillus ferroxidans. Met148Leu mutation was created in the rusticyanin protein, then molecular dynamics (MD) simulations and structural analysis were performed. The MD analysis of the wild-type and mutant protein demonstrated a slight instability in the mutant protein and significant instability in the active site of the mutant protein. The usefulness of this study is the genetic manipulation of the native Acidithiobacillus sp. FJ2 bacterium, which can boost the bioleaching efficiency of the bacterium to some extent, and investigating its effects on the structure of a mutant protein using computational methods.
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Affiliation(s)
- Roghayeh Jafarpour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faezeh Fatemi
- Materials and Nuclear Fuel Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Akram Eidi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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5
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Farahmand S, Fatemi F, Hajihosseini R. Sequencing of the rus gene before and after the mutation with DES in the bacterial Acidithiobacillus sp. FJ2. NOVA BIOLOGICA REPERTA 2019. [DOI: 10.29252/nbr.6.1.50] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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6
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Zhan Y, Yang M, Zhang S, Zhao D, Duan J, Wang W, Yan L. Iron and sulfur oxidation pathways of Acidithiobacillus ferrooxidans. World J Microbiol Biotechnol 2019; 35:60. [PMID: 30919119 DOI: 10.1007/s11274-019-2632-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022]
Abstract
Acidithiobacillus ferrooxidans is a gram-negative, autotrophic and rod-shaped bacterium. It can gain energy through the oxidation of Fe(II) and reduced inorganic sulfur compounds for bacterial growth when oxygen is sufficient. It can be used for bio-leaching and bio-oxidation and contributes to the geobiochemical circulation of metal elements and nutrients in acid mine drainage environments. The iron and sulfur oxidation pathways of A. ferrooxidans play key roles in bacterial growth and survival under extreme circumstances. Here, the electrons transported through the thermodynamically favourable pathway for the reduction to H2O (downhill pathway) and against the redox potential gradient reduce to NAD(P)(H) (uphill pathway) during the oxidation of Fe(II) were reviewed, mainly including the electron transport carrier, relevant operon and regulation of its expression. Similar to the electron transfer pathway, the sulfur oxidation pathway of A. ferrooxidans, related genes and operons, sulfur oxidation mechanism and sulfur oxidase system are systematically discussed.
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Affiliation(s)
- Yue Zhan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Mengran Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Jiangong Duan
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, Gansu Province, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China. .,College of Food Science, Heilongjiang Bayi Agricultural University, 5 Xinfeng Road, Daqing, 163319, Heilongjiang Province, People's Republic of China.
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7
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Forootanfar H, Arjmand S, Behzadi M, Faramarzi MA. Laccase-Mediated Treatment of Pharmaceutical Wastes. RESEARCH ADVANCEMENTS IN PHARMACEUTICAL, NUTRITIONAL, AND INDUSTRIAL ENZYMOLOGY 2018. [DOI: 10.4018/978-1-5225-5237-6.ch010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Laccases are versatile multi-copper enzymes belonging to the superfamily of oxidase enzymes, which have been known since the nineteenth century. Recent discoveries have refined investigators' views of the potential of laccase as a magic tool for remarkable biotechnological purposes. A literature review of the capabilities of laccases, their assorted substrates, and their molecular mechanism of action now indicates the emergence of a new direction for laccase application as part of an arsenal in the fight against the contamination of water supplies by a number of frequently prescribed medications. This chapter provides a critical review of the literature and reveals the pivotal role of laccases in the elimination and detoxification of pharmaceutical contaminants in aquatic environments and wastewaters.
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8
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Sinicropi A. DFT modeling of structures and redox potentials of wild-type, Nickel-substituted and mutated (N47S/M121L, HPAz) Azurin. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.08.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Zanetti-Polzi L, Corni S, Daidone I, Amadei A. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. Phys Chem Chem Phys 2016; 18:18450-9. [PMID: 27339768 DOI: 10.1039/c6cp03394f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, a methodology is proposed to investigate the collective fluctuation modes of an arbitrary set of observables, maximally contributing to the fluctuation of another functionally relevant observable. The methodology, based on the analysis of fully classical molecular dynamics (MD) simulations, exploits the essential dynamics (ED) method, originally developed to analyse the collective motions in proteins. We apply this methodology to identify the residues that are more relevant for determining the reduction potential (E(0)) of a redox-active protein. To this aim, the fluctuation modes of the single-residue electrostatic potentials mostly contributing to the fluctuations of the total electrostatic potential (the main determinant of E(0)) are investigated for wild-type azurin and two of its mutants with a higher E(0). By comparing the results here obtained with a previous study on the same systems [Zanetti-Polzi et al., Org. Biomol. Chem., 2015, 13, 11003] we show that the proposed methodology is able to identify the key sites that determine E(0). This information can be used for a general deeper understanding of the molecular mechanisms on the basis of the redox properties of the proteins under investigation, as well as for the rational design of mutants with a higher or lower E(0). From the results of the present analysis we propose a new azurin mutant that, according to our calculations, shows a further increase of E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy.
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10
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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11
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Pérez-Henarejos SA, Alcaraz LA, Donaire A. Blue Copper Proteins: A rigid machine for efficient electron transfer, a flexible device for metal uptake. Arch Biochem Biophys 2015; 584:134-48. [DOI: 10.1016/j.abb.2015.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/24/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
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12
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Komori H, Higuchi Y. Structure and molecular evolution of multicopper blue proteins. Biomol Concepts 2015; 1:31-40. [PMID: 25961983 DOI: 10.1515/bmc.2010.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The multicopper blue protein family, which contains cupredoxin-like domains as a structural unit, is one of the most diverse groups of proteins. This protein family is divided into two functionally different types of enzymes: multicopper oxidase and nitrite reductase. Multicopper oxidase catalyzes the oxidation of the substrate and then reduces dioxygen. The structures of many multicopper oxidases are already known, and until recently they were classified into two main groups: the three- and six-domain types. Both function as monomers and have three spectroscopically different copper sites: Types I (blue), II, and III (tri-nuclear). Nitrite reductase is a closely related protein that contains Types I and II (mono-nuclear) coppers but reduces nitrite instead of dioxygen. Nitrite reductase, which consists of two domains, forms a homotrimer. Multicopper oxidase and nitrite reductase share similar structural architectures and also contain Type I copper. Therefore, it is proposed that they have a common ancestor protein. Recently, some two-domain type multicopper oxidases have been found and their crystal structures have been determined. They have a trimeric quaternary structure and contain an active site at the molecular interface such as nitrite reductase. These results support previous hypotheses and provide an insight into the molecular evolution of multicopper blue proteins.
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13
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King JD, Harrington L, Lada BM, He G, Cooley JW, Blankenship RE. Site-directed mutagenesis of the highly perturbed copper site of auracyanin D. Arch Biochem Biophys 2014; 564:237-43. [DOI: 10.1016/j.abb.2014.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/01/2014] [Accepted: 10/07/2014] [Indexed: 10/24/2022]
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14
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Roger M, Biaso F, Castelle CJ, Bauzan M, Chaspoul F, Lojou E, Sciara G, Caffarri S, Giudici-Orticoni MT, Ilbert M. Spectroscopic characterization of a green copper site in a single-domain cupredoxin. PLoS One 2014; 9:e98941. [PMID: 24932914 PMCID: PMC4059628 DOI: 10.1371/journal.pone.0098941] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/09/2014] [Indexed: 12/13/2022] Open
Abstract
Cupredoxins are widespread copper-binding proteins, mainly involved in electron transfer pathways. They display a typical rigid greek key motif consisting of an eight stranded β-sandwich. A fascinating feature of cupredoxins is the natural diversity of their copper center geometry. These geometry variations give rise to drastic changes in their color, such as blue, green, red or purple. Based on several spectroscopic and structural analyses, a connection between the geometry of their copper-binding site and their color has been proposed. However, little is known about the relationship between such diversity of copper center geometry in cupredoxins and possible implications for function. This has been difficult to assess, as only a few naturally occurring green and red copper sites have been described so far. We report herein the spectrocopic characterization of a novel kind of single domain cupredoxin of green color, involved in a respiratory pathway of the acidophilic organism Acidithiobacillus ferrooxidans. Biochemical and spectroscopic characterization coupled to bioinformatics analysis reveal the existence of some unusual features for this novel member of the green cupredoxin sub-family. This protein has the highest redox potential reported to date for a green-type cupredoxin. It has a constrained green copper site insensitive to pH or temperature variations. It is a green-type cupredoxin found for the first time in a respiratory pathway. These unique properties might be explained by a region of unknown function never found in other cupredoxins, and by an unusual length of the loop between the second and the fourth copper ligands. These discoveries will impact our knowledge on non-engineered green copper sites, whose involvement in respiratory chains seems more widespread than initially thought.
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Affiliation(s)
- Magali Roger
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Frédéric Biaso
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America
| | - Marielle Bauzan
- Unité de Fermentation, Institut de Microbiologie de la Méditerranée, CNRS-FR 3479, Aix Marseille Université, Marseille, France
| | - Florence Chaspoul
- Unité Chimie Physique, Prévention des Risques et Nuisances Technologiques, Faculté de Pharmacie, CNRS-UMR 7263, Aix-Marseille Université, Marseille, France
| | - Elisabeth Lojou
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Giuliano Sciara
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Stefano Caffarri
- Unité de Biologie Végétale et Microbiologie Environnementales, CNRS-UMR 7265, CEA, Aix Marseille Université, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
| | - Marianne Ilbert
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-UMR7281, Aix-Marseille Université, Marseille, France
- * E-mail:
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15
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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16
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Hadt RG, Sun N, Marshall NM, Hodgson KO, Hedman B, Lu Y, Solomon EI. Spectroscopic and DFT studies of second-sphere variants of the type 1 copper site in azurin: covalent and nonlocal electrostatic contributions to reduction potentials. J Am Chem Soc 2012; 134:16701-16. [PMID: 22985400 PMCID: PMC3506006 DOI: 10.1021/ja306438n] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.
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Affiliation(s)
- Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Ning Sun
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nicholas M. Marshall
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Yi Lu
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
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18
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Santhanam N, Vivanco JM, Decker SR, Reardon KF. Expression of industrially relevant laccases: prokaryotic style. Trends Biotechnol 2011; 29:480-9. [DOI: 10.1016/j.tibtech.2011.04.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/15/2011] [Accepted: 04/19/2011] [Indexed: 01/11/2023]
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19
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Prasad NK, Vindal V, Narayana SL, V. R, Kunal SP, M. S. In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes. J Mol Model 2011; 18:2013-9. [DOI: 10.1007/s00894-011-1215-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/07/2011] [Indexed: 10/17/2022]
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20
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Rationally tuning the reduction potential of a single cupredoxin beyond the natural range. Nature 2009; 462:113-6. [PMID: 19890331 DOI: 10.1038/nature08551] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 09/30/2009] [Indexed: 11/08/2022]
Abstract
Redox processes are at the heart of numerous functions in chemistry and biology, from long-range electron transfer in photosynthesis and respiration to catalysis in industrial and fuel cell research. These functions are accomplished in nature by only a limited number of redox-active agents. A long-standing issue in these fields is how redox potentials are fine-tuned over a broad range with little change to the redox-active site or electron-transfer properties. Resolving this issue will not only advance our fundamental understanding of the roles of long-range, non-covalent interactions in redox processes, but also allow for design of redox-active proteins having tailor-made redox potentials for applications such as artificial photosynthetic centres or fuel cell catalysts for energy conversion. Here we show that two important secondary coordination sphere interactions, hydrophobicity and hydrogen-bonding, are capable of tuning the reduction potential of the cupredoxin azurin over a 700 mV range, surpassing the highest and lowest reduction potentials reported for any mononuclear cupredoxin, without perturbing the metal binding site beyond what is typical for the cupredoxin family of proteins. We also demonstrate that the effects of individual structural features are additive and that redox potential tuning of azurin is now predictable across the full range of cupredoxin potentials.
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21
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Choi M, Sukumar N, Liu A, Davidson VL. Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine. Biochemistry 2009; 48:9174-84. [PMID: 19715303 DOI: 10.1021/bi900836h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of replacing the axial methionine ligand of the type 1 copper site with leucine on the structure and function of amicyanin have been characterized. The crystal structures of the oxidized and reduced forms of the protein reveal that the copper site is now tricoordinate with no axial ligand, and that the copper coordination distances for the two ligands provided by histidines are significantly increased. Despite these structural changes, the absorption and EPR spectra of M98L amicyanin are only slightly altered and still consistent with that of a typical type 1 site. The oxidation-reduction midpoint potential (E(m)) value becomes 127 mV more positive as a consequence of the M98L mutation, most likely because of the increased hydrophobicity of the copper site. The most dramatic effect of the mutation was on the electron transfer (ET) reaction from reduced M98L amicyanin to cytochrome c(551i) within the protein ET complex. The rate decreased 435-fold, which was much more than expected from the change in E(m). Examination of the temperature dependence of the ET rate (k(ET)) revealed that the mutation caused a 13.6-fold decrease in the electronic coupling (H(AB)) for the reaction. A similar decrease was predicted from a comparative analysis of the crystal structures of reduced M98L and native amicyanins. The most direct route of ET for this reaction is through the Met98 ligand. Inspection of the structures suggests that the major determinant of the large decrease in the experimentally determined values of H(AB) and k(ET) is the increased distance from the copper to the protein within the type 1 site of M98L amicyanin.
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Affiliation(s)
- Moonsung Choi
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, Mississippi 39216-4505, USA
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22
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Si D, Li H. Quantum Chemical Calculation of Type-1 Cu Reduction Potential: Ligand Interaction and Solvation Effect. J Phys Chem A 2009; 113:12979-87. [DOI: 10.1021/jp905825q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dejun Si
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588
| | - Hui Li
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska 68588
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23
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Nicolle JLC, Simmons S, Bathe S, Norris PR. Ferrous iron oxidation and rusticyanin in halotolerant, acidophilic ‘Thiobacillus prosperus’. Microbiology (Reading) 2009; 155:1302-1309. [DOI: 10.1099/mic.0.023192-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The halotolerant acidophile ‘Thiobacillus prosperus’ was shown to require chloride for growth. With ferrous iron as substrate, growth occurred at a rate similar to that of the well-studied acidophile Acidithiobacillus ferrooxidans. Previously, the salt (NaCl) requirement of ‘T. prosperus’ was not clear and its growth on ferrous iron was described as poor. A subtractive hybridization of cDNAs from ferrous-iron-grown and sulfur-grown ‘T. prosperus’ strain V6 led to identification of a cluster of genes similar to the rus operon reported to encode ferrous iron oxidation in A. ferrooxidans. However, the ‘T. prosperus’ gene cluster did not contain a homologue of cyc1, which is thought to encode a key cytochrome c in the pathway of electron transport from ferrous iron in A. ferrooxidans. Rusticyanin, another key protein in ferrous iron oxidation by A. ferrooxidans, was present in ‘T. prosperus’ at similar concentrations in cells grown on either ferrous iron or sulfur.
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Affiliation(s)
- James Le C. Nicolle
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Susan Simmons
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Stephan Bathe
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Paul R. Norris
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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24
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Skálová T, Dohnálek J, Østergaard LH, Østergaard PR, Kolenko P, Dušková J, Štěpánková A, Hašek J. The Structure of the Small Laccase from Streptomyces coelicolor Reveals a Link between Laccases and Nitrite Reductases. J Mol Biol 2009; 385:1165-78. [DOI: 10.1016/j.jmb.2008.11.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 11/13/2008] [Accepted: 11/15/2008] [Indexed: 01/17/2023]
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25
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Ellis MJ, Grossmann JG, Eady RR, Hasnain SS. Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases. J Biol Inorg Chem 2007; 12:1119-27. [PMID: 17712582 DOI: 10.1007/s00775-007-0282-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/19/2007] [Indexed: 10/22/2022]
Abstract
Recently, the structure of a Cu-containing nitrite reductase (NiR) from Hyphomicrobium denitrificans (HdNiR) has been reported, establishing the existence of a new family of Cu-NiR where an additional type 1 Cu (T1Cu) containing cupredoxin domain is located at the N-terminus (Nojiri et al. in Proc. Natl. Acad. Sci. USA 104:4315-4320, 2007). HdNiR retains the well-characterised coupled T1Cu-type 2 Cu (T2Cu) core, where the T2Cu catalytic site is also built utilising ligands from neighbouring monomers. We have undertaken a genome analysis and found the wide occurrence of these NiRs, with members clustering in two groups, one showing an amino acid sequence similarity of around 80% with HdNiR, and a second group, including the NiR from the extremophile Acidothermus cellulolyticus, clustering around 50% similarity to HdNiR. This is reminiscent of the difference observed between the blue (Alcaligenes xylosoxidans) and green (Achromobacter cycloclastes and Alcaligenes faecalis) NiRs which have been extensively studied and may indicate that these also form two distinct subclasses of the new family. Genome analysis also showed the presence of Cu-NiRs with a C-terminal extension of 160-190 residues containing a class I cytochrome c domain with a characteristic beta-sheet extension. Currently no structural information exists for any member of this family. Genome analysis suggests the widespread occurrence of these novel NiRs with representatives in the alpha, beta and gamma subclasses of the Proteobacteria and in two species of the fungus Aspergillus. We selected the enzyme from Ralstonia pickettii for comparative modelling and produced a plausible structure highlighting an electron transfer mode in which the cytochrome c haem at the C-terminus can come within 16-A reach of the T1Cu centre of the T1Cu-T2Cu core.
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Affiliation(s)
- Mark J Ellis
- Molecular Biophysics Group, Science and Technology Facilities Council, Daresbury Laboratory, Warrington, Cheshire, UK
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26
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Zeng J, Geng M, Liu Y, Xia L, Liu J, Qiu G. The sulfhydryl group of Cys138 of rusticyanin from Acidithiobacillus ferrooxidans is crucial for copper binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:519-25. [PMID: 17395555 DOI: 10.1016/j.bbapap.2007.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 02/05/2007] [Accepted: 02/08/2007] [Indexed: 10/23/2022]
Abstract
Rusticyanin is a small blue copper protein isolated from Acidithiobacillus ferrooxidans with extreme acid stability and redox potential. The protein is thought to be a principal component in the iron respiratory electron transport chain in this microorganism, but its exact role in electron transfer remains controversial. The gene of rusticyanin was cloned then overexpressed in Escherichia coli, the soluble protein was purified by one-step affinity chromatography to apparent homogeneity. It was reported that Cys138, His85 and His143 were important residues for copper binding, but the significance of Cys138 was not verified so far. We constructed the mutant expression plasmids of these three residues using site-directed mutagenesis. Mutant proteins were expressed in E. coli and purified with a nickel metal affinity column. The EPR and atomic absorption spectroscopy results confirmed that Cys138 was crucial for copper binding. Removal of the sulfhydryl group of Cys138 resulted in copper loss. Mutations of His85 and His143 showed little effect on copper binding.
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Affiliation(s)
- Jia Zeng
- Department of Bioengineering, School of Resources Processing and Bioengineering, Central South University, Changsha, PR China
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27
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Mukhopadhyay BP, Ghosh B, Bairagya HR, Bera AK, Roy RK. Conserved Water Molecular Dynamics of the Different X-ray Structures of Rusticyanin: An Unique Aquation Potentiality of the Ligand Bonded Cu++Center. J Biomol Struct Dyn 2007; 24:369-78. [PMID: 17206852 DOI: 10.1080/07391102.2007.10507126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The invariant water molecular interaction involving in the Rusticyanin of Thiobacillus ferrooxidans is thought to be important for its molecular complexation with other proteins at differential acidophilic situation. The comparative analysis of the different x-ray, energy minimized, and auto solvated structures of Rusticyanin revealed the presence of five specific invariant bound water molecules (among the approximately 150 water molecules per monomer) in the crystals. The five W 205, W 206, W 112, W 214, and W 221 water molecules (in Rusticyanin PDB code: 1RCY) were seem to be invariant in all the seven structures (PDB codes: 1RCY, 1A3Z, 1A8Z, 1E3O, 1GY1, 1GY2, 2CAL). Among the five conserved water molecules the W 221 (of 1 RCY or the equivalent water molecules in the other oxidized form of Rusticyanin structures) had endowed an interesting coordination potentiality to Cu(+2) ion during the energy minimization. The W 221 was observed to approach toward the tetrahedrally bonded Cu(+2) ion through the opposite (or trans) route of metal-bonded Met 148. This direct water molecular coordination affected the tetrahedral geometry of Cu(+2) to trigonal bipyramidal. Presumably this structural dynamics at the Cu(+2) center could involve in the electron transport process during protein-protein complexation.
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Affiliation(s)
- B P Mukhopadhyay
- Department of Chemistry, National Institute Of Technology, Durgapur-713209, West Bengal, India.
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28
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Barrett ML, Harvey I, Sundararajan M, Surendran R, Hall JF, Ellis MJ, Hough MA, Strange RW, Hillier IH, Hasnain SS. Atomic Resolution Crystal Structures, EXAFS, and Quantum Chemical Studies of Rusticyanin and Its Two Mutants Provide Insight into Its Unusual Properties,. Biochemistry 2006; 45:2927-39. [PMID: 16503647 DOI: 10.1021/bi052372w] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rusticyanin from the extremophile Thiobacillus ferrooxidans is a blue copper protein with unusually high redox potential and acid stability. We present the crystal structures of native rusticyanin and of its Cu site mutant His143Met at 1.27 and 1.10 A, respectively. The very high resolution of these structures allows a direct comparison with EXAFS data and with quantum chemical models of the oxidized and reduced forms of the proteins, based upon both isolated and embedded clusters and density functional theory (DFT) methods. We further predict the structure of the Cu(II) form of the His143Met mutant which has been experimentally inaccessible due to its very high redox potential. We also present metrical EXAFS data and quantum chemical calculations for the oxidized and reduced states of the Met148Gln mutant, this protein having the lowest redox potential of all currently characterized mutants of rusticyanin. These data offer new insights into the structural factors which affect the redox potential in this important class of proteins. Calculations successfully predict the structure and the order of redox potentials for the three proteins. The calculated redox potential of H143M ( approximately 400 mV greater than native rusticyanin) is consistent with the failure of readily available chemical oxidants to restore a Cu(II) species of this mutant. The structural and energetic effects of mutating the equatorial cysteine to serine, yet to be studied experimentally, are predicted to be considerable by our calculations.
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Affiliation(s)
- Mark L Barrett
- School of Health and Life Sciences, De Montfort University, The Gateway, Leicester, UK
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29
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Yanagisawa S, Dennison C. Reduction Potential Tuning at a Type 1 Copper Site Does Not Compromise Electron Transfer Reactivity. J Am Chem Soc 2005; 127:16453-9. [PMID: 16305231 DOI: 10.1021/ja054426v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type 1 (T1) copper sites promote biological electron transfer (ET) and typically possess a weakly coordinated thioether sulfur from an axial Met [Cu(II)-Sdelta approximately 2.6 to 3.3 A] along with the conserved His2Cys equatorial ligands. A strong axial bond [Cu(II)-Oepsilon1 approximately 2.2 A] is sometimes provided by a Gln (as in the stellacyanins), and the axial ligand can be absent (a Val, Leu or Phe in the axial position) as in ceruloplasmin, Fet3p, fungal laccases and some plantacyanins (PLTs). Cucumber basic protein (CBP) is a PLT which has a relatively short Cu(II)-S(Met89) axial bond (2.6 A). The Met89Gln variant of CBP has an electron self-exchange (ESE) rate constant (k(ese), a measure of intrinsic ET reactivity) approximately 7 times lower than that of the wild-type protein. The Met89Val mutation to CBP results in a 2-fold increase in k(ese). As the axial interaction decreases from strong Oepsilon1 of Gln to relatively weak Sdelta of Met to no ligand (Val), ESE reactivity is therefore enhanced by approximately 1 order of magnitude while the reduction potential increases by approximately 350 mV. The variable coordination position at this ubiquitous ET site provides a mechanism for tuning the driving force to optimize ET with the correct partner without significantly compromising intrinsic reactivity. The enhanced reactivity of a three-coordinate T1 copper site will facilitate intramolecular ET in fungal laccases and Fet3p.
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Affiliation(s)
- Sachiko Yanagisawa
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, NE2 4HH, UK
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30
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Hough MA, Ellis MJ, Antonyuk S, Strange RW, Sawers G, Eady RR, Samar Hasnain S. High Resolution Structural Studies of Mutants Provide Insights into Catalysis and Electron Transfer Processes in Copper Nitrite Reductase. J Mol Biol 2005; 350:300-9. [PMID: 15927201 DOI: 10.1016/j.jmb.2005.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 04/01/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
We present high-resolution crystal structures and functional analysis of T1Cu centre mutants of nitrite reductase that perturb the redox potential and the Cys130-His129 "hard-wired" bridge through which electron transfer to the catalytic T2Cu centre occurs. These data provide insight into how activity can be altered through mutational manipulation of the electron delivery centre (T1Cu). The alteration of Cys to Ala results in loss of T1Cu and enzyme inactivation with azurin as electron donor despite the mutant enzyme retaining full nitrite-binding capacity. These data establish unequivocally that no direct transfer of electrons occurs from azurin to the catalytic type 2 Cu centre. The mutation of the axial ligand Met144 to Leu increases both the redox potential and catalytic activity, establishing that the rate-determining step of catalysis is the intermolecular electron transfer from azurin to nitrite reductase.
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Affiliation(s)
- Michael A Hough
- Molecular Biophysics Group, CCLRC Daresbury Laboratory, Warrington WA4 4AD, UK
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31
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Sato K, Crowley PB, Dennison C. Transient homodimer interactions studied using the electron self-exchange reaction. J Biol Chem 2005; 280:19281-8. [PMID: 15743773 DOI: 10.1074/jbc.m500842200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transient homodimer protein interactions have been investigated by analyzing the influence of ionic strength (NaCl) on the electron self-exchange (the bimolecular reaction whereby the two oxidation states of a redox protein interconvert) rate constant (k(ese)) of four plastocyanins. The k(ese) values for the plastocyanins from spinach, Dryopteris crassirhizoma (a fern), and the green alga Ulva pertusa, which possess acidic patches of varying size and locations, increase 190-, 29-, and 21-fold, respectively, at elevated ionic strength (I = 2.03 M). In contrast, the k(ese) for the almost neutral cyanobacterial plastocyanin from Anabaena variabilis exhibits very little dependence on ionic strength. The temperature dependence of the k(ese) for spinach plastocyanin (I = 0.28 M) provides evidence for poor packing at the homodimer interface. Representative structures of the transient homodimers involved in electron self-exchange, which are consistent with fits of the ionic strength dependence of k(ese) to van Leeuwen theory, have been obtained from protein modeling and docking simulations. The Coulombic energy of the docked homodimers follows the order spinach > D. crassirhizoma > U. pertusa > A. variabilis, which matches that of the overall influence of ionic strength on k(ese). Analysis of the homodimer structures indicates that poor packing and high planarity are features of the interface that favor transient interactions. The physiologically relevant Mg2+ ion has a much more pronounced influence on the k(ese) of spinach plastocyanin, which along with the known properties of the thylakoid lumen suggests a biological role for electron self-exchange.
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Affiliation(s)
- Katsuko Sato
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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32
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Jiménez B, Piccioli M, Moratal JM, Donaire A. Backbone dynamics of rusticyanin: the high hydrophobicity and rigidity of this blue copper protein is responsible for its thermodynamic properties. Biochemistry 2003; 42:10396-405. [PMID: 12950166 DOI: 10.1021/bi034692q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Local dynamics and solute-solvent exchange properties of rusticyanin (Rc) from Thiobacillus ferrooxidans have been studied by applying heteronuclear ((1)H, (15)N) NMR spectroscopy. (15)N relaxation parameters have been determined for the reduced protein, and a model-free analysis has been applied. The high average value of the generalized order parameter, S(2) (0.93), indicates that Rc is very rigid. The analysis of cross correlation rates recorded in both the reduced and the oxidized forms conclusively proves that Rc possesses the same dynamic features in both oxidation states. The accessibility of backbone amide protons to the solvent at different time scales has also been studied by applying specific heteronuclear pulse sequences and by H(2)O/D(2)O exchange experiments. These experiments reveal that rusticyanin is extremely hydrophobic. The first N-35 amino acids, not present in the other BCPs, protect the beta-barrel core from its interaction with the solvent, and thus, this is one of the main factors contributing to the hydrophobicity. Both characteristics (high rigidity and hydrophobicity) are maintained in the metal ion surroundings.
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Affiliation(s)
- Beatriz Jiménez
- Departamento de Química Inorgánica, Universitat de València, Burjassot, Spain
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33
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Claus H. Laccases and their occurrence in prokaryotes. Arch Microbiol 2003; 179:145-50. [PMID: 12610719 DOI: 10.1007/s00203-002-0510-7] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2002] [Revised: 11/15/2002] [Accepted: 12/02/2002] [Indexed: 10/20/2022]
Abstract
Laccases are copper-containing proteins that require O(2) to oxidize phenols, polyphenols, aromatic amines, and different non-phenolic substrates by one-electron transfer, resulting in the formation of reactive radicals. Although their specific physiological functions are not completely understood, there are several indications that laccases are involved in the morphogenesis of microorganisms (e.g., fungal spore development, melanization) and in the formation and/or degradation of complex organic substances such as lignin or humic matter. Owing to their high relative non-specific oxidation capacity, laccases are useful biocatalysts for diverse biotechnological applications. To date, laccases have been found only in eukaryotes (fungi, plants); however, databank searches and experimental data now provide evidence for their distribution in prokaryotes. This survey shows that laccase-like enzymes occur in many gram-negative and gram-positive bacteria. Corresponding genes have been found in prokaryotes that are thought to have branched off early during evolution, e.g., the extremely thermophilic Aquifex aeolicus and the archaeon Pyrobaculum aerophilum. Phylogenetically, the enzymes are members of the multi-copper protein family that have developed from small-sized prokaryotic azurins to eukaryotic plasma proteins.
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Affiliation(s)
- Harald Claus
- Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, Becherweg 15, Germany.
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34
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Donaire A, Jiménez B, Fernández CO, Pierattelli R, Niizeki T, Moratal JM, Hall JF, Kohzuma T, Hasnain SS, Vila AJ. Metal-ligand interplay in blue copper proteins studied by 1H NMR spectroscopy: Cu(II)-pseudoazurin and Cu(II)-rusticyanin. J Am Chem Soc 2002; 124:13698-708. [PMID: 12431099 DOI: 10.1021/ja0267019] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The blue copper proteins (BCPs), pseudoazurin from Achromobacter cycloclastes and rusticyanin from Thiobacillus ferrooxidans, have been investigated by (1)H NMR at a magnetic field of 18.8 T. Hyperfine shifts of the protons belonging to the coordinated ligands have been identified by exchange spectroscopy, including the indirect detection for those resonances that cannot be directly observed (the beta-CH(2) of the Cys ligand, and the NH amide hydrogen bonded to the S(gamma)(Cys) atom). These data reveal that the Cu(II)-Cys interaction in pseudoazurin and rusticyanin is weakened compared to that in classic blue sites (plastocyanin and azurin). This weakening is not induced by a stronger interaction with the axial ligand, as found in stellacyanin, but might be determined by the protein folding around the metal site. The average chemical shift of the beta-CH(2) Cys ligand in all BCPs can be correlated to geometric factors of the metal site (the Cu-S(gamma)(Cys) distance and the angle between the CuN(His)N(His) plane and the Cu-S(gamma)(Cys) vector). It is concluded that the degree of tetragonal distortion is not necessarily related to the strength of the Cu(II)-S(gamma)(Cys) bond. The copper-His interaction is similar in all BCPs, even for the solvent-exposed His ligand. It is proposed that the copper xy magnetic axes in blue sites are determined by subtle geometrical differences, particularly the orientation of the His ligands. Finally, the observed chemical shifts for beta-CH(2) Cys and Ser NH protons in rusticyanin suggest that a less negative charge at the sulfur atom could contribute to the high redox potential (680 mV) of this protein.
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Affiliation(s)
- Antonio Donaire
- Biophysics Section and Instituto de Biología Molecular y Celular de Rosario (IBR), University of Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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