1
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Chen A, Re RN, Davis TD, Tran K, Moriuchi YW, Wu S, La Clair JJ, Louie GV, Bowman ME, Clarke DJ, Mackay CL, Campopiano DJ, Noel JP, Burkart MD. Visualizing the Interface of Biotin and Fatty Acid Biosynthesis through SuFEx Probes. J Am Chem Soc 2024; 146:1388-1395. [PMID: 38176024 DOI: 10.1021/jacs.3c10181] [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: 01/06/2024]
Abstract
Site-specific covalent conjugation offers a powerful tool to identify and understand protein-protein interactions. In this study, we discover that sulfur fluoride exchange (SuFEx) warheads effectively crosslink the Escherichia coli acyl carrier protein (AcpP) with its partner BioF, a key pyridoxal 5'-phosphate (PLP)-dependent enzyme in the early steps of biotin biosynthesis by targeting a tyrosine residue proximal to the active site. We identify the site of crosslink by MS/MS analysis of the peptide originating from both partners. We further evaluate the BioF-AcpP interface through protein crystallography and mutational studies. Among the AcpP-interacting BioF surface residues, three critical arginine residues appear to be involved in AcpP recognition so that pimeloyl-AcpP can serve as the acyl donor for PLP-mediated catalysis. These findings validate an evolutionary gain-of-function for BioF, allowing the organism to build biotin directly from fatty acid biosynthesis through surface modifications selective for salt bridge formation with acidic AcpP residues.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Rebecca N Re
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Kelley Tran
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Yuta W Moriuchi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Sitong Wu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - David J Clarke
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Dominic J Campopiano
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
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2
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Jiang Z, Chen A, Chen J, Sekhon A, Louie GV, Noel JP, La Clair JJ, Burkart MD. Masked cerulenin enables a dual-site selective protein crosslink. Chem Sci 2023; 14:10925-10933. [PMID: 37829009 PMCID: PMC10566503 DOI: 10.1039/d3sc02864j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023] Open
Abstract
Protein-reactive natural products such as the fungal metabolite cerulenin are recognized for their value as therapeutic candidates, due to their ability to selectively react with catalytic residues within a protein active site or a complex of protein domains. Here, we explore the development of fatty-acid and polyketide-synthase probes by synthetically modulating cerulenin's functional moieties. Using a mechanism-based approach, we reveal unique reactivity within cerulenin and adapt it for fluorescent labeling and crosslinking of fatty-acid and iterative type-I polyketide synthases. We also describe two new classes of silylcyanohydrin and silylhemiaminal masked crosslinking probes that serve as new tools for activity and structure studies of these biosynthetic pathways.
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Affiliation(s)
- Ziran Jiang
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Jeffrey Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Arman Sekhon
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Gordon V Louie
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - Joseph P Noel
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
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3
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Loscalzo J. Molecular interaction networks and drug development: Novel approach to drug target identification and drug repositioning. FASEB J 2023; 37:e22660. [PMID: 36468661 PMCID: PMC10107166 DOI: 10.1096/fj.202201683r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/27/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
Conventional drug discovery requires identifying a protein target believed to be important for disease mechanism and screening compounds for those that beneficially alter the target's function. While this approach has been an effective one for decades, recent data suggest that its continued success is limited largely owing to the highly prevalent irreducibility of biologically complex systems that govern disease phenotype to a single primary disease driver. Network medicine, a new discipline that applies network science and systems biology to the analysis of complex biological systems and disease, offers a novel approach to overcoming these limitations of conventional drug discovery. Using the comprehensive protein-protein interaction network (interactome) as the template through which subnetworks that govern specific diseases are identified, potential disease drivers are unveiled and the effect of novel or repurposed drugs, used alone or in combination, is studied. This approach to drug discovery offers new and exciting unbiased possibilities for advancing our knowledge of disease mechanisms and precision therapeutics.
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Affiliation(s)
- Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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4
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Marincin KA, Hwang Y, Kengmana ES, Meyers DJ, Frueh DP. NMR as a readout to monitor and restore the integrity of complex chemoenzymatic reactions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107265. [PMID: 35849973 PMCID: PMC9463103 DOI: 10.1016/j.jmr.2022.107265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The non-invasive nature of NMR offers a means to monitor biochemical reactions in situ at the atomic level. We harness this advantage to monitor a complex chemoenzymatic reaction that sequentially modifies reagents and loads the product on a nonribosomal peptide synthetase carrier protein. We present a protocol including a pulse sequence that permits to assess both the integrity of reagents and the completion of each step in the reaction, thus alleviating otherwise time-consuming and costly approaches to debug and repeat inefficient reactions. This study highlights the importance of NMR as a tool to establish reliable and reproducible experimental conditions in biochemical studies.
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Affiliation(s)
- Kenneth A Marincin
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences Synthetic Core Facility, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Everett S Kengmana
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Whiting School of Engineering, Baltimore, MD 21218, USA
| | - David J Meyers
- Department of Pharmacology and Molecular Sciences Synthetic Core Facility, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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5
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Lv Z, Ma W, Zhang P, Lu Z, Zhou L, Meng F, Wang Z, Bie X. Deletion of COM donor and acceptor domains and the interaction between modules in bacillomycin D produced by Bacillus amyloliquefaciens. Synth Syst Biotechnol 2022; 7:989-1001. [PMID: 35782484 PMCID: PMC9213223 DOI: 10.1016/j.synbio.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | - Xiaomei Bie
- Corresponding author. Nanjing Agr Univ, Coll Food Sci & Technol, Nanjing, 210095, PR China.
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6
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McErlean M, Overbay J, Van Lanen S. Refining and expanding nonribosomal peptide synthetase function and mechanism. J Ind Microbiol Biotechnol 2019; 46:493-513. [PMID: 30673909 PMCID: PMC6460464 DOI: 10.1007/s10295-018-02130-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are involved in the biosynthesis of numerous peptide and peptide-like natural products that have been exploited in medicine, agriculture, and biotechnology, among other fields. As a consequence, there have been considerable efforts aimed at understanding how NRPSs orchestrate the assembly of these natural products. This review highlights several recent examples that continue to expand upon the fundamental knowledge of NRPS mechanism and includes (1) the discovery of new NRPS substrates and the mechanism by which these sometimes structurally complex substrates are made, (2) the characterization of new NRPS activities and domains that function during the process of peptide assembly, and (3) the various catalytic strategies that are utilized to release the NRPS product. These findings continue to strengthen the predictive power for connecting genes to products, thereby facilitating natural product discovery and development in the Genomics Era.
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Affiliation(s)
- Matt McErlean
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Jonathan Overbay
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Steven Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA.
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7
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Kim WE, Patel A, Hur GH, Tufar P, Wuo MG, McCammon JA, Burkart MD. Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases. Chembiochem 2018; 20:147-152. [PMID: 30194895 DOI: 10.1002/cbic.201800439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Indexed: 11/12/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are responsible for the synthesis of a variety of bioactive natural products with clinical and economic significance. Interestingly, these large multimodular enzyme machineries incorporate nonproteinogenic d-amino acids through the use of auxiliary epimerization domains, converting l-amino acids into d-amino acids that impart into the resulting natural products unique bioactivity and resistance to proteases. Due to the large and complex nature of NRPSs, several questions remain unanswered about the mechanism of the catalytic domain reactions. We have investigated the use of mechanism-based crosslinkers to probe the mechanism of an epimerization domain in gramicidin S biosynthesis. In addition, MD simulations were performed, showcasing the possible roles of catalytic residues within the epimerization domain.
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Affiliation(s)
- Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0636, USA
| | - Gene H Hur
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Peter Tufar
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Michael G Wuo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0636, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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8
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Schomer RA, Park H, Barkei JJ, Thomas MG. Alanine Scanning of YbdZ, an MbtH-like Protein, Reveals Essential Residues for Functional Interactions with Its Nonribosomal Peptide Synthetase Partner EntF. Biochemistry 2018; 57:4125-4134. [PMID: 29921120 DOI: 10.1021/acs.biochem.8b00552] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are megasynthetases that require complex and specific interactions between multiple domains and proteins to functionally produce a metabolite. MbtH-like proteins (MLPs) are integral components of many NRPSs and interact directly with the adenylation domain of the megasynthetases to stimulate functional enzymology. All of the MLP residues that are essential for functional interactions between the MLP and NRPS have yet to be defined. Here we probe the interactions between YbdZ, an MLP, and EntF, an NRPS, from Escherichia coli by performing a complete alanine scan of YbdZ. A phenotypic screen identified 11 YbdZ variants that are unable to replace the wild-type MLP, and these YbdZ variants were characterized using a series of in vivo and in vitro assays in an effort to explain why functional interactions with EntF were disrupted. All of the YbdZ variants enhanced the solubility of overproduced EntF, suggesting they were still capable of direct interactions with the megasynthase. Conversely, we show that EntF also influences the solubility of YbdZ and its variants. In vitro biochemical analyses of EntF function with each of the YbdZ variants found the impact that an amino acid substitution will have on NRPS function is difficult to predict, highlighting the complex interaction between these proteins.
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Affiliation(s)
- Rebecca A Schomer
- Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Hyunjun Park
- Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - John J Barkei
- Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Michael G Thomas
- Department of Bacteriology , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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9
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Skiba MA, Maloney FP, Dan Q, Fraley AE, Aldrich CC, Smith JL, Brown WC. PKS-NRPS Enzymology and Structural Biology: Considerations in Protein Production. Methods Enzymol 2018; 604:45-88. [PMID: 29779664 PMCID: PMC5992914 DOI: 10.1016/bs.mie.2018.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
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Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
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10
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Miyanaga A, Kudo F, Eguchi T. Protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrid assembly lines. Nat Prod Rep 2018; 35:1185-1209. [DOI: 10.1039/c8np00022k] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrids are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Fumitaka Kudo
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Tadashi Eguchi
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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11
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Kittilä T, Cryle MJ. An enhanced chemoenzymatic method for loading substrates onto carrier protein domains. Biochem Cell Biol 2017; 96:372-379. [PMID: 29172027 DOI: 10.1139/bcb-2017-0275] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) machineries produce many medically relevant peptides that cannot be easily accessed by chemical synthesis. Thus, understanding NRPS mechanism is of crucial importance to allow efficient redesign of these machineries to produce new compounds. During NRPS-mediated synthesis, substrates are covalently attached to peptidyl carrier proteins (PCPs), and studies of NRPSs are impeded by difficulties in producing PCPs loaded with substrates. Different approaches to load substrates onto PCP domains have been described, but all suffer from difficulties in either the complexity of chemical synthesis or low enzymatic efficiency. Here, we describe an enhanced chemoenzymatic loading method that combines 2 approaches into a single, highly efficient one-pot loading reaction. First, d-pantetheine and ATP are converted into dephospho-coenzyme A via the actions of 2 enzymes from coenzyme A (CoA) biosynthesis. Next, phosphoadenylates are dephosphorylated using alkaline phosphatase to allow linker attachment to PCP domain by Sfp mutant R4-4, which is inhibited by phosphoadenylates. This route does not depend on activity of the commonly problematic dephospho-CoA kinase and, therefore, offers an improved method for substrate loading onto PCP domains.
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Affiliation(s)
- Tiia Kittilä
- a Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J Cryle
- a Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,b The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,c EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
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12
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Yang L, Chumsae C, Kaplan JB, Moulton KR, Wang D, Lee DH, Zhou ZS. Detection of Alkynes via Click Chemistry with a Brominated Coumarin Azide by Simultaneous Fluorescence and Isotopic Signatures in Mass Spectrometry. Bioconjug Chem 2017; 28:2302-2309. [DOI: 10.1021/acs.bioconjchem.7b00354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lihua Yang
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Chris Chumsae
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Jenifer B. Kaplan
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Kevin Ryan Moulton
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Dongdong Wang
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - David H. Lee
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Zhaohui Sunny Zhou
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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13
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Fratila RM, Navascuez M, Idiago-López J, Eceiza M, Miranda JI, Aizpurua JM, de la Fuente JM. Covalent immobilisation of magnetic nanoparticles on surfaces via strain-promoted azide–alkyne click chemistry. NEW J CHEM 2017. [DOI: 10.1039/c7nj01822c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report a new family of clickable cyclooctynyl magnetic nanoparticles suitable for bioorthogonal click chemistry applications.
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Affiliation(s)
- Raluca M. Fratila
- Institute of Materials Science of Aragón (ICMA – CSIC/University of Zaragoza)
- Zaragoza
- Spain
- Centro de Investigación Biomédica en red en Bioingenieria Biomateriales y Nanomedicina (CIBER-BBN)
- Zaragoza
| | - Marcos Navascuez
- Institute of Materials Science of Aragón (ICMA – CSIC/University of Zaragoza)
- Zaragoza
- Spain
| | - Javier Idiago-López
- Institute of Materials Science of Aragón (ICMA – CSIC/University of Zaragoza)
- Zaragoza
- Spain
| | - Maite Eceiza
- José Mari Korta R&D Center
- Basque Country University
- UPV/EHU
- Donostia-San Sebastián
- Spain
| | - José I. Miranda
- José Mari Korta R&D Center
- Basque Country University
- UPV/EHU
- Donostia-San Sebastián
- Spain
| | - Jesús M. Aizpurua
- José Mari Korta R&D Center
- Basque Country University
- UPV/EHU
- Donostia-San Sebastián
- Spain
| | - Jesús M. de la Fuente
- Institute of Materials Science of Aragón (ICMA – CSIC/University of Zaragoza)
- Zaragoza
- Spain
- Centro de Investigación Biomédica en red en Bioingenieria Biomateriales y Nanomedicina (CIBER-BBN)
- Zaragoza
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14
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Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases. Cell Chem Biol 2016; 23:331-9. [PMID: 26991102 DOI: 10.1016/j.chembiol.2016.02.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/03/2016] [Accepted: 02/19/2016] [Indexed: 01/24/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.
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15
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Ulrich V, Cryle MJ. SNaPe: a versatile method to generate multiplexed protein fusions using synthetic linker peptides for in vitro applications. J Pept Sci 2016; 23:16-27. [PMID: 27910178 DOI: 10.1002/psc.2943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/26/2016] [Accepted: 11/06/2016] [Indexed: 11/10/2022]
Abstract
Understanding the structure and function of protein complexes and multi-domain proteins is highly important in biology, although the in vitro characterization of these systems is often complicated by their size or the transient nature of protein/protein interactions. To assist in the characterization of such protein complexes, we have developed a modular approach to fusion protein generation that relies upon Sortase-mediated and Native chemical ligation using synthetic Peptide linkers (SNaPe) to link two separately expressed proteins. In this approach, we utilize two separate linking steps - sortase-mediated and native chemical ligation - together with a library of peptide linkers to generate libraries of fusion proteins. We have demonstrated the viability of SNaPe to generate libraries from fusion protein constructs taken from the biosynthetic enzymes responsible for late stage aglycone assembly during glycopeptide antibiotic biosynthesis. Crucially, SNaPe was able to generate fusion proteins that are inaccessible via direct expression of the fusion construct itself. This highlights the advantages of SNaPe to not only access fusion proteins that have been previously unavailable for biochemical and structural characterization but also to do so in a manner that enables the linker itself to be controlled as an experimental parameter of fusion protein generation. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Veronika Ulrich
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.,EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia.,The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia
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16
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Mapping of the Communication-Mediating Interface in Nonribosomal Peptide Synthetases Using a Genetically Encoded Photocrosslinker Supports an Upside-Down Helix-Hand Motif. J Mol Biol 2016; 428:4345-4360. [DOI: 10.1016/j.jmb.2016.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/07/2016] [Accepted: 09/09/2016] [Indexed: 12/28/2022]
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17
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Zeng J, Wagner DT, Zhang Z, Moretto L, Addison JD, Keatinge-Clay AT. Portability and Structure of the Four-Helix Bundle Docking Domains of trans-Acyltransferase Modular Polyketide Synthases. ACS Chem Biol 2016; 11:2466-74. [PMID: 27362945 DOI: 10.1021/acschembio.6b00345] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The polypeptides of multimodular polyketide synthases self-assemble into biosynthetic factories. While the docking domains that mediate the assembly of cis-acyltransferase polyketide synthase polypeptides are well-studied, those of the more recently discovered trans-acyltransferase polyketide synthases have just started to be described. Located at the C- and N-termini of many polypeptides, these 25-residue, two-helix, pseudosymmetric motifs noncovalently connect domains both between and within modules. Domains expressed with their natural, cognate docking motifs formed complexes stable to size-exclusion chromatography with 1-10 μM dissociation constants as measured by isothermal titration calorimetry. Deletion and swapping experiments demonstrate portability of the docking motifs. A 1.72 Å-resolution structure of the N-terminal portion of the macrolactin synthase polypeptide MlnE shows an uncomplexed N-terminal docking motif to be preorganized in the conformation it assumes within the docking domain complex.
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Affiliation(s)
- Jia Zeng
- Department of Molecular Biosciences and ‡Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Drew T. Wagner
- Department of Molecular Biosciences and ‡Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhicheng Zhang
- Department of Molecular Biosciences and ‡Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Luisa Moretto
- Department of Molecular Biosciences and ‡Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Janci D. Addison
- Department of Molecular Biosciences and ‡Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences and ‡Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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18
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Chen WH, Li K, Guntaka NS, Bruner SD. Interdomain and Intermodule Organization in Epimerization Domain Containing Nonribosomal Peptide Synthetases. ACS Chem Biol 2016; 11:2293-303. [PMID: 27294598 DOI: 10.1021/acschembio.6b00332] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nonribosomal peptide synthetases are large, complex multidomain enzymes responsible for the biosynthesis of a wide range of peptidic natural products. Inherent to synthetase chemistry is the thioester templated mechanism that relies on protein/protein interactions and interdomain dynamics. Several questions related to structure and mechanism remain to be addressed, including the incorporation of accessory domains and intermodule interactions. The inclusion of nonproteinogenic d-amino acids into peptide frameworks is a common and important modification for bioactive nonribosomal peptides. Epimerization domains, embedded in nonribosomal peptide synthetases assembly lines, catalyze the l- to d-amino acid conversion. Here we report the structure of the epimerization domain/peptidyl carrier protein didomain construct from the first module of the cyclic peptide antibiotic gramicidin synthetase. Both holo (phosphopantethiene post-translationally modified) and apo structures were determined, each representing catalytically relevant conformations of the two domains. The structures provide insight into domain-domain recognition, substrate delivery during the assembly line process, in addition to the structural organization of homologous condensation domains, canonical players in all synthetase modules.
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Affiliation(s)
- Wei-Hung Chen
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Kunhua Li
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Naga Sandhya Guntaka
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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19
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Kokona B, Winesett ES, Nikolai von Krusenstiern A, Cryle MJ, Fairman R, Charkoudian LK. Probing the selectivity of β-hydroxylation reactions in non-ribosomal peptide synthesis using analytical ultracentrifugation. Anal Biochem 2016; 495:42-51. [DOI: 10.1016/j.ab.2015.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 12/17/2022]
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20
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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21
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Kitamura M, Kawasaki F, Ogawa K, Nakanishi S, Tanaka H, Yamada K, Kunishima M. Role of linkers in tertiary amines that mediate or catalyze 1,3,5-triazine-based amide-forming reactions. J Org Chem 2014; 79:3709-14. [PMID: 24650172 DOI: 10.1021/jo500376m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We studied 1,3,5-triazine-based amide-forming reactions that are mediated or catalyzed by various tert-amines. The representative tert-amine was trimethylamine, which has amido, 1,2,3-triazolyl, aryl, and alkyl linkers. It was found that electron-deficient aryl and heteroaryl linkers, particularly 1,2,3-triazolyl linkers, are superior. On the basis of our findings, we synthesized ligand catalysts, including a 1,2,3-triazolyl linker that connects a protein ligand to a trimethylamine moiety, and found that fluorescent-labeling of a targeting protein using the ligand catalysts proceeded in good yields.
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Affiliation(s)
- Masanori Kitamura
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical, and Health Sciences, Kanazawa University , Kakuma-machi, Kanazawa 920-1192, Japan
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22
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Crystal structures of the first condensation domain of CDA synthetase suggest conformational changes during the synthetic cycle of nonribosomal peptide synthetases. J Mol Biol 2013; 425:3137-50. [PMID: 23756159 DOI: 10.1016/j.jmb.2013.06.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/26/2013] [Accepted: 06/03/2013] [Indexed: 11/24/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large modular macromolecular machines that produce small peptide molecules with wide-ranging biological activities, such as antibiotics and green chemicals. The condensation (C) domain is responsible for amide bond formation, the central chemical step in nonribosomal peptide synthesis. Here we present two crystal structures of the first condensation domain of the calcium-dependent antibiotic (CDA) synthetase (CDA-C1) from Streptomyces coelicolor, determined at resolutions 1.8Å and 2.4Å. The conformations adopted by CDA-C1 are quite similar in these two structures yet distinct from those seen in other NRPS C domain structures. HPLC-based reaction assays show that this CDA-C1 construct is catalytically active, and small-angle X-ray scattering experiments suggest that the conformation observed in these crystal structures could faithfully represent the conformation in solution. We have performed targeted molecular dynamics simulations, normal mode analyses and energy-minimized linear interpolation to investigate the conformational changes required to transition between the observed structures. We discuss the implications of these conformational changes in the synthetic cycle and of the observation that the "latch" that covers the active site is consistently formed in all studied C domains.
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23
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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24
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Hur GH, Vickery CR, Burkart MD. Explorations of catalytic domains in non-ribosomal peptide synthetase enzymology. Nat Prod Rep 2012; 29:1074-98. [PMID: 22802156 DOI: 10.1039/c2np20025b] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Many pharmaceuticals on the market today belong to a large class of natural products called nonribosomal peptides (NRPs). Originating from bacteria and fungi, these peptide-based natural products consist not only of the 20 canonical L-amino acids, but also non-proteinogenic amino acids, heterocyclic rings, sugars, and fatty acids, generating tremendous chemical diversity. As a result, these secondary metabolites exhibit a broad array of bioactivity, ranging from antimicrobial to anticancer. The biosynthesis of these complex compounds is carried out by large multimodular megaenzymes called nonribosomal peptide synthetases (NRPSs). Each module is responsible for incorporation of a monomeric unit into the natural product peptide and is composed of individual domains that perform different catalytic reactions. Biochemical and bioinformatic investigations of these enzymes have uncovered the key principles of NRP synthesis, expanding the pharmaceutical potential of their enzymatic processes. Progress has been made in the manipulation of this biosynthetic machinery to develop new chemoenzymatic approaches for synthesizing novel pharmaceutical agents with increased potency. This review focuses on the recent discoveries and breakthroughs in the structural elucidation, molecular mechanism, and chemical biology underlying the discrete domains within NRPSs.
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25
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Hudak JE, Barfield RM, de Hart GW, Grob P, Nogales E, Bertozzi CR, Rabuka D. Synthesis of Heterobifunctional Protein Fusions Using Copper-Free Click Chemistry and the Aldehyde Tag. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108130] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Hudak JE, Barfield RM, de Hart GW, Grob P, Nogales E, Bertozzi CR, Rabuka D. Synthesis of heterobifunctional protein fusions using copper-free click chemistry and the aldehyde tag. Angew Chem Int Ed Engl 2012; 51:4161-5. [PMID: 22407566 PMCID: PMC3379715 DOI: 10.1002/anie.201108130] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Indexed: 01/16/2023]
Affiliation(s)
- Jason E Hudak
- Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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27
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van Geel R, Pruijn GJM, van Delft FL, Boelens WC. Preventing Thiol-Yne Addition Improves the Specificity of Strain-Promoted Azide–Alkyne Cycloaddition. Bioconjug Chem 2012; 23:392-8. [DOI: 10.1021/bc200365k] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Remon van Geel
- Biomolecular
Chemistry and ‡Synthetic Organic Chemistry, Nijmegen Center for Molecular
Life Sciences, Institute for Molecules and Materials and Netherlands Proteomics Centre, Radboud University
Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- Biomolecular
Chemistry and ‡Synthetic Organic Chemistry, Nijmegen Center for Molecular
Life Sciences, Institute for Molecules and Materials and Netherlands Proteomics Centre, Radboud University
Nijmegen, The Netherlands
| | - Floris L. van Delft
- Biomolecular
Chemistry and ‡Synthetic Organic Chemistry, Nijmegen Center for Molecular
Life Sciences, Institute for Molecules and Materials and Netherlands Proteomics Centre, Radboud University
Nijmegen, The Netherlands
| | - Wilbert C. Boelens
- Biomolecular
Chemistry and ‡Synthetic Organic Chemistry, Nijmegen Center for Molecular
Life Sciences, Institute for Molecules and Materials and Netherlands Proteomics Centre, Radboud University
Nijmegen, The Netherlands
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28
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Clifford-Nunn B, Showalter HDH, Andrews PC. Quaternary diamines as mass spectrometry cleavable crosslinkers for protein interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:201-12. [PMID: 22131227 PMCID: PMC3573217 DOI: 10.1007/s13361-011-0288-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/20/2011] [Accepted: 10/22/2011] [Indexed: 05/11/2023]
Abstract
Mapping protein interactions and their dynamics is crucial to defining physiologic states, building effective models for understanding cell function, and to allow more effective targeting of new drugs. Crosslinking studies can estimate the proximity of proteins, determine sites of protein-protein interactions, and have the potential to provide a snapshot of dynamic interactions by covalently locking them in place for analysis. Several major challenges are associated with the use of crosslinkers in mass spectrometry, particularly in complex mixtures. We describe the synthesis and characterization of a MS-cleavable crosslinker containing cyclic amines, which address some of these challenges. The DC4 crosslinker contains two intrinsic positive charges, which allow crosslinked peptides to fragment into their component peptides by collision-induced dissociation (CID) or in-source decay. Initial fragmentation events result in cleavage on either side of the positive charges so crosslinked peptides are identified as pairs of ions separated by defined masses. The structures of the component peptides can then be robustly determined by MS(3) because their fragmentation products rearrange to generate a mobile proton. The DC4 crosslinking reagent is stable to storage, highly reactive, highly soluble (1 M solutions), quite labile to CID, and MS(3) results in productive backbone fragmentation.
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Affiliation(s)
- Billy Clifford-Nunn
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, USA
| | - H. D. Hollis Showalter
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan Vahlteich Medicinal Chemistry Core, Ann Arbor, MI, USA
| | - Philip C. Andrews
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Room 1198, 300 North Ingalls Building, 300 North Ingalls St., Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
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29
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Liu Y, Zheng T, Bruner SD. Structural basis for phosphopantetheinyl carrier domain interactions in the terminal module of nonribosomal peptide synthetases. CHEMISTRY & BIOLOGY 2011; 18:1482-8. [PMID: 22118682 PMCID: PMC3238681 DOI: 10.1016/j.chembiol.2011.09.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/14/2011] [Accepted: 09/26/2011] [Indexed: 01/07/2023]
Abstract
Phosphopantetheine-modified carrier domains play a central role in the template-directed, biosynthesis of several classes of primary and secondary metabolites. Fatty acids, polyketides, and nonribosomal peptides are constructed on multidomain enzyme assemblies using phosphopantetheinyl thioester-linked carrier domains to traffic and activate building blocks. The carrier domain is a dynamic component of the process, shuttling pathway intermediates to sequential enzyme active sites. Here, we report an approach to structurally fix carrier domain/enzyme constructs suitable for X-ray crystallographic analysis. The structure of a two-domain construct of Escherichia coli EntF was determined with a conjugated phosphopantetheinyl-based inhibitor. The didomain structure is locked in an active orientation relevant to the chemistry of nonribosomal peptide biosynthesis. This structure provides details into the interaction of phosphopantetheine arm with the carrier domain and the active site of the thioesterase domain.
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Affiliation(s)
- Ye Liu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts USA 02167
| | - Tengfei Zheng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts USA 02167
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA 32611,Correspondence: Steven Bruner, , (352) 392-0525
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30
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Wong FT, Jin X, Mathews II, Cane DE, Khosla C. Structure and mechanism of the trans-acting acyltransferase from the disorazole synthase. Biochemistry 2011; 50:6539-48. [PMID: 21707057 DOI: 10.1021/bi200632j] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 1.51 Å resolution X-ray crystal structure of the trans-acyltransferase (AT) from the "AT-less" disorazole synthase (DSZS) and that of its acetate complex at 1.35 Å resolution are reported. Separately, comprehensive alanine-scanning mutagenesis of one of its acyl carrier protein substrates (ACP1 from DSZS) led to the identification of a conserved Asp45 residue on the ACP, which contributes to the substrate specificity of this unusual enzyme. Together, these experimental findings were used to derive a model for the selective association of the DSZS AT and its ACP substrate. With a goal of structurally characterizing the AT-ACP interface, a strategy was developed for covalently cross-linking the active site Ser → Cys mutant of the DSZS AT to its ACP substrate and for purifying the resulting AT-ACP complex to homogeneity. The S86C DSZS AT mutant was found to be functional, albeit with a transacylation efficiency 200-fold lower than that of its wild-type counterpart. Our findings provide new insights as well as new opportunities for high-resolution analysis of an important protein-protein interface in polyketide synthases.
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Affiliation(s)
- Fong T Wong
- Department of Chemical Engineering, Department of Chemistry, and §Department of Biochemistry, Stanford University , Stanford, California 94305, United States
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31
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Debets MF, van der Doelen CWJ, Rutjes FPJT, van Delft FL. Azide: a unique dipole for metal-free bioorthogonal ligations. Chembiochem 2010; 11:1168-84. [PMID: 20455238 DOI: 10.1002/cbic.201000064] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covalently bound azide on a (small) organic molecule or a (large) biomolecular structure has proven an important handle for bioconjugation. Azides are readily introduced, small, and stable, yet undergo smooth ligation with a range of reactive probes under mild conditions. In particular, the potential of azides to undergo metal-free reactions with strained unsaturated systems has inspired the development of an increasing number of reactive probes, which are comprehensively summarized here. For each individual probe, the synthetic preparation is described, together with reaction kinetics and the full range of applications, from materials science to glycoprofiling. Finally, a qualitative and quantitative comparison of azido-reactive probes is provided.
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Affiliation(s)
- Marjoke F Debets
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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32
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33
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Jewett JC, Bertozzi CR. Cu-free click cycloaddition reactions in chemical biology. Chem Soc Rev 2010; 39:1272-9. [PMID: 20349533 DOI: 10.1039/b901970g] [Citation(s) in RCA: 1254] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal chemical reactions are paving the way for new innovations in biology. These reactions possess extreme selectivity and biocompatibility, such that their participating reagents can form covalent bonds within richly functionalized biological systems--in some cases, living organisms. This tutorial review will summarize the history of this emerging field, as well as recent progress in the development and application of bioorthogonal copper-free click cycloaddition reactions.
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Affiliation(s)
- John C Jewett
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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34
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Park KD, Stables JP, Liu R, Kohn H. Proteomic searches comparing two (R)-lacosamide affinity baits: An electrophilic arylisothiocyanate and a photoactivated arylazide group. Org Biomol Chem 2010; 8:2803-13. [PMID: 20405068 DOI: 10.1039/c000987c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have advanced a novel strategy to search for lacosamide ((R)-1) targets in the brain proteome where protein binding is expected to be modest. Our approach used lacosamide agents containing affinity bait (AB) and chemical reporter (CR) units. The affinity bait moiety is designed to irreversibly react with the target, and the CR group permits protein detection and capture. In this study, we report the preparation and evaluation of (R)-N-(4-azido)benzyl 2-acetamido-3-(prop-2-ynyloxy)propionamide ((R)-3) and show that this compound exhibits potent anticonvulsant activities in the MES seizure model in rodents. We compared the utility of (R)-3 with its isostere, (R)-N-(4-isothiocyanato)benzyl 2-acetamido-3-(prop-2-ynyloxy)propionamide ((R)-2), in proteomic studies designed to identify potential (R)-1 targets. We showed that despite the two-fold improved anticonvulsant activity of (R)-3 compared with (R)-2, (R)-2 was superior in revealing potential binding targets in the mouse brain soluble proteome. The difference in these agents utility has been attributed to the reactivity of the affinity baits (i.e., (R)-2: aryl isothiocyanate moiety; (R)-3: photoactivated aryl azide intermediates) in the irreversible protein modification step, and we conclude that this factor is a critical determinant of successful target detection where ligand (drug) binding is modest. The utility of (R)-2 and (R)-3 in in situ proteome studies is explored.
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Affiliation(s)
- Ki Duk Park
- Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
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35
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Tosin M, Betancor L, Stephens E, Ariel Li WM, Spencer JB, Leadlay PF. Synthetic Chain Terminators Off-Load Intermediates from a Type I Polyketide Synthase. Chembiochem 2010; 11:539-46. [DOI: 10.1002/cbic.200900772] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Meier JL, Burkart MD. The chemical biology of modular biosynthetic enzymes. Chem Soc Rev 2009; 38:2012-45. [DOI: 10.1039/b805115c] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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