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Lee YZ, Han J, Zhang YN, Ward G, Gomes KB, Auclair S, Stanfield RL, He L, Wilson IA, Zhu J. A tale of two fusion proteins: understanding the metastability of human respiratory syncytial virus and metapneumovirus and implications for rational design of uncleaved prefusion-closed trimers. bioRxiv 2024:2024.03.07.583986. [PMID: 38496645 PMCID: PMC10942449 DOI: 10.1101/2024.03.07.583986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause human respiratory diseases and are major targets for vaccine development. In this study, we designed uncleaved prefusion-closed (UFC) trimers for the fusion (F) proteins of both viruses by examining mutations critical to F metastability. For RSV, we assessed four previous prefusion F designs, including the first and second generations of DS-Cav1, SC-TM, and 847A. We then identified key mutations that can maintain prefusion F in a native-like, closed trimeric form (up to 76%) without introducing any interprotomer disulfide bond. For hMPV, we developed a stable UFC trimer with a truncated F2-F1 linkage and an interprotomer disulfide bond. Tens of UFC constructs were characterized by negative-stain electron microscopy (nsEM), x-ray crystallography (11 RSV-F and one hMPV-F structures), and antigenic profiling. Using an optimized RSV-F UFC trimer as bait, we identified three potent RSV neutralizing antibodies (NAbs) from a phage-displayed human antibody library, with a public NAb lineage targeting sites Ø and V and two cross-pneumovirus NAbs recognizing site III. In mouse immunization, rationally designed RSV-F and hMPV-F UFC trimers induced robust antibody responses with high neutralizing titers. Our study provides a foundation for future prefusion F-based RSV and hMPV vaccine development.
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Affiliation(s)
- Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jerome Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Garrett Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Keegan Braz Gomes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Sarah Auclair
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, USA
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2
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Braz Gomes K, Zhang YN, Lee YZ, Eldad M, Lim A, Ward G, Auclair S, He L, Zhu J. Single-Component Multilayered Self-Assembling Protein Nanoparticles Displaying Extracellular Domains of Matrix Protein 2 as a Pan-influenza A Vaccine. ACS Nano 2023; 17:23545-23567. [PMID: 37988765 PMCID: PMC10722606 DOI: 10.1021/acsnano.3c06526] [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] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
The development of a cross-protective pan-influenza A vaccine remains a significant challenge. In this study, we designed and evaluated single-component self-assembling protein nanoparticles (SApNPs) presenting the conserved extracellular domain of matrix protein 2 (M2e) as vaccine candidates against influenza A viruses. The SApNP-based vaccine strategy was first validated for human M2e (hM2e) and then applied to tandem repeats of M2e from human, avian, and swine hosts (M2ex3). Vaccination with M2ex3 displayed on SApNPs demonstrated higher survival rates and less weight loss compared to the soluble M2ex3 antigen against the lethal challenges of H1N1 and H3N2 in mice. M2ex3 I3-01v9a SApNPs formulated with a squalene-based adjuvant were retained in the lymph node follicles over 8 weeks and induced long-lived germinal center reactions. Notably, a single low dose of M2ex3 I3-01v9a SApNP formulated with a potent adjuvant, either a Toll-like receptor 9 (TLR9) agonist or a stimulator of interferon genes (STING) agonist, conferred 90% protection against a lethal H1N1 challenge in mice. With the ability to induce robust and durable M2e-specific functional antibody and T cell responses, the M2ex3-presenting I3-01v9a SApNP provides a promising pan-influenza A vaccine candidate.
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Affiliation(s)
- Keegan Braz Gomes
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yi-Nan Zhang
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yi-Zong Lee
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Mor Eldad
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Alexander Lim
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Garrett Ward
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sarah Auclair
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Linling He
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jiang Zhu
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
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3
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Yoo Y, Gibson E, Zhao G, Sandu A, Re T, Das J, Hesheng W, Kim MM, Shen C, Lee YZ, Kondziolka D, Ibrahim M, Lian J, Jain R, Zhu T, Parmar H, Comaniciu D, Balter J, Cao Y. An Automated Brain Metastasis Detection and Segmentation System from MRI with a Large Multi-Institutional Dataset. Int J Radiat Oncol Biol Phys 2023; 117:S88-S89. [PMID: 37784596 DOI: 10.1016/j.ijrobp.2023.06.414] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Developments of automated systems for brain metastasis (BM) detection and segmentation from MRI for assisting early detection and stereotactic radiosurgery (SRS) have been reported but most based upon relatively small datasets from single institutes. This work aims to develop and evaluate a system using a large multi-institutional dataset, and to improve both identification of small/subtle BMs and segmentation accuracy of large BMs. MATERIALS/METHODS A 3D U-Net system was trained and evaluated to detect and segment intraparenchymal BMs with a size > 2mm using 1856 MRI volumes from 1791 patients treated with SRS from seven institutions (1539 volumes for training, 183 for validation, and 134 for testing). All patients had 3D post-Gd T1w MRI scans pre-SRS. Gross tumor volumes (GTVs) of BMs for SRS were curated by each institute first. Then, additional efforts were spent to create GTVs for the untreated and/or uncontoured BMs, including central reviews by two radiologists, to improve accuracy of ground truth. The training dataset was augmented with synthetic BMs of 3773 MRIs using a 3D generative pipeline. Our system consists of two U-Nets with one using small 3D patches dedicated for detecting small BMs and another using large 3D patches for segmenting large BMs, and a random-forest based fusion module for combining the two network outputs. The first U-Net was trained with 3D patches containing at least one BM < 0.1 cm3. For detection performance, we measured BM-level sensitivity and case-level false-positive (FP) rate. For segmentation performance, we measured BM-level Dice similarity coefficient (DSC) and 95-percentile Hausdorff distance (HD95). We also stratified performances based upon BM sizes. RESULTS For 739 BMs in the 134 testing cases, the overall lesion-level sensitivity was 0.870 with an average case-level FP of 1.34±1.92 (95% CI: 1.02-1.67). The sensitivity was >0.969 for the BMs >0.1 cm3, but dropped to 0.755 for the BMs < 0.1 cm3 (Table 1). The average DSC and HD95 for all detected BMs were 0.786 and 1.35mm. The worse performance for BMs > 20 cm3 was caused by a case with 83 cm3 GTV and artifacts in the MRI volume. CONCLUSION We achieved excellent detection sensitivity and segmentation accuracy for BMs > 0.1 cm3, and promising performance for small BMs (<0.1cm3) with a controlled FP rate using a large multi-institutional dataset. Clinical utility for assisting early detection and SRS planning will be investigated. Table 1: Per-lesion detection and segmentation performance stratified by individual BM size. N is the number of BMs in each category.
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Affiliation(s)
- Y Yoo
- Siemens Healthineers, Princeton, NJ
| | - E Gibson
- Siemens Healthineers, Princeton, NJ
| | - G Zhao
- Siemens Healthineers, Princeton, NJ
| | - A Sandu
- Siemens Healthineers, Princeton, NJ
| | - T Re
- Siemens Healthineers, Princeton, NJ
| | - J Das
- Siemens Healthineers, Princeton, NJ
| | | | - M M Kim
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - C Shen
- Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC
| | - Y Z Lee
- University of North Carolina, Chapel Hill, NC
| | - D Kondziolka
- Department of Neurosurgery, NYU Langone Health, New York, NY
| | - M Ibrahim
- University of Michigan, Ann Arbor, MI
| | - J Lian
- University of North Carolina, Chapel Hill, NC
| | - R Jain
- New York University, New York, NY
| | - T Zhu
- Washington University, St. Louis, MO
| | - H Parmar
- Department of Radiology, University of Michigan, Ann Arbor, MI
| | | | - J Balter
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
| | - Y Cao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI
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4
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Risner V, Huang B, McCullagh K, Benefield T, Lee YZ. The Development and Application of a Cost-Effective Cervical Spine Phantom for Use in Fluoroscopically Guided Lateral C1-C2 Spinal Puncture Training. AJNR Am J Neuroradiol 2023:ajnr.A7908. [PMID: 37321858 PMCID: PMC10337607 DOI: 10.3174/ajnr.a7908] [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] [Received: 02/25/2023] [Accepted: 05/21/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND PURPOSE Lateral C1-C2 spinal punctures are uncommon procedures performed by radiologists for access to CSF and contrast injection when a lumbar approach is contraindicated and an alternate method of access becomes necessary. There are limited opportunities to learn and practice the technique. We aimed to develop and assess the efficacy of a low-cost, reusable cervical spine phantom for training in fluoroscopically guided lateral C1-C2 spinal puncture. MATERIALS AND METHODS The phantom was constructed with a cervical spine model, an outer tube representing the thecal sac, an inner balloon representing the spinal cord, and polyalginate to replicate soft tissue. The total cost of materials was approximately US $70. Workshops were led by neuroradiology faculty experienced in the procedure using the model under fluoroscopy. Survey questions were assessed on a 5-point Likert scale. Participants were given pre- and postsurveys assessing comfort, confidence, and knowledge of steps. RESULTS Twenty-one trainees underwent training sessions. There was significant improvement in comfort level (Δ: 2.00, SD: 1.00, P value < .001); confidence (Δ: 1.52 points, SD: 0.87, P value < .001); and knowledge (Δ: 2.19, SD: 0.93, P value < .001). Eighty-one percent of participants found the model "very helpful" (5/5 on Likert scale), and all participants were "very likely" to recommend this workshop to others. CONCLUSIONS This cervical phantom model is affordable and replicable and demonstrates training utility to prepare residents for performing lateral C1-C2 spinal puncture. This is a rare procedure, so the use of a phantom model before patient encounters is invaluable to resident education and training.
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Affiliation(s)
- V Risner
- From the Department of Radiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - B Huang
- From the Department of Radiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - K McCullagh
- From the Department of Radiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - T Benefield
- From the Department of Radiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Y Z Lee
- From the Department of Radiology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
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5
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Zhang YN, Paynter J, Antanasijevic A, Allen JD, Eldad M, Lee YZ, Copps J, Newby ML, He L, Chavez D, Frost P, Goodroe A, Dutton J, Lanford R, Chen C, Wilson IA, Crispin M, Ward AB, Zhu J. Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimmers as HIV-1 vaccine candidates. Nat Commun 2023; 14:1985. [PMID: 37031217 PMCID: PMC10082823 DOI: 10.1038/s41467-023-37742-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 10/03/2022] [Accepted: 03/29/2023] [Indexed: 04/10/2023] Open
Abstract
Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 native-like Env trimers as vaccine candidates. We characterize the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. For 1c-SApNPs, glycan trimming improves recognition of the CD4 binding site without affecting broadly neutralizing antibodies (bNAbs) to major glycan epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increases the frequency of vaccine responders (FVR) and steers antibody responses away from immunodominant glycan holes and glycan patches. The mechanism of vaccine-induced immunity is examined in mice. Compared with the UFO trimer, the multilayered E2p and I3-01v9 1c-SApNPs show 420 times longer retention in lymph node follicles, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions. These findings can inform future HIV-1 vaccine development.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Joel D Allen
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mor Eldad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi-Zong Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Maddy L Newby
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deborah Chavez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Pat Frost
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Anna Goodroe
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - John Dutton
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert Lanford
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Christopher Chen
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Max Crispin
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, SO17 1BJ, UK
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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6
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Liu YH, Chuang CH, Lee YZ, Lee ET, Lo CL, Wu CY, Huang LK, Bikfalvi A, Sue SC. Structural Properties of CXCL4L1 and Its Recognition of the CXCR3 N-Terminus. Biochemistry 2023; 62:722-734. [PMID: 36626574 DOI: 10.1021/acs.biochem.2c00525] [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: 01/12/2023]
Abstract
Chemokine CXCL4L1, a homologue of CXCL4, is a more potent antiangiogenic ligand. Its structural property is correlated with the downstream receptor binding. The two chemokines execute their functions by binding the receptors of CXCR3A and CXCR3B. The receptors differ by an extra 51-residue extension in the CXCR3B N-terminus. To understand the binding specificity, a GB1 protein scaffold was used to carry different CXCR3 extracellular elements, and artificial CXCL4 and CXCL4L1 monomers were engineered for the binding assay. We first characterized the molten globule property of CXCL4L1. The structural property causes the CXCL4L1 tetramer to dissociate into monomers in low concentrations, but native CXCL4 adopts a stable tetramer structure in solution. In the titration experiments, the combination of the CXCR3A N-terminus and receptor extracellular loop 2 provided moderate and comparable binding affinities to CXCL4 and CXCL4L1, while sulfation on the CXCR3A N-terminal tyrosine residues provided binding specificity. However, the CXCR3B N-terminal extension did not show significant enhancement in the binding of CXCL4 or CXCL4L1. This result indicates that the tendency to form a chemokine monomer and the binding affinity together contribute the high antiangiogenic activity of CXCL4L1.
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Affiliation(s)
- Ya-Hsin Liu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chia-Hsuan Chuang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yi-Zong Lee
- Instrumentation Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Eh-Tzen Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chiao-Ling Lo
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chu-Ya Wu
- Instrumentation Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Li-Kun Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | | | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.,Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
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7
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Wu CY, Hu IC, Yang YC, Ding WC, Lai CH, Lee YZ, Liu YC, Cheng HC, Lyu PC. An essential role of acetyl coenzyme A in the catalytic cycle of insect arylalkylamine N-acetyltransferase. Commun Biol 2020; 3:441. [PMID: 32796911 PMCID: PMC7427786 DOI: 10.1038/s42003-020-01177-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
Acetyl coenzyme A (Ac-CoA)-dependent N-acetylation is performed by arylalkylamine N-acetyltransferase (AANAT) and is important in many biofunctions. AANAT catalyzes N-acetylation through an ordered sequential mechanism in which cofactor (Ac-CoA) binds first, with substrate binding afterward. No ternary structure containing AANAT, cofactor, and substrate was determined, meaning the details of substrate binding and product release remain unclear. Here, two ternary complexes of dopamine N-acetyltransferase (Dat) before and after N-acetylation were solved at 1.28 Å and 1.36 Å resolution, respectively. Combined with the structures of Dat in apo form and Ac-CoA bound form, we addressed each stage in the catalytic cycle. Isothermal titration calorimetry (ITC), crystallography, and nuclear magnetic resonance spectroscopy (NMR) were utilized to analyze the product release. Our data revealed that Ac-CoA regulates the conformational properties of Dat to form the catalytic site and substrate binding pocket, while the release of products is facilitated by the binding of new Ac-CoA.
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Affiliation(s)
- Chu-Ya Wu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - I-Chen Hu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Chen Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wei-Cheng Ding
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chih-Hsuan Lai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Instrumentation Center, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Chung Liu
- Institute of Population Sciences, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Hui-Chun Cheng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Department of Medical Sciences, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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8
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Li JY, Chen YC, Lee YZ, Huang CH, Sue SC. N-terminal Backbone Pairing Shifts in CCL5- 12AAA 14 Dimer Interface: Structural Significance of the FAY Sequence. Int J Mol Sci 2020; 21:ijms21051689. [PMID: 32121575 PMCID: PMC7084690 DOI: 10.3390/ijms21051689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 01/13/2023] Open
Abstract
CC-type chemokine ligand 5 (CCL5) has been known to regulate immune responses by mediating the chemotaxis of leukocytes. Depending on the environment, CCL5 forms different orders of oligomers to interact with targets and create functional diversity. A recent CCL5 trimer structure revealed that the N-terminal conversed F12-A13-Y14 (12FAY14) sequence is involved in CCL5 aggregation. The CCL5-12AAA14 mutant with two mutations had a deficiency in the formation of high-order oligomers. In the study, we clarify the respective roles of F12 and Y14 through NMR analysis and structural determination of the CCL5-12AAA14 mutant where F12 is involved in the dimer assembly and Y14 is involved in aggregation. The CCL5-12AAA14 structure contains a unique dimer packing. The backbone pairing shifts for one-residue in the N-terminal interface, when compared to the native CCL5 dimer. This difference creates a new structural orientation and leads to the conclusion that F12 confines the native CCL5 dimer configuration. Without F12 anchoring in the position, the interfacial backbone pairing is permitted to slide. Structural plasticity occurs in the N-terminal interaction. This is the first case to report this structural rearrangement through mutagenesis. The study provides a new idea for chemokine engineering and complements the understanding of CCL5 oligomerization and the role of the 12FAY14 sequence.
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Affiliation(s)
- Jin-Ye Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
| | - Yi-Chen Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
- Instrument Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chun-Hsiang Huang
- Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan;
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan; (J.-Y.L.); (Y.-C.C.); (Y.-Z.L.)
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
- Correspondence: ; Tel.: +886-3-5742025; Fax: +886-3-5715934
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9
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Chen YC, Chen SP, Li JY, Chen PC, Lee YZ, Li KM, Zarivach R, Sun YJ, Sue SC. Integrative Model to Coordinate the Oligomerization and Aggregation Mechanisms of CCL5. J Mol Biol 2020; 432:1143-1157. [PMID: 31931012 DOI: 10.1016/j.jmb.2019.12.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 11/25/2022]
Abstract
CC-type chemokine ligand 5 (CCL5) is involved in the pathogenesis of many inflammatory conditions. Under physiological conditions, CCL5 oligomerization and aggregation are considered to be responsible for its inflammatory properties. The structural basis of CCL5 oligomerization remains controversial because the current oligomer models contain no consensus interactions. In this study, NMR and biophysical analyses proposed evidence that the CC-type CCL5 dimer acts as the basic unit to constitute the oligomer and that CCL5 oligomerizes alternatively through E66-K25 and E66-R44/K45 interactions. In addition, a newly determined trimer structure, constituted by CCL5 and the E66S mutant, reported an interfacial interaction through the N-terminal 12FAY14 sequence. The interaction contributes to CCL5 aggregation and precipitation but not to oligomerization. In accordance with the observations, an integrative model explains the CCL5 oligomerization and aggregation mechanism in which CCL5 assembly consists of two types of dimer-dimer interactions and one aggregation mechanism. For full-length CCL5, the molecular accumulation triggers oligomerization through the E66-K25 and E66-R44/K45 interactions, and the 12FAY14 interaction acts as a secondary effect to derive aggregation and precipitation. In contrast, the E66-R44/K45 interaction might dominate in CCL5 N-terminal truncations, and the interaction would lead to the filament-like formation in solution.
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Affiliation(s)
- Yi-Chen Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Siou-Pei Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jin-Ye Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Pei-Chun Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Instrument Center, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Kun-Mou Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Raz Zarivach
- Department of Life Sciences, The National Institute for Biotechnology in the Negev and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.
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10
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Chen SH, Chao A, Tsai CL, Sue SC, Lin CY, Lee YZ, Hung YL, Chao AS, Cheng AJ, Wang HS, Wang TH. Utilization of HEPES for Enhancing Protein Transfection into Mammalian Cells. Mol Ther Methods Clin Dev 2018; 13:99-111. [PMID: 30740472 PMCID: PMC6357789 DOI: 10.1016/j.omtm.2018.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/13/2018] [Indexed: 01/12/2023]
Abstract
The delivery of active proteins into cells (protein transfection) for biological purposes offers considerable potential for clinical applications. Herein we demonstrate that, with a readily available, inexpensive organic agent, the 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) method can be used for simple and efficient protein transfection. By mixing proteins with a pure HEPES solution before they are applied to live cells, proteins with various molecular weights (including antibodies, recombinant proteins, and peptides) were successfully delivered into the cytoplasm of different cell types. The protein transfection efficiency of the HEPES method was not inferior to that of commercially available systems that are both more expensive and time consuming. Studies using endocytotic inhibitors and endosomal markers have revealed that cells internalize HEPES-protein mixtures through endocytosis. Results that HEPES-protein mixtures exhibited a low diffusion coefficient suggest that HEPES might neutralize the charges of proteins and, thus, facilitate their cellular internalization. Upon internalization, the cytosolic antibodies caused the degradation of targeted proteins in TRIM21-expressing cells. In summary, the HEPES method is efficient for protein transfection and has potential for myriad clinical applications.
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Affiliation(s)
- Shun-Hua Chen
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University, Taoyuan, Taiwan
| | - Angel Chao
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University, Taoyuan, Taiwan.,Gynecologic Cancer Research Center, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chiao-Yun Lin
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Lin Hung
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - An-Shine Chao
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University, Taoyuan, Taiwan
| | - Ann-Joy Cheng
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Shih Wang
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University, Taoyuan, Taiwan
| | - Tzu-Hao Wang
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital Linkou Medical Center and Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan
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11
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Nudelman H, Lee YZ, Hung YL, Kolusheva S, Upcher A, Chen YC, Chen JY, Sue SC, Zarivach R. Understanding the Biomineralization Role of Magnetite-Interacting Components (MICs) From Magnetotactic Bacteria. Front Microbiol 2018; 9:2480. [PMID: 30405554 PMCID: PMC6206293 DOI: 10.3389/fmicb.2018.02480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/28/2018] [Indexed: 11/20/2022] Open
Abstract
Biomineralization is a process that takes place in all domains of life and which usually helps organisms to harden soft tissues by creating inorganic structures that facilitate their biological functions. It was shown that biominerals are under tight biological control via proteins that are involved in nucleation initiation and/or which act as structural skeletons. Magnetotactic bacteria (MTB) use iron biomineralization to create nano-magnetic particles in a specialized organelle, the magnetosome, to align to the geomagnetic field. A specific set of magnetite-associated proteins (MAPs) is involved in regulating magnetite nucleation, size, and shape. These MAPs are all predicted to contain specific 17–22 residue-long sequences involved in magnetite formation. To understand the mechanism of magnetite formation, we focused on three different MAPs, MamC, Mms6 and Mms7, and studied the predicted iron-binding sequences. Using nuclear magnetic resonance (NMR), we differentiated the recognition mode of each MAP based on ion specificity, affinity, and binding residues. The significance of critical residues in each peptide was evaluated by mutation followed by an iron co-precipitation assay. Among the peptides, MamC showed weak ion binding but created the most significant effect in enhancing magnetite particle size, indicating the potency in controlling magnetite particle shape and size. Alternatively, Mms6 and Mms7 had strong binding affinities but less effect in modulating magnetite particle size, representing their major role potentially in initiating nucleation by increasing local metal concentration. Overall, our results explain how different MAPs affect magnetite synthesis, interact with Fe2+ ions and which residues are important for the MAPs functions.
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Affiliation(s)
- Hila Nudelman
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Instrumentation Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Lin Hung
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.,Instrumentation Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Alexander Upcher
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yi-Chen Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jih-Ying Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Raz Zarivach
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel.,Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
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12
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Boyé K, Pujol N, D Alves I, Chen YP, Daubon T, Lee YZ, Dedieu S, Constantin M, Bello L, Rossi M, Bjerkvig R, Sue SC, Bikfalvi A, Billottet C. The role of CXCR3/LRP1 cross-talk in the invasion of primary brain tumors. Nat Commun 2017; 8:1571. [PMID: 29146996 PMCID: PMC5691136 DOI: 10.1038/s41467-017-01686-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 10/10/2017] [Indexed: 11/09/2022] Open
Abstract
CXCR3 plays important roles in angiogenesis, inflammation, and cancer. However, the precise mechanism of regulation and activity in tumors is not well known. We focused on CXCR3-A conformation and on the mechanisms controlling its activity and trafficking and investigated the role of CXCR3/LRP1 cross talk in tumor cell invasion. Here we report that agonist stimulation induces an anisotropic response with conformational changes of CXCR3-A along its longitudinal axis. CXCR3-A is internalized via clathrin-coated vesicles and recycled by retrograde trafficking. We demonstrate that CXCR3-A interacts with LRP1. Silencing of LRP1 leads to an increase in the magnitude of ligand-induced conformational change with CXCR3-A focalized at the cell membrane, leading to a sustained receptor activity and an increase in tumor cell migration. This was validated in patient-derived glioma cells and patient samples. Our study defines LRP1 as a regulator of CXCR3, which may have important consequences for tumor biology.
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Affiliation(s)
- Kevin Boyé
- INSERM U1029, Pessac, 33615, France.,Université de Bordeaux, Pessac, 33615, France
| | - Nadège Pujol
- INSERM U1029, Pessac, 33615, France.,Université de Bordeaux, Pessac, 33615, France
| | | | - Ya-Ping Chen
- Institute of Bioinformatics and Structural Biology, NTHU, Hsinchu, 30055, Taiwan
| | - Thomas Daubon
- INSERM U1029, Pessac, 33615, France.,Université de Bordeaux, Pessac, 33615, France.,K.G. Jebsen Brain Tumour Research Centre, Department of Biomedicine, University of Bergen, Bergen, 5009, Norway.,Department of Oncology, Luxembourg Institute of Health, Luxembourg, L-1526, Luxembourg
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, NTHU, Hsinchu, 30055, Taiwan
| | - Stephane Dedieu
- CNRS UMR 7369 MEDyC, Université de Reims Champagne-Ardenne, Reims, 51687, France
| | - Marion Constantin
- INSERM U1029, Pessac, 33615, France.,Université de Bordeaux, Pessac, 33615, France
| | - Lorenzo Bello
- Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Humanitas Resarch Hospital, Milan, 20089, Italy
| | - Marco Rossi
- Neurosurgical Oncology Unit, Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Humanitas Resarch Hospital, Milan, 20089, Italy
| | - Rolf Bjerkvig
- K.G. Jebsen Brain Tumour Research Centre, Department of Biomedicine, University of Bergen, Bergen, 5009, Norway.,Department of Oncology, Luxembourg Institute of Health, Luxembourg, L-1526, Luxembourg
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, NTHU, Hsinchu, 30055, Taiwan
| | - Andreas Bikfalvi
- INSERM U1029, Pessac, 33615, France. .,Université de Bordeaux, Pessac, 33615, France.
| | - Clotilde Billottet
- INSERM U1029, Pessac, 33615, France. .,Université de Bordeaux, Pessac, 33615, France.
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13
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Abstract
Split inteins have emerged as a powerful tool in protein engineering. We describe a reliable in silico method to predict viable split sites for the design of new split inteins. A computational circular permutation (CP) prediction method facilitates the search for internal permissive sites to create artificial circular permutants. In this procedure, the original amino- and carboxyl-termini are connected and new termini are created. The identified new terminal sites are promising candidates for the generation of new split sites with the backbone opening being tolerated by the structural scaffold. Here we show how to integrate the online usage of the CP predictor, CPred, in the search of new split intein sites.
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Affiliation(s)
- Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, 30013, Hsinchu, Taiwan
| | - Wei-Cheng Lo
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, 30013, Hsinchu, Taiwan.
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.
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14
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Hung YL, Jiang I, Lee YZ, Wen CK, Sue SC. NMR Study Reveals the Receiver Domain of Arabidopsis ETHYLENE RESPONSE1 Ethylene Receptor as an Atypical Type Response Regulator. PLoS One 2016; 11:e0160598. [PMID: 27486797 PMCID: PMC4972365 DOI: 10.1371/journal.pone.0160598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 06/08/2016] [Accepted: 07/21/2016] [Indexed: 11/26/2022] Open
Abstract
The gaseous plant hormone ethylene, recognized by plant ethylene receptors, plays a pivotal role in various aspects of plant growth and development. ETHYLENE RESPONSE1 (ETR1) is an ethylene receptor isolated from Arabidopsis and has a structure characteristic of prokaryotic two-component histidine kinase (HK) and receiver domain (RD), where the RD structurally resembles bacteria response regulators (RRs). The ETR1 HK domain has autophosphorylation activity, and little is known if the HK can transfer the phosphoryl group to the RD for receptor signaling. Unveiling the correlation of the receptor structure and phosphorylation status would advance the studies towards the underlying mechanisms of ETR1 receptor signaling. In this study, using the nuclear magnetic resonance technique, our data suggested that the ETR1-RD is monomeric in solution and the rigid structure of the RD prevents the conserved aspartate residue phosphorylation. Comparing the backbone dynamics with other RRs, we propose that backbone flexibility is critical to the RR phosphorylation. Besides the limited flexibility, ETR1-RD has a unique γ loop conformation of opposite orientation, which makes ETR1-RD unfavorable for phosphorylation. These two features explain why ETR1-RD cannot be phosphorylated and is classified as an atypical type RR. As a control, phosphorylation of the ETR1-RD was also impaired when the sequence was swapped to the fragment of the bacterial typical type RR, CheY. Here, we suggest a molecule insight that the ETR1-RD already exists as an active formation and executes its function through binding with the downstream factors without phosphorylation.
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Affiliation(s)
- Yi-Lin Hung
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Instrumentation Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ingjye Jiang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chi-Kuang Wen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail:
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15
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Tseng KL, Lee YZ, Chen YR, Lyu PC. 1H, 15N and 13C resonance assignments of light organ-associated fatty acid-binding protein of Taiwanese fireflies. Biomol NMR Assign 2016; 10:71-74. [PMID: 26373428 DOI: 10.1007/s12104-015-9640-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
Fatty acid-binding proteins (FABPs) are a family of proteins that modulate the transfer of various fatty acids in the cytosol and constitute a significant portion in many energy-consuming cells. The ligand binding properties and specific functions of a particular type of FABP seem to be diverse and depend on the respective binding cavity as well as the cell type from which this protein is derived. Previously, a novel FABP (lcFABP; lc: Luciola cerata) was identified in the light organ of Taiwanese fireflies. The lcFABP was proved to possess fatty acids binding capabilities, especially for fatty acids of length C14-C18. However, the structural details are unknown, and the structure-function relationship has remained to be further investigated. In this study, we finished the (1)H, (15)N and (13)C chemical shift assignments of (15)N/(13)C-enriched lcFABP by solution NMR spectroscopy. In addition, the secondary structure distribution was revealed based on the backbone N, H, Cα, Hα, C and side chain Cβ assignments. These results can provide the basis for further structural exploration of lcFABP.
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Affiliation(s)
- Kai-Li Tseng
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Yun-Ru Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, No. 101, Sec. 2, Kuang Fu Rd, Hsinchu, 30013, Taiwan, ROC.
- Department of Medical Sciences, National Tsing Hua University, Hsinchu, Taiwan, ROC.
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16
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Lee YZ, Lee YT, Lin YJ, Chen YJ, Sue SC. A streamlined method for preparing split intein for NMR study. Protein Expr Purif 2014; 99:106-12. [PMID: 24751877 DOI: 10.1016/j.pep.2014.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 12/27/2013] [Revised: 03/19/2014] [Accepted: 04/10/2014] [Indexed: 11/16/2022]
Abstract
A protein ligase, intein, mediates a protein-splicing reaction. It can be split into two complementary fragments and reconstituted as a whole intein scaffold to perform protein trans-splicing. To understand the association of intein fragments and the splicing mechanism, it is necessary to produce a large quantity of split intein for structural study. Conventionally, two fragments are prepared separately and assembled in solution, but severe aggregation of intein fragments occurs, and precise control of the relative concentration of each fragment is difficult. Here, we present a streamlined method to incorporate a circular permutation concept into the production of split intein. By circular permutation of the native split Nostoc punctiforme DnaE intein (NpuInt), a new backbone opening is relocated to the native split site at residue 102. As the protein splicing activity is preserved, the expressed NpuInt can immediately self-cleave into a two-piece split NpuInt. Because of a tight association between the two complementary fragments, split NpuInt can be purified in one step. The idea is simple and applicable to other split inteins. Employing the new preparation, we use NMR spectra to assign the backbone and side chain resonances for the native split NpuInt.
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Affiliation(s)
- Yi-Zong Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yun-Tzai Lee
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Jan Lin
- Graduate Institute of Natural Products and Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Ju Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan.
| | - Shih-Che Sue
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan; Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.
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17
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Cao G, Lee YZ, Peng R, Liu Z, Rajaram R, Calderon-Colon X, An L, Wang P, Phan T, Sultana S, Lalush DS, Lu JP, Zhou O. A dynamic micro-CT scanner based on a carbon nanotube field emission x-ray source. Phys Med Biol 2009; 54:2323-40. [PMID: 19321922 DOI: 10.1088/0031-9155/54/8/005] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Current commercial micro-CT scanners have the capability of imaging objects ex vivo with high spatial resolution, but performing in vivo micro-CT on free-breathing small animals is still challenging because their physiological motions are non-periodic and much faster than those of humans. In this paper, we present a prototype physiologically gated micro-computed tomography (micro-CT) scanner based on a carbon nanotube field emission micro-focus x-ray source. The novel x-ray source allows x-ray pulses and imaging sequences to be readily synchronized and gated to non-periodic physiological signals from small animals. The system performance is evaluated using phantoms and sacrificed and anesthetized mice. Prospective respiratory-gated micro-CT images of anesthetized free-breathing mice were collected using this scanner at 50 ms temporal resolution and 6.2 lp mm(-1) at 10% system MTF. The high spatial and temporal resolutions of the micro-CT scanner make it well suited for high-resolution imaging of free-breathing small animals.
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Affiliation(s)
- G Cao
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27599, USA.
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18
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Rajaram R, Yang G, Lee YZ, Lalush D, Lu J, Zhou O. TH-C-332-08: Calibration of the Geometry in a Stationary Digital Breast Tomosynthesis System. Med Phys 2008. [DOI: 10.1118/1.2962874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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19
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Lee YZ, Chen X, Chen SA, Wei PK, Fann WS. Soluble electroluminescent poly(phenylene vinylene)s with balanced electron- and hole injections. J Am Chem Soc 2001; 123:2296-307. [PMID: 11456878 DOI: 10.1021/ja003135d] [Citation(s) in RCA: 254] [Impact Index Per Article: 11.0] [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
We report a new route for the design of efficient soluble electroluminescent PPV-based copolymers bearing electron-deficient oxadiazole (OXD) moieties on side chains. The introduction of OXD through a long alkylene spacer with PPV backbone provides a molecular dispersion of OXD in the film; both the side chain OXD and the main chain PPV do retain their own electron-transport and emissive properties, respectively. The use of phenylene vinylene derivatives with asymmetric and branched substituents and a long spacer provides solubility for ease of device fabrication as well as amorphous structure to allow a well-mixing of OXD groups with the main chains. By properly adjusting the OXD content through copolymerization, we can tailor the chemical structure of electroluminescent material to give a balance of hole- and electron injections for various metal cathodes, such that the quantum efficiency is significantly improved and the turn-on voltage is reduced for the devices with aluminum and calcium. For the device with calcium fabricated in open air, a maximum brightness of 15000 cd/m(2) at 15 V/100 nm and a maximum luminance efficiency of 2.27 cd/A can be obtained, respectively, about 30 times brighter and 9.4 times more efficient than those with the corresponding homopolymer, poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylenevinylene] (MEH-PPV). The use of physical blends to simulate the copolymers provides no significant improvement, since phase-separation structures appear, causing an inefficient utilization of OXD and sometimes voltage-dependent emission spectra. The present route permits a fabrication of single layer PLED with high brightness, high efficiency, and low turn-on voltage.
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Affiliation(s)
- Y Z Lee
- Contribution from the Chemical Engineering Department, National Tsing-Hua University, Hsinchu, 30043, Taiwan, Republic of China
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20
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Sirlin CB, Lee YZ, Girard MS, Peterson TM, Steinbach GC, Baker KG, Mattrey RF. Contrast-enhanced B-mode US angiography in the assessment of experimental in vivo and in vitro atherosclerotic disease. Acad Radiol 2001; 8:162-72. [PMID: 11227645 DOI: 10.1016/s1076-6332(01)90133-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
RATIONALE AND OBJECTIVES This study was performed to (a) test the hypothesis that filling the arterial lumen with echoes at B-mode ultrasound (US) enables the assessment of wall and luminal abnormalities and (b) compare contrast material-enhanced B-mode US with color and power Doppler US angiography. MATERIALS AND METHODS Atherosclerotic lesions were created in 14 rabbit aortas and imaged with color Doppler and B-mode US before and after the intravenous administration of 0.3 mL of AF0150, a US contrast agent. In addition, four replicas of diseased human carotid arteries were immersed in a tissue-mimicking phantom and imaged with B-mode and color and power Doppler US before and after the administration of 1 mL of AF0150 per liter of porcine blood. Radiopaque plastic casts of the rabbit aortas and contact radiographs of the plastic replicas served as standards. RESULTS Although color and power Doppler US allowed immediate localization of the lumen, precise estimation of stenoses and reliable visualization of surface irregularities were not possible. After AF0150 administration, angiogram-like images of the lumen were created with B-mode US, allowing rapid assessment of the entire vessel lumen and wall. Consequently, luminal stenoses were more accurately measured than with unenhanced B-mode US (r2 = 0.94, P < .0001 vs r2 = 0.21, P = .25) or Doppler (r2 = 0.42, P < .03). In addition, plaques and ulcerations were visible only with contrast-enhanced B-mode US. CONCLUSION Microbubbles fill the arterial lumen with echoes at B-mode US, creating an angiogram-like image. The ability to visualize the inner and outer surfaces of the vascular wall improved the evaluation of luminal and wall abnormalities.
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Affiliation(s)
- C B Sirlin
- Department of Radiology, University of California, San Diego Medical Center, USA
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Lee YZ, Suzuki S, Kawada T, Wang J, Koyama H, Rivai IF, Herawati N. Content of cadmium in carrots compared with rice in Japan. Bull Environ Contam Toxicol 1999; 63:711-9. [PMID: 10594144 DOI: 10.1007/s001289901038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- Y Z Lee
- Department of Public Health, Gunma University, School of Medicine, Showa-3, Maebashi 371-8511, Japan
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Yoon JH, Lee YZ, Park HR. Thermal relaxation of the deposition-induced nonequilibrium state and steady-state defect density in hydrogenated amorphous silicon. Phys Rev B Condens Matter 1994; 49:10303-10306. [PMID: 10009850 DOI: 10.1103/physrevb.49.10303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Wang SS, Hsieh JT, Chen SY, Lee YZ, Wong WJ, Chang KC. Functional voiding disorders in women. Taiwan Yi Xue Hui Za Zhi 1989; 88:377-80. [PMID: 2794938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
From July 1986 to Dec 1987, 78 women complaining of frequency, urgency, dysuria and suprapubic discomfort were evaluated at our clinic. Their ages ranged from 20 to 68 (mean age: 38.2). The patients who were noted to have evidence of pyuria, neurological or gynecological abnormalities were excluded from the study. Urodynamic examinations including uroflowmetry, cystometry (CMG), urethral pressure profiles (UPP) and electromyography (EMG) of the external urethral sphincter were performed. The results revealed low flow rates in 56 patients (71.8%), non-relaxation of the external sphincter during voiding in 55 patients (70.5%), unstable bladder in 6 patients (7.7%) and a high maximal urethral closure pressure (MUCP) (greater than 80 cmH2O) in 44 patients (56.4%). The average volume of the cystometric capacity (250 +/- 86 ml) was decreased. The association between the low flow rate, non-relaxation of the external sphincter and a high MUCP was statistically significant. Urethral hypersensitivity has been recognized as being the major cause of these symptoms.
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Rahimtula AD, Lee YZ, Silva J. Induction of epidermal and hepatic ornithine decarboxylase by a Prudhoe Bay crude oil. Fundam Appl Toxicol 1987; 8:408-14. [PMID: 3569711 DOI: 10.1016/0272-0590(87)90090-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Application of a Prudhoe Bay crude oil (PBCO) to the backs of mice caused a rapid induction of epidermal ornithine decarboxylase (ODC). A maximum induction of over 60-fold was seen at 6 hr after application of 50 microliters of PBCO. Concurrently, epidermal putrescine levels were elevated 4.7-fold over controls. Intraperitoneal administration of PBCO led to a 15-20-fold increase in hepatic ODC activity but to a 45% decrease in the renal enzyme activity. Maximum induction of ODC was seen at 12 hr following the administration of 4 ml/kg body wt of PBCO. Hepatic putrescine levels were elevated 34-fold over controls. Pretreatment of mice with the protein synthesis inhibitor cycloheximide abolished both epidermal and hepatic ODC induction.
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Chen DH, Yang HB, Wang GH, Chang HQ, Ni DS, He H, Lee YZ, Zhou L. [Electron microscopic study of the morphology of virus of hemorrhagic fever with renal syndrome in suckling mice]. Wei Sheng Wu Xue Bao 1986; 26:112-5. [PMID: 2875562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Leighton FA, Lee YZ, Rahimtula AD, O'Brien PJ, Peakall DB. Biochemical and functional disturbances in red blood cells of herring gulls ingesting Prudhoe Bay crude oil. Toxicol Appl Pharmacol 1985; 81:25-31. [PMID: 4049418 DOI: 10.1016/0041-008x(85)90116-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heinz body hemolytic anemia developed in Herring Gull (Larus argentatus) nestlings given oral doses of 10 ml of Prudhoe Bay crude oil per kilogram of body weight per day for 5 days. Associated disturbances in red blood cells were increased amounts of reduced glutathione (GSH), peroxidation of membrane lipids, an increase in membrane permeability, and a decrease in the oxygen-carrying capacity of cyanomethemoglobin-convertible hemoglobin. Among groups of gulls given different cumulative doses of oil over a 6-day period, significant covariance with dose and dependence on dose was demonstrated for packed cell volume, hemoglobin, and red cell GSH. Rapid defecation of oil by gulls indicated that the effective dose was substantially less than the administered dose. Pronounced damage to red cells occurred in some birds administered oil for only 2 days. These data imply that the toxic effects of ingested oil may contribute significantly to the morbidity and mortality of oil-contaminated birds.
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Abstract
Lipopolysaccharide from a strain of Aeromonas salmonicida salmonicida was isolated from cells by the aqueous phenol method in 2.3% yield (based on dry weight of bacteria). Hydrolysis of the lipopolysaccharide in 1% acetic acid afforded O-polysaccharide (19% by weight), core-oligosaccharide (12.2%) and lipid A (44.6%). Analysis indicated that 3-deoxy-D-manno-2-octulosonic acid was absent from the lipopolysaccharide and that no low-molecular-weight compounds were released by the mild hydrolysis. The O-polysaccharide had the monosaccharide composition of rhamnose, glucose and N-acetylmannosamine in molar ratio of 1.0:1.58:0.83. 75% of the N-acetylmannosamine residues were substituted at position 4 by O-acetyl groups. Hydrolysis of the methylated polysaccharide proved to be both difficult and dependent on the method of hydrolysis chosen, in all cases a partially methylated disaccharide of rhamnose and N-acetylmannosamine was identified in the hydrolysate. Methylation analysis, periodate oxidation and proton magnetic resonance analysis were used to confirm the structure of the repeating unit as: (formula; see text).
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Abstract
A search was undertaken for bacteria which degrade chondroitin sulfate in nature and to find bacteria with a usefully high rate of chondroitinase (ChSase) productivity. First, 253 ChSase-producing bacteria were obtained from aquatic and land environments in Japan by aerobic and anaerobic screening methods. Identification according to Bergey's Manual of Determinative Bacteriology or Bain and Shewan (1968) permitted assignment of the majority of the isolates to seven genera, Aeromonas, Vibrio, Flavobacterium, Beneckea, Proteus, Micrococcus, and Arthrobacter. Next, ChSase productivities of all the isolates were compared with those of two established ChSase-producing stock strains, Proteus vulgaris NCTC 4636 and Flavobacterium heparinum ATCC 13125. As a result, special attention was given to production by a strain of Aeromonas sp. of large quantities of extracellular ChSase-AC. None of the isolates from the current study displayed significant ChSase-ABC productivity. Finally, ChSase-AC was prepared from the culture fluid of the Aeromonas strain by fractional precipitation with ammonium sulfate, chromatography on phospho-cellulose and diethylaminoethyl-cellulose, and gel filtration on Sephadex G-200. It was concluded that the Aeromonas strain may represent a profitable source of the enzyme ChSase-AC.
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