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Khoury F, Su Z, Banta S. Rare Earth Element Binding and Recovery by a Beta Roll-Forming RTX Domain. Inorg Chem 2024; 63:13223-13230. [PMID: 38986039 DOI: 10.1021/acs.inorgchem.4c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
The Block V of the RTX domain of the adenylate cyclase protein from Bordetella pertussis is disordered, and upon binding eight calcium ions, it folds into a beta roll domain with a C-terminal capping group. Due to their similar ionic radii and coordination geometries, trivalent lanthanide ions have been used to probe and identify calcium-binding sites in many proteins. Here, we report using a FRET-based assay that the RTX domain can bind rare earth elements (REEs) with higher affinities than calcium. The apparent disassociation constants for lanthanide ions ranged from 20 to 75 μM, which are an order of magnitude higher than the affinity for calcium, with a higher selectivity toward heavy REEs over light REEs. Most proteins release bound ions at mildly acidic conditions (pH 5-6), and the high affinity REE-binding lanmodulin protein can bind 3-4 REE ions at pH as low as ∼2.5. Circular dichroism (CD) spectra of the RTX domain demonstrate pH-induced folding of the beta roll domain in the absence of ions, indicating that protonation of key amino acids enables structure formation in low pH solutions. The beta roll domain coordinates up to four ions in extreme pH conditions (pH < 1), as determined by equilibrium ultrafiltration experiments. Finally, to demonstrate a potential application of the RTX domain, REE ions (Nd3+ and Dy3+) were recovered from other non-REEs (Fe2+ and Co2+) in a NdFeB magnet simulant solution (at pH 6).
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Affiliation(s)
- Farid Khoury
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Zihang Su
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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Wang H, Chen G, Li H. Templated folding of the RTX domain of the bacterial toxin adenylate cyclase revealed by single molecule force spectroscopy. Nat Commun 2022; 13:2784. [PMID: 35589788 PMCID: PMC9120197 DOI: 10.1038/s41467-022-30448-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
Abstract
The RTX (repeats-in-toxin) domain of the bacterial toxin adenylate cyclase (CyaA) contains five RTX blocks (RTX-i to RTX-v) and its folding is essential for CyaA’s functions. It was shown that the C-terminal capping structure of RTX-v is critical for the whole RTX to fold. However, it is unknown how the folding signal transmits within the RTX domain. Here we use optical tweezers to investigate the interplay between the folding of RTX-iv and RTX-v. Our results show that RTX-iv alone is disordered, but folds into a Ca2+-loaded-β-roll structure in the presence of a folded RTX-v. Folding trajectories of RTX-iv-v reveal that the folding of RTX-iv is strictly conditional upon the folding of RTX-v, suggesting that the folding of RTX-iv is templated by RTX-v. This templating effect allows RTX-iv to fold rapidly, and provides significant mutual stabilization. Our study reveals a possible mechanism for transmitting the folding signal within the RTX domain. The authors use optical tweezers to show that the folding of repeats-in-toxin (RTX) block-iv in adenylate cyclase is templated by the folded RTX block-v. The findings suggest a possible mechanism for transmitting the folding signal in the RTX domain.
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Affiliation(s)
- Han Wang
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.,State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, 300072, Tianjin, P. R. China
| | - Guojun Chen
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
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Bulutoglu B, Banta S. Calcium-Dependent RTX Domains in the Development of Protein Hydrogels. Gels 2019; 5:E10. [PMID: 30823512 PMCID: PMC6473919 DOI: 10.3390/gels5010010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022] Open
Abstract
The RTX domains found in some pathogenic proteins encode repetitive peptide sequences that reversibly bind calcium and fold into the unique the β-roll secondary structure. Several of these domains have been studied in isolation, yielding key insights into their structure/function relationships. These domains are increasingly being used in protein engineering applications, where the calcium-induced control over structure can be exploited to gain new functions. Here we review recent advances in the use of RTX domains in the creation of calcium responsive biomaterials.
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Affiliation(s)
- Beyza Bulutoglu
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA.
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA.
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Abdallah W, Solanki K, Banta S. Insertion of a Calcium-Responsive β-Roll Domain into a Thermostable Alcohol Dehydrogenase Enables Tunable Control over Cofactor Selectivity. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03809] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Walaa Abdallah
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Kusum Solanki
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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Liu L, Wang H, Han Y, Lv S, Chen J. Using single molecule force spectroscopy to facilitate a rational design of Ca2+-responsive β-roll peptide-based hydrogels. J Mater Chem B 2018; 6:5303-5312. [DOI: 10.1039/c8tb01511b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mechanical stability of Ca2+-responsive β-roll peptides (RTX) is largely responsible for the Ca2+-dependent mechanical properties of the RTX-based hydrogels.
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Affiliation(s)
- Lichao Liu
- State Key Laboratory of Organic–Inorganic Composite Materials
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Han Wang
- Department of Chemistry
- The University of British Columbia
- Vancouver
- Canada
| | - Yueying Han
- State Key Laboratory of Organic–Inorganic Composite Materials
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shanshan Lv
- State Key Laboratory of Organic–Inorganic Composite Materials
- Beijing University of Chemical Technology
- Beijing 100029
- China
- Department of Chemistry
| | - Jianfeng Chen
- State Key Laboratory of Organic–Inorganic Composite Materials
- Beijing University of Chemical Technology
- Beijing 100029
- China
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Bulutoglu B, Banta S. Block V RTX Domain of Adenylate Cyclase from Bordetella pertussis: A Conformationally Dynamic Scaffold for Protein Engineering Applications. Toxins (Basel) 2017; 9:E289. [PMID: 28926974 PMCID: PMC5618222 DOI: 10.3390/toxins9090289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/27/2023] Open
Abstract
The isolated Block V repeats-in-toxin (RTX) peptide domain of adenylate cyclase (CyaA) from Bordetella pertussis reversibly folds into a β-roll secondary structure upon calcium binding. In this review, we discuss how the conformationally dynamic nature of the peptide is being engineered and employed as a switching mechanism to mediate different protein functions and protein-protein interactions. The peptide has been used as a scaffold for diverse applications including: a precipitation tag for bioseparations, a cross-linking domain for protein hydrogel formation and as an alternative scaffold for biomolecular recognition applications. Proteins and peptides such as the RTX domains that exhibit natural stimulus-responsive behavior are valuable building blocks for emerging synthetic biology applications.
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Affiliation(s)
- Beyza Bulutoglu
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA.
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Structural and functional dissection reveals distinct roles of Ca2+-binding sites in the giant adhesin SiiE of Salmonella enterica. PLoS Pathog 2017; 13:e1006418. [PMID: 28558023 PMCID: PMC5466336 DOI: 10.1371/journal.ppat.1006418] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 06/09/2017] [Accepted: 05/18/2017] [Indexed: 11/20/2022] Open
Abstract
The giant non-fimbrial adhesin SiiE of Salmonella enterica mediates the first contact to the apical site of epithelial cells and enables subsequent invasion. SiiE is a 595 kDa protein composed of 53 repetitive bacterial immunoglobulin (BIg) domains and the only known substrate of the SPI4-encoded type 1 secretion system (T1SS). The crystal structure of BIg50-52 of SiiE revealed two distinct Ca2+-binding sites per BIg domain formed by conserved aspartate or glutamate residues. In a mutational analysis Ca2+-binding sites were disrupted by aspartate to serine exchange at various positions in the BIg domains of SiiE. Amounts of secreted SiiE diminish with a decreasing number of intact Ca2+-binding sites. BIg domains of SiiE contain distinct Ca2+-binding sites, with type I sites being similar to other T1SS-secreted proteins and type II sites newly identified in SiiE. We functionally and structurally dissected the roles of type I and type II Ca2+-binding sites in SiiE, as well as the importance of Ca2+-binding sites in various positions of SiiE. Type I Ca2+-binding sites were critical for efficient secretion of SiiE and a decreasing number of type I sites correlated with reduced secretion. Type II sites were less important for secretion, stability and surface expression of SiiE, however integrity of type II sites in the C-terminal portion was required for the function of SiiE in mediating adhesion and invasion. The interaction of Salmonella enterica with polarized epithelial cells depends on the function of SiiE, a 595 kDa adhesin containing 53 repeats of a bacterial immunoglobulin (BIg) domain. SiiE is secreted and surface-expressed by a cognate type I secretion system (T1SS). We found that BIg domains contain amino acid (aa) residues forming binding sites for Ca2+ ions. Two types of Ca2+-binding sites can be distinguished, termed type I and type II sites. We performed a structural and functional dissection of Ca2+-binding sites of SiiE. After mutation of aa residues forming type I and/or type II Ca2+-binding sites, we investigated the secretion, surface expression and function as adhesin for interaction with polarized epithelial cells of the SiiE variants. We found that Ca2+-binding sites are critical for supporting the secretion of SiiE. Integrity of type I sites in any position of SiiE is essential for efficient secretion and surface expression. In contrast integrity of type II sites is less important for secretion. However, loss of type II in the C-terminal, most distal portion of SiiE ablated SiiE-mediated adhesion, while loss of the type II sites in middle or N-terminal portions of SiiE had less or no effect on SiiE function. We propose a novel mechanism of Ca2+-dependent secretion and conformational fine tuning of SiiE as a large T1SS substrate with a central role in the interaction of S. enterica with host cells.
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Masin J, Osickova A, Sukova A, Fiser R, Halada P, Bumba L, Linhartova I, Osicka R, Sebo P. Negatively charged residues of the segment linking the enzyme and cytolysin moieties restrict the membrane-permeabilizing capacity of adenylate cyclase toxin. Sci Rep 2016; 6:29137. [PMID: 27581058 PMCID: PMC5007505 DOI: 10.1038/srep29137] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/15/2016] [Indexed: 11/10/2022] Open
Abstract
The whooping cough agent, Bordetella pertussis, secretes an adenylate cyclase toxin-hemolysin (CyaA) that plays a crucial role in host respiratory tract colonization. CyaA targets CR3-expressing cells and disrupts their bactericidal functions by delivering into their cytosol an adenylate cyclase enzyme that converts intracellular ATP to cAMP. In parallel, the hydrophobic domain of CyaA forms cation-selective pores that permeabilize cell membrane. The invasive AC and pore-forming domains of CyaA are linked by a segment that is unique in the RTX cytolysin family. We used mass spectrometry and circular dichroism to show that the linker segment forms α-helical structures that penetrate into lipid bilayer. Replacement of the positively charged arginine residues, proposed to be involved in target membrane destabilization by the linker segment, reduced the capacity of the toxin to translocate the AC domain across cell membrane. Substitutions of negatively charged residues then revealed that two clusters of negative charges within the linker segment control the size and the propensity of CyaA pore formation, thereby restricting the cell-permeabilizing capacity of CyaA. The ‘AC to Hly-linking segment’ thus appears to account for the smaller size and modest cell-permeabilizing capacity of CyaA pores, as compared to typical RTX hemolysins.
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Affiliation(s)
- Jiri Masin
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Adriana Osickova
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Anna Sukova
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Radovan Fiser
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Irena Linhartova
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Radim Osicka
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
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Tang NC, Chilkoti A. Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins. NATURE MATERIALS 2016; 15:419-24. [PMID: 26726995 PMCID: PMC4809025 DOI: 10.1038/nmat4521] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/25/2015] [Indexed: 05/08/2023]
Abstract
Most genes are synthesized using seamless assembly methods that rely on the polymerase chain reaction (PCR). However, PCR of genes encoding repetitive proteins either fails or generates nonspecific products. Motivated by the need to efficiently generate new protein polymers through high-throughput gene synthesis, here we report a codon-scrambling algorithm that enables the PCR-based gene synthesis of repetitive proteins by exploiting the codon redundancy of amino acids and finding the least-repetitive synonymous gene sequence. We also show that the codon-scrambling problem is analogous to the well-known travelling salesman problem, and obtain an exact solution to it by using De Bruijn graphs and a modern mixed integer linear programme solver. As experimental proof of the utility of this approach, we use it to optimize the synthetic genes for 19 repetitive proteins, and show that the gene fragments are amenable to PCR-based gene assembly and recombinant expression.
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Affiliation(s)
- Nicholas C Tang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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