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Luan M, Hou Z, Zhang B, Ma L, Yuan S, Liu Y, Huang G. Inter-Domain Repulsion of Dumbbell-Shaped Calmodulin during Electrospray Ionization Revealed by Molecular Dynamics Simulations. Anal Chem 2023; 95:8798-8806. [PMID: 37309130 DOI: 10.1021/acs.analchem.2c05630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The mechanisms whereby protein ions are released from nanodroplets at the liquid-gas interface have continued to be controversial since electrospray ionization (ESI) mass spectrometry was widely applied in biomolecular structure analysis in solution. Several viable pathways have been proposed and verified for single-domain proteins. However, the ESI mechanism of multi-domain proteins with more complicated and flexible structures remains unclear. Herein, dumbbell-shaped calmodulin was chosen as a multi-domain protein model to perform molecular dynamics simulations to investigate the structural evolution during the ESI process. For [Ca4CAM], the protein followed the classical charge residue model. As the inter-domain electrostatic repulsion increased, the droplet was found to split into two sub-droplets, while stronger-repulsive apo-calmodulin unfolded during the early evaporation stage. We designated this novel ESI mechanism as the domain repulsion model, which provides new mechanistic insights into further exploration of proteins containing more domains. Our results suggest that greater attention should be paid to the effect of domain-domain interactions on structure retention during liquid-gas interface transfer when mass spectrometry is used as the developing technique in gas phase structural biology.
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Affiliation(s)
- Moujun Luan
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Zhuanghao Hou
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Buchun Zhang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Likun Ma
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Siming Yuan
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Yangzhong Liu
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
| | - Guangming Huang
- Department of Cardiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
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2
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Lipstein N, Göth M, Piotrowski C, Pagel K, Sinz A, Jahn O. Presynaptic Calmodulin targets: lessons from structural proteomics. Expert Rev Proteomics 2017; 14:223-242. [DOI: 10.1080/14789450.2017.1275966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Noa Lipstein
- Department of Molecular Neurobiology, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| | - Melanie Göth
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin & Fritz Haber Institute of the Max-Planck-Society, Berlin, Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin & Fritz Haber Institute of the Max-Planck-Society, Berlin, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
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3
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Liu Y, Wang T, Calabrese AN, Carver JA, Cummins SF, Bowie JH. The membrane-active amphibian peptide caerin 1.8 inhibits fibril formation of amyloid β1-42. Peptides 2015; 73:1-6. [PMID: 26275335 DOI: 10.1016/j.peptides.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/04/2015] [Accepted: 08/04/2015] [Indexed: 12/21/2022]
Abstract
The amphibian host-defense peptide caerin 1.8 [(1)GLFKVLGSV(10)AKHLLPHVVP(20)VIAEKL(NH2)] inhibits fibril formation of amyloid β 1-42 [(1)DAEFRHDSG(10)YEVHHQKLVF(20)FAEDVGSNKG(30)AIIGLMVGGV(40)VIA] [Aβ42] (the major precursor of the extracellular fibrillar deposits of Alzheimer's disease). Some truncated forms of caerin 1.8 also inhibit fibril formation of Aβ42. For example, caerin 1.8 (1-13) [(1)GLFKVLGSV(10)AKHL(NH2) and caerin 1.8 (22-25) [KVLGSV(10)AKHLLPHVVP(20)VIAEKL(NH2)] show 85% and 75% respectively of the inhibition activity of the parent caerin 1.8. The synthetic peptide KLVFFKKKKKK is a known inhibitor of Aβ42 fibril formation, and was used as a standard in this study. Caerin 1.8 is the more effective fibril inhibitor. IC50 values (± 15%) are caerin 1.8 (75 μM) and KLVFFKKKKKK (370 μM). MALDI mass spectrometry shows the presence of a small peak corresponding to a protonated 1:1 adduct [caerin 1.8/Aβ42]H(+). Molecular dynamics simulation suggests that both hydrogen bonding and hydrophobic interactions between Aβ42 and caerin 1.8 facilitate the formation of a 1:1 complex in water. Fibril formation from Aβ42 has been proposed to be based around the (16)KLVF(20)F region of Aβ42; this region in the 1:1 complex is partially blocked from attachment of a further molecule of Aβ42.
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Affiliation(s)
- Yanqin Liu
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Antonio N Calabrese
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Canberra, Australian Capital Chemistry, 2601, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - John H Bowie
- Department of Chemistry, The University of Adelaide, South Australia 5005, Australia.
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Chen WF, Huang SY, Liao CY, Sung CS, Chen JY, Wen ZH. The use of the antimicrobial peptide piscidin (PCD)-1 as a novel anti-nociceptive agent. Biomaterials 2015; 53:1-11. [PMID: 25890701 DOI: 10.1016/j.biomaterials.2015.02.069] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 02/10/2015] [Accepted: 02/15/2015] [Indexed: 02/09/2023]
Abstract
The antimicrobial peptide piscidin (PCD)-1 has been reported to have antibacterial and immunomodulatory functions. Here, we investigated the anti-neuropathic properties of PCD-1, in order to determine its potential as a compound to alleviate pain. Treatment with PCD-1 suppressed the inflammatory proteins COX-2 and iNOS in murine macrophage (RAW264.7) and microglial (BV2) cell lines stimulated by lipopolysaccharide (LPS). For studies of the effect of PCD-1 in vivo, mononeuropathy in rats was induced by chronic constriction injury (CCI), and the resulting anti-nociceptive behaviors were compared between CCI controls and CCI rats given intrathecal injections of PCD-1. Much like gabapentin, PCD-1 exerts anti-nociceptive effects against thermal hyperalgesia, with a median effective dose (ED50) of 9.5 μg in CCI rats. In CCI rats, PCD-1 exerted effects against mechanical and cold allodynia, thermal hyperalgesia, and weight-bearing deficits. Furthermore, CCI-mediated activation of microglia and astrocytes in the dorsal horn of the lumbar spinal cord were decreased by PCD-1. In addition, PCD-1 suppressed up-regulation of interleukin-1β (IL-1β) and phosphorylated mammalian target of rapamycin (phospho-mTOR) in CCI rats. Finally, CCI-induced down-regulation of transforming growth factor-β1 (TGF-β1) in rats was attenuated by injection of PCD-1. Taken together, the present findings demonstrate that the marine antimicrobial peptide PCD-1 has anti-nociceptive effects, and thus may have potential for development as an alternative pain-alleviating agent.
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Affiliation(s)
- Wu-Fu Chen
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123 Ta Pei Rd, Kaohsiung 833, Taiwan; Center for Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123 Ta Pei Rd, Kaohsiung 833, Taiwan
| | - Shi-Ying Huang
- Center for Neuroscience, National Sun Yat-Sen University, 70 Lien-Hai Rd, Kaohsiung 804, Taiwan
| | - Chang-Yi Liao
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, 70 Lien-Hai Rd, Kaohsiung 804, Taiwan
| | - Chun-Sung Sung
- Department of Anesthesiology, Taipei Veterans General Hospital, 201 Sec 2, Shih-Pai Rd, Taipei 112, Taiwan; School of Medicine, National Yang-Ming University, 155 Sec 2, Li-Nong St, Taipei 112, Taiwan
| | - Jyh-Yih Chen
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd, Jiaushi, Ilan 262, Taiwan.
| | - Zhi-Hong Wen
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, 70 Lien-Hai Rd, Kaohsiung 804, Taiwan; Marine Biomedical Laboratory and Center for Translational Biopharmaceuticals, Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, 70 Lien-Hai Rd, Kaohsiung 804, Taiwan.
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5
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Xu X, Lai R. The chemistry and biological activities of peptides from amphibian skin secretions. Chem Rev 2015; 115:1760-846. [PMID: 25594509 DOI: 10.1021/cr4006704] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Xueqing Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology , Kunming 650223, Yunnan, China
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Calabrese AN, Bowie JH, Pukala TL. Structural analysis of calmodulin binding by nNOS inhibitory amphibian peptides. Biochemistry 2014; 54:567-76. [PMID: 25436860 DOI: 10.1021/bi5004124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Calmodulin (CaM) is a ubiquitous protein in nature and plays a regulatory role in numerous biological processes, including the upregulation of nitric oxide (NO) synthesis in vivo. Several peptides that prevent NO production by interacting with CaM have been isolated in the cutaneous secretions of Australian amphibians, and are thought to serve as a defense mechanism against predators. In this work, we probe the mechanism by which three of these peptides, namely, caerin 1.8, dahlein 5.6, and a synthetic modification of citropin 1.1, interact with CaM to inhibit NO signaling. Isothermal titration calorimetry was used to determine thermodynamic parameters of the binding interactions and revealed that all the peptides bind to CaM in a similar fashion, with the peptide encapsulated between the two lobes of CaM. Ion mobility-mass spectrometry was used to investigate the changes in collision cross section that occur as a result of complexation, providing additional evidence for this binding mode. Finally, nuclear magnetic resonance spectroscopy was used to track chemical shift changes upon binding. The results obtained confirm that these complexes adopt canonical collapsed structures and demonstrate the strength of the interaction between the peptides and CaM. An understanding of these molecular recognition events provides insights into the underlying mechanism of the amphibian host-defense system.
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Affiliation(s)
- Antonio N Calabrese
- School of Chemistry and Physics, The University of Adelaide , Adelaide, SA Australia 5005
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Muller L, Jackson SN, Woods AS. ETD and sequential ETD localize the residues involved in D2-A2A heteromerization. RSC Adv 2014. [DOI: 10.1039/c4ra04757e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ETD2to identify binding site in NCX.
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Affiliation(s)
- Ludovic Muller
- Structural Biology Unit
- NIDA IRP
- NIH
- Baltimore, USA
- University of Pittsburgh
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Abstract
Deciphering the biological and clinical significance of the proteins is investigated by mass spectrometry in a relatively new field, named proteomics. Mass spectrometry is, however, also used in chemistry for many years. In this Research Front we try to show the potential use of mass spectrometry in chemical, environmental and biomedical research and also to illustrate the applications of mass spectrometry in proteomics.
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Bowie JH, Separovic F, Tyler MJ. Host-defense peptides of Australian anurans. Part 2. Structure, activity, mechanism of action, and evolutionary significance. Peptides 2012; 37:174-88. [PMID: 22771617 DOI: 10.1016/j.peptides.2012.06.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 06/26/2012] [Accepted: 06/26/2012] [Indexed: 01/01/2023]
Abstract
A previous review summarized research prior to 2004 carried out on the bioactive host-defense peptides contained in the skin secretions of Australian anurans (frogs and toads). This review covers the extension of that research from 2004 to 2012, and includes membrane-active peptides (including antibacterial, anticancer, antifungal and antiviral peptides) together with the mechanisms by which these peptides interact with model membranes, peptides that may be classified as "neuropeptides" (including smooth muscle active peptides, opioids and immunomodulators) and peptides which inhibit the formation of nitric oxide from neuronal nitric oxide synthase. The review discusses the outcome of cDNA sequencing of signal-spacer-active peptides from an evolutionary viewpoint, and also lists those peptides for which activities have not been found to this time.
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Affiliation(s)
- John H Bowie
- Department of Chemistry, School of Chemistry and Physics, The University of Adelaide, South Australia 5005, Australia.
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Calabrese AN, Speechley LA, Pukala TL. Characterisation of Calmodulin Structural Transitions by Ion Mobility Mass Spectrometry. Aust J Chem 2012. [DOI: 10.1071/ch12047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This study demonstrates the ability of travelling wave ion mobility-mass spectrometry to measure collision cross-sections of ions in the negative mode, using a calibration based approach. Here, negative mode ion mobility-mass spectrometry was utilised to understand structural transitions of calmodulin upon Ca2+ binding and complexation with model peptides melittin and the plasma membrane Ca2+ pump C20W peptide. Coexisting calmodulin conformers were distinguished on the basis of their mass and cross-section, and identified as relatively folded and unfolded populations, with good agreement in collision cross-section to known calmodulin geometries. Titration of calcium tartrate to physiologically relevant Ca2+ levels provided evidence for intermediately metalated species during the transition from apo- to holo-calmodulin, with collision cross-section measurements indicating that higher Ca2+ occupancy is correlated with more compact structures. The binding of two representative peptides which exemplify canonical compact (melittin) and extended (C20W) peptide-calmodulin binding models has also been interrogated by ion mobility mass spectrometry. Peptide binding to calmodulin involves intermediates with metalation states from 1–4 Ca2+, which demonstrate relatively collapsed structures, suggesting neither the existence of holo-calmodulin or a pre-folded calmodulin conformation is a prerequisite for binding target peptides or proteins. The biological importance of the different metal unsaturated calmodulin complexes, if any, is yet to be understood.
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Pan J, Konermann L. Calcium-Induced Structural Transitions of the Calmodulin−Melittin System Studied by Electrospray Mass Spectrometry: Conformational Subpopulations and Metal-Unsaturated Intermediates. Biochemistry 2010; 49:3477-86. [DOI: 10.1021/bi100261c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jingxi Pan
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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12
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Pan J, Xu K, Yang X, Choy WY, Konermann L. Solution-Phase Chelators for Suppressing Nonspecific Protein−Metal Interactions in Electrospray Mass Spectrometry. Anal Chem 2009; 81:5008-15. [DOI: 10.1021/ac900423x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jingxi Pan
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Kun Xu
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Xiaoda Yang
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Wing-Yiu Choy
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
| | - Lars Konermann
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People’s Republic of China, and School of Pharmaceutical Sciences and National Research Laboratories of Natural and Biomimetic Drugs, Peking University, Beijing 100083, People’s Republic of China
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