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Hunt WD, McCarty NA, Marin EM, Westafer RS, Yamin PR, Cui G, Eckford AW, Denison DR. A transistor model for the cystic fibrosis transmembrane conductance regulator. BIOPHYSICAL REPORTS 2023; 3:100108. [PMID: 37351179 PMCID: PMC10282560 DOI: 10.1016/j.bpr.2023.100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/07/2023] [Indexed: 06/24/2023]
Abstract
In this paper we present a transistor circuit model for cystic fibrosis transmembrane conductance regulator (CFTR) that seeks to map the functional form of CFTR both in wild type and mutants. The circuit architecture is configured so that the function, and as much as possible the form, faithfully represents what is known about CFTR from cryo-electron microscopy and molecular dynamics. The model is a mixed analog-digital topology with an AND gate receiving the input from two separate ATP-nucleotide-binding domain binding events. The analog portion of the circuit takes the output from the AND gate as its input. The input to the circuit model and its noise characteristics are extracted from single-channel patch-clamp experiments. The chloride current predicted by the model is then compared with single-channel patch-clamp recordings for wild-type CFTR. We also consider the patch-clamp recordings from CFTR with a G551D point mutation, a clinically relevant mutant that is responsive to therapeutic management. Our circuit model approach enables bioengineering approaches to CFTR and allows biophysicists to use efficient circuit simulation tools to analyze its behavior.
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Affiliation(s)
| | | | | | | | | | - Guiying Cui
- Emory University School of Medicine, Atlanta, Georgia
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Recovery of ΔF508-CFTR Function by Citrate. Nutrients 2022; 14:nu14204283. [PMID: 36296967 PMCID: PMC9610893 DOI: 10.3390/nu14204283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Treatment of cystic fibrosis relies so far on expensive and sophisticated drugs. A logical approach to rescuing the defective ΔF508-CFTR protein has not yet been published. Therefore, virtual docking of ATP and CFTR activators to the open conformation of the CFTR protein was performed. A new ATP binding site outside of the two known locations was identified. It was located in the cleft between the nucleotide binding domains NBD1 and NBD2 and comprised six basic amino acids in close proximity. Citrate and isocitrate were also bound to this site. Citrate was evaluated for its action on epithelial cells with intact CFTR and defective ΔF508-CFTR. It activated hyaluronan export from human breast carcinoma cells and iodide efflux, and recovered ΔF508-CFTR from premature intracellular degradation. In conclusion, citrate is an activator for ΔF508-CFTR and increases export by defective ΔF508-CFTR into the extracellular matrix of epithelial cells.
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Wakabayashi-Nakao K, Yu Y, Nakakuki M, Hwang TC, Ishiguro H, Sohma Y. Characterization of Δ(G970-T1122)-CFTR, the most frequent CFTR mutant identified in Japanese cystic fibrosis patients. J Physiol Sci 2019; 69:103-112. [PMID: 29951967 PMCID: PMC10717160 DOI: 10.1007/s12576-018-0626-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/19/2018] [Indexed: 12/24/2022]
Abstract
A massive deletion over three exons 16-17b in the CFTR gene was identified in Japanese CF patients with the highest frequency (about 70% of Japanese CF patients definitely diagnosed). This pathogenic mutation results in a deletion of 153 amino acids from glycine at position 970 (G970) to threonine at 1122 (T1122) in the CFTR protein without a frameshift. We name it Δ(G970-T1122)-CFTR. In the present study, we characterized the Δ(G970-T1122)-CFTR expressed in CHO cells using immunoblots and a super resolution microscopy. Δ(G970-T1122)-CFTR proteins were synthesized and core-glycosylated but not complex-glycosylated. This observation suggests that the Δ(G970-T1122) mutation can be categorized into the class II mutation like ΔF508. However, VX-809 a CFTR corrector that can help maturation of ΔF508, had no effect on Δ(G970-T1122). Interestingly C-terminal FLAG tag seems to partially rescue the trafficking defect of Δ(G970-T1122)-CFTR; however the rescued Δ(G970-T1122)-CFTR proteins do not assume channel function. Japanese, and perhaps people in other Asian nations, carry a class II mutation Δ(G970-T1122) with a higher frequency than previously appreciated. Further study of the Δ(G970-T1122)-CFTR is essential for understanding CF and CFTR-related diseases particularly in Asian countries.
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Affiliation(s)
- Kanako Wakabayashi-Nakao
- Department of Pharmaceutical Sciences and Center for Medical Sciences, International University of Health and Welfare, 2600-1 Kitakanemaru, Otawara, Tochigi, 324-8501, Japan
- Department of Pharmacology, Keio University School of Medicine, Tokyo, Japan
| | - Yingchun Yu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO, 65211, USA
| | - Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO, 65211, USA
| | - Hiroshi Ishiguro
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiro Sohma
- Department of Pharmaceutical Sciences and Center for Medical Sciences, International University of Health and Welfare, 2600-1 Kitakanemaru, Otawara, Tochigi, 324-8501, Japan.
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO, 65211, USA.
- Department of Pharmacology, Keio University School of Medicine, Tokyo, Japan.
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Ge J, Wang C, Huang S, Du R, Liu K, Song G, Ping W. Biosynthesis regulation of natamycin production from Streptomyces natalensis HDMNTE-01 enhanced by response surface methodology. Prep Biochem Biotechnol 2017; 47:939-944. [PMID: 28816611 DOI: 10.1080/10826068.2017.1365244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Natamycin has been widely applied in medical treatments and food protection widely due to its effective inhibition to the growth of yeast and mold. As polyene macrolide antibiotic, the biosynthesis pathway of natamycin is relatively clear. To regulate the biosynthesis of natamycin, additions of precursors affecting cell growth and natamycin production were investigated. The results showed that 0.003% (w/v) potassium ferrocyanide and sodium propionate: n-butanol at a ratio of 4:1 was added into the broth at 0 and 24 hr, respectively, and they contributed to yield natamycin, reaching 1.62 g L-1 (174.6% higher than control). Furthermore, response surface methodology was undertaken to enhance natamycin production by Streptomyces natalensis HDMNTE-01 (a wild strain). The optimum conditions determined were: glucose 3.97%; soya peptone 2%; yeast extract 0.5%; original pH 7.0; inoculum volume 6%; growth in a 250-mL flask containing 24.68 mL of medium; shaken (220 rpm) at 28°C for 4 days. Under the optimized conditions, the yield was 2.81 g L-1 natamycin in 5-L fermentor when the fermentation was processed.
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Affiliation(s)
- Jingping Ge
- a Key Laboratory of Microbiology, College of Life Science , Heilongjiang University , Harbin , P. R. China
| | - Changli Wang
- a Key Laboratory of Microbiology, College of Life Science , Heilongjiang University , Harbin , P. R. China
| | - Shoufeng Huang
- a Key Laboratory of Microbiology, College of Life Science , Heilongjiang University , Harbin , P. R. China
| | - Renpeng Du
- a Key Laboratory of Microbiology, College of Life Science , Heilongjiang University , Harbin , P. R. China
| | - Kun Liu
- a Key Laboratory of Microbiology, College of Life Science , Heilongjiang University , Harbin , P. R. China
| | - Gang Song
- a Key Laboratory of Microbiology, College of Life Science , Heilongjiang University , Harbin , P. R. China
| | - Wenxiang Ping
- a Key Laboratory of Microbiology, College of Life Science , Heilongjiang University , Harbin , P. R. China
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Prehm P. Curcumin analogue identified as hyaluronan export inhibitor by virtual docking to the ABC transporter MRP5. Food Chem Toxicol 2013; 62:76-81. [PMID: 23978416 DOI: 10.1016/j.fct.2013.08.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 08/13/2013] [Accepted: 08/16/2013] [Indexed: 11/29/2022]
Abstract
Hyaluronan is overproduced in many diseases including metastasis, inflammation or ischemia, but there is no drug to attenuate hyaluronan production. Hyaluronan is exported from fibroblasts by the multidrug resistance associated protein 5 (MRP5) which is inhibited by the plant phenols curcumin or xanthohumol. We performed virtual docking and chemical synthesis of analogues to optimize the inhibitors. The AutoDock software was used to identify the binding cavity within the open conformation of MRP5. Inhibitory plant phenols bound to the ATP binding site between the two nucleotide binding domains NBD1 and NBD2. This binding cavity was chosen to screen about 120 derivatives and analogues. The superior hyaluronan export inhibitor was 1,5-bis(4-hydroxy-3-methoxyphenyl)-1,4-pentadien-3-one (hylin). It inhibited hyaluronan export from fibroblasts with an IC50 of 4.9 μM. Hylin is a minor component in natural curcumin preparations and has previously been described as anti-metastatic and anti-inflammatory. Since curcumin itself is unstable under physiological conditions, the active component for many cell biological and pharmaceutical effects of natural curcumin preparations could be hylin that acts by hyaluronan export inhibition.
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Affiliation(s)
- Peter Prehm
- Muenster University Hospital, Institute of Physiological Chemistry and Pathobiochemistry, Waldeyerstrasse 15, D-48149 Muenster, Germany.
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Krasilnikov OV, Sabirov RZ, Okada Y. ATP hydrolysis-dependent asymmetry of the conformation of CFTR channel pore. J Physiol Sci 2011; 61:267-78. [PMID: 21461971 PMCID: PMC10717511 DOI: 10.1007/s12576-011-0144-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 03/20/2011] [Indexed: 01/13/2023]
Abstract
Despite substantial efforts, the entire cystic fibrosis transmembrane conductance regulator (CFTR) protein proved to be difficult for structural analysis at high resolution, and little is still known about the actual dimensions of the anion-transporting pathway of CFTR channel. In the present study, we therefore gauged geometrical features of the CFTR Cl(-) channel pore by a nonelectrolyte exclusion technique. Polyethylene glycols with a hydrodynamic radius (R (h)) smaller than 0.95 nm (PEG 300-1,000) added from the intracellular side greatly suppressed the inward unitary anionic conductance, whereas only molecules with R (h) ≤ 0.62 nm (PEG 200-400) applied extracellularly were able to affect the outward unitary anionic currents. Larger molecules with R (h) = 1.16-1.84 nm (PEG 1,540-3,400) added from either side were completely excluded from the pore and had no significant effect on the single-channel conductance. The cut-off radius of the inner entrance of CFTR channel pore was assessed to be 1.19 ± 0.02 nm. The outer entrance was narrower with its cut-off radius of 0.70 ± 0.16 nm and was dilated to 0.93 ± 0.23 nm when a non-hydrolyzable ATP analog, 5'-adenylylimidodiphosphate (AMP-PNP), was added to the intracellular solution. Thus, it is concluded that the structure of CFTR channel pore is highly asymmetric with a narrower extracellular entrance and that a dilating conformational change of the extracellular entrance is associated with the channel transition to a non-hydrolytic, locked-open state.
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Affiliation(s)
- Oleg V. Krasilnikov
- Department of Cell Physiology, National Institute for Physiological Sciences, Okazaki, 444-8585 Japan
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Recife, PE 50670-901 Brazil
| | - Ravshan Z. Sabirov
- Department of Cell Physiology, National Institute for Physiological Sciences, Okazaki, 444-8585 Japan
- Laboratory of Molecular Physiology, Institute of Physiology and Biophysics, Academy of Science RUz, Niyazova 1, 100095 Tashkent, Uzbekistan
- Department of Biophysics, National University, Niyazova 1, 100095 Tashkent, Uzbekistan
| | - Yasunobu Okada
- Department of Cell Physiology, National Institute for Physiological Sciences, Okazaki, 444-8585 Japan
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