1
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Babu K, Kathiresan V, Kumari P, Newsom S, Parameshwaran HP, Chen X, Liu J, Qin PZ, Rajan R. Coordinated Actions of Cas9 HNH and RuvC Nuclease Domains Are Regulated by the Bridge Helix and the Target DNA Sequence. Biochemistry 2021; 60:3783-3800. [PMID: 34757726 PMCID: PMC8675354 DOI: 10.1021/acs.biochem.1c00354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/23/2021] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas systems are RNA-guided nucleases that provide adaptive immune protection in bacteria and archaea against intruding genomic materials. Cas9, a type-II CRISPR effector protein, is widely used for gene editing applications since a single guide RNA can direct Cas9 to cleave specific genomic targets. The conformational changes associated with RNA/DNA binding are being modulated to develop Cas9 variants with reduced off-target cleavage. Previously, we showed that proline substitutions in the arginine-rich bridge helix (BH) of Streptococcus pyogenes Cas9 (SpyCas9-L64P-K65P, SpyCas92Pro) improve target DNA cleavage selectivity. In this study, we establish that kinetic analysis of the cleavage of supercoiled plasmid substrates provides a facile means to analyze the use of two parallel routes for DNA linearization by SpyCas9: (i) nicking by HNH followed by RuvC cleavage (the TS (target strand) pathway) and (ii) nicking by RuvC followed by HNH cleavage (the NTS (nontarget strand) pathway). BH substitutions and DNA mismatches alter the individual rate constants, resulting in changes in the relative use of the two pathways and the production of nicked and linear species within a given pathway. The results reveal coordinated actions between HNH and RuvC to linearize DNA, which is modulated by the integrity of the BH and the position of the mismatch in the substrate, with each condition producing distinct conformational energy landscapes as observed by molecular dynamics simulations. Overall, our results indicate that BH interactions with RNA/DNA enable target DNA discrimination through the differential use of the parallel sequential pathways driven by HNH/RuvC coordination.
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Affiliation(s)
- Kesavan Babu
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Venkatesan Kathiresan
- Department
of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, California 90089, United States
| | - Pratibha Kumari
- Department
of Pharmaceutical Sciences, University of North Texas System College
of Pharmacy, University of North Texas Health
Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United
States
| | - Sydney Newsom
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Hari Priya Parameshwaran
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Xiongping Chen
- Department
of Pharmaceutical Sciences, University of North Texas System College
of Pharmacy, University of North Texas Health
Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United
States
| | - Jin Liu
- Department
of Pharmaceutical Sciences, University of North Texas System College
of Pharmacy, University of North Texas Health
Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United
States
| | - Peter Z. Qin
- Department
of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, California 90089, United States
| | - Rakhi Rajan
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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2
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Kathiresan V, Karthik S. Efficient Detection Using Soft Computing Approach of Modified Fuzzy C-Means Based Outlier Detection in Electronics Patient Records Systems. j med imaging hlth inform 2021. [DOI: 10.1166/jmihi.2021.3857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Outliers are the data objects or data elements which are deviated from the observation or population in the dataset. Normally outliers are considered as noise data but in recent days outliers are taken vital role in the applications like healthcare systems to energetically check for
any malignant, irregular, or abnormal behaviour. Accuracy of the outlier detection is purely based upon the efficiency of outlier detection methods and application where the outlier detection is involved. In this paper we design hybrid three phase modified fuzzy c-means and diverse distance
based outlier detection method for distributed dataset to detect the unusual usage of data and illegitimate approach in large-scale integral networks, especially in healthcare sectors (EPR systems). The proposed algorithm combining the features of modified C-Means Fuzzification, Z-score and
Manhattan distance in outlier identification. The proposed algorithm provides efficiency in outlier detection on univariate EPRdata. This paper also mainly focuses the application intrusion detection in healthcare data. The algorithm is tested on real world dataset of machine learning database
repository (UCIML).
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Affiliation(s)
- V. Kathiresan
- Department of Computer Science and Engineering, Coimbatore Institute of Engineering and Technology, Coimbatore 641109, TamilNadu, India
| | - S. Karthik
- Department of Computer Science and Engineering, S.N.S College of Technology, Coimbatore 641035, TamilNadu, India
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3
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Parameshwaran HP, Babu K, Tran C, Guan K, Allen A, Kathiresan V, Qin PZ, Rajan R. The bridge helix of Cas12a imparts selectivity in cis-DNA cleavage and regulates trans-DNA cleavage. FEBS Lett 2021; 595:892-912. [PMID: 33523494 PMCID: PMC8044059 DOI: 10.1002/1873-3468.14051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 12/26/2022]
Abstract
Cas12a is an RNA-guided DNA endonuclease of the type V-A CRISPR-Cas system that has evolved convergently with the type II Cas9 protein. We previously showed that proline substitutions in the bridge helix (BH) impart target DNA cleavage selectivity in Streptococcus pyogenes (Spy) Cas9. Here, we examined a BH variant of Cas12a from Francisella novicida (FnoCas12aKD2P ) to test mechanistic conservation. Our results show that for RNA-guided DNA cleavage (cis-activity), FnoCas12aKD2P accumulates nicked products while cleaving supercoiled DNA substrates with mismatches, with certain mismatch positions being more detrimental for linearization. FnoCas12aKD2P also possess reduced trans-single-stranded DNA cleavage activity. These results implicate the BH in substrate selectivity in both cis- and trans-cleavages and show its conserved role in target discrimination among Cas nucleases.
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Affiliation(s)
- Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Christine Tran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Kevin Guan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
| | - Aleique Allen
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | | | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, OK, USA
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4
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Wang Y, Kathiresan V, Chen Y, Hu Y, Jiang W, Bai G, Liu G, Qin PZ, Fang X. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chem Sci 2020; 11:9655-9664. [PMID: 33224460 PMCID: PMC7667596 DOI: 10.1039/d0sc01717e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/19/2020] [Indexed: 12/25/2022] Open
Abstract
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date.
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron–Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.
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Affiliation(s)
- Yan Wang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Yaoyi Chen
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Wei Jiang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
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5
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Jiang W, Singh J, Allen A, Li Y, Kathiresan V, Qureshi O, Tangprasertchai N, Zhang X, Parameshwaran HP, Rajan R, Qin PZ. CRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA/DNA Complementarity. ACS Omega 2019; 4:17140-17147. [PMID: 31656887 PMCID: PMC6811856 DOI: 10.1021/acsomega.9b01469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/25/2019] [Indexed: 05/03/2023]
Abstract
Cas12a (also known as "Cpf1") is a class 2 type V-A CRISPR-associated nuclease that can cleave double-stranded DNA at specific sites. The Cas12a effector enzyme comprises a single protein and a CRISPR-encoded small RNA (crRNA) and has been used for genome editing and manipulation. Work reported here examined in vitro interactions between the Cas12a effector enzyme and DNA duplexes with varying states of base-pairing between the two strands. The data revealed that in the absence of complementarity between the crRNA guide and the DNA target-strand, Cas12a binds duplexes with unpaired segments. These off-target duplexes were bound at the Cas12a site responsible for RNA-guided double-stranded DNA binding but were not cleaved due to the lack of RNA/DNA hybrid formation. Such promiscuous binding was attributed to increased DNA flexibility induced by the unpaired segment present next to the protospacer-adjacent-motif. The results suggest that target discrimination of Cas12a can be influenced by flexibility of the DNA. As such, in addition to the linear sequence, flexibility and other physical properties of the DNA should be considered in Cas12a-based genome engineering applications.
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Affiliation(s)
- Wei Jiang
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Jaideep Singh
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Aleique Allen
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Yue Li
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Venkatesan Kathiresan
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Omair Qureshi
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Narin Tangprasertchai
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Xiaojun Zhang
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Hari Priya Parameshwaran
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Rakhi Rajan
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Peter Z. Qin
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
- E-mail: . Phone: (213) 821-2461. Fax: (213) 740-2701
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6
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Ding Y, Kathiresan V, Zhang X, Haworth IS, Qin PZ. Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes. J Phys Chem A 2019; 123:3592-3598. [PMID: 30978022 DOI: 10.1021/acs.jpca.9b01027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Measurement of distances between spectroscopic labels (e.g., spin labels, fluorophores) attached to specific sites of biomolecules is an important method for studying biomolecular complexes. ALLNOX (Addition of Labels and Linkers) has been developed as a program to model interlabel distances based on an input macromolecule structure. Here, we report validation of ALLNOX using measured distances between nitroxide spin labels attached to specific sites of a protein-DNA complex. The results demonstrate that ALLNOX predicts average interspin distances that matched with values measured with pairs of labels attached at the protein and/or DNA. This establishes a solid foundation for using spin labeling in conjunction with ALLNOX to investigate complexes without high-resolution structures. With its high degree of flexibility for the label or the target biomolecule, ALLNOX provides a useful tool for investigating the structure-function relationship in a large variety of biological molecules.
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Affiliation(s)
- Yuan Ding
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Xiaojun Zhang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Ian S Haworth
- Department of Pharmacology and Pharmaceutical Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States.,Department of Biological Sciences , University of Southern California , Los Angeles , California 90089 , United States
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7
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McWilliams SF, Bunting PC, Kathiresan V, Mercado BQ, Hoffman BM, Long JR, Holland PL. Isolation and characterization of a high-spin mixed-valent iron dinitrogen complex. Chem Commun (Camb) 2018; 54:13339-13342. [PMID: 30403226 DOI: 10.1039/c8cc07294a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a rare example of a mixed-valence iron compound with an FeNNFe core, which gives insight into the structural, spectroscopic, and magnetic influences of single-electron reductions and oxidations. In the new compound, the odd electron is localized as judged from Mössbauer spectra at 80 K and infrared spectra at room temperature, and the backbonding into the N2 unit is intermediate between diiron(i) and diiron(0) congeners. Magnetic susceptibility and relaxation studies on the series of FeNNFe compounds show significant magnetic anisotropy, but through-barrier pathways enable fairly rapid magnetic relaxation.
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Affiliation(s)
- Sean F McWilliams
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06520, USA.
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8
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Byer A, Yang H, McDaniel EC, Kathiresan V, Impano S, Pagnier A, Watts H, Denler C, Vagstad AL, Piel J, Duschene KS, Shepard EM, Shields TP, Scott LG, Lilla EA, Yokoyama K, Broderick WE, Hoffman BM, Broderick JB. Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis. J Am Chem Soc 2018; 140:8634-8638. [PMID: 29954180 PMCID: PMC6053644 DOI: 10.1021/jacs.8b04061] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an intermediate under a variety of mixing order conditions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double resonance spectroscopy establish that Ω involves an Fe-C5' bond between 5'-dAdo· and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (coenzyme B12) cofactor used to initiate radical reactions via a 5'-dAdo· intermediate. Liberation of a reactive 5'-dAdo· intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However, coenzyme B12 is involved in enzymes catalyzing only a small number (∼12) of distinct reactions, whereas the RS superfamily has more than 100 000 distinct sequences and over 80 reaction types characterized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.
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Affiliation(s)
- Amanda
S. Byer
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Hao Yang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Elizabeth C. McDaniel
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Venkatesan Kathiresan
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Stella Impano
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Adrien Pagnier
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Hope Watts
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Carly Denler
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Anna L. Vagstad
- Institute
of Microbiology, Eidgenössische Technische
Hochschule Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Jörn Piel
- Institute
of Microbiology, Eidgenössische Technische
Hochschule Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Kaitlin S. Duschene
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Thomas P. Shields
- Cassia,
LLC, 3030 Bunker Hill
Street, Ste. 214, San Diego, California 92109, United States
| | - Lincoln G. Scott
- Cassia,
LLC, 3030 Bunker Hill
Street, Ste. 214, San Diego, California 92109, United States
| | - Edward A. Lilla
- Department
of Biochemistry, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - Kenichi Yokoyama
- Department
of Biochemistry, Duke University Medical
Center, Durham, North Carolina 27710, United States
| | - William E. Broderick
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States,
| | - Joan B. Broderick
- Department
of Chemistry & Biochemistry, Montana
State University, Bozeman, Montana 59717, United States,
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9
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Dong M, Kathiresan V, Fenwick MK, Torelli AT, Zhang Y, Caranto JD, Dzikovski B, Sharma A, Lancaster KM, Freed JH, Ealick SE, Hoffman BM, Lin H. Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis. Science 2018; 359:1247-1250. [PMID: 29590073 DOI: 10.1126/science.aao6595] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 01/30/2018] [Indexed: 12/31/2022]
Abstract
Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.
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Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew T Torelli
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jonathan D Caranto
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA. .,Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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10
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Gallagher AT, Lee JY, Kathiresan V, Anderson JS, Hoffman BM, Harris TD. A structurally-characterized peroxomanganese(iv) porphyrin from reversible O 2 binding within a metal-organic framework. Chem Sci 2017; 9:1596-1603. [PMID: 29675204 PMCID: PMC5890324 DOI: 10.1039/c7sc03739b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/13/2017] [Indexed: 11/22/2022] Open
Abstract
Within a MOF, a side-on peroxomanganese(iv) porphyrin has been isolated and comprehensively examined.
The role of peroxometal species as reactive intermediates in myriad biological processes has motivated the synthesis and study of analogous molecular model complexes. Peroxomanganese(iv) porphyrin complexes are of particular interest, owing to their potential ability to form from reversible O2 binding, yet have been exceedingly difficult to isolate and characterize in molecular form. Alternatively, immobilization of metalloporphyrin sites within a metal–organic framework (MOF) can enable the study of interactions between low-coordinate metal centers and gaseous substrates, without interference from bimolecular reactions and axial ligation by solvent molecules. Here, we employ this approach to isolate the first rigorously four-coordinate manganese(ii) porphyrin complex and examine its reactivity with O2 using infrared spectroscopy, single-crystal X-ray diffraction, EPR spectroscopy, and O2 adsorption analysis. X-ray diffraction experiments reveal for the first time a peroxomanganese(iv) porphyrin species, which exhibits a side-on, η2 binding mode. Infrared and EPR spectroscopic data confirm the formulation of a peroxomanganese(iv) electronic structure, and show that O2 binding is reversible at ambient temperature, in contrast to what has been observed in molecular form. Finally, O2 gas adsorption measurements are employed to quantify the enthalpy of O2 binding as hads = –49.6(8) kJ mol–1. This enthalpy is considerably higher than in the corresponding Fe- and Co-based MOFs, and is found to increase with increasing reductive capacity of the MII/III redox couple.
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Affiliation(s)
- Audrey T Gallagher
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
| | - Jung Yoon Lee
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
| | - Venkatesan Kathiresan
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
| | - John S Anderson
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
| | - Brian M Hoffman
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
| | - T David Harris
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , IL 60208-3113 , USA .
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Kathiresan V, Subburaman S, Krishna AV, Natarajan M, Rathinasamy G, Ganesan K, Ramachandran M. Naringenin Ameliorates Doxorubicin Toxicity and Hypoxic Condition in Dalton's Lymphoma Ascites Tumor Mouse Model: Evidence from Electron Paramagnetic Resonance Imaging. J Environ Pathol Toxicol Oncol 2016; 35:249-262. [DOI: 10.1615/jenvironpatholtoxicoloncol.2016013997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mohandas K, Awang Y, Duraisamy G, Kathiresan V. Autologous blood transfusion in cardiac surgery. Med J Malaysia 1988; 43:21-7. [PMID: 3244315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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