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Liu X, Tao J, Zhang S, Lan W, Yao Y, Wang C, Xue H, Ji Y, Li G, Cao C. Development of charybdotoxin Q18F variant as a selective peptide blocker of neuronal BK(α + β4) channel for the treatment of epileptic seizures. Protein Sci 2022; 31:e4506. [PMID: 36369672 PMCID: PMC9703589 DOI: 10.1002/pro.4506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/14/2022]
Abstract
Epilepsy is the results from the imbalance between inhibition and excitation in neural circuits, which is mainly treated by some chemical drugs with side effects. Gain-of-function of BK channels or knockout of its β4 subunit associates with spontaneous epilepsy. Currently, few reports were published about the efficacy of BK(α + β4) channel modulators in epilepsy prevention. Charybdotoxin is a non-specific inhibitor of BK and other K+ channels. Here, by nuclear magnetic resonance (NMR) and other biochemical techniques, we found that charybdotoxin might interact with the extracellular loop of human β4 subunit (i.e., hβ4-loop) of BK(α + β4) channel at a molar ratio 4:1 (hβ4-loop vs. charybdotoxin). Charybdotoxin enhanced its ability to prevent K+ current of BK(α + β4 H101Y) channel. The charybdotoxin Q18F variant selectively reduced the neuronal spiking frequency and increased interspike intervals of BK(α + β4) channel by π-π stacking interactions between its residue Phe18 and residue His101 of hβ4-loop. Moreover, intrahippocampal infusion of charybdotoxin Q18F variant significantly increased latency time of seizure, reduced seizure duration and seizure numbers on pentylenetetrazole-induced pre-sensitized rats, inhibited hippocampal hyperexcitability and c-Fos expression, and displayed neuroprotective effects on hippocampal neurons. These results implied that charybdotoxin Q18F variant could be potentially used for intractable epilepsy treatment by therapeutically targeting BK(α + β4) channel.
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Affiliation(s)
- Xinlian Liu
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of ScienceBeijingChina
| | - Jie Tao
- Department of Neurology and Central Laboratory, Putuo HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of Biomembrane and BiopharmaceuticsShanghai UniversityShanghaiChina
| | - Shuzhang Zhang
- Institute of Biomembrane and BiopharmaceuticsShanghai UniversityShanghaiChina
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina
| | - Yu Yao
- Institute of Biomembrane and BiopharmaceuticsShanghai UniversityShanghaiChina
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, Zhangjiang LabShanghai Advanced Research Institute, Chinese Academy of SciencesShanghaiChina
| | - Yonghua Ji
- Institute of Biomembrane and BiopharmaceuticsShanghai UniversityShanghaiChina
| | - Guoyi Li
- Department of Neurology and Central Laboratory, Putuo HospitalShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of ScienceBeijingChina
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Liu X, Tao J, Zhang S, Lan W, Wang C, Ji Y, Cao C. Selective Blockade of Neuronal BK (α + β4) Channels Preventing Epileptic Seizure. J Med Chem 2019; 63:216-230. [DOI: 10.1021/acs.jmedchem.9b01241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xinlian Liu
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Science, No. 19A, Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jie Tao
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, 164 Lanxi Road, Putuo District, Shanghai 200062, China
- Institute of Biomembrane and Biopharmaceutics, Shanghai University, 99 Shangda Road,
BaoShan District, Shanghai 200444, China
| | - Shuzhang Zhang
- Institute of Biomembrane and Biopharmaceutics, Shanghai University, 99 Shangda Road,
BaoShan District, Shanghai 200444, China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yonghua Ji
- Institute of Biomembrane and Biopharmaceutics, Shanghai University, 99 Shangda Road,
BaoShan District, Shanghai 200444, China
- Xinhua Hospital (Chongming) Affiliated to Shanghai JiaoTong University School of Medicine, Shanghai Chongming Xinhua Translational Medical Institute for Cancer Pain, 25 Nanmen Port Street, Chongming Branch, Shanghai 202150, China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Science, No. 19A, Yuquan Road, Shijingshan District, Beijing 100049, China
- Institute of Drug Discovery Technology, Ningbo University, No 818 Fenghua Road, Ningbo, Zhejiang 313211, China
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Scholten A, Visser NFC, van den Heuvel RHH, Heck AJR. Analysis of protein-protein interaction surfaces using a combination of efficient lysine acetylation and nanoLC-MALDI-MS/MS applied to the E9:Im9 bacteriotoxin--immunity protein complex. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:983-994. [PMID: 16713291 DOI: 10.1016/j.jasms.2006.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 03/13/2006] [Accepted: 03/13/2006] [Indexed: 05/09/2023]
Abstract
To understand how proteins perform their function, knowledge about their structure and dynamics is essential. Here we use a combination of an efficient chemical lysine acetylation reaction and nanoLC-MALDI tandem mass spectrometry to probe the accessibility of every lysine residue in a protein complex. To demonstrate the applicability of this approach, we studied the interaction between the DNase domain of Colicin E9 (E9) and its immunity protein Im9. Free E9 and E9 in complex with Im9 were rapidly acetylated, followed by proteolytic digestion and analysis by LC-MALDI-TOF/TOF MS/MS. Acetylated peptides could be filtered out of the complex peptide mixtures using selective ion chromatograms of the specific immonium marker ions. Additionally, isobaric acetylated peptides, acetylated at different sites, could be separated by their LC retention times. The combination of LC and MALDI-TOF/TOF MS/MS provided information about the amount of acetylation on each individual lysine even for peptides containing several lysine residues. In general, our data agree well with those derived from the crystal structure of E9 and the E9:Im9 complex. Interestingly, next to in the binding interface expected lysines, K89 and K97, two from the crystal structure data unexpected lysines, K81 and K76, were observed to become less exposed upon Im9 binding. Moreover, K55 and K63, positioned in the predicted DNA binding region, were also found to be less accessible upon Im9 binding. These findings may illustrate some of the described differences in the solution-phase structure of the E9:Im9 complex compared with the crystal structure.
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Affiliation(s)
- Arjen Scholten
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands
| | - Natasja F C Visser
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands
| | - Robert H H van den Heuvel
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands
| | - Albert J R Heck
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht, The Netherlands.
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Keeble AH, Kleanthous C. The Kinetic Basis for Dual Recognition in Colicin Endonuclease–Immunity Protein Complexes. J Mol Biol 2005; 352:656-71. [PMID: 16109424 DOI: 10.1016/j.jmb.2005.07.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 07/04/2005] [Accepted: 07/13/2005] [Indexed: 11/26/2022]
Abstract
The antibacterial activity of E colicin endonucleases (DNases) is counteracted by the binding of immunity proteins; the affinities of cognate and non-cognate complexes differing by up to ten orders of magnitude. Here, we address the mechanism of complex formation using a combination of protein engineering, pre-steady-state kinetics and isothermal titration calorimetry, in order to understand the underlying basis for specificity. Contrary to previous work, we show that a pre-equilibrium mechanism does not explain the binding kinetics. Instead, the data are best explained by a modified induced-fit mechanism where cognate and non-cognate complexes alike form a non-specific, conformationally dynamic encounter complex, most likely centred on conserved interactions at the interface. The dynamics appear to be an intrinsic property of the encounter complex where the proteins move relative to one another, thereby sampling different conformations rather than being "induced" by binding. This allows optimal alignment of interface specificity sites, without producing energetically costly conformational changes, essential for high-affinity binding. Importantly, specificity is achieved without slowing the rate of association, an important requirement for rapid inhibition of the colicin in the producing bacterial cell. A rigid-body rotation model is also consistent with the observation that specificity contacts in colicin-immunity protein complexes can involve different regions of the interface. Such a kinetic discrimination mechanism explains the ability of DNase-specific immunity proteins to display dual recognition specificity, wherein they are broadly cross-reactive yet are highly specific, achieving femtomolar binding affinities in complexes with their cognate DNases.
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Affiliation(s)
- Anthony H Keeble
- Department of Biology (Area 10), P.O. Box 373, University of York, Heslington, York YO10 5YW, UK.
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Gao G, Prutzman KC, King ML, Scheswohl DM, DeRose EF, London RE, Schaller MD, Campbell SL. NMR Solution Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase in Complex with a Paxillin LD Peptide. J Biol Chem 2004; 279:8441-51. [PMID: 14662767 DOI: 10.1074/jbc.m309808200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that is regulated by integrins. Upon activation, FAK generates signals that modulate crucial cell functions, including cell proliferation, migration, and survival. The C-terminal focal adhesion targeting (FAT) sequence mediates localization of FAK to discrete regions in the cell called focal adhesions. Several binding partners for the FAT domain of FAK have been identified, including paxillin. We have determined the solution structure of the avian FAT domain in complex with a peptide mimicking the LD2 motif of paxillin by NMR spectroscopy. The FAT domain retains a similar fold to that found in the unliganded form when complexed to the paxillin-derived LD2 peptide, an antiparallel four-helix bundle. However, noticeable conformational changes were observed upon the LD2 peptide binding, especially the position of helix 4. Multiple lines of evidence, including the results obtained from isothermal titration calorimetry, intermolecular nuclear Overhauser effects, mutagenesis, and protection from paramagnetic line broadening, support the existence of two distinct paxillin-binding sites on the opposite faces of the FAT domain. The structure of the FAT domain-LD2 complex was modeled using the program HADDOCK based on our solution structure of the LD2-bound FAT domain and mutagenesis data. Our model of the FAT domain-LD2 complex provides insight into the molecular basis of FAK-paxillin binding interactions, which will aid in understanding the role of paxillin in FAK targeting and signaling.
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Affiliation(s)
- Guanghua Gao
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Kirby TW, Mueller GA, DeRose EF, Lebetkin MS, Meiss G, Pingoud A, London RE. The nuclease A inhibitor represents a new variation of the rare PR-1 fold. J Mol Biol 2002; 320:771-82. [PMID: 12095254 DOI: 10.1016/s0022-2836(02)00460-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nuclease A (NucA) from Anabaena sp. is a non-specific endonuclease able to degrade single and double-stranded DNA and RNA. The endonucleolytic activity is inhibited by the nuclease A inhibitor (NuiA), which binds to NucA with 1:1 stoichiometry and picomolar affinity. In order to better understand the mechanism of inhibition, the solution structure of NuiA was determined by NMR methods. The fold of NuiA is an alpha-beta-alpha sandwich but standard database searches by DALI and TOP revealed no structural homologies. A visual inspection of alpha-beta-alpha folds in the CATH database revealed similarities to the PR-1-like fold (SCOP nomenclature). The similarities include the ordering of secondary structural elements, a single helix on one face of the alpha-beta-alpha sandwich, and three helices on the other face. However, a major difference is in the IV helix, which in the PR-1 fold is short and perpendicular to the I and III helices, but in NuiA is long and parallel to the I and III helices. Additionally, a strand insertion in the beta-sheet makes the NuiA beta-sheet completely antiparallel in organization. The fast time-scale motions of NuiA, characterized by enhanced flexibility of the extended loop between helices III and IV, also show similarities to P14a, which is a PR-1 fold. We propose that the purpose of the PR-1 fold is to form a stable scaffold to present this extended structure for biological interactions with other proteins. This hypothesis is supported by data that show that when NuiA is bound to NucA significant changes in chemical shift occur in the extended loop between helices III and IV.
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Affiliation(s)
- Thomas W Kirby
- National Institute of Environmental Health Sciences, P.O. Box 12233, MD MR-01, Research Triangle Park, NC 27709, USA
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