1
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Bartlett B, Stitt-Bergh M, Kantar M, Bingham JP. A data science practicum to introduce undergraduate students to bioinformatics for research. Biochem Mol Biol Educ 2023; 51:520-528. [PMID: 37401749 PMCID: PMC10621008 DOI: 10.1002/bmb.21762] [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: 06/21/2022] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 07/05/2023]
Abstract
An explosion of data available in the life sciences has shifted the discipline toward genomics and quantitative data science research. Institutions of higher learning have been addressing this shift by modifying undergraduate curriculums resulting in an increasing number of bioinformatics courses and research opportunities for undergraduates. The goal of this study was to explore how a newly designed introductory bioinformatics seminar could leverage the combination of in-class instruction and independent research to build the practical skill sets of undergraduate students beginning their careers in the life sciences. Participants were surveyed to assess learning perceptions toward the dual curriculum. Most students had a neutral or positive interest in these topics before the seminar and reported increased interest after the seminar. Students had increases in confidence level in their bioinformatic proficiency and understanding of ethical principles for data/genomic science. By combining undergraduate research with directed bioinformatics skills, classroom seminars facilitated a connection between student's life sciences knowledge and emerging research tools in computational biology.
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Affiliation(s)
- Bjarne Bartlett
- The University of Hawaii at Manoa, Department of Molecular Biosystems and Bioengineering, Honolulu, Hawaii, United States
| | - Monica Stitt-Bergh
- Assessment and Curriculum Support Center, The University of Hawaii at Manoa, Honolulu, Hawaii, United States
| | - Michael Kantar
- Department of Tropical Plant and Soil Sciences, The University of Hawaii at Manoa, Honolulu, Hawaii, United States
| | - Jon-Paul Bingham
- The University of Hawaii at Manoa, Department of Molecular Biosystems and Bioengineering, Honolulu, Hawaii, United States
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2
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Espiritu MJ, Taylor JK, Sugai CK, Thapa P, Loening NM, Gusman E, Baoanan ZG, Baumann MH, Bingham JP. Characterization of the Native Disulfide Isomers of the Novel χ-Conotoxin PnID: Implications for Further Increasing Conotoxin Diversity. Mar Drugs 2023; 21:61. [PMID: 36827103 PMCID: PMC9964023 DOI: 10.3390/md21020061] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
χ-Conotoxins are known for their ability to selectively inhibit norepinephrine transporters, an ability that makes them potential leads for treating various neurological disorders, including neuropathic pain. PnID, a peptide isolated from the venom of Conus pennaceus, shares high sequence homology with previously characterized χ-conotoxins. Whereas previously reported χ-conotoxins seem to only have a single native disulfide bonding pattern, PnID has three native isomers due to the formation of different disulfide bond patterns during its maturation in the venom duct. In this study, the disulfide connectivity and three-dimensional structure of these disulfide isomers were explored using regioselective synthesis, chromatographic coelution, and solution-state nuclear magnetic resonance spectroscopy. Of the native isomers, only the isomer with a ribbon disulfide configuration showed pharmacological activity similar to other χ-conotoxins. This isomer inhibited the rat norepinephrine transporter (IC50 = 10 ± 2 µM) and has the most structural similarity to previously characterized χ-conotoxins. In contrast, the globular isoform of PnID showed more than ten times less activity against this transporter and the beaded isoform did not display any measurable biological activity. This study is the first report of the pharmacological and structural characterization of an χ-conotoxin from a species other than Conus marmoreus and is the first report of the existence of natively-formed conotoxin isomers.
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Affiliation(s)
- Michael J. Espiritu
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
- School of Pharmacy, Pacific University, 222 SE 8th Ave, Ste. 451, Hillsboro, OR 97123, USA
| | - Jonathan K. Taylor
- School of Pharmacy, Pacific University, 222 SE 8th Ave, Ste. 451, Hillsboro, OR 97123, USA
| | - Christopher K. Sugai
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Nikolaus M. Loening
- Department of Chemistry, Lewis & Clark College, 615 S Palatine Hill Road, Portland, OR 97219, USA
| | - Emma Gusman
- School of Pharmacy, Pacific University, 222 SE 8th Ave, Ste. 451, Hillsboro, OR 97123, USA
| | - Zenaida G. Baoanan
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
- Department of Biology, College of Science, University of the Philippines Baguio, Baguio City 2600, Philippines
| | - Michael H. Baumann
- Designer Drug Research Unit, Intramural Research Program, National Institute on Drug Abuse (NIDA), National Institutes of Health (NIH), 333 Cassell Drive Suite 4400, Baltimore, MD 21224, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
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3
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DeLude A, Wells R, Boomla S, Chuang SC, Urena F, Shipman A, Rubas N, Kuehu DL, Bickerton B, Peterson T, Dobhal S, Arizala D, Klair D, Ochoa-Corona F, Ali ME, Odani J, Bingham JP, Jenkins DM, Fletcher J, Stack JP, Alvarez AM, Arif M. Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. Sci Rep 2022; 12:19193. [PMID: 36357509 PMCID: PMC9649655 DOI: 10.1038/s41598-022-22023-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Dickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae) causes soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deployable loop-mediated isothermal amplification (LAMP) assay using a unique genomic region, present exclusively in D. fangzhongdai. Multiple genomes of D. fangzhongdai, and other species of Dickeya, Pectobacterium and unrelated genera were used for comparative genomic analyses to identify an exclusive and conserved target sequence from the major facilitator superfamily (MFS) transporter gene region. This gene region had broad detection capability for D. fangzhongdai and thus was used to design primers for endpoint PCR and LAMP assays. In-silico validation showed high specificity with D. fangzhongdai genome sequences available in the NCBI GenBank genome database as well as the in-house sequenced genome. The specificity of the LAMP assay was determined with 96 strains that included all Dickeya species and Pectobacterium species as well as other closely related genera and 5 hosts; no false positives or false negatives were detected. The detection limit of the assay was determined by performing four sensitivity assays with tenfold serially diluted purified genomic DNA of D. fangzhongdai with and without the presence of crude host extract (taro, orchid, and onion). The detection limit for all sensitivity assays was 100 fg (18-20 genome copies) with no negative interference by host crude extracts. The assays were performed by five independent operators (blind test) and on three instruments (Rotor-Gene, thermocycler and dry bath); the assay results were concordant. The assay consistently detected the target pathogen from artificially inoculated and naturally infected host samples. The developed assay is highly specific for D. fangzhongdai and has applications in routine diagnostics, phytosanitary and seed certification programs, and epidemiological studies.
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Affiliation(s)
- Anuhea DeLude
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Riley Wells
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Sherine Boomla
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shu-Cheng Chuang
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Frank Urena
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Aaron Shipman
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Noelle Rubas
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Donna Lee Kuehu
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Buster Bickerton
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Taylor Peterson
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shefali Dobhal
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Dario Arizala
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Diksha Klair
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Francisco Ochoa-Corona
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - Md Emran Ali
- grid.213876.90000 0004 1936 738XDepartment of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Jenee Odani
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jon-Paul Bingham
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Daniel M. Jenkins
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jacqueline Fletcher
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - James P. Stack
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Anne M. Alvarez
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Mohammad Arif
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
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4
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Wiere S, Sugai C, Espiritu MJ, Aurelio VP, Reyes CD, Yuzon N, Whittal RM, Tytgat J, Peigneur S, Bingham JP. Research into the Bioengineering of a Novel α-Conotoxin from the Milked Venom of Conus obscurus. Int J Mol Sci 2022; 23:12096. [PMID: 36292948 PMCID: PMC9602734 DOI: 10.3390/ijms232012096] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022] Open
Abstract
The marine cone snail produces one of the fastest prey strikes in the animal kingdom. It injects highly efficacious venom, often causing prey paralysis and death within seconds. Each snail has hundreds of conotoxins, which serve as a source for discovering and utilizing novel analgesic peptide therapeutics. In this study, we discovered, isolated, and synthesized a novel α3/5-conotoxins derived from the milked venom of Conus obscurus (α-conotoxin OI) and identified the presence of α-conotoxin SI-like sequence previously found in the venom of Conus striatus. Five synthetic analogs of the native α-conotoxin OI were generated. These analogs incorporated single residue or double residue mutations. Three synthetic post-translational modifications (PTMs) were synthetically incorporated into these analogs: N-terminal truncation, proline hydroxylation, and tryptophan bromination. The native α-conotoxin OI demonstrated nanomolar potency in Poecilia reticulata and Homosapiens muscle-type nicotinic acetylcholine receptor (nAChR) isoforms. Moreover, the synthetic α-[P9K] conotoxin OI displayed enhanced potency in both bioassays, ranging from a 2.85 (LD50) to 18.4 (IC50) fold increase in comparative bioactivity. The successful incorporation of PTMs, with retention of both potency and nAChR isoform selectivity, ultimately pushes new boundaries of peptide bioengineering and the generation of novel α-conotoxin-like sequences.
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Affiliation(s)
- Sean Wiere
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Christopher Sugai
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Michael J. Espiritu
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
- School of Pharmacy, Pacific University Oregon, Hillsboro, OR 97123, USA
| | - Vincent P. Aurelio
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Chloe D. Reyes
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Nicole Yuzon
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
| | - Randy M. Whittal
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, 3000 Leuven, Belgium
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, 3000 Leuven, Belgium
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai’i, Honolulu, HI 96822, USA
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5
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Domingo R, Perez C, Klair D, Vu H, Candelario-Tochiki A, Wang X, Camson A, Uy JN, Salameh M, Arizala D, Dobhal S, Boluk G, Bingham JP, Ochoa-Corona F, Ali ME, Stack JP, Fletcher J, Odani J, Jenkins D, Alvarez AM, Arif M. Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil. Sci Rep 2021; 11:21948. [PMID: 34753982 PMCID: PMC8578433 DOI: 10.1038/s41598-021-01196-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
Pectobacterium parmentieri (formerly Pectobacterium wasabiae), which causes soft rot disease in potatoes, is a newly established species of pectinolytic bacteria within the family Pectobacteriaceae. Despite serious damage caused to the potato industry worldwide, no field-deployable diagnostic tests are available to detect the pathogen in plant samples. In this study, we aimed to develop a reliable, rapid, field-deployable loop-mediated isothermal amplification (LAMP) assay for the specific detection of P. parmentieri. Specific LAMP primers targeting the petF1 gene region, found in P. parmentieri but no other Pectobacterium spp., were designed and validated in silico and in vitro using extensive inclusivity (15 strains of P. parmentieri) and exclusivity (94 strains including all other species in the genus Pectobacterium and host DNA) panels. No false positives or negatives were detected when the assay was tested directly with bacterial colonies, and with infected plant and soil samples. Sensitivity (analytical) assays using serially diluted bacterial cell lysate and purified genomic DNA established the detection limit at 10 CFU/mL and 100 fg (18-20 genome copies), respectively, even in the presence of host crude DNA. Consistent results obtained by multiple users/operators and field tests suggest the assay's applicability to routine diagnostics, seed certification programs, biosecurity, and epidemiological studies.
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Affiliation(s)
- Ryan Domingo
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Cristian Perez
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Diksha Klair
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Huong Vu
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Alika Candelario-Tochiki
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Amihan Camson
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jaclyn Nicole Uy
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mouauia Salameh
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Gamze Boluk
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Francisco Ochoa-Corona
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - James P Stack
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jacqueline Fletcher
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Jenee Odani
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Daniel Jenkins
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
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6
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Laurora A, Bingham JP, Poojary MM, Wall MM, Ho KK. Carotenoid composition and bioaccessibility of papaya cultivars from Hawaii. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103984] [Citation(s) in RCA: 1] [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: 10/21/2022]
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7
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Laczko R, Chang A, Watanabe L, Petelo M, Kahaleua K, Bingham JP, Csiszar K. Anti-inflammatory activities of Waltheria indica extracts by modulating expression of IL-1B, TNF-α, TNFRII and NF-κB in human macrophages. Inflammopharmacology 2019; 28:525-540. [PMID: 31686273 DOI: 10.1007/s10787-019-00658-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022]
Abstract
In Hawaiian traditional medicinal practices, the indigenous 'uhaloa, Waltheria indica var. Americana is one of the most recognized plants. Waltheria is also known in various cultures as a medicinal plant for the treatment of inflammatory conditions. Results in human subjects and cell and animal models supported anti-inflammatory activity for the Waltheria flavonoid quercetin, and for crude plant extracts, limited animal studies also confirmed anti-inflammatory effects. Yet no systematic studies have examined immune or inflammatory responses affected by these extracts. In order to gain insight into inflammatory cascades modulated by Waltheria extracts, and to uncover the mechanistic bases for the effective use of this medicinal plant as a natural anti-inflammatory agent, we have undertaken analyses of LPS and TNF-α/IF-γ-stimulated human macrophages treated with Waltheria extracts using targeted qRT-PCR and Inflammation Panels to test differential mRNA expression of two hundred immune-related genes, furthermore, ELISA assays and Inflammatory Protein arrays to determine extracts-modulated intracellular and secreted levels of prominent cytokines. Results demonstrate that Waltheria extracts inhibit key inflammatory cytokines and cytokine receptors including protein levels of IL-1B, IL-1ra, IL-8 and IL-6, reduce both mRNA and protein levels of TNF-α and protein levels of its receptor, TNF RII, predicting diminished TNF-α-associated inflammatory signaling that, together with significant reduction of NF-κB mRNA and protein, can effectively diminish activities of multiple pro-inflammatory signaling pathways and mitigate key processes in diseases with inflammatory components.
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Affiliation(s)
- Rozalia Laczko
- Department of Integrative Medicine and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Andrew Chang
- Department of Integrative Medicine and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Lindsey Watanabe
- Department of Integrative Medicine and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Maria Petelo
- Department of Integrative Medicine and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Kimberly Kahaleua
- Department of Integrative Medicine and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, USA
| | - Katalin Csiszar
- Department of Integrative Medicine and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA.
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8
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Affiliation(s)
- Anthony Mau
- College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jon-Paul Bingham
- College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Fabio Soller
- Aquatic Feeds and Nutrition Department, Oceanic Institute of Hawaii Pacific University, Waimanalo, HI, USA
| | - Rajesh Jha
- College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, USA
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9
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Zhang RY, Thapa P, Espiritu MJ, Menon V, Bingham JP. From nature to creation: Going around in circles, the art of peptide cyclization. Bioorg Med Chem 2018; 26:1135-1150. [DOI: 10.1016/j.bmc.2017.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 02/02/2023]
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10
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Thapa P, Cabalteja CC, Philips EE, Espiritu MJ, Peigneur S, Mille BG, Tytgat J, Cummins TR, Bingham JP. t-boc synthesis of huwentoxin-i through native chemical ligation incorporating a trifluoromethanesulfonic acid cleavage strategy. Biopolymers 2017; 106:737-45. [PMID: 27271997 DOI: 10.1002/bip.22887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 02/04/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 11/10/2022]
Abstract
Tert-butyloxycarbonyl (t-Boc)-based native chemical ligation (NCL) techniques commonly employ hydrogen fluoride (HF) to create the thioester fragment required for the ligation process. Our research aimed to assess the replacement of HF with Trifluoromethanesulfonic acid (TFMSA). Here we examined a 33 amino acid test peptide, Huwentoxin-I (HwTx-I) as a novel candidate for our TFMSA cleavage protocol. Structurally HwTx-I has an X-Cys(16) -Cys(17) -X sequence mid-region, which makes it an ideal candidate for NCL. Experiments determined that the best yields (16.8%) obtained for 50 mg of a thioester support resin were achieved with a TFMSA volume of 100 μL with a 0.5-h incubation on ice, followed by 2.0 h at room temperature. RP-HPLC/UV and mass spectra indicated the appropriate parent mass and retention of the cleaved HwTx-I N-terminal thioester fragment (Ala(1) -Cys(16) ), which was used in preparation for NCL. The resulting chemically ligated HwTx-I was oxidized/folded, purified, and then assessed for pharmacological target selectivity. Native-like HwTx-I produced by this method yielded an EC50 value of 340.5 ± 26.8 nM for Nav 1.2 and an EC50 value of 504.1 ± 81.3 nM for Nav 1.3, this being similar to previous literature results using native material. This article represents the first NCL based synthesis of this potent sodium channel blocker. Our illustrated approach removes potential restrictions in the advancement of NCL as a common peptide laboratory technique with minimal investment, and removes the hazards associated with HF usage. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 737-745, 2016.
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Affiliation(s)
- Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Chino C Cabalteja
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Edwin E Philips
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Michael J Espiritu
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822
| | - Steve Peigneur
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, 3000, Belgium
| | - Bea G Mille
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, 3000, Belgium
| | - Jan Tytgat
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, 3000, Belgium
| | - Theodore R Cummins
- Department of Pharmacology and Toxicology, Indiana University, Indianapolis, IN.,Department of Pharmacology and Toxicology, Stark Neurosciences Research Institute, 320 West 25th Street, NB-414F, Indianapolis, IN, 46202-2266
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, 96822.
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Maldonado A, Johnson A, Gochfeld D, Slattery M, Ostrander GK, Bingham JP, Schlenk D. Hard coral (Porites lobata) extracts and homarine on cytochrome P450 expression in Hawaiian butterflyfishes with different feeding strategies. Comp Biochem Physiol C Toxicol Pharmacol 2016; 179:57-63. [PMID: 26297807 DOI: 10.1016/j.cbpc.2015.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 12/27/2022]
Abstract
Dietary specialists tend to be less susceptible to the effects of chemical defenses produced by their prey compared to generalist predators that feed upon a broader range of prey species. While many researchers have investigated the ability of insects to detoxify dietary allelochemicals, little research has been conducted in marine ecosystems. We investigated metabolic detoxification pathways in three species of butterflyfishes: the hard coral specialist feeder, Chaetodon multicinctus, and two generalist feeders, Chaetodon auriga and Chaetodon kleinii. Each species was fed tissue homogenate of the hard coral Porites lobata or the feeding deterrent compound homarine (found in the coral extract), and the expression and catalytic activity of cytochrome P450 (CYP) 3A-like and CYP2-like enzymes were examined after one-week of treatment. The P. lobata homogenate significantly induced content and catalytic activity of CYP2-like and CYP3A-like forms, by 2-3 fold and by 3-9 fold, respectively, in C. multicinctus. Homarine caused a significant decrease of CYP2-like and CYP3A-like proteins at the high dose in C. kleinii and 60-80% mortality in that species. Homarine also induced CYP3A-like content by 3-fold and catalytic activity by 2-fold in C. auriga, while causing non-monotonic increases in CYP2-like and CYP3A-like catalytic activity in C. multicinctus. Our results indicate that dietary exposure to coral homogenates and the feeding deterrent constituent within these homogenates caused species-specific modulation of detoxification enzymes consistent with the prey selection strategies of generalist and specialist butterflyfishes.
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Affiliation(s)
- Aileen Maldonado
- Department of Environmental Science, University of California, Riverside, 2258 Geology, 900 University Ave., Riverside, CA 92521, USA.
| | - Amber Johnson
- Department of Environmental Science, University of California, Riverside, 2258 Geology, 900 University Ave., Riverside, CA 92521, USA
| | - Deborah Gochfeld
- National Center for Natural Products Research and Department of BioMolecular Science, University of Mississippi, P.O. Box 1848, University, MS 38677, USA
| | - Marc Slattery
- National Center for Natural Products Research and Department of BioMolecular Science, University of Mississippi, P.O. Box 1848, University, MS 38677, USA
| | - Gary K Ostrander
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306-1330, USA
| | - Jon-Paul Bingham
- Department of Molecular Bioscience and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Ag. Science 218, Honolulu, HI 96822, USA
| | - Daniel Schlenk
- Department of Environmental Science, University of California, Riverside, 2258 Geology, 900 University Ave., Riverside, CA 92521, USA
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Colmegna B, Uboldi S, Frapolli R, Licandro SA, Panini N, Galmarini CM, Badri N, Spanswick VJ, Bingham JP, Kiakos K, Erba E, Hartley JA, D'Incalci M. Increased sensitivity to platinum drugs of cancer cells with acquired resistance to trabectedin. Br J Cancer 2015; 113:1687-93. [PMID: 26633559 PMCID: PMC4701998 DOI: 10.1038/bjc.2015.407] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/29/2015] [Accepted: 11/06/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND In order to investigate the mechanisms of acquired resistance to trabectedin, trabectedin-resistant human myxoid liposarcoma (402-91/T) and ovarian carcinoma (A2780/T) cell lines were derived and characterised in vitro and in vivo. METHODS Resistant cell lines were obtained by repeated exposures to trabectedin. Characterisation was performed by evaluating drug sensitivity, cell cycle perturbations, DNA damage and DNA repair protein expression. In vivo experiments were performed on A2780 and A2780/T xenografts. RESULTS 402-91/T and A2780/T cells were six-fold resistant to trabectedin compared with parental cells. Resistant cells were found to be hypersensitive to UV light and did not express specific proteins involved in the nucleotide excision repair (NER) pathway: XPF and ERCC1 in 402-91/T and XPG in A2780/T. NER deficiency in trabectedin-resistant cells was associated with the absence of a G2/M arrest induced by trabectedin and with enhanced sensitivity (two-fold) to platinum drugs. In A2780/T, this collateral sensitivity, confirmed in vivo, was associated with an increased formation of DNA interstrand crosslinks. CONCLUSIONS Our finding that resistance to trabectedin is associated with the loss of NER function, with a consequent increased sensitivity to platinum drugs, provides the rational for sequential use of these drugs in patients who have acquired resistance to trabectedin.
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Affiliation(s)
- B Colmegna
- Department of Oncology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, Milan 20156, Italy
| | - S Uboldi
- Department of Oncology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, Milan 20156, Italy
| | - R Frapolli
- Department of Oncology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, Milan 20156, Italy
| | - S A Licandro
- Department of Oncology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, Milan 20156, Italy
| | - N Panini
- Department of Oncology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, Milan 20156, Italy
| | - C M Galmarini
- Department of Research and Development (R&D), PharmaMar S.A., Colmenar Viejo, Madrid 28770, Spain
| | - Nadia Badri
- Department of Research and Development (R&D), PharmaMar S.A., Colmenar Viejo, Madrid 28770, Spain
| | - V J Spanswick
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - J P Bingham
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - E Erba
- Department of Oncology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, Milan 20156, Italy
| | - J A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK
| | - M D'Incalci
- Department of Oncology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, via La Masa 19, Milan 20156, Italy
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Abstract
Two classes of small homologous basic proteins, mamba snake dendrotoxins (DTX) and bovine pancreatic trypsin inhibitor (BPTI), block the large conductance Ca(2+)-activated K(+) channel (BKCa, KCa1.1) by production of discrete subconductance events when added to the intracellular side of the membrane. This toxin-channel interaction is unlikely to be pharmacologically relevant to the action of mamba venom, but as a fortuitous ligand-protein interaction, it has certain biophysical implications for the mechanism of BKCa channel gating. In this work we examined the subconductance behavior of 9 natural dendrotoxin homologs and 6 charge neutralization mutants of δ-dendrotoxin in the context of current structural information on the intracellular gating ring domain of the BKCa channel. Calculation of an electrostatic surface map of the BKCa gating ring based on the Poisson-Boltzmann equation reveals a predominantly electronegative surface due to an abundance of solvent-accessible side chains of negatively charged amino acids. Available structure-activity information suggests that cationic DTX/BPTI molecules bind by electrostatic attraction to site(s) on the gating ring located in or near the cytoplasmic side portals where the inactivation ball peptide of the β2 subunit enters to block the channel. Such an interaction may decrease the apparent unitary conductance by altering the dynamic balance of open versus closed states of BKCa channel activation gating.
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Halford ZA, Yu PY, Likeman RK, Hawley-Molloy JS, Thomas C, Bingham JP. Cone shell envenomation: epidemiology, pharmacology and medical care. Diving Hyperb Med 2015; 45:200-207. [PMID: 26415072] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/11/2015] [Indexed: 06/05/2023]
Abstract
The marine environment presents much danger, specifically in regards to the numerous venomous inhabitants within tropical and subtropical waters. The toxins from one such group of venomous marine snails, commonly referred to as 'cone snails', have been well documented in causing human fatalities. Yet information regarding medical treatment for cone snail envenomation is limited and poorly accessible. To correct this, medical and scientific expertise and literary review on Conus provide a basic and comprehensive directive focused on the medical treatment and post-mortem investigative analysis of cone snail envenomation. We emphasize what we expect to be the most lethal feeding group of Conus and provide a brief background to the epidemiology of their stings. We describe the venom apparatus of Conus and its utility of rapid venom delivery. We have compiled the documented incidences of Conus envenomation to offer thorough reference of known signs and symptoms - this too drawing on personal experiences in the field. We have also made available a brief background to the biochemistry and pharmacology of Conus venoms to highlight their complex nature.
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Affiliation(s)
- Zan A Halford
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Peter Yc Yu
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Robert K Likeman
- Directorate of Army Health, Department of Defense, Canberra, ACT, Australia, formerly Director of Army Health, Department of Defense, Canberra, Australia
| | | | - Craig Thomas
- Hawaii Emergency Physicians Associated, 407 Uluniu St, Suite 411, Kailua, HI
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii HI, 96822, USA, E-mail:
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15
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Thapa P, Zhang RY, Menon V, Bingham JP. Native chemical ligation: a boon to peptide chemistry. Molecules 2014; 19:14461-83. [PMID: 25221869 PMCID: PMC6271921 DOI: 10.3390/molecules190914461] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/02/2014] [Accepted: 09/02/2014] [Indexed: 11/16/2022] Open
Abstract
The use of chemical ligation within the realm of peptide chemistry has opened various opportunities to expand the applications of peptides/proteins in biological sciences. Expansion and refinement of ligation chemistry has made it possible for the entry of peptides into the world of viable oral therapeutic drugs through peptide backbone cyclization. This progression has been a journey of chemical exploration and transition, leading to the dominance of native chemical ligation in the present advances of peptide/protein applications. Here we illustrate and explore the historical and current nature of peptide ligation, providing a clear indication to the possibilities and use of these novel methods to take peptides outside their typically defined boundaries.
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Affiliation(s)
- Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Rui-Yang Zhang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Vinay Menon
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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Thapa P, Espiritu MJ, Cabalteja C, Bingham JP. The Emergence of Cyclic Peptides: The Potential of Bioengineered Peptide Drugs. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9421-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Espiritu MJ, Collier AC, Bingham JP. A 21st-century approach to age-old problems: the ascension of biologics in clinical therapeutics. Drug Discov Today 2014; 19:1109-13. [DOI: 10.1016/j.drudis.2014.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 12/31/2013] [Accepted: 01/20/2014] [Indexed: 01/07/2023]
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19
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Thapa P, Espiritu MJ, Cabalteja CC, Bingham JP. Conotoxins and their regulatory considerations. Regul Toxicol Pharmacol 2014; 70:197-202. [PMID: 25013992 DOI: 10.1016/j.yrtph.2014.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 06/29/2014] [Accepted: 06/30/2014] [Indexed: 01/21/2023]
Abstract
Venom derived peptides from marine cone snails, conotoxins, have demonstrated unique pharmacological targeting properties that have been pivotal in advancing medical research. The awareness of their true toxic origins and potent pharmacological nature is emphasized by their 'select agent' classification by the US Centers for Disease Control and Prevention. We briefly introduce the biochemical and pharmacological aspects of conotoxins, highlighting current advancements into their biological engineering, and provide details to the present regulations that govern their use in research.
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Affiliation(s)
- Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai'i, Honolulu, HI 96822, USA
| | - Michael J Espiritu
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai'i, Honolulu, HI 96822, USA
| | - Chino C Cabalteja
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai'i, Honolulu, HI 96822, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai'i, Honolulu, HI 96822, USA.
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Yafuso JT, Negi VS, Bingham JP, Borthakur D. An O-Acetylserine (thiol) Lyase from Leucaena leucocephala Is a Cysteine Synthase But Not a Mimosine Synthase. Appl Biochem Biotechnol 2014; 173:1157-68. [DOI: 10.1007/s12010-014-0917-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/09/2014] [Indexed: 10/25/2022]
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21
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Negi VS, Bingham JP, Li QX, Borthakur D. A carbon-nitrogen lyase from Leucaena leucocephala catalyzes the first step of mimosine degradation. Plant Physiol 2014; 164:922-34. [PMID: 24351687 PMCID: PMC3912116 DOI: 10.1104/pp.113.230870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 12/16/2013] [Indexed: 05/22/2023]
Abstract
The tree legume Leucaena leucocephala contains a large amount of a toxic nonprotein aromatic amino acid, mimosine, and also an enzyme, mimosinase, for mimosine degradation. In this study, we isolated a 1,520-bp complementary DNA (cDNA) for mimosinase from L. leucocephala and characterized the encoded enzyme for mimosine-degrading activity. The deduced amino acid sequence of the coding region of the cDNA was predicted to have a chloroplast transit peptide. The nucleotide sequence, excluding the sequence for the chloroplast transit peptide, was codon optimized and expressed in Escherichia coli. The purified recombinant enzyme was used in mimosine degradation assays, and the chromatogram of the major product was found to be identical to that of 3-hydroxy-4-pyridone (3H4P), which was further verified by electrospray ionization-tandem mass spectrometry. The enzyme activity requires pyridoxal 5'-phosphate but not α-keto acid; therefore, the enzyme is not an aminotransferase. In addition to 3H4P, we also identified pyruvate and ammonia as other degradation products. The dependence of the enzyme on pyridoxal 5'-phosphate and the production of 3H4P with the release of ammonia indicate that it is a carbon-nitrogen lyase. It was found to be highly efficient and specific in catalyzing mimosine degradation, with apparent Km and Vmax values of 1.16×10(-4) m and 5.05×10(-5) mol s(-1) mg(-1), respectively. The presence of other aromatic amino acids, including l-tyrosine, l-phenylalanine, and l-tryptophan, in the reaction did not show any competitive inhibition. The isolation of the mimosinase cDNA and the biochemical characterization of the recombinant enzyme will be useful in developing transgenic L. leucocephala with reduced mimosine content in the future.
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Bingham JP. The Emergence of Cyclic Peptides: The Potential of Bioengineered Peptide Drugs. Med Chem 2014. [DOI: 10.4172/2161-0444.1000180] [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: 11/09/2022]
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Bergeron ZL, Chun JB, Baker MR, Sandall DW, Peigneur S, Yu PY, Thapa P, Milisen JW, Tytgat J, Livett BG, Bingham JP. A 'conovenomic' analysis of the milked venom from the mollusk-hunting cone snail Conus textile--the pharmacological importance of post-translational modifications. Peptides 2013; 49:145-58. [PMID: 24055806 PMCID: PMC6013274 DOI: 10.1016/j.peptides.2013.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 09/08/2013] [Accepted: 09/09/2013] [Indexed: 12/19/2022]
Abstract
Cone snail venoms provide a largely untapped source of novel peptide drug leads. To enhance the discovery phase, a detailed comparative proteomic analysis was undertaken on milked venom from the mollusk-hunting cone snail, Conus textile, from three different geographic locations (Hawai'i, American Samoa and Australia's Great Barrier Reef). A novel milked venom conopeptide rich in post-translational modifications was discovered, characterized and named α-conotoxin TxIC. We assign this conopeptide to the 4/7 α-conotoxin family based on the peptide's sequence homology and cDNA pre-propeptide alignment. Pharmacologically, α-conotoxin TxIC demonstrates minimal activity on human acetylcholine receptor models (100 μM, <5% inhibition), compared to its high paralytic potency in invertebrates, PD50 = 34.2 nMol kg(-1). The non-post-translationally modified form, [Pro](2,8)[Glu](16)α-conotoxin TxIC, demonstrates differential selectivity for the α3β2 isoform of the nicotinic acetylcholine receptor with maximal inhibition of 96% and an observed IC50 of 5.4 ± 0.5 μM. Interestingly its comparative PD50 (3.6 μMol kg(-1)) in invertebrates was ~100 fold more than that of the native peptide. Differentiating α-conotoxin TxIC from other α-conotoxins is the high degree of post-translational modification (44% of residues). This includes the incorporation of γ-carboxyglutamic acid, two moieties of 4-trans hydroxyproline, two disulfide bond linkages, and C-terminal amidation. These findings expand upon the known chemical diversity of α-conotoxins and illustrate a potential driver of toxin phyla-selectivity within Conus.
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Affiliation(s)
- Zachary L. Bergeron
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i, Honolulu, HI, USA, 96822
| | - Joycelyn B. Chun
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i, Honolulu, HI, USA, 96822
| | - Margaret R. Baker
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i, Honolulu, HI, USA, 96822
| | - David W. Sandall
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Steve Peigneur
- Laboratory of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, Belgium, 3000
| | - Peter Y.C. Yu
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i, Honolulu, HI, USA, 96822
| | - Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i, Honolulu, HI, USA, 96822
| | - Jeffrey W. Milisen
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i, Honolulu, HI, USA, 96822
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, University of Leuven (KU Leuven), Campus Gasthuisberg O&N II, Leuven, Belgium, 3000
| | - Bruce G. Livett
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia, 3010
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i, Honolulu, HI, USA, 96822
- Corresponding Author: Dr. Jon-Paul Bingham, , Fax: (808) 965-3542, Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawai'i, HI, 96822, USA
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Kapono CA, Thapa P, Cabalteja CC, Guendisch D, Collier AC, Bingham JP. Conotoxin truncation as a post-translational modification to increase the pharmacological diversity within the milked venom of Conus magus. Toxicon 2013; 70:170-8. [DOI: 10.1016/j.toxicon.2013.04.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/15/2013] [Accepted: 04/23/2013] [Indexed: 01/07/2023]
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25
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Negi VS, Bingham JP, Li QX, Borthakur D. midD-encoded 'rhizomimosinase' from Rhizobium sp. strain TAL1145 is a C-N lyase that catabolizes L-mimosine into 3-hydroxy-4-pyridone, pyruvate and ammonia. Amino Acids 2013; 44:1537-47. [PMID: 23462928 DOI: 10.1007/s00726-013-1479-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
Rhizobium sp. strain TAL1145 catabolizes mimosine, which is a toxic non-protein amino acid present in Leucaena leucocephala (leucaena). The objective of this investigation was to study the biochemical and catalytic properties of the enzyme encoded by midD, one of the TAL1145 genes involved in mimosine degradation. The midD-encoded enzyme, MidD, was expressed in Escherichia coli, purified and used for biochemical and catalytic studies using mimosine as the substrate. The reaction products in the enzyme assay were analyzed by HPLC and mass spectrometry. MidD has a molecular mass of ~45 kDa and its catalytic activity was found to be optimal at 37 °C and pH 8.5. The major product formed in the reaction had the same retention time as that of synthetic 3-hydroxy-4-pyridone (3H4P). It was confirmed to be 3H4P by MS/MS analysis of the HPLC-purified product. The K m, V max and K cat of MidD were 1.27 × 10(-4) mol, 4.96 × 10(-5) mol s(-1) mg(-1), and 2,256.05 s(-1), respectively. Although MidD has sequence similarities with aminotransferases, it is not an aminotransferase because it does not require a keto acid as the co-substrate in the degradation reaction. It is a pyridoxal-5'-phosphate (PLP)-dependent enzyme and the addition of 50 μM hydroxylamine completely inhibited the reaction. However, the supplementation of the reaction with 0.1 μM PLP restored the catalytic activity of MidD in the reaction containing 50 μM hydroxylamine. The catalytic activity of MidD was found to be specific to mimosine, and the presence of its structural analogs including L-tyrosine, L-tryptophan and L-phenylalanine did not show any competitive inhibition. In addition to 3H4P, we also identified pyruvate and ammonia as other degradation products in equimolar quantities of the substrate used. The degradation of mimosine into a ring compound, 3H4P with the release of ammonia indicates that MidD of Rhizobium sp. strain TAL1145 is a C-N lyase.
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Affiliation(s)
- Vishal Singh Negi
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
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Abstract
Scorpion toxins have been central to the investigation and understanding of the physiological role of potassium (K+) channels and their expansive function in membrane biophysics. As highly specific probes, toxins have revealed a great deal about channel structure and the correlation between mutations, altered regulation and a number of human pathologies. Radio- and fluorescently-labeled toxin isoforms have contributed to localization studies of channel subtypes in expressing cells, and have been further used in competitive displacement assays for the identification of additional novel ligands for use in research and medicine. Chimeric toxins have been designed from multiple peptide scaffolds to probe channel isoform specificity, while advanced epitope chimerization has aided in the development of novel molecular therapeutics. Peptide backbone cyclization has been utilized to enhance therapeutic efficiency by augmenting serum stability and toxin half-life in vivo as a number of K+-channel isoforms have been identified with essential roles in disease states ranging from HIV, T-cell mediated autoimmune disease and hypertension to various cardiac arrhythmias and Malaria. Bioengineered scorpion toxins have been monumental to the evolution of channel science, and are now serving as templates for the development of invaluable experimental molecular therapeutics.
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Affiliation(s)
- Zachary L Bergeron
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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Bingham JP, Andrews EA, Kiyabu SM, Cabalteja CC. Drugs from slugs. Part II--conopeptide bioengineering. Chem Biol Interact 2012; 200:92-113. [PMID: 23063744 DOI: 10.1016/j.cbi.2012.09.021] [Citation(s) in RCA: 12] [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] [Received: 06/30/2012] [Revised: 08/27/2012] [Accepted: 09/17/2012] [Indexed: 11/27/2022]
Abstract
The biological transformation of toxins as research probes, or as pharmaceutical drug leads, is an onerous and drawn out process. Issues regarding changes to pharmacological specificity, desired potency, and bioavailability are compounded naturally by their inherent toxicity. These often scuttle their progress as they move up the narrowing drug development pipeline. Yet one class of peptide toxins, from the genus Conus, has in many ways spearheaded the expansion of new peptide bioengineering techniques to aid peptide toxin pharmaceutical development. What has now emerged is the sequential bioengineering of new research probes and drug leads that owe their lineage to these highly potent and isoform specific peptides. Here we discuss the progressive bioengineering steps that many conopeptides have transitioned through, and specifically illustrate some of the biochemical approaches that have been established to maximize their biological research potential and pharmaceutical worth.
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Affiliation(s)
- Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA.
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Bingham JP, Baker MR, Chun JB. Analysis of a cone snail's killer cocktail--the milked venom of Conus geographus. Toxicon 2012; 60:1166-70. [PMID: 22884604 DOI: 10.1016/j.toxicon.2012.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/19/2012] [Accepted: 07/25/2012] [Indexed: 11/27/2022]
Abstract
"Snails can kill" is a statement that receives much disbelief. Yet the venom from Conus geographus, as delivered by a disposable hypodermic-like needle, has indeed killed many unsuspecting human victims. Our understanding of their milked venom the essence of these fatalities, is in itself non-existent. Here, we present the molecular mass analysis of the milked venom of C. geographus, providing the first insight into the composition of its deadly cocktail.
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Affiliation(s)
- Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI 96822, USA.
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Chun JBS, Baker MR, Kim DH, Leroy M, Toribo P, Bingham JP. Cone snail milked venom dynamics--a quantitative study of Conus purpurascens. Toxicon 2012; 60:83-94. [PMID: 22497788 DOI: 10.1016/j.toxicon.2012.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 03/10/2012] [Accepted: 03/22/2012] [Indexed: 11/16/2022]
Abstract
Milked venom from cone snails represent a novel biological resource with a proven track record for drug discovery. To strengthen this correlation, we undertook a chromatographic and mass spectrometric study of individual milked venoms from Conus purpurascens. Milked venoms demonstrate extensive peptide differentiation amongst individual specimens and during captivity. Individual snails were found to lack a consistent set of described conopeptides, but instead demonstrated the ability to change venom expression, composition and post-translational modification incorporation; all variations contribute to an increase in chemical diversity and prey targeting strategies. Quantitative amino acid analysis revealed that milked venom peptides are expressed at ranges up to 3.51-121.01 μM within single milked venom samples. This provides for a 6.37-20,965 fold-excess of toxin to induce apparent IC₅₀ for individual conopeptides identified in this study. Comparative molecular mass analysis of duct venom, milked venom and radula tooth extracts from single C. purpurascens specimens demonstrated a level of peptide continuity. Numerous highly abundant and unique conopeptides remain to be characterized. This study strengthens the notion that approaches in conopeptide drug lead discovery programs will potentially benefit from a greater understanding of the toxinological nature of the milked venoms of Conus.
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Affiliation(s)
- Joycelyn B S Chun
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI 96822, USA
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Gilly WF, Richmond TA, Duda TF, Elliger C, Lebaric Z, Schulz J, Bingham JP, Sweedler JV. A diverse family of novel peptide toxins from an unusual cone snail, Conus californicus. ACTA ACUST UNITED AC 2011; 214:147-61. [PMID: 21147978 DOI: 10.1242/jeb.046086] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Diversity among Conus toxins mirrors the high species diversity in the Indo-Pacific region, and evolution of both is thought to stem from feeding-niche specialization derived from intra-generic competition. This study focuses on Conus californicus, a phylogenetic outlier endemic to the temperate northeast Pacific. Essentially free of congeneric competitors, it preys on a wider variety of organisms than any other cone snail. Using molecular cloning of cDNAs and mass spectrometry, we examined peptides isolated from venom ducts to elucidate the sequences and post-translational modifications of two eight-cysteine toxins (cal12a and cal12b of type 12 framework) that block voltage-gated Na(+) channels. Based on homology of leader sequence and mode of action, these toxins are related to the O-superfamily, but differ significantly from other members of that group. Six of the eight cysteine residues constitute the canonical framework of O-members, but two additional cysteine residues in the N-terminal region define an O+2 classification within the O-superfamily. Fifteen putative variants of Cal12.1 toxins have been identified by mRNAs that differ primarily in two short hypervariable regions and have been grouped into three subtypes (Cal12.1.1-3). This unique modular variation has not been described for other Conus toxins and suggests recombination as a diversity-generating mechanism. We propose that these toxin isoforms show specificity for similar molecular targets (Na(+) channels) in the many species preyed on by C. californicus and that individualistic utilization of specific toxin isoforms may involve control of gene expression.
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Affiliation(s)
- W F Gilly
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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Bingham JP, Mitsunaga E, Bergeron ZL. Drugs from slugs--past, present and future perspectives of omega-conotoxin research. Chem Biol Interact 2010; 183:1-18. [PMID: 19800874 DOI: 10.1016/j.cbi.2009.09.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 09/03/2009] [Accepted: 09/24/2009] [Indexed: 12/18/2022]
Abstract
Peptides from the venom of carnivorous cone shells have provided six decades of intense research, which has led to the discovery and development of novel analgesic peptide therapeutics. Our understanding of this unique natural marine resource is however somewhat limited. Given the past pharmacological record, future investigations into the toxinology of these highly venomous tropical marine snails will undoubtedly yield other highly selective ion channel inhibitors and modulators. With over a thousand conotoxin-derived sequences identified to date, those identified as ion channel inhibitors represent only a small fraction of the total. Here we discuss our present understanding of conotoxins, focusing on the omega-conotoxin peptide family, and illustrate how such a seemingly simple snail has yielded a highly effective clinical drug.
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Affiliation(s)
- Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA.
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Bingham JP, Chun JB, Ruzicka MR, Li QX, Tan ZY, Kaulin YA, Englebretsen DR, Moczydlowski EG. Synthesis of an iberiotoxin derivative by chemical ligation: a method for improved yields of cysteine-rich scorpion toxin peptides. Peptides 2009; 30:1049-57. [PMID: 19463736 PMCID: PMC2998342 DOI: 10.1016/j.peptides.2009.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 03/10/2009] [Accepted: 03/10/2009] [Indexed: 10/21/2022]
Abstract
Automated and manual solid phase peptide synthesis techniques were combined with chemical ligation to produce a 37-residue peptide toxin derivative of iberiotoxin which contained: (i) substitution of Val(16) to Ala, to facilitate kinetic feasibility of native chemical ligation, and; (ii) substitution of Asp(19) to orthogonally protected Cys-4-MeOBzl for chemical conjugate derivatization following peptide folding and oxidation. This peptide ligation approach increased synthetic yields approximately 12-fold compared to standard linear peptide synthesis. In a functional inhibition assay, the ligated scorpion toxin derivative, iberiotoxin V16A/D19-Cys-4-MeOBzl, exhibited 'native-like' affinity (K(d)=1.9 nM) and specificity towards the BK Ca(2+)-activated K(+) Channel (K(Ca)1.1). This was characterized by the rapid association and slow dissociation rates (k(on)=4.59 x 10(5)M(-1)s(-1); k(off)=8.65 x 10(-4) s(-1)) as determined by inhibition of macroscopic whole-cell currents of cloned human K(Ca)1.1 channel. These results illustrate the successful application of peptide chemical ligation to improve yield of cysteine-rich peptide toxins over traditional solid phase peptide synthesis. Native chemical ligation is a promising method for improving production of biologically active disulfide containing peptide toxins, which have diverse applications in studies of ion-channel function.
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Affiliation(s)
- Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI 96822, USA.
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Xiao Y, Bingham JP, Zhu W, Moczydlowski E, Liang S, Cummins TR. Tarantula huwentoxin-IV inhibits neuronal sodium channels by binding to receptor site 4 and trapping the domain ii voltage sensor in the closed configuration. J Biol Chem 2008; 283:27300-13. [PMID: 18628201 DOI: 10.1074/jbc.m708447200] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Peptide toxins with high affinity, divergent pharmacological functions, and isoform-specific selectivity are powerful tools for investigating the structure-function relationships of voltage-gated sodium channels (VGSCs). Although a number of interesting inhibitors have been reported from tarantula venoms, little is known about the mechanism for their interaction with VGSCs. We show that huwentoxin-IV (HWTX-IV), a 35-residue peptide from tarantula Ornithoctonus huwena venom, preferentially inhibits neuronal VGSC subtypes rNav1.2, rNav1.3, and hNav1.7 compared with muscle subtypes rNav1.4 and hNav1.5. Of the five VGSCs examined, hNav1.7 was most sensitive to HWTX-IV (IC(50) approximately 26 nM). Following application of 1 microm HWTX-IV, hNav1.7 currents could only be elicited with extreme depolarizations (>+100 mV). Recovery of hNav1.7 channels from HWTX-IV inhibition could be induced by extreme depolarizations or moderate depolarizations lasting several minutes. Site-directed mutagenesis analysis indicated that the toxin docked at neurotoxin receptor site 4 located at the extracellular S3-S4 linker of domain II. Mutations E818Q and D816N in hNav1.7 decreased toxin affinity for hNav1.7 by approximately 300-fold, whereas the reverse mutations in rNav1.4 (N655D/Q657E) and the corresponding mutations in hNav1.5 (R812D/S814E) greatly increased the sensitivity of the muscle VGSCs to HWTX-IV. Our data identify a novel mechanism for sodium channel inhibition by tarantula toxins involving binding to neurotoxin receptor site 4. In contrast to scorpion beta-toxins that trap the IIS4 voltage sensor in an outward configuration, we propose that HWTX-IV traps the voltage sensor of domain II in the inward, closed configuration.
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Affiliation(s)
- Yucheng Xiao
- Department of Pharmacology and Toxicology, Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Bingham JP, Bian S, Tan ZY, Takacs Z, Moczydlowski E. Synthesis of a biotin derivative of iberiotoxin: binding interactions with streptavidin and the BK Ca2+-activated K+ channel expressed in a human cell line. Bioconjug Chem 2006; 17:689-99. [PMID: 16704206 PMCID: PMC2505059 DOI: 10.1021/bc060002u] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iberiotoxin (IbTx) is a scorpion venom peptide that inhibits BK Ca2+-activated K+ channels with high affinity and specificity. Automated solid-phase synthesis was used to prepare a biotin-labeled derivative (IbTx-LC-biotin) of IbTx by substitution of Asp19 of the native 37-residue peptide with N--(D-biotin-6-amidocaproate)-L-lysine. Both IbTx-LC-biotin and its complex with streptavidin (StrAv) block single BK channels from rat skeletal muscle with nanomolar affinity, indicating that the biotin-labeled residue, either alone or in complex with StrAv, does not obstruct the toxin binding interaction with the BK channel. IbTx-LC-biotin exhibits high affinity (KD = 26 nM) and a slow dissociation rate (koff = 5.4 x 10(-4) s(-1)) in a macroscopic blocking assay of whole-cell current of the cloned human BK channel. Titration of IbTx-LC-biotin with StrAv monitored by high performance size exclusion chromatography is consistent with a stoichiometry of two binding sites for IbTx-LC-biotin per StrAv tetramer, indicating that steric interference hinders simultaneous binding of two toxin molecules on each of the two biotin-binding faces of StrAv. In combination with fluorescent conjugates of StrAv or anti-biotin antibody, IbTx-LC-biotin was used to image the surface distribution of BK channels on a transfected cell line. Fluorescence microscopy revealed a patch-like surface distribution of BK channel protein. The results support the feasibility of using IbTx-LC-biotin and similar biotin-tagged K+ channel toxins for diverse applications in cellular neurobiology. .
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Affiliation(s)
| | - Shumin Bian
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven CT 06520
| | - Zhi-Yong Tan
- Department of Internal Medicine, University of Iowa, Iowa City IA 52242
| | - Zoltan Takacs
- The Department of Pediatrics; University of Chicago, Chicago, IL 60637
| | - Edward Moczydlowski
- Department of Biology, Clarkson University, Potsdam, NY 13699
- Corresponding Author: Edward Moczydlowski, Department of Biology, Box 5805, Clarkson University, Potsdam, NY 13699-5805; Tel.: 315-268-6641; Fax: 315-268-7118; e-mail:
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Krishnan MN, Bingham JP, Lee SH, Trombley P, Moczydlowski E. Functional role and affinity of inorganic cations in stabilizing the tetrameric structure of the KcsA K+ channel. J Gen Physiol 2005; 126:271-83. [PMID: 16129774 PMCID: PMC2266582 DOI: 10.1085/jgp.200509323] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 08/02/2005] [Indexed: 11/20/2022] Open
Abstract
Crystal structures of the tetrameric KcsA K+ channel reveal seven distinct binding sites for K+ ions within the central pore formed at the fourfold rotational symmetry axis. Coordination of an individual K+ ion by eight protein oxygen atoms within the selectivity filter suggests that ion-subunit bridging by cation-oxygen interactions contributes to structural stability of the tetramer. To test this hypothesis, we examined the effect of inorganic cations on the temperature dependence of the KcsA tetramer as monitored by SDS-PAGE. Inorganic cations known to permeate or strongly block K+ channels (K+, Rb+, Cs+, Tl+, NH4+, Ba2+, and Sr2+) confer tetramer stability at higher temperatures (T0.5 range = 87 degrees C to >99 degrees C) than impermeant cations and weak blockers (Li+, Na+, Tris+, choline+; T0.5 range = 59 degrees C to 77 degrees C). Titration of K+, Ba2+, and other stabilizing cations protects against rapid loss of KcsA tetramer observed in 100 mM choline Cl at 90 degrees C. Tetramer protection titrations of K+, Rb+, Cs+, Tl+, and NH4+ at 85 degrees C or 90 degrees C exhibit apparent Hill coefficients (N) ranging from 1.7 to 3.3 and affinity constants (K0.5) ranging from 1.1 to 9.6 mM. Ba2+ and Sr2+ titrations exhibit apparent one-site behavior (N congruent with 1) with K0.5 values of 210 nM and 11 microM, respectively. At 95 degrees C in the presence of 5 mM K+, titration of Li+ or Na+ destabilizes the tetramer with K0.5 values of 57 mM and 109 mM, respectively. We conclude that specific binding interactions of inorganic cations with the selectivity filter are an important determinant of tetramer stability of KscA.
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Affiliation(s)
- Manoj N Krishnan
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
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Bingham JP, Broxton NM, Livett BG, Down JG, Jones A, Moczydlowski EG. Optimizing the connectivity in disulfide-rich peptides: α-conotoxin SII as a case study. Anal Biochem 2005; 338:48-61. [PMID: 15707935 DOI: 10.1016/j.ab.2004.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2004] [Indexed: 10/25/2022]
Abstract
We describe a strategy for the efficient, unambiguous assignment of disulfide connectivities in alpha-conotoxin SII, of which approximately 30% of its mass is cysteine, as an example of a generalizable technique for investigation of cysteine-rich peptides. alpha-Conotoxin SII was shown to possess 3-8, 2-18, and 4-14 disulfide bond connectivity. Sequential disulfide bond connectivity analysis was performed by partial reduction with Tris(2-carboxyethyl)phosphine and real-time mass monitoring by direct-infusion electrospray mass spectrometry (ESMS). This method achieved high yields of the differentially reduced disulfide bonded intermediates and economic use of reduced peptide. Intermediates were alkylated with either N-phenylmaleimide or 4-vinylpyridine. The resulting alkyl products were assigned by ESMS and their alkyl positions sequentially identified via conventional Edman degradation. The methodology described allows a more efficient, rapid, and reliable assignment of disulfide bond connectivity in synthetic and native cysteine-rich peptides.
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Affiliation(s)
- Jon-Paul Bingham
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA.
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Jakubowski JA, Keays DA, Kelley WP, Sandall DW, Bingham JP, Livett BG, Gayler KR, Sweedler JV. Determining sequences and post-translational modifications of novel conotoxins in Conus victoriae using cDNA sequencing and mass spectrometry. J Mass Spectrom 2004; 39:548-557. [PMID: 15170751 DOI: 10.1002/jms.624] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A combination of cDNA cloning and detailed mass spectrometric analyses was employed to identify novel conotoxins from Conus victoriae. Eleven conotoxin sequences were determined using molecular methods: one belonging to the A superfamily (Vc1.1), six belonging to the O superfamily (Vc6.1-Vc6.6) and four members of the T superfamily (Vc5.1-Vc5.4). In order to verify the sequences and identify the post-translational modifications (excluding the disulfide connectivity) of three Conus victoriae conotoxins, vc1a, vc5a and vc6a, deduced from sequences Vc1.1, Vc5.1, and Vc6.1, respectively, liquid chromatography/electrospray ionization ion trap mass spectrometry, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nanospray ionization ion trap mass spectrometry with collisionally induced dissociation were performed on reduced and alkylated venom fractions. We report that vc1a, the native form of alpha-conotoxin Vc1.1 (an unmodified 16 amino acid residue peptide that has notable pain-relieving capabilities), includes a hydroxyproline and a gamma-carboxyglutamate residue. Conotoxin vc5a is a 10-residue peptide with two disulfide bonds and a hydroxyproline and vc6a is a 25 amino acid peptide with three disulfide bonds.
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Affiliation(s)
- Jennifer A Jakubowski
- Department of Chemistry and the Beckman Institute, University of Illinois, Urbana-Champaign, Illinois 61801, USA
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Duda TF, Bingham JP, Livett BG, Kohn AJ, Massilia GR, Schultz JR, Down J, Sandall D, Sweedler JV. How Much at Risk Are Cone Snails? Science 2004; 303:955-7; author reply 955-7. [PMID: 14963310 DOI: 10.1126/science.303.5660.955] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Marshall J, Kelley WP, Rubakhin SS, Bingham JP, Sweedler JV, Gilly WF. Anatomical correlates of venom production in Conus californicus. Biol Bull 2002; 203:27-41. [PMID: 12200253 DOI: 10.2307/1543455] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Like all members of the genus, Conus californicus has a specialized venom apparatus, including a modified radular tooth, with which it injects paralyzing venom into its prey. In this paper the venom duct and its connection to the pharynx, along with the radular sac and teeth, were examined using light and transmission electron microscopy. The general anatomy of the venom apparatus resembles that in other members of the genus, but several features are described that have not been previously reported for other species. The proximal (posterior) quarter of the venom duct is composed of a complex epithelium that may be specialized for active transport rather than secretion. The distal portion of the duct is composed of a different type of epithelium, suggestive of holocrine secretion, and the cells display prominent intracellular granules of at least two types. Similar granules fill the lumen of the duct. The passageway between the lumen of the venom duct and pharynx is a flattened branching channel that narrows to a width of 10 micro m and is lined by a unique cell type of unknown function. Granular material similar to that in the venom duct was also found in the lumen of individual teeth within the radular sac. Mass spectrometry (MALDI-TOF) demonstrated the presence of putative peptides in material derived from the tooth lumen, and all of the more prominent species were also evident in the anterior venom duct. Radular teeth thus appear to be loaded with peptide toxins while they are still in the radular sac.
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Affiliation(s)
- Jennifer Marshall
- Hopkins Marine Station and Department of Biological Sciences of Stanford University, Pacific Grove, California 93950, USA
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Grimaldi KA, Bingham JP, Hartley JA. PCR-based assays for strand-specific measurement of DNA damage and repair. I. Strand-specific quantitative PCR. Methods Mol Biol 1999; 113:227-40. [PMID: 10443424 DOI: 10.1385/1-59259-675-4:227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- K A Grimaldi
- Department of Oncology, University College London Medical School, UK
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Hill JM, Oomen CJ, Miranda LP, Bingham JP, Alewood PF, Craik DJ. Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: effects of solution environment on helicity. Biochemistry 1998; 37:15621-30. [PMID: 9843366 DOI: 10.1021/bi981535w] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [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: 11/29/2022]
Abstract
alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha3 beta2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha3 beta2 interface. Here we describe the three-dimensional solution structure of MII determined using 2D 1H NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 A for the backbone atoms and 0.34 A for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha3beta2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.
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Affiliation(s)
- J M Hill
- Centre for Drug Design and Development, The University of Queensland, Brisbane, Australia
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Bingham JP, Hartley JA, Souhami RL, Grimaldi KA. Strand-specific measurement of cisplatin-induced DNA damage and repair using quantitative PCR. Nucleic Acids Res 1996; 24:987-9. [PMID: 8600473 PMCID: PMC145736 DOI: 10.1093/nar/24.5.987] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- J P Bingham
- Department of Oncology, University College London Medical School, UK
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Jones A, Bingham JP, Gehrmann J, Bond T, Loughnan M, Atkins A, Lewis RJ, Alewood PF. Isolation and characterization of conopeptides by high-performance liquid chromatography combined with mass spectrometry and tandem mass spectrometry. Rapid Commun Mass Spectrom 1996; 10:138-143. [PMID: 8563013 DOI: 10.1002/(sici)1097-0231(19960115)10:1<138::aid-rcm442>3.0.co;2-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- A Jones
- Centre for DrugDesign and Development, The University of Queensland, Brisbane, Australia
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Grimaldi KA, Bingham JP, Souhami RL, Hartley JA. DNA damage by anticancer agents and its repair: mapping in cells at the subgene level with quantitative polymerase chain reaction. Anal Biochem 1994; 222:236-42. [PMID: 7856855 DOI: 10.1006/abio.1994.1479] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [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: 01/27/2023]
Abstract
The quantitative polymerase chain reaction (QPCR)-based assay was used to measure DNA damage and repair to a small (523 bp) fragment of the single-copy human N-ras gene in K562 cells. Compared with previous methods DNA preparation from treated cells and the subsequent detection of the radioactive product were considerably simplified. The results demonstrated that QPCR can be used to measure damage in a small gene segment, caused by cisplatin, nitrogen, and quinacrine mustards. Drug-DNA adducts produced by two novel minor groove binding, sequence-specific molecules (AT-486 and DSB-120) could be detected at physiologically relevant concentrations of drug. For both cisplatin and nitrogen mustard the concentrations required to cause damage in cells were higher than those needed to cause equivalent damage in isolated DNA. In contrast both AT-486 and quinacrine mustard caused more damage at equimolar concentrations in cells than in isolated DNA. DSB-120, which is closely related to AT-486, was found to be 15-fold less effective than the latter at causing damage in treated cells despite similar reactivity with isolated DNA. Repair of damage caused by quinacrine mustard to the same small gene fragment was found to proceed at a constant rate over 24 h. The QPCR assay presented here is a simple quantitative method to measure damage and repair in subgene functional units such as promoters, introns, and exons.
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Affiliation(s)
- K A Grimaldi
- Department of Oncology, University College London Medical School, United Kingdom
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Lewis RJ, Bingham JP, Jones A, Alewood PF, Andrews PR. Drugs from the peptide venoms of marine cone shells. Australas Biotechnol 1994; 4:298-300. [PMID: 7765678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Australian cone shell venoms are being investigated as an exciting new source of bioactive peptides as part of a new collaborative project between the 3D Centre and AMRAD. Initial studies have already revealed a number of new and novel acting peptides amongst the hundred or so small, heavily constrained peptides present in the venom of each cone shell. The aim of the project is to develop peptidomimetic drugs based on a selection of these native peptides.
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Affiliation(s)
- R J Lewis
- Drug Design and Development (3D) Centre, Gehrmann Laboratories, University of Queensland, St Lucia
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Holley JL, Mather A, Wheelhouse RT, Cullis PM, Hartley JA, Bingham JP, Cohen GM. Targeting of tumor cells and DNA by a chlorambucil-spermidine conjugate. Cancer Res 1992; 52:4190-5. [PMID: 1638533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many tumor cells, including murine ADJ/PC6 plasmacytoma cells, possess an active energy dependent polyamine uptake system which selectively accumulates endogenous polyamines and structurally related compounds. We have attempted to target the cytotoxic drug chlorambucil to a tumor possessing this uptake system by conjugating it to the polyamine spermidine. Furthermore, since polyamines have a high affinity for DNA, the attachment of spermidine to chlorambucil should also facilitate its targeting to DNA. This was supported by the observation that the chlorambucil-spermidine conjugate was approximately 10,000-fold more active than chlorambucil at forming interstrand crosslinks with naked DNA. In vitro cytotoxicity and in vivo antitumor studies were carried out using the ADJ/PC6 plasmacytoma. In vitro, using [3H]thymidine incorporation to assess cell viability following a 1-h exposure to control and polyamine depleted ADJ/PC6 cells, chlorambucil-spermidine was 35- and 225-fold, respectively, more toxic than chlorambucil. The increased toxicity of the conjugate compared to chlorambucil was possibly due to enhanced DNA binding and/or facilitated uptake via the polyamine uptake system. The enhanced toxicity of the conjugate but not chlorambucil by prior polyamine depletion with difluoromethylornithine, together with the observation that the conjugate but not chlorambucil competitively inhibited spermidine uptake into tumor cells, supported the suggestion that the conjugate utilized the polyamine uptake system. In vivo following a single i.p. dose, the conjugate was 4-fold more potent than chlorambucil in its ability to inhibit ADJ/PC6 tumor growth in BALB/c mice. However, the therapeutic index was not increased. Our results support the hypothesis that polyamines linked to cytotoxics facilitate their entry into tumor cells possessing a polyamine uptake system and increase their selectivity to DNA. This may have therapeutic application in the delivery of cytotoxic agents linked to polyamines to certain tumors.
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Affiliation(s)
- J L Holley
- Medical Research Council Toxicology Unit, Carshalton, Surrey, United Kingdom
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Hartley JA, Bingham JP, Souhami RL. DNA sequence selectivity of guanine-N7 alkylation by nitrogen mustards is preserved in intact cells. Nucleic Acids Res 1992; 20:3175-8. [PMID: 1620613 PMCID: PMC312455 DOI: 10.1093/nar/20.12.3175] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [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: 12/27/2022] Open
Abstract
Nitrogen mustard alkylating agents react with isolated DNA in a sequence selective manner, and the substituent attached to the drug reactive group can impose a distinct sequence preference. It is not clear however to what extent the observed DNA sequence preferences are preserved in intact cells. The highly reiterated sequence of human alpha DNA has been used to determine the sites of guanine-N7 alkylation following treatment of cells with three nitrogen mustards, mechlorethamine, uracil mustard and quinacrine mustard, known to react in isolated DNA with distinctly different sequence preferences. Alpha DNA from drug treated cells was extracted, purified, end-labeled, and a 296 base pair, singly end-labelled, fragment isolated. Following the quantitative conversion of alkylation sites to strand breaks the fragments were separated on DNA sequencing gels. Clear differences were observed between the alkylation patterns of the three compounds, and the selectivities were qualitatively similar to those predicted and observed in the same sequence alkylated in vitro. In particular the unique preferences of uracil and quinacrine mustards for 5'-PyGC-3' and 5'-GT/GPu-3' sequences, respectively, were preserved in intact cells suggesting that the pattern of sequence dependent reactivity is not grossly affected by the nuclear milieu.
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Affiliation(s)
- J A Hartley
- Department of Oncology, University College and Middlesex School of Medicine, London, UK
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