1
|
Bonomi F, Iametti S, Barbiroli A. Protein interactions in the biological assembly of iron-sulfur clusters in Escherichia coli: Molecular and mechanistic aspects of the earliest assembly steps. IUBMB Life 2022; 74:723-732. [PMID: 35611886 PMCID: PMC9321986 DOI: 10.1002/iub.2622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/24/2022] [Indexed: 11/11/2022]
Abstract
This contribution focuses on the earliest steps of the assembly of FeS clusters and their insertion into acceptor apoproteins, that call for transient formation of a 2Fe2S cluster on a scaffold protein from sulfide and iron salts. For the sake of simplicity, this report is essentially limited to the Escherichia coli isc-encoded proteins and does not take into account agents that modulate the enzymatic synthesis of sulfide by protein in the same operon or the redox events associated with both sulfide generation and conversion of 2Fe2S structures in clusters of higher nuclearity. Therefore, the results discussed here are based on chemical reconstitution systems using inorganic sulfide, ferric salts, and excess thiols. This simplification offers the possibility to address some mechanistic issues related to the role of protein/protein interaction as for modulating: (a) the rate of cluster assembly on scaffold proteins; (b) the stability of the cluster on the scaffold protein; and (c) the rate of transfer to acceptor apoproteins as also influenced by the acceptor concentration. The emerging picture highlights the mechanistic versatility of the systems, that is discussed in terms of the capability of such an apparently simple combination of proteins to cope with various physiological situation. The hypothetical mechanism presented here may represent an additional way of modulating the rate and outcome of the overall process while avoiding potential toxicity issues.
Collapse
Affiliation(s)
- Francesco Bonomi
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Stefania Iametti
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
2
|
Iametti S, Bonomi F, Barbiroli A. Circular Dichroism to Probe the Synthesis, Transfer, and Stability of Fe-S Clusters. Methods Mol Biol 2021; 2353:209-229. [PMID: 34292552 DOI: 10.1007/978-1-0716-1605-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All Fe-S proteins are characterized by distinctive circular dichroism (CD) features in the visible region of the spectrum due to chiral interaction between the cluster itself and the protein backbone. Therefore, the presence of a CD signal in the visible region relates to the presence of the cluster, whereas the disappearance of the signal refers to cluster breakdown or redox changes. The position of the CD features in the spectrum and the intensity of individual components of the CD signal show great variations among different Fe-S proteins. This feature can provide information on transfer processes between proteins, as well as on possible changes in cluster nuclearity. This method can also be used to detect changes in the chemical nature or spatial organization of cluster ligands that may be concurrent with cluster transfer and associated events.
Collapse
Affiliation(s)
- Stefania Iametti
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy
| | - Francesco Bonomi
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy.
| | - Alberto Barbiroli
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy
| |
Collapse
|
3
|
Li J, Li H. Single molecule force spectroscopy reveals that a two-coordinate ferric site is critical for the folding of holo-rubredoxin. NANOSCALE 2020; 12:22564-22573. [PMID: 33169779 DOI: 10.1039/d0nr06275h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metalloproteins play important roles in a wide range of biological processes. The folding process of metalloproteins is complex due to the synergistic effects of the folding of their polypeptide chains and the incorporation of metal cofactors. The folding mechanism of the simplest iron-sulfur protein rubredoxin, which contains one ferric ion coordinated by four cysteinyl sulfurs, is revealed using optical tweezers for the first time. The folding of the rubredoxin polypeptide chain is rapid and robust, while the reconstitution of the iron-sulfur center is greatly dependent upon the coordination state of the ferric ion on the unfolded polypeptide chain. If the ferric ion is coordinated by two neighboring cysteines, rubredoxin can readily fold with the iron-sulfur center fully reconstituted. However, if the ferric ion is only mono-coordinated, rubredoxin can fold but the iron-sulfur center is not reconstituted. Our results suggested that the folding of holo-rubredoxin follows a novel binding-folding-reconstitution mechanism, which is distinct from the folding mechanisms proposed for the folding of metalloproteins. Our study highlights the critical importance of the two-coordinate ferric site in the folding of holo-rubredoxin, which may have some important implications to our understanding of the folding mechanism of more complex metalloproteins in vivo.
Collapse
Affiliation(s)
- Jiayu Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | | |
Collapse
|
4
|
Li J, Li H. Mechanical Unfolding Pathway of the High-Potential Iron-Sulfur Protein Revealed by Single-Molecule Atomic Force Microscopy: Toward a General Unfolding Mechanism for Iron-sulfur Proteins. J Phys Chem B 2018; 122:9340-9349. [PMID: 30212202 DOI: 10.1021/acs.jpcb.8b07614] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-potential iron-sulfur proteins (HiPIPs) are an important class of metalloproteins with a [4Fe-4S] cluster coordinated by four cysteine residues. Distinct from other iron-sulfur proteins, the cluster in HiPIP has a high reduction potential, making it an essential electron carrier in bacterial photosynthesis. Here, we combined single-molecule atomic force microscopy and protein engineering techniques to investigate the mechanical unfolding mechanism of HiPIP from Chromatium tepidum (cHiPIP). We found that cHiPIP unfolds in a two-step fashion with the protein sequence sequestered by the iron-sulfur center as a stable unfolding intermediate state. The rupture of the iron-sulfur center of cHiPIP proceeds in two distinct parallel pathways; one pathway involves the concurrent rupture of multiple iron-thiolate bonds, and the other one involves the sequential rupture of the iron-thiolate bonds. This mechanistic information was further confirmed by mutational studies. We found that the rupture of the iron-thiolate bonds in reduced and oxidized cHiPIP occurred in the range of 150-180 pN at a pulling speed of 400 nm/s, similar to that measured for iron-thiolate bonds in rubredoxin and ferredoxin. Our results may have important implications for understanding the general unfolding mechanism governing iron-sulfur proteins, as well as the mechanism governing the mechanical rupture of the iron-sulfur center.
Collapse
Affiliation(s)
- Jiayu Li
- Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada
| | - Hongbin Li
- Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada
| |
Collapse
|
5
|
Maiti BK, Maia LB, Moro AJ, Lima JC, Cordas CM, Moura I, Moura JJG. Unusual Reduction Mechanism of Copper in Cysteine-Rich Environment. Inorg Chem 2018; 57:8078-8088. [PMID: 29956539 DOI: 10.1021/acs.inorgchem.8b00121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Copper-cysteine interactions play an important role in Biology and herein we used the copper-substituted rubredoxin (Cu-Rd) from Desulfovibrio gigas to gain further insights into the copper-cysteine redox chemistry. EPR spectroscopy results are consistent with Cu-Rd harboring a CuII center in a sulfur-rich coordination, in a distorted tetrahedral structure ( g∥,⊥ = 2.183 and 2.032 and A∥,⊥ = 76.4 × 10-4 and 12 × 10-4 cm-1). In Cu-Rd, two oxidation states at Cu-center (CuII and CuI) are associated with Cys oxidation-reduction, alternating in the redox cycle, as pointed by electrochemical studies that suggest internal geometry rearrangements associated with the electron transfer processes. The midpoint potential of [CuI(S-Cys)2(Cys-S-S-Cys)]/[CuII(S-Cys)4] redox couple was found to be -0.15 V vs NHE showing a large separation of cathodic and anodic peaks potential (Δ Ep = 0.575 V). Interestingly, sulfur-rich CuII-Rd is highly stable under argon in dark conditions, which is thermodynamically unfavorable to Cu-thiol autoreduction. The reduction of copper and concomitant oxidation of Cys can both undergo two possible pathways: oxidative as well as photochemical. Under O2, CuII plays the role of the electron carrier from one Cys to O2 followed by internal geometry rearrangement at the Cu site, which facilitates reduction at Cu-center to yield CuI(S-Cys)2(Cys-S-S-Cys). Photoinduced (irradiated at λex = 280 nm) reduction of the CuII center is observed by UV-visible photolysis (above 300 nm all bands disappeared) and tryptophan fluorescence (∼335 nm peak enhanced) experiments. In both pathways, geometry reorganization plays an important role in copper reduction yielding an energetically compatible donor-acceptor system. This model system provides unusual stability and redox chemistry rather than the universal Cu-thiol auto redox chemistry in cysteine-rich copper complexes.
Collapse
Affiliation(s)
- Biplab K Maiti
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Luisa B Maia
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Artur J Moro
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - João C Lima
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - Isabel Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| | - José J G Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade Nova de Lisboa , 2829-516 Caparica , Portugal
| |
Collapse
|
6
|
Lei H, Guo Y, Hu X, Hu C, Hu X, Li H. Reversible Unfolding and Folding of the Metalloprotein Ferredoxin Revealed by Single-Molecule Atomic Force Microscopy. J Am Chem Soc 2017; 139:1538-1544. [DOI: 10.1021/jacs.6b11371] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hai Lei
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yabin Guo
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Xiaodong Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Chunguang Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiaotang Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Hongbin Li
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
7
|
Saini AK, Kumari P, Sharma V, Mathur P, Mobin SM. Varying structural motifs in the salen based metal complexes of Co(ii), Ni(ii) and Cu(ii): synthesis, crystal structures, molecular dynamics and biological activities. Dalton Trans 2016; 45:19096-19108. [DOI: 10.1039/c6dt03573f] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four new metal complexes which demonstrates varying structural motifs from monomeric to dimeric to tetrameric complexes by slightly altering the reaction conditions and their biological applications.
Collapse
Affiliation(s)
- Anoop Kumar Saini
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Pratibha Kumari
- Centre for Biosciences and Bio-Medical Engineering
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Vinay Sharma
- Centre for Biosciences and Bio-Medical Engineering
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Pradeep Mathur
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Shaikh M. Mobin
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
- Centre for Biosciences and Bio-Medical Engineering
| |
Collapse
|
8
|
Li W, Wang J, Zhang J, Wang W. Molecular simulations of metal-coupled protein folding. Curr Opin Struct Biol 2015; 30:25-31. [DOI: 10.1016/j.sbi.2014.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/24/2014] [Accepted: 11/24/2014] [Indexed: 01/22/2023]
|
9
|
Zheng P, Wang Y, Li H. Reversible Unfolding-Refolding of Rubredoxin: A Single-Molecule Force Spectroscopy Study. Angew Chem Int Ed Engl 2014; 53:14060-3. [DOI: 10.1002/anie.201408105] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Indexed: 11/11/2022]
|
10
|
Zheng P, Wang Y, Li H. Reversible Unfolding-Refolding of Rubredoxin: A Single-Molecule Force Spectroscopy Study. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
11
|
Miriani M, Iametti S, Kurtz DM, Bonomi F. Rubredoxin refolding on nanostructured hydrophobic surfaces: evidence for a new type of biomimetic chaperones. Proteins 2014; 82:3154-62. [PMID: 25143010 DOI: 10.1002/prot.24675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/04/2014] [Accepted: 08/11/2014] [Indexed: 11/08/2022]
Abstract
Rubredoxins (Rds) are small proteins containing a tetrahedral Fe(SCys)4 site. Folded forms of metal free Rds (apoRds) show greatly impaired ability to incorporate iron compared with chaotropically unfolded apoRds. In this study, formation of the Rd holoprotein (holoRd) on addition of iron to a structured, but iron-uptake incompetent apoRd was investigated in the presence of polystyrene nanoparticles (NP). In our rationale, hydrophobic contacts between apoRd and the NP surface would expose protein regions (including ligand cysteines) buried in the structured apoRd, allowing iron incorporation and folding to the native holoRd. Burial of the hydrophobic regions in the folded holoRd would allow its detachment from the NP surface. We found that both rate and yield of holoRd formation increased significantly in the presence of NP and were influenced by the NP concentration and size. Rates and yields had an optimum at "catalytic" NP concentrations (0.2 g/L NP) when using relatively small NP (46 nm diameter). At these optimal conditions, only a fraction of the apoRd was bound to the NP, consistent with the occurrence of turnover events on the NP surface. Lower rates and yields at higher NP concentrations or when using larger NP (200 nm) suggest that steric effects and molecular crowding on the NP surface favor specific "iron-uptake-competent" conformations of apoRd on the NP surface. This bio-mimetic chaperone system may be applicable to other proteins requiring an unfolding step before cofactor-triggered refolding, particularly when over-expressed under limited cofactor accessibility.
Collapse
Affiliation(s)
- Matteo Miriani
- Section of Chemistry and Biomolecular Sciences, DeFENS, University of Milan, Milan, Italy
| | | | | | | |
Collapse
|
12
|
Schwaid AG, Shannon DA, Ma J, Slavoff SA, Levin JZ, Weerapana E, Saghatelian A. Chemoproteomic discovery of cysteine-containing human short open reading frames. J Am Chem Soc 2013; 135:16750-3. [PMID: 24152191 PMCID: PMC3868496 DOI: 10.1021/ja406606j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The application of ribosome profiling and mass spectrometry technologies has recently revealed that the human proteome is larger than previously appreciated. Short open reading frames (sORFs), which are difficult to identify using traditional gene-finding algorithms, constitute a significant fraction of unknown protein-coding genes. Thus, experimental approaches to identify sORFs provide invaluable insight into the protein-coding potential of genomes. Here, we report an affinity-based approach to enrich and identify cysteine-containing human sORF-encoded polypeptides (ccSEPs) from cells. This approach revealed 16 novel ccSEPs, each derived from an uncharacterized sORF, demonstrating its potential for discovering new genes. We validated expression of a SEP from its endogenous RNA, and demonstrated the specificity of our labeling approach using synthetic SEP. The discovery of additional human SEPs and their conservation indicate the potential importance of these molecules in biology.
Collapse
Affiliation(s)
- Adam G. Schwaid
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - D. Alexander Shannon
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Jiao Ma
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Sarah A. Slavoff
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Joshua Z. Levin
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Eranthie Weerapana
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| |
Collapse
|
13
|
Yan R, Adinolfi S, Iannuzzi C, Kelly G, Oregioni A, Martin S, Pastore A. Cluster and fold stability of E. coli ISC-type ferredoxin. PLoS One 2013; 8:e78948. [PMID: 24265733 PMCID: PMC3827102 DOI: 10.1371/journal.pone.0078948] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/22/2013] [Indexed: 11/25/2022] Open
Abstract
Iron-sulfur clusters are essential protein prosthetic groups that provide their redox potential to several different metabolic pathways. Formation of iron-sulfur clusters is assisted by a specialised machine that comprises, among other proteins, a ferredoxin. As a first step to elucidate the precise role of this protein in cluster assembly, we have studied the factors governing the stability and the dynamic properties of E. coli ferredoxin using different spectroscopic techniques. The cluster-loaded protein is monomeric and well structured with a flexible C-terminus but is highly oxygen sensitive so that it readily loses the cluster leading to an irreversible unfolding under aerobic conditions. This process is slowed down by reducing conditions and high ionic strengths. NMR relaxation experiments on the cluster-loaded protein also show that, once the cluster is in place, the protein forms a globular and relatively rigid domain. These data indicate that the presence of the iron-sulfur cluster is the switch between a functional and a non-functional state.
Collapse
Affiliation(s)
- Robert Yan
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Salvatore Adinolfi
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Clara Iannuzzi
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Geoff Kelly
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Alain Oregioni
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Stephen Martin
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Annalisa Pastore
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| |
Collapse
|
14
|
Zheng P, Takayama SIJ, Mauk AG, Li H. Single Molecule Force Spectroscopy Reveals That Iron Is Released from the Active Site of Rubredoxin by a Stochastic Mechanism. J Am Chem Soc 2013; 135:7992-8000. [DOI: 10.1021/ja402150q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia V6T 1Z1, Canada
| | - Shin-ichi J. Takayama
- Department of Biochemistry and
Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British
Columbia V6T 1Z3, Canada
| | - A. Grant Mauk
- Department of Biochemistry and
Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British
Columbia V6T 1Z1, Canada
| |
Collapse
|
15
|
Caranto JD, Gebhardt LL, MacGowan CE, Limberger RJ, Kurtz DM. Treponema denticola superoxide reductase: in vivo role, in vitro reactivities, and a novel [Fe(Cys)(4)] site. Biochemistry 2012; 51:5601-10. [PMID: 22715932 DOI: 10.1021/bi300667s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In vitro and in vivo results are presented demonstrating that superoxide reductase (SOR) from the air-sensitive oral spirochete, Treponema denticola (Td), is a principal enzymatic scavenger of superoxide in this organism. This SOR contains the characteristic non-heme [Fe(His)(4)Cys] active sites. No other metal-binding domain has been annotated for Td SOR. However, we found that Td SOR also accommodates a [Fe(Cys)(4)] site whose spectroscopic and redox properties resemble those in so-called 2Fe-SORs. Spectroscopic comparisons of the wild type and engineered Cys → Ser variants indicate that three of the Cys ligands correspond to those in [Fe(Cys)(4)] sites of "canonical" 2Fe-SORs, whereas the fourth Cys ligand residue has no counterpart in canonical 2Fe-SORs or in any other known [Fe(Cys)(4)] protein. Structural modeling is consistent with iron ligation of the "noncanonical" Cys residue across subunit interfaces of the Td SOR homodimer. The Td SOR was isolated with only a small percentage of [Fe(Cys)(4)] sites. However, quantitative formation of stable [Fe(Cys)(4)] sites was readily achieved by exposing the as-isolated protein to an iron salt, a disulfide reducing agent and air. The disulfide/dithiol status and iron occupancy of the Td SOR [Fe(Cys)(4)] sites could, thus, reflect intracellular redox status, particularly during periods of oxidative stress.
Collapse
Affiliation(s)
- Jonathan D Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | | | | | | | | |
Collapse
|
16
|
Lai M, Yam KC, Andrews D, Hill BC. Copper binding traps the folded state of the SCO protein from Bacillus subtilis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:292-302. [DOI: 10.1016/j.bbapap.2011.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/15/2011] [Accepted: 10/10/2011] [Indexed: 11/29/2022]
|
17
|
Kaluarachchi H, Siebel JF, Kaluarachchi-Duffy S, Krecisz S, Sutherland DEK, Stillman MJ, Zamble DB. Metal selectivity of the Escherichia coli nickel metallochaperone, SlyD. Biochemistry 2011; 50:10666-77. [PMID: 22047179 DOI: 10.1021/bi2014882] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SlyD is a Ni(II)-binding protein that contributes to nickel homeostasis in Escherichia coli. The C-terminal domain of SlyD contains a rich variety of metal-binding amino acids, suggesting broader metal binding capabilities, and previous work demonstrated that the protein can coordinate several types of first-row transition metals. However, the binding of SlyD to metals other than Ni(II) has not been previously characterized. To improve our understanding of the in vitro metal-binding activity of SlyD and how it correlates with the in vivo function of this protein, the interactions between SlyD and the series of biologically relevant transition metals [Mn(II), Fe(II), Co(II), Cu(I), and Zn(II)] were examined by using a combination of optical spectroscopy and mass spectrometry. Binding of SlyD to Mn(II) or Fe(II) ions was not detected, but the protein coordinates multiple ions of Co(II), Zn(II), and Cu(I) with appreciable affinity (K(D) values in or below the nanomolar range), highlighting the promiscuous nature of this protein. The order of affinities of SlyD for the metals examined is as follows: Mn(II) and Fe(II) < Co(II) < Ni(II) ~ Zn(II) ≪ Cu(I). Although the purified protein is unable to overcome the large thermodynamic preference for Cu(I) and exclude Zn(II) chelation in the presence of Ni(II), in vivo studies reveal a Ni(II)-specific function for the protein. Furthermore, these latter experiments support a specific role for SlyD as a [NiFe]-hydrogenase enzyme maturation factor. The implications of the divergence between the metal selectivity of SlyD in vitro and the specific activity in vivo are discussed.
Collapse
Affiliation(s)
- Harini Kaluarachchi
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
| | | | | | | | | | | | | |
Collapse
|
18
|
Botelho HM, Gomes CM. Structural reorganization renders enhanced metalloprotein stability. Chem Commun (Camb) 2011; 47:11149-51. [PMID: 21894348 DOI: 10.1039/c1cc13354c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enhanced stability of a mesophilic metalloprotein was assessed using biophysical spectroscopies. Significant local structural interconversions during thermal insult account for a reorganization of the protein scaffold, without disturbing the active metal site. This cushioning mechanism is proposed to be a generic property of metalloproteins contributing to enhanced stability.
Collapse
Affiliation(s)
- Hugo M Botelho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, EAN 2785-572, Oeiras, Portugal
| | | |
Collapse
|
19
|
Zheng P, Li H. Direct measurements of the mechanical stability of zinc-thiolate bonds in rubredoxin by single-molecule atomic force microscopy. Biophys J 2011; 101:1467-73. [PMID: 21943428 DOI: 10.1016/j.bpj.2011.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/28/2011] [Accepted: 08/09/2011] [Indexed: 01/09/2023] Open
Abstract
Zinc (Zn) is one of the most abundant metals and is essential for life. Through ligand interactions, often with thiolate from cysteine residues in proteins, Zn can play important structural roles in organizing protein structure and augmenting protein folding and stability. However, it is difficult to separate the contributions of Zn-ligand interactions from those originating from intrinsic protein folding in experimental studies of Zn-containing metalloproteins, which makes the study of Zn-ligand interactions in proteins challenging. Here, we used single-molecule force spectroscopy to directly measure the mechanical rupture force of the Zn-thiolate bond in Zn-rubredoxin. Our results show that considerable force is needed to rupture Zn-thiolate bonds (~170 pN, which is significantly higher than the force necessary to rupture the coordination bond between Zn and histidines). To our knowledge, our study not only provides new information about Zn-thiolate bonds in rubredoxin, it also opens a new avenue for studying metal-ligand bonds in proteins using single-molecule force spectroscopy.
Collapse
Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | |
Collapse
|