1
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Tsai CY, Chen PH, Chen AL, Wang TSA. Spatiotemporal Investigation of Intercellular Heterogeneity via Multiple Photocaged Probes. Chemistry 2023; 29:e202301067. [PMID: 37382047 DOI: 10.1002/chem.202301067] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/03/2023] [Revised: 06/14/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
Intercellular heterogeneity occurs widely under both normal physiological environments and abnormal disease-causing conditions. Several attempts to couple spatiotemporal information to cell states in a microenvironment were performed to decipher the cause and effect of heterogeneity. Furthermore, spatiotemporal manipulation can be achieved with the use of photocaged/photoactivatable molecules. Here, we provide a platform to spatiotemporally analyze differential protein expression in neighboring cells by multiple photocaged probes coupled with homemade photomasks. We successfully established intercellular heterogeneity (photoactivable ROS trigger) and mapped the targets (directly ROS-affected cells) and bystanders (surrounding cells), which were further characterized by total proteomic and cysteinomic analysis. Different protein profiles were shown between bystanders and target cells in both total proteome and cysteinome. Our strategy should expand the toolkit of spatiotemporal mapping for elucidating intercellular heterogeneity.
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Affiliation(s)
- Chun-Yi Tsai
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
| | - Po-Hsun Chen
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
| | - Ai-Lin Chen
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
| | - Tsung-Shing Andrew Wang
- Department of Chemistry, National Taiwan University and Center for, Emerging Material and Advanced Devices, National Taiwan University, Taipei, 10617, Taiwan (R.O.C
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2
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Wang TSA, Zhang YW, Chen HA, Lin ST, Lee HM. Constructing pH-Responsive and Tunable Azo-Phenol-Based o-Nitrobenzyl Photocages. Chemistry 2023:e202300884. [PMID: 37154791 DOI: 10.1002/chem.202300884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
Multiple triggered-release strategies are widely utilized to control the release of caged target molecules. Among them, photocages with conditional triggers provide extra layers of control in photorelease. In this work, we designed a series of pH-responsive photocages that could be triggered under irradiation and specific intracellular pH values. We conjugated the pH-sensitive phenolic groups with o-nitrobenzyl (oNB) to form azo-phenolic NPX photocages with tunable pKa. Our azo-phenol-based oNB photocages showed differentiable photoreleasing profiles at pH 5.0, 7.2 and 9.0. By attaching fluorogenic cargos, we were able to show that one of the photocages, NPdiCl, could be used to differentiate between acidic pH 5.0 and neutral pH 7.2 in cells under artificial pH conditions. Finally, we demonstrated that NPdiCl is a promising pH-responsive photocage for photoreleasing cargo inside acidic tumor cells.
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Affiliation(s)
- Tsung-Shing Andrew Wang
- National Taiwan University College of Science, Department of Chemistry, No. 1, Sec. 4, Roosevelt Road, 10617, Taipei, TAIWAN
| | - Ya-Wen Zhang
- National Taiwan University College of Science, Department of Chemistry, TAIWAN
| | - Huai-An Chen
- Institute of Chemistry Academia Sinica, Institute of Chemistry, TAIWAN
| | - Shiou-Ting Lin
- National Taiwan University College of Science, Department of Chemistry, TAIWAN
| | - Hsien-Ming Lee
- Institute of Chemistry Academia Sinica, Institute of Chemistry, TAIWAN
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3
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Io WS, Wang TSA. A Versatile Strategy to Manipulate and Probe Native Carbonic Anhydrases In Cellulo Utilizing Two-Step Ligand-Directed Functionalization. ACS Chem Biol 2023; 18:1208-1217. [PMID: 37122236 DOI: 10.1021/acschembio.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Elucidating the biological logistics and functional interplay of proteins in their natural context has long been a great challenge in biological research. Chemical modification of proteins allows understanding of their roles and their interactions. Over decades, numerous strategies have been developed to modify target proteins with desired probes in test tubes and even biological systems. Nevertheless, these approaches require the design and synthesis of different probes for different applications, even for the same target protein, which is very time- and labor-consuming. Herein, we developed a general two-step protein functionalization strategy that utilizes ligand-directed chemistry to modify a clickable tag on the intact protein in the first step. Then, the desired functional moiety can be conjugated onto the target protein via a simple bioorthogonal click reaction in the second step, thus achieving probing and activity regulation of the target protein. In this work, carbonic anhydrase (CA) was chosen as our model protein for functionalization. We successfully labeled endogenous CAs with fluorophores to allow cellular imaging. In addition, a photoswitchable ligand was conjugated to CAs such that its activity could be manipulated in a light-responsive manner.
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Affiliation(s)
- Wai-Seng Io
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (R.O.C.)
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4
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Hung HM, Wang TSA. A Double Photocage Strategy to Construct Light-Controllable and Spatiotemporally Trackable Cathepsin B Activity-Based Probes. ACS Chem Biol 2022; 17:11-16. [PMID: 34965108 DOI: 10.1021/acschembio.1c00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Utilizing multiple cages to selectively modulate the activity of biomolecules is indispensable to achieving controllable and trackable activity manipulation. However, trackable cages that can be used to monitor the activation of biomolecules are rare. In this work, we utilized a double photocage strategy to achieve light-controllable and spatiotemporally trackable activation. To demonstrate biological applicability, we used the well-known cancer cell biomarker cathepsin B as the target and constructed double photocaged cathepsin B activity-based probe 2PPG-FK-AcRha that performed well in cancer cell cultures. Using our probe, we could monitor the light-activation by the blue fluorescence of 7-diethylamino-4-hydroxymethyl-coumarin (DEACM) and simultaneously probe the activity of cathepsin B through the green fluorescence of acetyl rhodamine (AcRha). Additionally, by partially irradiating the cell cultures, the regional photoactivation experiments also demonstrated great spatial controllability and trackability of our probe.
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Affiliation(s)
- Hsuan-Min Hung
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Tsung-Shing Andrew Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan, Republic of China
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5
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Wang TSA, Chen PL, Chen YCS, Hung HM, Huang JY. Selectively Targeting and Differentiating Vancomycin-Resistant Staphylococcus aureus via Dual Synthetic Fluorescent Probes. ACS Infect Dis 2021; 7:2584-2590. [PMID: 34410687 DOI: 10.1021/acsinfecdis.1c00235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Many Staphylococcus bacteria are pathogenic and harmful to humans. Noticeably, some Staphylococcus, including vancomycin-resistant S. aureus (VRSA), have become notoriously resistant to antibiotics and have spread rapidly, becoming threats to public health. Here, we designed a dual fluorescent probe scheme combining siderophores and antibiotics as the guiding units to selectively target VRSA and vancomycin-sensitive S. aureus (VSSA) in complex bacterial samples. Siderophore-mediated iron uptake is the key pathway by which S. aureus acquires iron in limited environments. Therefore, the siderophore-derivative probe could differentiate between S. aureus and other bacteria. Moreover, by fine-tuning the vancomycin-derivative probes, we could selectively target only VSSA, further differentiating VRSA and VSSA. Finally, by combining the siderophore-derivative probe and the vancomycin-derivative probe, we successfully targeted and differentiated between VRSA and VSSA in complicated bacterial mixtures.
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Affiliation(s)
| | - Pin-Lung Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (R.O.C.)
| | - Yi-Chen Sarah Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (R.O.C.)
| | - Hsuan-Min Hung
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (R.O.C.)
| | - Jhih-Yi Huang
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (R.O.C.)
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6
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Fan CH, Wei KC, Chiu NH, Liao EC, Wang HC, Wu RY, Ho YJ, Chan HL, Wang TSA, Huang YZ, Hsieh TH, Lin CH, Lin YC, Yeh CK. Sonogenetic-Based Neuromodulation for the Amelioration of Parkinson's Disease. Nano Lett 2021; 21:5967-5976. [PMID: 34264082 DOI: 10.1021/acs.nanolett.1c00886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sonogenetics is a promising strategy allowing the noninvasive and selective activation of targeted neurons in deep brain regions; nevertheless, its therapeutic outcome for neurodegeneration diseases that need long-term treatment remains to be verified. We previously enhanced the ultrasound (US) sensitivity of targeted cells by genetic modification with an engineered auditory-sensing protein, mPrestin (N7T, N308S). In this study, we expressed mPrestin in the dopaminergic neurons of the substantia nigra in Parkinson's disease (PD) mice and used 0.5 MHz US for repeated and localized brain stimulation. The mPrestin expression in dopaminergic neurons persisted for at least 56 days after a single shot of adeno-associated virus, suggesting that the period of expression was long enough for US treatment in mice. Compared to untreated mice, US stimulation ameliorated the dopaminergic neurodegeneration 10-fold and mitigated the PD symptoms of the mice 4-fold, suggesting that this sonogenetic strategy has the clinical potential to treat neurodegenerative diseases.
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Affiliation(s)
| | - Kuo-Chen Wei
- New Taipei Municipal TuCheng Hospital, New Taipei City 236017, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan 33305, Taiwan
| | | | | | | | - Ruo-Yu Wu
- Department of Chemistry, National Taiwan University, Taipei 106319, Taiwan
| | | | | | | | | | | | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei 106319, Taiwan
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7
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Wang TSA, Wu RY, Hong Y, Wang ZC, Li TL, Shie JJ, Hsu CC. Labeling and Characterization of Phenol-Containing Glycopeptides Using Chemoselective Probes with Isotope Tags. Chembiochem 2021; 22:2415-2419. [PMID: 33915022 DOI: 10.1002/cbic.202100169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/29/2021] [Indexed: 11/07/2022]
Abstract
Secondary metabolites are structurally diverse natural products (NPs) and have been widely used for medical applications. Developing new tools to enrich NPs can be a promising solution to isolate novel NPs from the native and complex samples. Here, we developed native and deuterated chemoselective labeling probes to target phenol-containing glycopeptides by the ene-type labeling used in proteomic research. The clickable azido-linker was included for further biotin functionalization to facilitate the enrichment of labeled substrates. Afterward, our chemoselective method, in conjunction with LC-MS and MSn analysis, was demonstrated in bacterial cultures. A vancomycin-related phenol-containing glycopeptide was labeled and characterized by our labeling strategy, showing its potential in glycopeptide discovery in complex environments.
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Affiliation(s)
- Tsung-Shing Andrew Wang
- Department of Chemistry, College of Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan (R.O.C
| | - Ruo-Yu Wu
- Department of Chemistry, College of Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan (R.O.C
| | - Yu Hong
- Department of Chemistry, College of Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan (R.O.C
| | - Zhe-Chong Wang
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 115, Taiwan (R.O.C
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 115, Taiwan (R.O.C
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nankang, Taipei, 115, Taiwan (R.O.C
| | - Cheng-Chih Hsu
- Department of Chemistry, College of Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan (R.O.C
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8
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Chung HH, Kao CY, Wang TSA, Chu J, Pei J, Hsu CC. Reaction Tracking and High-Throughput Screening of Active Compounds in Combinatorial Chemistry by Tandem Mass Spectrometry Molecular Networking. Anal Chem 2021; 93:2456-2463. [PMID: 33416326 DOI: 10.1021/acs.analchem.0c04481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Combinatorial synthesis has been widely used as an efficient strategy to screen for active compounds. Mass spectrometry is the method of choice in the identification of hits resulting from high-throughput screenings due to its high sensitivity, specificity, and speed. However, manual data processing of mass spectrometry data, especially for structurally diverse products in combinatorial chemistry, is extremely time-consuming and one of the bottlenecks in this process. In this study, we demonstrated the effectiveness of a tandem mass spectrometry molecular networking-based strategy for product identification, reaction dynamics monitoring, and active compound targeting in combinatorial synthesis. Molecular networking connects compounds with similar tandem mass spectra into a cluster and has been widely used in natural products analysis. We show that both the expected and side products can be readily characterized using molecular networking based on their mass spectrometry fragmentation patterns. Additionally, time-dependent molecular networking was integrated to track reaction dynamics to determine the optimal reaction time to maximize target product yields. We also present a proof-of-concept experiment that successfully identified and isolated active molecules from a dynamic combinatorial library. These results demonstrated the potential of using molecular networking for identifying, tracking, and high-throughput screening of active compounds in combinatorial synthesis.
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Affiliation(s)
- Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Chih-Yao Kao
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Tsung-Shing Andrew Wang
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - John Chu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Jiying Pei
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.,School of Marine Sciences, Guangxi University, No.100, East Daxue Rd., Nanning City, Guangxi 530015, China
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
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9
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Chen PHC, Ho SY, Chen PL, Hung TC, Liang AJ, Kuo TF, Huang HC, Wang TSA. Selective Targeting of Vibrios by Fluorescent Siderophore-Based Probes. ACS Chem Biol 2017; 12:2720-2724. [PMID: 28991433 DOI: 10.1021/acschembio.7b00667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Siderophores are small molecules used to specifically transport iron into bacteria via related receptors. By adapting siderophores and hijacking their pathways, we may discover an efficient and selective way to target microbes. Herein, we report the synthesis of a siderophore-fluorophore conjugate VF-FL derived from vibrioferrin (VF). Using flow cytometry and fluorescence microscopy, the probe selectively labeled vibrios, including V. parahaemolyticus, V. cholerae, and V. vulnificus, even in the presence of other species such as S. aureus and E. coli. The labeling is siderophore-related and both iron-limited conditions and the siderophore moiety are required. The competitive relationship between VF-FL and VF in vibrios implies an unreported VF-related transport mechanism in V. cholerae and V. vulnificus. These studies demonstrate that the siderophore scaffold provides a method to selectively target microbes expressing cognate receptors under iron-limited conditions.
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Affiliation(s)
- Peng-Hsun Chase Chen
- Department
of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
| | - Sheng-Yang Ho
- Department
of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
| | - Pin-Lung Chen
- Department
of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
| | - Tzu-Chiao Hung
- Institute
of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
| | - An-Jou Liang
- Institute
of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
| | - Tang-Feng Kuo
- Department
of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
| | - Hsiao-Chun Huang
- Institute
of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
| | - Tsung-Shing Andrew Wang
- Department
of Chemistry, National Taiwan University, Taipei, 10617, Taiwan (Republic of China)
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10
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Fan CH, Huang YS, Huang WE, Lee AA, Ho SY, Kao YL, Wang CL, Lian YL, Ueno T, Andrew Wang TS, Yeh CK, Lin YC. Manipulating Cellular Activities Using an Ultrasound-Chemical Hybrid Tool. ACS Synth Biol 2017; 6:2021-2027. [PMID: 28945972 DOI: 10.1021/acssynbio.7b00162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We developed an ultrasound-chemical hybrid tool to precisely manipulate cellular activities. A focused ultrasound coupled with gas-filled microbubbles was used to rapidly trigger the influx of membrane-impermeable chemical dimerizers into living cells to regulate protein dimerization and location without inducing noticeable toxicity. With this system, we demonstrated the successful modulation of phospholipid metabolism triggered by a short pulse of ultrasound exposure. Our technique offers a powerful and versatile tool for using ultrasound to spatiotemporally manipulate the cellular physiology in living cells.
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Affiliation(s)
| | | | | | | | - Sheng-Yang Ho
- Department
of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | | | | | | | - Tasuku Ueno
- Graduate
School of Pharmaceutical Sciences, University of Tokyo, Tokyo, 113-8654, Japan
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11
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Ho YH, Ho SY, Hsu CC, Shie JJ, Wang TSA. Utilizing an iron(iii)-chelation masking strategy to prepare mono- and bis-functionalized aerobactin analogues for targeting pathogenic bacteria. Chem Commun (Camb) 2017; 53:9265-9268. [DOI: 10.1039/c7cc05197b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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 present a facile functionalization of native siderophoresviaan Fe(iii)-chelation masking strategy to prepare fluorophore conjugates for targeting pathogenic bacteria.
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Affiliation(s)
- Yu-Hin Ho
- Department of Chemistry
- National Taiwan University
- Taipei 10617
- Taiwan
| | - Sheng-Yang Ho
- Department of Chemistry
- National Taiwan University
- Taipei 10617
- Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry
- National Taiwan University
- Taipei 10617
- Taiwan
| | - Jiun-Jie Shie
- Institute of Chemistry
- Academia Sinica
- Taipei 11529
- Taiwan
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12
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Lee AA, Chen YCS, Ekalestari E, Ho SY, Hsu NS, Kuo TF, Wang TSA. Facile and Versatile Chemoenzymatic Synthesis of Enterobactin Analogues and Applications in Bacterial Detection. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Albert A. Lee
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Yi-Chen S. Chen
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Elisa Ekalestari
- Department of Chemistry & Biochemistry; University of California, Los Angeles; Los Angeles CA 90095 USA
| | - Sheng-Yang Ho
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Nai-Shu Hsu
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Tang-Feng Kuo
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Tsung-Shing Andrew Wang
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
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13
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Lee AA, Chen YCS, Ekalestari E, Ho SY, Hsu NS, Kuo TF, Wang TSA. Facile and Versatile Chemoenzymatic Synthesis of Enterobactin Analogues and Applications in Bacterial Detection. Angew Chem Int Ed Engl 2016; 55:12338-42. [DOI: 10.1002/anie.201603921] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/07/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Albert A. Lee
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Yi-Chen S. Chen
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Elisa Ekalestari
- Department of Chemistry & Biochemistry; University of California, Los Angeles; Los Angeles CA 90095 USA
| | - Sheng-Yang Ho
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Nai-Shu Hsu
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Tang-Feng Kuo
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
| | - Tsung-Shing Andrew Wang
- Department of Chemistry; National Taiwan University; No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan) (R.O.C
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14
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Zhang Y, Goswami D, Wang D, Wang TSA, Sen S, Magliery TJ, Griffin PR, Wang F, Schultz PG. An antibody with a variable-region coiled-coil "knob" domain. Angew Chem Int Ed Engl 2013; 53:132-5. [PMID: 24254636 DOI: 10.1002/anie.201307939] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 01/24/2023]
Abstract
The X-ray crystal structure of a bovine antibody (BLV1H12) revealed a unique structure in its ultralong heavy chain complementarity determining region 3 (CDR3H) that folds into a solvent-exposed β-strand "stalk" fused to a disulfide crosslinked "knob" domain. We have substituted an antiparallel heterodimeric coiled-coil motif for the β-strand stalk in this antibody. The resulting antibody (Ab-coil) expresses in mammalian cells and has a stability similar to that of the parent bovine antibody. MS analysis of H-D exchange supports the coiled-coil structure of the substituted peptides. Substitution of the knob-domain of Ab-coil with bovine granulocyte colony-stimulating factor (bGCSF) results in a stably expressed chimeric antibody, which proliferates mouse NFS-60 cells with a potency comparable to that of bGCSF. This work demonstrates the utility of this novel coiled-coil CDR3 motif as a means for generating stable, potent antibody fusion proteins with useful pharmacological properties.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA); Present address: California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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15
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Zhang Y, Goswami D, Wang D, Wang TSA, Sen S, Magliery TJ, Griffin PR, Wang F, Schultz PG. An Antibody with a Variable-Region Coiled-Coil “Knob” Domain. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Gampe CM, Tsukamoto H, Wang TSA, Walker S, Kahne D. Modular synthesis of diphospholipid oligosaccharide fragments of the bacterial cell wall and their use to study the mechanism of moenomycin and other antibiotics. Tetrahedron 2011; 67:9771-9778. [PMID: 22505780 PMCID: PMC3322638 DOI: 10.1016/j.tet.2011.09.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a flexible, modular route to GlcNAc-MurNAc-oligosaccharides that can be readily converted into peptidoglycan (PG) fragments to serve as reagents for the study of bacterial enzymes that are targets for antibiotics. Demonstrating the utility of these synthetic PG substrates, we show that the tetrasaccharide substrate lipid IV (3), but not the disaccharide substrate lipid II (2), significantly increases the concentration of moenomycin A required to inhibit a prototypical PG-glycosyltransferase (PGT). These results imply that lipid IV and moenomycin A bind to the same site on the enzyme. We also show the moenomycin A inhibits the formation of elongated polysaccharide product but does not affect length distribution. We conclude that moenomycin A blocks PG-strand initiation rather than elongation or chain termination. Synthetic access to diphospholipid oligosaccharides will enable further studies of bacterial cell wall synthesis with the long-term goal of identifying novel antibiotics.
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Affiliation(s)
- Christian M. Gampe
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Hirokazu Tsukamoto
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Tsung-Shing Andrew Wang
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Suzanne Walker
- Harvard Medical School, Department of Microbiology and Molecular Genetics, Boston, Massachusetts 02115, USA
| | - Daniel Kahne
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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17
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Oman TJ, Lupoli TJ, Wang TSA, Kahne D, Walker S, van der Donk WA. Haloduracin α binds the peptidoglycan precursor lipid II with 2:1 stoichiometry. J Am Chem Soc 2011; 133:17544-7. [PMID: 22003874 PMCID: PMC3206492 DOI: 10.1021/ja206281k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [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: 07/06/2011] [Indexed: 11/30/2022]
Abstract
The two-peptide lantibiotic haloduracin is composed of two post-translationally modified polycyclic peptides that synergistically act on gram-positive bacteria. We show here that Halα inhibits the transglycosylation reaction catalyzed by PBP1b by binding in a 2:1 stoichiometry to its substrate lipid II. Halβ and the mutant Halα-E22Q were not able to inhibit this step in peptidoglycan biosynthesis, but Halα with its leader peptide still attached was a potent inhibitor. Combined with previous findings, the data support a model in which a 1:2:2 lipid II:Halα:Halβ complex inhibits cell wall biosynthesis and mediates pore formation, resulting in loss of membrane potential and potassium efflux.
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Affiliation(s)
- Trent J. Oman
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Tania J. Lupoli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Tsung-Shing Andrew Wang
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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18
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Lupoli TJ, Tsukamoto H, Doud EH, Wang TSA, Walker S, Kahne D. Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan. J Am Chem Soc 2011; 133:10748-51. [PMID: 21682301 DOI: 10.1021/ja2040656] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The β-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.
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Affiliation(s)
- Tania J Lupoli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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19
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Wang TSA, Lupoli TJ, Sumida Y, Tsukamoto H, Wu Y, Rebets Y, Kahne DE, Walker S. Primer preactivation of peptidoglycan polymerases. J Am Chem Soc 2011; 133:8528-30. [PMID: 21568328 DOI: 10.1021/ja2028712] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidoglycan glycosyltransferases are highly conserved bacterial enzymes that catalyze glycan strand polymerization to build the cell wall. Because the cell wall is essential for bacterial cell survival, these glycosyltransferases are potential antibiotic targets, but a detailed understanding of their mechanisms is lacking. Here we show that a synthetic peptidoglycan fragment that mimics the elongating polymer chain activates peptidoglycan glycosyltransferases by bypassing the rate-limiting initiation step.
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Affiliation(s)
- Tsung-Shing Andrew Wang
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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20
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Fuse S, Tsukamoto H, Yuan Y, Wang TSA, Zhang Y, Bolla M, Walker S, Sliz P, Kahne D. Functional and structural analysis of a key region of the cell wall inhibitor moenomycin. ACS Chem Biol 2010; 5:701-11. [PMID: 20496948 DOI: 10.1021/cb100048q] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Moenomycin A (MmA) belongs to a family of natural products that inhibit peptidoglycan biosynthesis by binding to the peptidoglycan glycosyltransferases, the enzymes that make the glycan chains of peptidoglycan. MmA is remarkably potent, but its clinical utility has been hampered by poor physicochemical properties. Moenomycin contains three structurally distinct regions: a pentasaccharide, a phosphoglycerate, and a C25 isoprenyl (moenocinyl) lipid tail that gives the molecule its name. The phosphoglycerate moiety links the pentasaccharide to the moenocinyl chain. This moiety contains two negatively charged groups, a phosphoryl group and a carboxylate. Both the phosphoryl group and the carboxylate have previously been implicated in target binding but the role of the carboxylate has not been explored in detail. Here we report the synthesis of six MmA analogues designed to probe the importance of the phosphoglycerate. These analogues were evaluated for antibacterial and enzyme inhibitory activity; the specific contacts between the phosphoglycerate and the protein target were assessed by X-ray crystallography in conjunction with molecular modeling. Both the phosphoryl group and the carboxylate of the phosphoglycerate chain play roles in target binding. The negative charge of the carboxylate, and not its specific structure, appears to be the critical feature in binding since replacing it with a negatively charged acylsulfonamide group produces a more active compound than replacing it with the isosteric amide. Analysis of the ligand-protein contacts suggests that the carboxylate makes a critical contact with an invariant lysine in the active site. The reported work provides information and validated computational methods critical for the design of analogues based on moenomycin scaffolds.
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Affiliation(s)
- Shinichiro Fuse
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Hirokazu Tsukamoto
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Yanqiu Yuan
- Department of Microbiology and Molecular Genetics
| | - Tsung-Shing Andrew Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Yi Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Megan Bolla
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | | | - Piotr Sliz
- Department of Pediatrics
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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21
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Perlstein DL, Wang TSA, Doud EH, Kahne D, Walker S. The role of the substrate lipid in processive glycan polymerization by the peptidoglycan glycosyltransferases. J Am Chem Soc 2010; 132:48-9. [PMID: 20017480 DOI: 10.1021/ja909325m] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The peptidoglycan glycosyltransferases (PGTs) catalyze the processive polymerization of a C55 lipid-linked disaccharide (Lipid II) to form peptidoglycan, the main component of the bacterial cell wall. Our ability to understand this reaction has been limited due to challenges identifying the appropriate substrate analogues to selectively interrogate the donor (the elongating strand) and acceptor (Lipid II) sites. To address this problem, we have developed an assay using synthetic substrates that can discriminate between the donor and acceptor sites of the PGTs. We have shown that each site has a distinct lipid length preference. We have also established that processive polymerization depends on the length of the lipid attached to the donor.
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Affiliation(s)
- Deborah L Perlstein
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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22
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Wang TSA, Manning SA, Walker S, Kahne D. Isolated peptidoglycan glycosyltransferases from different organisms produce different glycan chain lengths. J Am Chem Soc 2008; 130:14068-9. [PMID: 18834124 DOI: 10.1021/ja806016y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidoglycan is an essential component of bacterial cell wall. The glycan strands of peptidoglycan are synthesized by enzymes called peptidoglycan glycosyltransferases (PGTs). Using a high-resolution SDS-PAGE assay, we compared the glycan strand lengths of four different PGTs from three different organisms (Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus). We report that each enzyme makes a polymer having an intrinsic characteristic length that is independent of the enzyme:substrate ratio. The glycan strand lengths vary considerably, depending on the enzyme. These results indicate that each enzyme must have some mechanism, as yet unknown, for controlling product length. The observation that different PGTs produce different length glycan chains may have implications for their cellular roles and for the three-dimensional structure of bacterial peptidoglycan.
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Affiliation(s)
- Tsung-Shing Andrew Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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23
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Abstract
Bacterial cells are surrounded by a cross-linked polymer called peptidoglycan, the integrity of which is necessary for cell survival. The carbohydrate chains that form the backbone of peptidoglycan are made by peptidoglycan glycosyltransferases (PGTs), highly conserved membrane-bound enzymes that are thought to be excellent targets for the development of new antibacterials. Although structural information on these enzymes recently became available, their mechanism is not well understood because of a dearth of methods to monitor PGT activity. Here we describe a direct, sensitive, and quantitative SDS-PAGE method to analyze PGT reactions. We apply this method to characterize the substrate specificity and product length profile for two different PGT domains, PBP1A from Aquifex aeolicus and PBP1A from Escherichia coli. We show that both disaccharide and tetrasaccharide diphospholipids (Lipid II and Lipid IV) serve as substrates for these PGTs, but the product distributions differ significantly depending on which substrate is used as the starting material. Reactions using the disaccharide substrate are more processive and yield much longer glycan products than reactions using the tetrasaccharide substrate. We also show that the SDS-PAGE method can be applied to provide information on the roles of invariant residues in catalysis. A comprehensive mutational analysis shows that the biggest contributor to turnover of 14 mutated residues is an invariant glutamate located in the center of the active site cleft. The assay and results described provide new information about the process by which PGTs assemble bacterial cell walls.
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Affiliation(s)
- Dianah Barrett
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Tsung-Shing Andrew Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Yanqiu Yuan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Yi Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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24
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Zhang Y, Fechter EJ, Wang TSA, Barrett D, Walker S, Kahne DE. Synthesis of heptaprenyl-lipid IV to analyze peptidoglycan glycosyltransferases. J Am Chem Soc 2007; 129:3080-1. [PMID: 17323951 PMCID: PMC3222299 DOI: 10.1021/ja069060g] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yi Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Eric J. Fechter
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Tsung-Shing Andrew Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
| | - Dianah Barrett
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115
- ;
| | - Daniel E. Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- ;
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