1
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Budusan E, Payne CD, Gonzalez TI, Obergrussberger A, Becker N, Clark RJ, Johan Rosengren K, Rash LD, Cristofori-Armstrong B. The funnel-web spider venom derived single knot peptide Hc3a modulates acid-sensing ion channel 1a desensitisation. Biochem Pharmacol 2024; 228:116175. [PMID: 38552850 DOI: 10.1016/j.bcp.2024.116175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
Acid-sensing ion channel 1a (ASIC1a) is a proton-gated channel involved in synaptic transmission, pain signalling, and several ischemia-associated pathological conditions. The spider venom-derived peptides PcTx1 and Hi1a are two of the most potent ASIC1a inhibitors known and have been instrumental in furthering our understanding of the structure, function, and biological roles of ASICs. To date, homologous spider peptides with different pharmacological profiles at ASIC1a have yet to be discovered. Here we report the characterisation of Hc3a, a single inhibitor cystine knot peptide from the Australian funnel-web spider Hadronyche cerberea with sequence similarity to PcTx1. We show that Hc3a has complex pharmacology and binds different ASIC1a conformational states (closed, open, and desensitised) with different affinities, with the most prominent effect on desensitisation. Hc3a slows the desensitisation kinetics of proton-activated ASIC1a currents across multiple application pHs, and when bound directly to ASIC1a in the desensitised conformation promotes current inhibition. The solution structure of Hc3a was solved, and the peptide-channel interaction examined via mutagenesis studies to highlight how small differences in sequence between Hc3a and PcTx1 can lead to peptides with distinct pharmacology. The discovery of Hc3a expands the pharmacological diversity of spider venom peptides targeting ASIC1a and adds to the toolbox of compounds to study the intricacies of ASIC1 gating.
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Affiliation(s)
- Elena Budusan
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Colton D Payne
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Tye I Gonzalez
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | | | | | - Richard J Clark
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia.
| | - Lachlan D Rash
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, Australia.
| | - Ben Cristofori-Armstrong
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.
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2
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Kuschert S, Stroet M, Chin YKY, Conibear AC, Jia X, Lee T, Bartling CRO, Strømgaard K, Güntert P, Rosengren KJ, Mark AE, Mobli M. Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:57-72. [PMID: 37904802 PMCID: PMC10583272 DOI: 10.5194/mr-4-57-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 11/01/2023]
Abstract
Peptides and proteins containing non-canonical amino acids (ncAAs) are a large and important class of biopolymers. They include non-ribosomally synthesised peptides, post-translationally modified proteins, expressed or synthesised proteins containing unnatural amino acids, and peptides and proteins that are chemically modified. Here, we describe a general procedure for generating atomic descriptions required to incorporate ncAAs within popular NMR structure determination software such as CYANA, CNS, Xplor-NIH and ARIA. This procedure is made publicly available via the existing Automated Topology Builder (ATB) server (https://atb.uq.edu.au, last access: 17 February 2023) with all submitted ncAAs stored in a dedicated database. The described procedure also includes a general method for linking of side chains of amino acids from CYANA templates. To ensure compatibility with other systems, atom names comply with IUPAC guidelines. In addition to describing the workflow, 3D models of complex natural products generated by CYANA are presented, including vancomycin. In order to demonstrate the manner in which the templates for ncAAs generated by the ATB can be used in practice, we use a combination of CYANA and CNS to solve the structure of a synthetic peptide designed to disrupt Alzheimer-related protein-protein interactions. Automating the generation of structural templates for ncAAs will extend the utility of NMR spectroscopy to studies of more complex biomolecules, with applications in the rapidly growing fields of synthetic biology and chemical biology. The procedures we outline can also be used to standardise the creation of structural templates for any amino acid and thus have the potential to impact structural biology more generally.
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Affiliation(s)
- Sarah Kuschert
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martin Stroet
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yanni Ka-Yan Chin
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne Claire Conibear
- Institute of Applied Synthetic Chemistry, Technische Universität Wien, Getreidemarkt 9/163, Wien 1060, Vienna, Austria
| | - Xinying Jia
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zurich, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, Hachiōji, Tokyo 192-0397, Japan
| | - Karl Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan Edward Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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3
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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] [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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4
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Willems P, Huang J, Messens J, Van Breusegem F. Functionally annotating cysteine disulfides and metal binding sites in the plant kingdom using AlphaFold2 predicted structures. Free Radic Biol Med 2023; 194:220-229. [PMID: 36493985 DOI: 10.1016/j.freeradbiomed.2022.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Deep learning algorithms such as AlphaFold2 predict three-dimensional protein structure with high confidence. The recent release of more than 200 million structural models provides an unprecedented resource for functional protein annotation. Here, we used AlphaFold2 predicted structures of fifteen plant proteomes to functionally and evolutionary analyze cysteine residues in the plant kingdom. In addition to identification of metal ligands coordinated by cysteine residues, we systematically analyzed cysteine disulfides present in these structural predictions. Our analysis demonstrates most of these predicted disulfides are trustworthy due their high agreement (∼96%) with those present in X-ray and NMR protein structures, their characteristic disulfide stereochemistry, the biased subcellular distribution of their proteins and a higher degree of oxidation of their respective cysteines as measured by proteomics. Adopting an evolutionary perspective, zinc binding sites are increasingly present at the expense of iron-sulfur clusters in plants. Interestingly, disulfide formation is increased in secreted proteins of land plants, likely promoting sequence evolution to adapt to changing environments encountered by plants. In summary, Alphafold2 predicted structural models are a rich source of information for studying the role of cysteines residues in proteins of interest and for protein redox biology in general.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, 9052, Ghent, Belgium.
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050, Brussels, Belgium; Brussels Center for Redox Biology, Vrije Universiteit Brussel, B-1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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5
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Luo J, Guo Y, Li P, Sue ACH, Cheng C. Dynamic combinatorial libraries of a dimercapto-pillar[5]arene. Chem Commun (Camb) 2022; 58:8646-8649. [PMID: 35822240 DOI: 10.1039/d2cc02752f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis and dynamic covalent chemistry (DCvC) of an A1/A2-dimercapto-functionalized pillar[5]arene (Di-SH-P5). The introduction of thiol moieties into this macrocyclic host makes it an effective building block for making a dynamic combinatorial library (DCL), giving rise to a set of cyclic trimers with intriguing host-guest properties as the dominant constituents.
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Affiliation(s)
- Jinwen Luo
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yunlong Guo
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Ping Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Andrew C-H Sue
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chuyang Cheng
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
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6
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Nair AG, Perumalla DS, Anjukandi P. Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D. Phys Chem Chem Phys 2022; 24:7691-7699. [PMID: 35311864 DOI: 10.1039/d1cp05819c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-terminal disulfide bond oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys103-Cys109) in its active site. The enzymatic functions are believed to be regulated by an electron transfer mediated redox switching of the disulfide bond, which is vital in controlling bacterial virulence factors. In light of the disulfide bond's inclination towards nucleophilic cleavage, it is also plausible that an internal nucleophile could second the existing electron transfer mechanism in nDsbD. Using QM/MM MD metadynamics simulations, we explore different possibilities of generating an internal nucleophile near the nDsbD active site, which could serve as a fail-over mechanism in cleaving the disulfide bond. The simulations show the formation of the internal nucleophile Tyr42O- (F ≈ 9 kcal mol-1) and its stabilization through the solvent medium. The static gas-phase calculations show that Tyr42O- could be a potential nucleophile for cleaving the S-S bond. Most strikingly, it is also seen that Tyr42O- and Asp68OH communicate with each other through a proton-hole like water wire (F ≈ 12 kcal mol-1), thus modulating the nucleophile formation. Accordingly, we propose the role of a solvent in regulating the internal nucleophilic reactions and the subsequent self-activation of nDsbD. We believe that this could be deterministic while designing enzyme-targeted inhibitor compounds.
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Affiliation(s)
- Aparna G Nair
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
| | | | - Padmesh Anjukandi
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
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7
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Derry A, Carpenter KA, Altman RB. Training data composition affects performance of protein structure analysis algorithms. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022; 27:10-21. [PMID: 34890132 PMCID: PMC8669736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The three-dimensional structures of proteins are crucial for understanding their molecular mechanisms and interactions. Machine learning algorithms that are able to learn accurate representations of protein structures are therefore poised to play a key role in protein engineering and drug development. The accuracy of such models in deployment is directly influenced by training data quality. The use of different experimental methods for protein structure determination may introduce bias into the training data. In this work, we evaluate the magnitude of this effect across three distinct tasks: estimation of model accuracy, protein sequence design, and catalytic residue prediction. Most protein structures are derived from X-ray crystallography, nuclear magnetic resonance (NMR), or cryo-electron microscopy (cryo-EM); we trained each model on datasets consisting of either all three structure types or of only X-ray data. We Find that across these tasks, models consistently perform worse on test sets derived from NMR and cryo-EM than they do on test sets of structures derived from X-ray crystallography, but that the difference can be mitigated when NMR and cryo-EM structures are included in the training set. Importantly, we show that including all three types of structures in the training set does not degrade test performance on X-ray structures, and in some cases even increases it. Finally, we examine the relationship between model performance and the biophysical properties of each method, and recommend that the biochemistry of the task of interest should be considered when composing training sets.
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Affiliation(s)
- Alexander Derry
- Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA
| | - Kristy A. Carpenter
- Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA
| | - Russ B. Altman
- Departments of Bioengineering, Genetics, Biomedical Data Science, and Medicine, Stanford University, Stanford, CA 94305, USA
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8
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Payne CD, Vadlamani G, Hajiaghaalipour F, Muhammad T, Fisher MF, Andersson HS, Göransson U, Clark RJ, Bond CS, Mylne JS, Rosengren KJ. Solution NMR and racemic crystallography provide insights into a novel structural class of cyclic plant peptides. RSC Chem Biol 2021; 2:1682-1691. [PMID: 34977583 PMCID: PMC8637875 DOI: 10.1039/d1cb00155h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
Head-to-tail cyclic and disulfide-rich peptides are natural products with applications in drug design. Among these are the PawS-Derived Peptides (PDPs) produced in seeds of the daisy plant family. PDP-23 is a unique member of this class in that it is twice the typical size and adopts two β-hairpins separated by a hinge region. The β-hairpins, both stabilised by a single disulfide bond, fold together into a V-shaped tertiary structure creating a hydrophobic core. In water two PDP-23 molecules merge their hydrophobic cores to form a square prism quaternary structure. Here, we synthesised PDP-23 and its enantiomer comprising d-amino acids and achiral glycine, which allowed us to confirm these solution NMR structural data by racemic crystallography. Furthermore, we discovered the related PDP-24. NMR analysis showed that PDP-24 does not form a dimeric structure and it has poor water solubility, but in less polar solvents adopts near identical secondary and tertiary structure to PDP-23. The natural role of these peptides in plants remains enigmatic, as we did not observe any antimicrobial or insecticidal activity. However, the plasticity of these larger PDPs and their ability to change structure under different conditions make them appealing peptide drug scaffolds. Larger members of the PawS-Derived family of cyclic plant peptides form complex structures. The graphical abstract shows the racemic crystal structure of the homodimeric PDP-23 as well as the solution NMR structure of PDP-24.![]()
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Affiliation(s)
- Colton D Payne
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Grishma Vadlamani
- Curtin University, Centre for Crop and Disease Management, School of Molecular and Life Sciences Bentley WA 6102 Australia.,The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia.,The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences Crawley WA 6009 Australia
| | | | - Taj Muhammad
- Uppsala University, Division of Pharmacognosy, Department of Pharmaceutical Biosciences 75124 Uppsala Sweden
| | - Mark F Fisher
- Curtin University, Centre for Crop and Disease Management, School of Molecular and Life Sciences Bentley WA 6102 Australia.,The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia.,The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences Crawley WA 6009 Australia
| | - Håkan S Andersson
- Uppsala University, Division of Pharmacognosy, Department of Pharmaceutical Biosciences 75124 Uppsala Sweden.,Karolinska Institute, Department of Medical Biochemistry and Biophysics 17177 Stockholm Sweden
| | - Ulf Göransson
- Uppsala University, Division of Pharmacognosy, Department of Pharmaceutical Biosciences 75124 Uppsala Sweden
| | - Richard J Clark
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Charles S Bond
- The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia
| | - Joshua S Mylne
- Curtin University, Centre for Crop and Disease Management, School of Molecular and Life Sciences Bentley WA 6102 Australia.,The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia.,The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences Crawley WA 6009 Australia
| | - K Johan Rosengren
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
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9
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Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon 2021; 201:127-140. [PMID: 34454969 DOI: 10.1016/j.toxicon.2021.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
Peptide toxins are potent and often exquisitely selective probes of the structure and function of ion channels and receptors, and are therefore of significant interest to the pharmaceutical and biotech industries as both pharmacological tools and therapeutic leads. The three-dimensional structures of peptide toxins are essential as a basis for understanding their structure-activity relationships and their binding to target receptors, as well as in guiding the design of analogues with modified potency and/or selectivity for key targets. NMR spectroscopy has played a key role in elucidating the structures of peptide toxins and probing their structure-function relationships. In this article, we highlight the additional important contribution of NMR to characterising the dynamics of peptide toxins. We also compare the information available from NMR measurements with that afforded by molecular dynamics simulations. We describe several examples of the importance of dynamics measurements over a range of timescales for understanding the structure-function relationships of peptide toxins and their receptor engagement. Peptide toxins that inhibit the voltage-gated potassium channel KV1.3 with pM affinities display different degrees of conformational flexibility, even though they contain multiple disulfide bonds, and this flexibility can affect the relative orientation of residues that have been shown to be critical for channel binding. Information on the dynamic properties of peptide toxins is important in the design of analogues or mimetics where receptor-bound structures are not available.
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Affiliation(s)
- Karoline Sanches
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia.
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10
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Ploetz EA, Karunaweera S, Bentenitis N, Chen F, Dai S, Gee MB, Jiao Y, Kang M, Kariyawasam NL, Naleem N, Weerasinghe S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20. J Chem Theory Comput 2021; 17:2964-2990. [PMID: 33878263 DOI: 10.1021/acs.jctc.1c00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nikolaos Bentenitis
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Feng Chen
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Shu Dai
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Moon B Gee
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Yuanfang Jiao
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Myungshim Kang
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nilusha L Kariyawasam
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | | | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
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11
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Belgi A, Burnley JV, MacRaild CA, Chhabra S, Elnahriry KA, Robinson SD, Gooding SG, Tae HS, Bartels P, Sadeghi M, Zhao FY, Wei H, Spanswick D, Adams DJ, Norton RS, Robinson AJ. Alkyne-Bridged α-Conotoxin Vc1.1 Potently Reverses Mechanical Allodynia in Neuropathic Pain Models. J Med Chem 2021; 64:3222-3233. [PMID: 33724033 DOI: 10.1021/acs.jmedchem.0c02151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Several Conus-derived venom peptides are promising lead compounds for the management of neuropathic pain, with α-conotoxins being of particular interest. Modification of the interlocked disulfide framework of α-conotoxin Vc1.1 has been achieved using on-resin alkyne metathesis. Although introduction of a metabolically stable alkyne motif significantly disrupts backbone topography, the structural modification generates a potent and selective GABAB receptor agonist that inhibits Cav2.2 channels and exhibits dose-dependent reversal of mechanical allodynia in a behavioral rat model of neuropathic pain. The findings herein support the hypothesis that analgesia can be achieved via activation of GABABRs expressed in dorsal root ganglion (DRG) sensory neurons.
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Affiliation(s)
- Alessia Belgi
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - James V Burnley
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Sandeep Chhabra
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Khaled A Elnahriry
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Samuel D Robinson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Simon G Gooding
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
| | - Han-Shen Tae
- Illawarra Health & Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Peter Bartels
- Illawarra Health & Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Mahsa Sadeghi
- Illawarra Health & Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales 2522, Australia
| | | | | | - David Spanswick
- NeuroSolutions Ltd., Coventry CV4 7AL, U.K
- Biomedicine Discovery Institute and the Department of Physiology, Monash University, Clayton, Victoria 3800, Australia
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, U.K
| | - David J Adams
- Illawarra Health & Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
- ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia
| | - Andrea J Robinson
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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12
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Armstrong DA, Jin AH, Braga Emidio N, Lewis RJ, Alewood PF, Rosengren KJ. Chemical Synthesis and NMR Solution Structure of Conotoxin GXIA from Conus geographus. Mar Drugs 2021; 19:md19020060. [PMID: 33530397 PMCID: PMC7912261 DOI: 10.3390/md19020060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
Conotoxins are disulfide-rich peptides found in the venom of cone snails. Due to their exquisite potency and high selectivity for a wide range of voltage and ligand gated ion channels they are attractive drug leads in neuropharmacology. Recently, cone snails were found to have the capability to rapidly switch between venom types with different proteome profiles in response to predatory or defensive stimuli. A novel conotoxin, GXIA (original name G117), belonging to the I3-subfamily was identified as the major component of the predatory venom of piscivorous Conus geographus. Using 2D solution NMR spectroscopy techniques, we resolved the 3D structure for GXIA, the first structure reported for the I3-subfamily and framework XI family. The 32 amino acid peptide is comprised of eight cysteine residues with the resultant disulfide connectivity forming an ICK+1 motif. With a triple stranded β-sheet, the GXIA backbone shows striking similarity to several tarantula toxins targeting the voltage sensor of voltage gated potassium and sodium channels. Supported by an amphipathic surface, the structural evidence suggests that GXIA is able to embed in the membrane and bind to the voltage sensor domain of a putative ion channel target.
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Affiliation(s)
- David A. Armstrong
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Ai-Hua Jin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - Richard J. Lewis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - Paul F. Alewood
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (A.-H.J.); (N.B.E.); (R.J.L.); (P.F.A.)
| | - K. Johan Rosengren
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia;
- Correspondence:
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13
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Krumpe LRH, Wilson BAP, Marchand C, Sunassee SN, Bermingham A, Wang W, Price E, Guszczynski T, Kelley JA, Gustafson KR, Pommier Y, Rosengren KJ, Schroeder CI, O'Keefe BR. Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I. J Am Chem Soc 2020; 142:21178-21188. [PMID: 33263997 DOI: 10.1021/jacs.0c10418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a molecular target for the sensitization of cancer cells to the FDA-approved topoisomerase inhibitors topotecan and irinotecan. High-throughput screening of natural product extract and fraction libraries for inhibitors of TDP1 activity resulted in the discovery of a new class of knotted cyclic peptides from the marine sponge Axinella sp. Bioassay-guided fractionation of the source extract resulted in the isolation of the active component which was determined to be an unprecedented 42-residue cysteine-rich peptide named recifin A. The native NMR structure revealed a novel fold comprising a four strand antiparallel β-sheet and two helical turns stabilized by a complex disulfide bond network that creates an embedded ring around one of the strands. The resulting structure, which we have termed the Tyr-lock peptide family, is stabilized by a tyrosine residue locked into three-dimensional space. Recifin A inhibited the cleavage of phosphodiester bonds by TDP1 in a FRET assay with an IC50 of 190 nM. Enzyme kinetics studies revealed that recifin A can specifically modulate the enzymatic activity of full-length TDP1 while not affecting the activity of a truncated catalytic domain of TDP1 lacking the N-terminal regulatory domain (Δ1-147), suggesting an allosteric binding site for recifin A on the regulatory domain of TDP1. Recifin A represents both the first of a unique structural class of knotted disulfide-rich peptides and defines a previously unseen mechanism of TDP1 inhibition that could be productively exploited for potential anticancer applications.
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Affiliation(s)
- Lauren R H Krumpe
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States.,Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Brice A P Wilson
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - Suthananda N Sunassee
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Alun Bermingham
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Wenjie Wang
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - Edmund Price
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Tad Guszczynski
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - James A Kelley
- Chemical Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Kirk R Gustafson
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christina I Schroeder
- Chemical Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Barry R O'Keefe
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States.,Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, Maryland 21702, United States
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14
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Payne CD, Vadlamani G, Fisher MF, Zhang J, Clark RJ, Mylne JS, Rosengren KJ. Defining the Familial Fold of the Vicilin-Buried Peptide Family. JOURNAL OF NATURAL PRODUCTS 2020; 83:3030-3040. [PMID: 32997497 DOI: 10.1021/acs.jnatprod.0c00594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Plants and their seeds have been shown to be a rich source of cystine-stabilized peptides. Recently a new family of plant seed peptides whose sequences are buried within precursors for seed storage vicilins was identified. Members of this Vicilin-Buried Peptide (VBP) family are found in distantly related plant species including the monocot date palm, as well as dicotyledonous species like pumpkin and sesame. Genetic evidence for their widespread occurrence indicates that they are of ancient origin. Limited structural studies have been conducted on VBP family members, but two members have been shown to adopt a helical hairpin fold. We present an extensive characterization of VBPs using solution NMR spectroscopy, to better understand their structural features. Four peptides were produced by solid phase peptide synthesis and shown to favor a helix-loop-helix hairpin fold, as a result of the I-IV/II-III ladderlike connectivity of their disulfide bonds. Interhelical interactions, including hydrophobic contacts and salt bridges, are critical for the fold stability and control the angle at which the antiparallel α-helices interface. Activities reported for VBPs include trypsin inhibitory activity and inhibition of ribosomal function; however, their diverse structural features despite a common fold suggest that additional bioactivities yet to be revealed are likely.
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Affiliation(s)
- Colton D Payne
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | | | | | - Richard J Clark
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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15
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McMahon KL, Tran HN, Deuis JR, Lewis RJ, Vetter I, Schroeder CI. Discovery, Pharmacological Characterisation and NMR Structure of the Novel µ-Conotoxin SxIIIC, a Potent and Irreversible Na V Channel Inhibitor. Biomedicines 2020; 8:biomedicines8100391. [PMID: 33023152 PMCID: PMC7599555 DOI: 10.3390/biomedicines8100391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium (NaV) channel subtypes, including NaV1.7, are promising targets for the treatment of neurological diseases, such as chronic pain. Cone snail-derived µ-conotoxins are small, potent NaV channel inhibitors which represent potential drug leads. Of the 22 µ-conotoxins characterised so far, only a small number, including KIIIA and CnIIIC, have shown inhibition against human NaV1.7. We have recently identified a novel µ-conotoxin, SxIIIC, from Conus striolatus. Here we present the isolation of native peptide, chemical synthesis, characterisation of human NaV channel activity by whole-cell patch-clamp electrophysiology and analysis of the NMR solution structure. SxIIIC displays a unique NaV channel selectivity profile (1.4 > 1.3 > 1.1 ≈ 1.6 ≈ 1.7 > 1.2 >> 1.5 ≈ 1.8) when compared to other µ-conotoxins and represents one of the most potent human NaV1.7 putative pore blockers (IC50 152.2 ± 21.8 nM) to date. NMR analysis reveals the structure of SxIIIC includes the characteristic α-helix seen in other µ-conotoxins. Future investigations into structure-activity relationships of SxIIIC are expected to provide insights into residues important for NaV channel pore blocker selectivity and subsequently important for chronic pain drug development.
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Affiliation(s)
- Kirsten L. McMahon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (K.L.M.); (H.N.T.T.); (J.R.D.); (R.J.L.)
| | - Hue N.T. Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (K.L.M.); (H.N.T.T.); (J.R.D.); (R.J.L.)
| | - Jennifer R. Deuis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (K.L.M.); (H.N.T.T.); (J.R.D.); (R.J.L.)
| | - Richard J. Lewis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (K.L.M.); (H.N.T.T.); (J.R.D.); (R.J.L.)
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (K.L.M.); (H.N.T.T.); (J.R.D.); (R.J.L.)
- The School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
- Correspondence: (I.V.); (C.I.S.)
| | - Christina I. Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (K.L.M.); (H.N.T.T.); (J.R.D.); (R.J.L.)
- National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Correspondence: (I.V.); (C.I.S.)
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16
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McMahon KL, Tay B, Deuis JR, Tanaka BS, Peigneur S, Jin AH, Tytgat J, Waxman SG, Dib-Hajj SD, Vetter I, Schroeder CI. Pharmacological activity and NMR solution structure of the leech peptide HSTX-I. Biochem Pharmacol 2020; 181:114082. [PMID: 32524995 DOI: 10.1016/j.bcp.2020.114082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 10/24/2022]
Abstract
The role of voltage-gated sodium (NaV) channels in pain perception is indisputable. Of particular interest as targets for the development of pain therapeutics are the tetrodotoxin-resistant isoforms NaV1.8 and NaV1.9, based on animal as well as human genetic studies linking these ion channel subtypes to the pathogenesis of pain. However, only a limited number of inhibitors selectively targeting these channels have been reported. HSTX-I is a peptide toxin identified from saliva of the leech Haemadipsa sylvestris. The native 23-residue peptide, stabilised by two disulfide bonds, has been reported to inhibit rat NaV1.8 and mouse NaV1.9 with low micromolar activity, and may therefore represent a scaffold for development of novel modulators with activity at human tetrodotoxin-resistant NaV isoforms. We synthetically produced this hydrophobic peptide in high yield using a one-pot oxidation and single step purification and determined the three-dimensional solution structure of HSTX-I using NMR solution spectroscopy. However, in our hands, the synthetic HSTX-I displayed only very modest activity at human NaV1.8 and NaV1.9, and lacked analgesic efficacy in a murine model of inflammatory pain.
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Affiliation(s)
- Kirsten L McMahon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bryan Tay
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Brian S Tanaka
- Center for Neuroscience and Regeneration Research, New Haven, CT, United States; Department of Neurology, Yale University School of Medicine, New Haven, CT, United States; Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, United States
| | - Steve Peigneur
- Toxicology and Pharmacology, Katholieke Universiteit (KU) Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Ai-Hua Jin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jan Tytgat
- Toxicology and Pharmacology, Katholieke Universiteit (KU) Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Stephen G Waxman
- Center for Neuroscience and Regeneration Research, New Haven, CT, United States; Department of Neurology, Yale University School of Medicine, New Haven, CT, United States; Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, United States
| | - Sulayman D Dib-Hajj
- Center for Neuroscience and Regeneration Research, New Haven, CT, United States; Department of Neurology, Yale University School of Medicine, New Haven, CT, United States; Rehabilitation Research Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, United States
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; School of Pharmacy, The University of Queensland, Woolloongabba, Queensland 4103, Australia.
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States.
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17
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Wiedemann C, Kumar A, Lang A, Ohlenschläger O. Cysteines and Disulfide Bonds as Structure-Forming Units: Insights From Different Domains of Life and the Potential for Characterization by NMR. Front Chem 2020; 8:280. [PMID: 32391319 PMCID: PMC7191308 DOI: 10.3389/fchem.2020.00280] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
Disulfide bridges establish a fundamental element in the molecular architecture of proteins and peptides which are involved e.g., in basic biological processes or acting as toxins. NMR spectroscopy is one method to characterize the structure of bioactive compounds including cystine-containing molecules. Although the disulfide bridge itself is invisible in NMR, constraints obtained via the neighboring NMR-active nuclei allow to define the underlying conformation and thereby to resolve their functional background. In this mini-review we present shortly the impact of cysteine and disulfide bonds in the proteasome from different domains of life and give a condensed overview of recent NMR applications for the characterization of disulfide-bond containing biomolecules including advantages and limitations of the different approaches.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Amit Kumar
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Andras Lang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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18
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Ramanujam V, Shen Y, Ying J, Mobli M. Residual Dipolar Couplings for Resolving Cysteine Bridges in Disulfide-Rich Peptides. Front Chem 2020; 7:889. [PMID: 32039137 PMCID: PMC6987419 DOI: 10.3389/fchem.2019.00889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Disulfide bridges in proteins are formed by the oxidation of pairs of cysteine residues. These cross-links play a critical role in stabilizing the 3D-structure of small disulfide rich polypeptides such as hormones and venom toxins. The arrangement of the multiple disulfide bonds directs the peptide fold into distinct structural motifs that have evolved for resistance against biochemical and physical insults. These structural scaffolds have, therefore, proven to be very attractive in bioengineering efforts to develop novel biologics with applications in health and agriculture. Structural characterization of small disulfide rich peptides (DRPs) presents unique challenges when using commonly applied biophysical methods. NMR is the most commonly used method for studying such molecules, where the relatively small size of these molecules results in highly precise structural ensembles defined by a large number of distance and dihedral angle restraints per amino acid. However, in NMR the sulfur atoms that are involved in three of the five dihedral angles in a disulfide bond cannot be readily measured. Given the central role of disulfide bonds in the structure of these molecules, it is unclear what the inherent resolution of such NMR structures is when using traditional NMR methods. Here, we use an extensive set of long-range residual dipolar couplings (RDCs) to assess the resolution of the NMR structure of a disulfide-rich peptide. We find that structures based primarily on NOEs, yield ensembles that are equivalent to a crystallographic resolution of 2-3 Å in resolution, and that incorporation of RDCs reduces this to ~1-1.5 Å resolution. At this resolution the sidechain of ordered amino acids can be defined accurately, allowing the geometry of the cysteine bridges to be better defined, and allowing for disulfide-bond connectivities to be determined with high confidence. The observed improvements in resolution when using RDCs is remarkable considering the small size of these peptides.
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Affiliation(s)
- Venkatraman Ramanujam
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
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19
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Three-Dimensional Structure Determination of Peptides Using Solution Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2020; 2068:129-162. [PMID: 31576526 DOI: 10.1007/978-1-4939-9845-6_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has over the last few decades proven to be an extremely useful technique for, and indeed an integral part of, investigating the structural features of peptides and small proteins directly in solution, without the need for crystallization. This advantage over X-ray methods is important when dealing with peptides and small proteins that do not readily form crystals. In this chapter we outline what specific NMR experiments are useful, considerations about how to acquire and interpret these experiments, and how information derived from the NMR data can be used to determine solution structures of small peptides.
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20
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Iwakawa N, Baxter NJ, Wai DCC, Fowler NJ, Morales RAV, Sugase K, Norton RS, Williamson MP. Conformational exchange in the potassium channel blocker ShK. Sci Rep 2019; 9:19307. [PMID: 31848433 PMCID: PMC6917819 DOI: 10.1038/s41598-019-55806-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022] Open
Abstract
ShK is a 35-residue disulfide-linked polypeptide produced by the sea anemone Stichodactyla helianthus, which blocks the potassium channels Kv1.1 and Kv1.3 with pM affinity. An analogue of ShK has been developed that blocks Kv1.3 > 100 times more potently than Kv1.1, and has completed Phase 1b clinical trials for the treatment of autoimmune diseases such as psoriasis and rheumatoid arthritis. Previous studies have indicated that ShK undergoes a conformational exchange that is critical to its function, but this has proved difficult to characterise. Here, we have used high hydrostatic pressure as a tool to increase the population of the alternative state, which is likely to resemble the active form that binds to the Kv1.3 channel. By following changes in chemical shift with pressure, we have derived the chemical shift values of the low- and high-pressure states, and thus characterised the locations of structural changes. The main difference is in the conformation of the Cys17-Cys32 disulfide, which is likely to affect the positions of the critical Lys22-Tyr23 pair by twisting the 21–24 helix and increasing the solvent exposure of the Lys22 sidechain, as indicated by molecular dynamics simulations.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.,Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Dorothy C C Wai
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Nicholas J Fowler
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Rodrigo A V Morales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.,CSL Limited (Bio21), 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia. .,ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria, 3052, Australia.
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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21
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Conibear AC, Rosengren KJ, Becker CFW, Kaehlig H. Random coil shifts of posttranslationally modified amino acids. JOURNAL OF BIOMOLECULAR NMR 2019; 73:587-599. [PMID: 31317299 PMCID: PMC6859290 DOI: 10.1007/s10858-019-00270-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/09/2019] [Indexed: 05/14/2023]
Abstract
Most eukaryotic proteins are modified during and/or after translation, regulating their structure, function and localisation. The role of posttranslational modifications (PTMs) in both normal cellular processes and in diseases is already well recognised and methods for detection of PTMs and generation of specifically modified proteins have developed rapidly over the last decade. However, structural consequences of PTMs and their specific effects on protein dynamics and function are not well understood. Furthermore, while random coil NMR chemical shifts of the 20 standard amino acids are available and widely used for residue assignment, dihedral angle predictions and identification of structural elements or propensity, they are not available for most posttranslationally modified amino acids. Here, we synthesised a set of random coil peptides containing common naturally occurring PTMs and determined their random coil NMR chemical shifts under standardised conditions. We highlight unique NMR signatures of posttranslationally modified residues and their effects on neighbouring residues. This comprehensive dataset complements established random coil shift datasets of the 20 standard amino acids and will facilitate identification and assignment of posttranslationally modified residues. The random coil shifts will also aid in determination of secondary structure elements and prediction of structural parameters of proteins and peptides containing PTMs.
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Affiliation(s)
- Anne C Conibear
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria.
- School of Biomedical Sciences, The University of Queensland, QLD, 4072, Brisbane, Australia.
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, QLD, 4072, Brisbane, Australia
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
| | - Hanspeter Kaehlig
- Faculty of Chemistry, Institute of Organic Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria
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22
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Jin AH, Muttenthaler M, Dutertre S, Himaya SWA, Kaas Q, Craik DJ, Lewis RJ, Alewood PF. Conotoxins: Chemistry and Biology. Chem Rev 2019; 119:11510-11549. [PMID: 31633928 DOI: 10.1021/acs.chemrev.9b00207] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The venom of the marine predatory cone snails (genus Conus) has evolved for prey capture and defense, providing the basis for survival and rapid diversification of the now estimated 750+ species. A typical Conus venom contains hundreds to thousands of bioactive peptides known as conotoxins. These mostly disulfide-rich and well-structured peptides act on a wide range of targets such as ion channels, G protein-coupled receptors, transporters, and enzymes. Conotoxins are of interest to neuroscientists as well as drug developers due to their exquisite potency and selectivity, not just against prey but also mammalian targets, thereby providing a rich source of molecular probes and therapeutic leads. The rise of integrated venomics has accelerated conotoxin discovery with now well over 10,000 conotoxin sequences published. However, their structural and pharmacological characterization lags considerably behind. In this review, we highlight the diversity of new conotoxins uncovered since 2014, their three-dimensional structures and folds, novel chemical approaches to their syntheses, and their value as pharmacological tools to unravel complex biology. Additionally, we discuss challenges and future directions for the field.
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Affiliation(s)
- Ai-Hua Jin
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , 1090 Vienna , Austria
| | - Sebastien Dutertre
- Département des Acides Amines, Peptides et Protéines, Unité Mixte de Recherche 5247, Université Montpellier 2-Centre Nationale de la Recherche Scientifique , Institut des Biomolécules Max Mousseron , Place Eugène Bataillon , 34095 Montpellier Cedex 5 , France
| | - S W A Himaya
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
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23
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Zhang J, Payne CD, Pouvreau B, Schaefer H, Fisher MF, Taylor NL, Berkowitz O, Whelan J, Rosengren KJ, Mylne JS. An Ancient Peptide Family Buried within Vicilin Precursors. ACS Chem Biol 2019; 14:979-993. [PMID: 30973714 DOI: 10.1021/acschembio.9b00167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
New proteins can evolve by duplication and divergence or de novo, from previously noncoding DNA. A recently observed mechanism is for peptides to evolve within a "host" protein and emerge by proteolytic processing. The first examples of such interstitial peptides were ones hosted by precursors for seed storage albumin. Interstitial peptides have also been observed in precursors for seed vicilins, but current evidence for vicilin-buried peptides (VBPs) is limited to seeds of the broadleaf plants pumpkin and macadamia. Here, an extensive sequence analysis of vicilin precursors suggested that peptides buried within the N-terminal region of preprovicilins are widespread and truly ancient. Gene sequences indicative of interstitial peptides were found in species from Amborellales to eudicots and include important grass and legume crop species. We show the first protein evidence for a monocot VBP in date palm seeds as well as protein evidence from other crops including the common tomato, sesame and pumpkin relatives, cucumber, and the sponge loofah ( Luffa aegyptiaca). Their excision was consistent with asparaginyl endopeptidase-mediated maturation, and sequences were confirmed by tandem mass spectrometry. Our findings suggest that the family is large and ancient and that based on the NMR solution structures for loofah Luffin P1 and tomato VBP-8, VBPs adopt a helical hairpin fold stapled by two internal disulfide bonds. The first VBPs characterized were a protease inhibitor, antimicrobials, and a ribosome inactivator. The age and evolutionary retention of this peptide family suggest its members play important roles in plant biology.
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Affiliation(s)
| | - Colton D. Payne
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Hanno Schaefer
- Department of Ecology and Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, 85354, Freising, Germany
| | | | | | - Oliver Berkowitz
- Department of Animal, Plant, and Soil Sciences, School of Life Sciences and ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria 3086 Australia
| | - James Whelan
- Department of Animal, Plant, and Soil Sciences, School of Life Sciences and ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria 3086 Australia
| | - K. Johan Rosengren
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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Structure and Synthesis of Antifungal Disulfide β-Strand Proteins from Filamentous Fungi. Microorganisms 2018; 7:microorganisms7010005. [PMID: 30591636 PMCID: PMC6352176 DOI: 10.3390/microorganisms7010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 02/03/2023] Open
Abstract
The discovery and understanding of the mode of action of new antimicrobial agents is extremely urgent, since fungal infections cause 1.5 million deaths annually. Antifungal peptides and proteins represent a significant group of compounds that are able to kill pathogenic fungi. Based on phylogenetic analyses the ascomycetous, cysteine-rich antifungal proteins can be divided into three different groups: Penicillium chrysogenum antifungal protein (PAF), Neosartorya fischeri antifungal protein 2 (NFAP2) and “bubble-proteins” (BP) produced, for example, by P. brevicompactum. They all dominantly have β-strand secondary structures that are stabilized by several disulfide bonds. The PAF group (AFP antifungal protein from Aspergillus giganteus, PAF and PAFB from P. chrysogenum,Neosartorya fischeri antifungal protein (NFAP)) is the best characterized with their common β-barrel tertiary structure. These proteins and variants can efficiently be obtained either from fungi production or by recombinant expression. However, chemical synthesis may be a complementary aid for preparing unusual modifications, e.g., the incorporation of non-coded amino acids, fluorophores, or even unnatural disulfide bonds. Synthetic variants up to ca. 6–7 kDa can also be put to good use for corroborating structure determination. A short overview of the structural peculiarities of antifungal β-strand disulfide bridged proteins will be given. Here, we describe the structural propensities of some known antifungal proteins from filamentous fungi which can also be prepared with modern synthetic chemistry methods.
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