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Madsen JJ, Petersen JE, Christensen DP, Hansen JB, Schwartz TW, Frimurer TM, Olsen OH. Deciphering specificity and cross-reactivity in tachykinin NK1 and NK2 receptors. J Biol Chem 2023; 299:105438. [PMID: 37944618 PMCID: PMC10724690 DOI: 10.1016/j.jbc.2023.105438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
The tachykinin receptors neurokinin 1 (NK1R) and neurokinin 2 (NK2R) are G protein-coupled receptors that bind preferentially to the natural peptide ligands substance P and neurokinin A, respectively, and have been targets for drug development. Despite sharing a common C-terminal sequence of Phe-X-Gly-Leu-Met-NH2 that helps direct biological function, the peptide ligands exhibit some degree of cross-reactivity toward each other's non-natural receptor. Here, we investigate the detailed structure-activity relationships of the ligand-bound receptor complexes that underlie both potent activation by the natural ligand and cross-reactivity. We find that the specificity and cross-reactivity of the peptide ligands can be explained by the interactions between the amino acids preceding the FxGLM consensus motif of the bound peptide ligand and two regions of the receptor: the β-hairpin of the extracellular loop 2 (ECL2) and a N-terminal segment leading into transmembrane helix 1. Positively charged sidechains of the ECL2 (R177 of NK1R and K180 of NK2R) are seen to play a vital role in the interaction. The N-terminal positions 1 to 3 of the peptide ligand are entirely dispensable. Mutated and chimeric receptor and ligand constructs neatly swap around ligand specificity as expected, validating the structure-activity hypotheses presented. These findings will help in developing improved agonists or antagonists for NK1R and NK2R.
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Affiliation(s)
- Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida, USA; Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Jacob E Petersen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Thue W Schwartz
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas M Frimurer
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ole H Olsen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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2
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O'Brien BCV, Weber L, Hueffer K, Weltzin MM. SARS-CoV-2 spike ectodomain targets α7 nicotinic acetylcholine receptors. J Biol Chem 2023; 299:104707. [PMID: 37061001 PMCID: PMC10101490 DOI: 10.1016/j.jbc.2023.104707] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 03/13/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Virus entry into animal cells is initiated by attachment to target macromolecules located on host cells. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) trimeric spike glycoprotein targets host angiotensin converting enzyme 2 to gain cellular access. The SARS-CoV-2 glycoprotein contains a neurotoxin-like region that has sequence similarities to the rabies virus and the HIV glycoproteins, as well as to snake neurotoxins, which interact with nicotinic acetylcholine receptor (nAChR) subtypes via this region. Using a peptide of the neurotoxin-like region of SARS-CoV-2 (SARS-CoV-2 glycoprotein peptide [SCoV2P]), we identified that this area moderately inhibits α3β2, α3β4, and α4β2 subtypes, while potentiating and inhibiting α7 nAChRs. These nAChR subtypes are found in target tissues including the nose, lung, central nervous system, and immune cells. Importantly, SCoV2P potentiates and inhibits ACh-induced α7 nAChR responses by an allosteric mechanism, with nicotine enhancing these effects. Live-cell confocal microscopy was used to confirm that SCoV2P interacts with α7 nAChRs in transfected neuronal-like N2a and human embryonic kidney 293 cells. The SARS-CoV-2 ectodomain functionally potentiates and inhibits the α7 subtype with nanomolar potency. Our functional findings identify that the α7 nAChR is a target for the SARS-CoV-2 glycoprotein, providing a new aspect to our understanding of SARS-CoV-2 and host cell interactions, in addition to disease pathogenesis.
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Affiliation(s)
- Brittany C V O'Brien
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Lahra Weber
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Maegan M Weltzin
- Department of Chemistry and Biochemistry, University of Alaska Fairbanks, Fairbanks, Alaska, USA.
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3
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Vaitaitis GM, Wagner DH. Modulating CD40 and integrin signaling in the proinflammatory nexus using a 15-amino-acid peptide, KGYY 15. J Biol Chem 2023; 299:104625. [PMID: 36944397 PMCID: PMC10141526 DOI: 10.1016/j.jbc.2023.104625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
CD40 signaling has long been a target in autoimmunity. Attempts to block signaling between CD40 and CD154 during clinical trials using monoclonal antibodies suffered severe adverse events. Previously, we developed a peptide, KGYY15, that targets CD40 and, in preclinical trials, prevents type 1 diabetes in >90% of cases and reverses new-onset hyperglycemia in 56% of cases. It did so by establishing normal effector T-cell levels rather than ablating the cells and causing immunosuppression. However, the relationship between KGYY15 and other elements of the complex signaling network of CD40 is not clear. Studying interactions between proteins from autoimmune and nonautoimmune mice, we demonstrate interactions between CD40 and integrin CD11a/CD18, which complicates the understanding of the inflammatory nexus and how to prevent autoinflammation. In addition to interacting with CD40, KGYY15 interacts with the integrins CD11a/CD18 and CD11b/CD18. We argue that modulation of CD40-CD154 signaling may be more advantageous than complete inhibition because it may preserve normal immunity to pathogens.
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Affiliation(s)
- Gisela M Vaitaitis
- Webb-Waring Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - David H Wagner
- Webb-Waring Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
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4
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Sheehan CT, Hampton TH, Madden DR. Tryptophan mutations in G3BP1 tune the stability of a cellular signaling hub by weakening transient interactions with Caprin1 and USP10. J Biol Chem 2022; 298:102552. [PMID: 36183834 DOI: 10.1016/j.jbc.2022.102552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) often coordinate transient interactions with multiple proteins to mediate complex signals within large protein networks. Among these, the IDP hub protein G3BP1 can form complexes with cytoplasmic phosphoprotein Caprin1 and ubiquitin peptidase USP10; the resulting control of USP10 activity contributes to a pathogenic virulence system that targets endocytic recycling of the ion channel CFTR. However, while the identities of protein interactors are known for many IDP hub proteins, the relationship between pairwise affinities and the extent of protein recruitment and activity is not well understood. Here, we describe in vitro analysis of these G3BP1 affinities and show tryptophan substitutions of specific G3BP1 residues reduce its affinity for both USP10 and Caprin1. We show that these same mutations reduce the stability of complexes between the full-length proteins, suggesting that copurification can serve as a surrogate measure of interaction strength. The crystal structure of G3BP1 TripleW (F15W/F33W/F124W) mutant reveals a clear reorientation of the side chain of W33, creating a steric clash with USP10 and Caprin1. Furthermore, an amino-acid scan of USP10 and Caprin1 peptides reveals similarities and differences in the ability to substitute residues in the core motifs as well as specific substitutions with the potential to create higher affinity peptides. Taken together, these data show that small changes in component binding affinities can have significant effects on the composition of cellular interaction hubs. These specific protein mutations can be harnessed to manipulate complex protein networks, informing future investigations into roles of these networks in cellular processes.
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5
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Ko MS, Cohen SN, Polley S, Mahata SK, Biswas T, Huxford T, Ghosh G. Regulatory subunit NEMO promotes polyubiquitin-dependent induction of NF-κB through a targetable second interaction with upstream activator IKK2. J Biol Chem 2022; 298:101864. [PMID: 35339487 PMCID: PMC9035715 DOI: 10.1016/j.jbc.2022.101864] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 01/16/2023] Open
Abstract
Canonical NF-κB signaling through the inhibitor of κB kinase (IKK) complex requires induction of IKK2/IKKβ subunit catalytic activity via specific phosphorylation within its activation loop. This process is known to be dependent upon the accessory ubiquitin (Ub)-binding subunit NF-κB essential modulator (NEMO)/IKKγ as well as poly-Ub chains. However, the mechanism through which poly-Ub binding serves to promote IKK catalytic activity is unclear. Here, we show that binding of NEMO/IKKγ to linear poly-Ub promotes a second interaction between NEMO/IKKγ and IKK2/IKKβ, distinct from the well-characterized interaction of the NEMO/IKKγ N terminus to the "NEMO-binding domain" at the C terminus of IKK2/IKKβ. We mapped the location of this second interaction to a stretch of roughly six amino acids immediately N-terminal to the zinc finger domain in human NEMO/IKKγ. We also showed that amino acid residues within this region of NEMO/IKKγ are necessary for binding to IKK2/IKKβ through this secondary interaction in vitro and for full activation of IKK2/IKKβ in cultured cells. Furthermore, we identified a docking site for this segment of NEMO/IKKγ on IKK2/IKKβ within its scaffold-dimerization domain proximal to the kinase domain-Ub-like domain. Finally, we showed that a peptide derived from this region of NEMO/IKKγ is capable of interfering specifically with canonical NF-κB signaling in transfected cells. These in vitro biochemical and cell culture-based experiments suggest that, as a consequence of its association with linear poly-Ub, NEMO/IKKγ plays a direct role in priming IKK2/IKKβ for phosphorylation and that this process can be inhibited to specifically disrupt canonical NF-κB signaling.
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Affiliation(s)
- Myung Soo Ko
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA; Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Samantha N Cohen
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Smarajit Polley
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Sushil K Mahata
- Department of Medicine, University of California, San Diego, La Jolla, California, USA; Medicine, VA San Diego Health Care System, San Diego, California, USA
| | - Tapan Biswas
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA.
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Liu Y, Yang X, Zhou M, Yang Y, Li F, Yan X, Zhang M, Wei Z, Qin S, Min J. Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain. J Biol Chem 2022; 298:101623. [PMID: 35074427 PMCID: PMC8861120 DOI: 10.1016/j.jbc.2022.101623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.
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Affiliation(s)
- Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China.
| | - Xiajie Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Yinxue Yang
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Fangzhou Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Xuemei Yan
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | | | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Su Qin
- Life Science Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China.
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7
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Hussain M, Cummins MC, Endo-Streeter S, Sondek J, Kuhlman B. Designer proteins that competitively inhibit Gα q by targeting its effector site. J Biol Chem 2021; 297:101348. [PMID: 34715131 PMCID: PMC8633581 DOI: 10.1016/j.jbc.2021.101348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 10/12/2021] [Accepted: 10/22/2021] [Indexed: 11/30/2022] Open
Abstract
During signal transduction, the G protein, Gαq, binds and activates phospholipase C-β isozymes. Several diseases have been shown to manifest upon constitutively activating mutation of Gαq, such as uveal melanoma. Therefore, methods are needed to directly inhibit Gαq. Previously, we demonstrated that a peptide derived from a helix-turn-helix (HTH) region of PLC-β3 (residues 852-878) binds Gαq with low micromolar affinity and inhibits Gαq by competing with full-length PLC-β isozymes for binding. Since the HTH peptide is unstructured in the absence of Gαq, we hypothesized that embedding the HTH in a folded protein might stabilize the binding-competent conformation and further improve the potency of inhibition. Using the molecular modeling software Rosetta, we searched the Protein Data Bank for proteins with similar HTH structures near their surface. The candidate proteins were computationally docked against Gαq, and their surfaces were redesigned to stabilize this interaction. We then used yeast surface display to affinity mature the designs. The most potent design bound Gαq/i with high affinity in vitro (KD = 18 nM) and inhibited activation of PLC-β isozymes in HEK293 cells. We anticipate that our genetically encoded inhibitor will help interrogate the role of Gαq in healthy and disease model systems. Our work demonstrates that grafting interaction motifs into folded proteins is a powerful approach for generating inhibitors of protein-protein interactions.
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Affiliation(s)
- Mahmud Hussain
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Matthew C Cummins
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Stuart Endo-Streeter
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - John Sondek
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA.
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8
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Atali S, Dorandish S, Devos J, Williams A, Price D, Taylor J, Guthrie J, Heyl D, Evans HG. Interaction of amyloid beta with humanin and acetylcholinesterase is modulated by ATP. FEBS Open Bio 2020; 10:2805-2823. [PMID: 33145964 PMCID: PMC7714071 DOI: 10.1002/2211-5463.13023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Humanin (HN) is known to bind amyloid beta (Aβ)‐inducing cytoprotective effects, while binding of acetylcholinesterase (AChE) to Aβ increases its aggregation and cytotoxicity. Previously, we showed that binding of HN to Aβ blocks aggregation induced by AChE and that HN decreases but does not abolish Aβ‐AChE interactions in A549 cell media. Here, we set out to shed light on factors that modulate the interactions of Aβ with HN and AChE. We found that binding of either HN or AChE to Aβ is not affected by heparan sulfate, while ATP, thought to reduce misfolding of Aβ, weakened interactions between AChE and Aβ but strengthened those between Aβ and HN. Using media from either A549 or H1299 lung cancer cells, we observed that more HN was bound to Aβ upon addition of ATP, while levels of AChE in a complex with Aβ were decreased by ATP addition to A549 cell media. Exogenous addition of ATP to either A549 or H1299 cell media increased interactions of endogenous HN with Aβ to a comparable extent despite differences in AChE expression in the two cell lines, and this was correlated with decreased binding of exogenously added HN to Aβ. Treatment with exogenous ATP had no effect on cell viability under all conditions examined. Exogenously added ATP did not affect viability of cells treated with AChE‐immunodepleted media, and there was no apparent protection against the cytotoxicity resulting from immunodepletion of HN. Moreover, exogenously added ATP had no effect on the relative abundance of oligomer versus total Aβ in either cell line.
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Affiliation(s)
- Sarah Atali
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Sadaf Dorandish
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Jonathan Devos
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Asana Williams
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Deanna Price
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Jaylen Taylor
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Jeffrey Guthrie
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Deborah Heyl
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
| | - Hedeel Guy Evans
- Chemistry Department, Eastern Michigan University, Ypsilanti, MI, USA
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9
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Torpey JH, Meade RM, Mistry R, Mason JM, Madine J. Insights Into Peptide Inhibition of Alpha-Synuclein Aggregation. Front Neurosci 2020; 14:561462. [PMID: 33177976 PMCID: PMC7594713 DOI: 10.3389/fnins.2020.561462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
α-Synuclein (aSyn) aggregation is an attractive target for therapeutic development for a range of neurodegenerative conditions, collectively termed synucleinopathies. Here, we probe the mechanism of action of a peptide 4554W, (KDGIVNGVKA), previously identified through intracellular library screening, to prevent aSyn aggregation and associated toxicity. We utilize NMR to probe association and identify that 4554W associates with a "partially aggregated" form of aSyn, with enhanced association occurring over time. We also report the ability of 4554W to undergo modification through deamidation of the central asparagine residue, occurring on the same timescale as aSyn aggregation in vitro, with peptide modification enhancing its association with aSyn. Additionally, we report that 4554W can act to reduce fibril formation of five Parkinson's disease associated aSyn mutants. Inhibitory peptide binding to partially aggregated forms of aSyn, as identified here, is particularly attractive from a therapeutic perspective, as it would eliminate the need to administer the therapy at pre-aggregation stages, which are difficult to diagnose. Taken together the data suggest that 4554W could be a suitable candidate for future therapeutic development against wild-type, and most mutant aSyn aggregation.
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Affiliation(s)
- James H Torpey
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard M Meade
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Ravina Mistry
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jody M Mason
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jillian Madine
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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10
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Wang CK, Amiss AS, Weidmann J, Craik DJ. Structure-activity analysis of truncated albumin-binding domains suggests new lead constructs for potential therapeutic delivery. J Biol Chem 2020; 295:12143-12152. [PMID: 32647013 PMCID: PMC7443490 DOI: 10.1074/jbc.ra120.014168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Rapid clearance by renal filtration is a major impediment to the translation of small bioactive biologics into drugs. To extend serum t1/2, a commonly used approach is to attach drug leads to the G-related albumin-binding domain (ABD) to bind albumin and evade clearance. Despite the success of this approach in extending half-lives of a wide range of biologics, it is unclear whether the existing constructs are optimized for binding and size; any improvements along these lines could lead to improved drugs. Characterization of the biophysics of binding of an ABD to albumin in solution could shed light on this question. Here, we examine the binding of an ABD to human serum albumin using isothermal titration calorimetry and assess the structural integrity of the ABD using CD, NMR, and molecular dynamics. A structure-activity analysis of truncations of the ABD suggests that downsized variants could replace the full-length domain. Reducing size could have the benefit of reducing potential immunogenicity problems. We further showed that one of these variants could be used to design a bifunctional molecule with affinity for albumin and a serum protein involved in cholesterol metabolism, PCSK9, demonstrating the potential utility of these fragments in the design of cholesterol-lowering drugs. Future work could extend these in vitro binding studies to other ABD variants to develop therapeutics. Our study presents new understanding of the solution structural and binding properties of ABDs, which has implications for the design of next-generation long-lasting therapeutics.
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Affiliation(s)
- Conan K. Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Anna S. Amiss
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J. Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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11
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Ronan T, Garnett R, Naegle KM. New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data. J Biol Chem 2020; 295:11346-11363. [PMID: 32540967 DOI: 10.1074/jbc.ra120.012503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/11/2020] [Indexed: 11/06/2022] Open
Abstract
Protein domain interactions with short linear peptides, such as those of the Src homology 2 (SH2) domain with phosphotyrosine-containing peptide motifs (pTyr), are ubiquitous and important to many biochemical processes of the cell. The desire to map and quantify these interactions has resulted in the development of high-throughput (HTP) quantitative measurement techniques, such as microarray or fluorescence polarization assays. For example, in the last 15 years, experiments have progressed from measuring single interactions to covering 500,000 of the 5.5 million possible SH2-pTyr interactions in the human proteome. However, high variability in affinity measurements and disagreements about positive interactions between published data sets led us here to reevaluate the analysis methods and raw data of published SH2-pTyr HTP experiments. We identified several opportunities for improving the identification of positive and negative interactions and the accuracy of affinity measurements. We implemented model-fitting techniques that are more statistically appropriate for the nonlinear SH2-pTyr interaction data. We also developed a method to account for protein concentration errors due to impurities and degradation or protein inactivity and aggregation. Our revised analysis increases the reported affinity accuracy, reduces the false-negative rate, and increases the amount of useful data by adding reliable true-negative results. We demonstrate improvement in classification of binding versus nonbinding when using machine-learning techniques, suggesting improved coherence in the reanalyzed data sets. We present revised SH2-pTyr affinity results and propose a new analysis pipeline for future HTP measurements of domain-peptide interactions.
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Affiliation(s)
- Tom Ronan
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Roman Garnett
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kristen M Naegle
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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12
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Darlot B, Eaton JRO, Geis-Asteggiante L, Yakala GK, Karuppanan K, Davies G, Robinson CV, Kawamura A, Bhattacharya S. Engineered anti-inflammatory peptides inspired by mapping an evasin-chemokine interaction. J Biol Chem 2020; 295:10926-10939. [PMID: 32471866 PMCID: PMC7415964 DOI: 10.1074/jbc.ra120.014103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/23/2020] [Indexed: 12/27/2022] Open
Abstract
Chemokines mediate leukocyte migration and homeostasis and are key targets in inflammatory diseases including atherosclerosis, cytokine storm, and chronic autoimmune disease. Chemokine redundancy and ensuing network robustness has frustrated therapeutic development. Salivary evasins from ticks bind multiple chemokines to overcome redundancy and are effective in several preclinical disease models. Their clinical development has not progressed because of concerns regarding potential immunogenicity, parenteral delivery, and cost. Peptides mimicking protein activity can overcome the perceived limitations of therapeutic proteins. Here we show that peptides possessing multiple chemokine-binding and anti-inflammatory activities can be developed from the chemokine-binding site of an evasin. We used hydrogen-deuterium exchange MS to map the binding interface of the evasin P672 that physically interacts with C-C motif chemokine ligand (CCL) 8 and synthesized a 16-mer peptide (BK1.1) based on this interface region in evasin P672. Fluorescent polarization and native MS approaches showed that BK1.1 binds CCL8, CCL7, and CCL18 and disrupts CCL8 homodimerization. We show that a BK1.1 derivative, BK1.3, has substantially improved ability to disrupt P672 binding to CCL8, CCL2, and CCL3 in an AlphaScreen assay. Using isothermal titration calorimetry, we show that BK1.3 directly binds CCL8. BK1.3 also has substantially improved ability to inhibit CCL8, CCL7, CCL2, and CCL3 chemotactic function in vitro We show that local as well as systemic administration of BK1.3 potently blocks inflammation in vivo Identification and characterization of the chemokine-binding interface of evasins could thus inspire the development of novel anti-inflammatory peptides that therapeutically target the chemokine network in inflammatory diseases.
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Affiliation(s)
- Benoit Darlot
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - James R O Eaton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lucia Geis-Asteggiante
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Gopala K Yakala
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Kalimuthu Karuppanan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Graham Davies
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Carol V Robinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom .,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Shoumo Bhattacharya
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
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13
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Agwa AJ, Tran P, Mueller A, Tran HNT, Deuis JR, Israel MR, McMahon KL, Craik DJ, Vetter I, Schroeder CI. Manipulation of a spider peptide toxin alters its affinity for lipid bilayers and potency and selectivity for voltage-gated sodium channel subtype 1.7. J Biol Chem 2020; 295:5067-5080. [PMID: 32139508 PMCID: PMC7152767 DOI: 10.1074/jbc.ra119.012281] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/03/2020] [Indexed: 02/05/2023] Open
Abstract
Huwentoxin-IV (HwTx-IV) is a gating modifier peptide toxin from spiders that has weak affinity for the lipid bilayer. As some gating modifier toxins have affinity for model lipid bilayers, a tripartite relationship among gating modifier toxins, voltage-gated ion channels, and the lipid membrane surrounding the channels has been proposed. We previously designed an HwTx-IV analogue (gHwTx-IV) with reduced negative charge and increased hydrophobic surface profile, which displays increased lipid bilayer affinity and in vitro activity at the voltage-gated sodium channel subtype 1.7 (NaV1.7), a channel targeted in pain management. Here, we show that replacements of the positively-charged residues that contribute to the activity of the peptide can improve gHwTx-IV's potency and selectivity for NaV1.7. Using HwTx-IV, gHwTx-IV, [R26A]gHwTx-IV, [K27A]gHwTx-IV, and [R29A]gHwTx-IV variants, we examined their potency and selectivity at human NaV1.7 and their affinity for the lipid bilayer. [R26A]gHwTx-IV consistently displayed the most improved potency and selectivity for NaV1.7, examined alongside off-target NaVs, compared with HwTx-IV and gHwTx-IV. The lipid affinity of each of the three novel analogues was weaker than that of gHwTx-IV, but stronger than that of HwTx-IV, suggesting a possible relationship between in vitro potency at NaV1.7 and affinity for lipid bilayers. In a murine NaV1.7 engagement model, [R26A]gHwTx-IV exhibited an efficacy comparable with that of native HwTx-IV. In summary, this study reports the development of an HwTx-IV analogue with improved in vitro selectivity for the pain target NaV1.7 and with an in vivo efficacy similar to that of native HwTx-IV.
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Affiliation(s)
- Akello J Agwa
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Poanna Tran
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alexander Mueller
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hue N T Tran
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mathilde R Israel
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kirsten L McMahon
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, Centre for Pain Research, 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, Centre for Pain Research, The University of Queensland, Brisbane, Queensland 4072, Australia
- National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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14
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Reyes-Vargas E, Barker AP, Zhou Z, He X, Jensen PE. HLA-DM catalytically enhances peptide dissociation by sensing peptide-MHC class II interactions throughout the peptide-binding cleft. J Biol Chem 2020; 295:2959-2973. [PMID: 31969393 PMCID: PMC7062162 DOI: 10.1074/jbc.ra119.010645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/13/2020] [Indexed: 11/06/2022] Open
Abstract
Human leukocyte antigen-DM (HLA-DM) is an integral component of the major histocompatibility complex class II (MHCII) antigen-processing and -presentation pathway. HLA-DM shapes the immune system by differentially catalyzing peptide exchange on MHCII molecules, thereby editing the peptide-MHCII (pMHCII) repertoire by imposing a bias on the foreign and self-derived peptide cargos that are presented on the cell surface for immune surveillance and tolerance induction by CD4+ T cells. To better understand DM selectivity, here we developed a real-time fluorescence anisotropy assay to delineate the pMHCII intrinsic stability, DM-binding affinity, and catalytic turnover, independent kinetic parameters of HLA-DM enzymatic activity. We analyzed prominent pMHCII contacts by differentiating the kinetic parameters in pMHCII homologs, observing that peptide interactions throughout the MHCII-binding cleft influence both the rate of peptide dissociation from the DM-pMHCII catalytic complex and the binding affinity of HLA-DM for a pMHCII. We show that the intrinsic stability of a pMHCII linearly correlates with DM catalytic turnover, but is nonlinearly correlated with its binding affinity. Surprisingly, interactions at the peptides N terminus up to and including MHCII position one (P1) anchor affected the catalytic turnover, suggesting that the active DM-pMHCII catalytic complex operates on pMHCII complexes with full peptide occupancy. Furthermore, interactions at the peptide C terminus modulated DM-binding affinity, suggesting distal communication between peptide interactions with the MHCII and the DM-pMHCII binding interface. Our results imply an intimate linkage between the DM-pMHCII interface and peptide-MHCII interactions throughout the peptide-binding cleft.
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Affiliation(s)
- Eduardo Reyes-Vargas
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Adam P Barker
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112; Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah 84108
| | - Zemin Zhou
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Xiao He
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112.
| | - Peter E Jensen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112; Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah 84108.
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15
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Li H, Zhu H, Sarbeng EB, Liu Q, Tian X, Yang Y, Lyons C, Zhou L, Liu Q. An unexpected second binding site for polypeptide substrates is essential for Hsp70 chaperone activity. J Biol Chem 2019; 295:584-596. [PMID: 31806707 DOI: 10.1074/jbc.ra119.009686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/02/2019] [Indexed: 12/14/2022] Open
Abstract
Heat shock proteins of 70 kDa (Hsp70s) are ubiquitous and highly conserved molecular chaperones. They play multiple essential roles in assisting with protein folding and maintaining protein homeostasis. Their chaperone activity has been proposed to require several rounds of binding to and release of polypeptide substrates at the substrate-binding domain (SBD) of Hsp70s. All available structures have revealed a single substrate-binding site in the SBD that binds a single segment of an extended polypeptide of 3-4 residues. However, this well-established single peptide-binding site alone has made it difficult to explain the efficient chaperone activity of Hsp70s. In this study, using purified proteins and site-directed mutagenesis, along with fluorescence polarization and luciferase-refolding assays, we report the unexpected discovery of a second peptide-binding site in Hsp70s. More importantly, the biochemical analyses suggested that this novel binding site, named here P2, is essential for Hsp70 chaperone activity. Furthermore, cross-linking and mutagenesis studies indicated that this second binding site is in the SBD adjacent to the first binding site. Taken together, our results suggest that these two essential binding sites of Hsp70s cooperate in protein folding.
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Affiliation(s)
- Hongtao Li
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Huanyu Zhu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Evans Boateng Sarbeng
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Qingdai Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Xueli Tian
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Ying Yang
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Charles Lyons
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Lei Zhou
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298.
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16
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Han H, Schubert HL, McCullough J, Monroe N, Purdy MD, Yeager M, Sundquist WI, Hill CP. Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation. J Biol Chem 2019; 295:435-443. [PMID: 31767681 DOI: 10.1074/jbc.ac119.009890] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/11/2019] [Indexed: 11/06/2022] Open
Abstract
Many members of the AAA+ ATPase family function as hexamers that unfold their protein substrates. These AAA unfoldases include spastin, which plays a critical role in the architecture of eukaryotic cells by driving the remodeling and severing of microtubules, which are cytoskeletal polymers of tubulin subunits. Here, we demonstrate that a human spastin binds weakly to unmodified peptides from the C-terminal segment of human tubulin α1A/B. A peptide comprising alternating glutamate and tyrosine residues binds more tightly, which is consistent with the known importance of glutamylation for spastin microtubule severing activity. A cryo-EM structure of the spastin-peptide complex at 4.2 Å resolution revealed an asymmetric hexamer in which five spastin subunits adopt a helical, spiral staircase configuration that binds the peptide within the central pore, whereas the sixth subunit of the hexamer is displaced from the peptide/substrate, as if transitioning from one end of the helix to the other. This configuration differs from a recently published structure of spastin from Drosophila melanogaster, which forms a six-subunit spiral without a transitioning subunit. Our structure resembles other recently reported AAA unfoldases, including the meiotic clade relative Vps4, and supports a model in which spastin utilizes a hand-over-hand mechanism of tubulin translocation and microtubule remodeling.
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Affiliation(s)
- Han Han
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - John McCullough
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Nicole Monroe
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Michael D Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Mark Yeager
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908; Department of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, Virginia 22908; Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, Virginia 22908; Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112.
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112.
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17
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Atkinson JM, Ye Y, Gebru MT, Liu Q, Zhou S, Young MM, Takahashi Y, Lin Q, Tian F, Wang HG. Time-resolved FRET and NMR analyses reveal selective binding of peptides containing the LC3-interacting region to ATG8 family proteins. J Biol Chem 2019; 294:14033-14042. [PMID: 31362979 DOI: 10.1074/jbc.ra119.008723] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/24/2019] [Indexed: 11/06/2022] Open
Abstract
Selective autophagy sequesters cytoplasmic cargo for lysosomal degradation via the binding of autophagy receptors to Atg8 (autophagy-related 8) family proteins on the autophagic membrane. The sole yeast Atg8 gene has six mAtg8 (mammalian Atg8) homologs, including the MAP1LC3 (microtubule-associated protein-1 light chain 3) family and the GABA receptor-associated proteins. Selective autophagy receptors interact with two conserved hydrophobic pockets (termed the W-site and L-site) of mATG8 proteins through a linear motif called the LC3-interacting region (LIR) with the general composition (W/F/Y)XX(I/L/V). To address a lack in our knowledge regarding LIR peptide specificity toward each mATG8 homolog, here we used competitive time-resolved FRET to sensitively and quantitatively characterize the interactions between LIRs and mAtg8. We report that 14 representative LIR-containing peptides display differential binding affinities toward the mAtg8 proteins and identified the LIR domain peptide of TP53INP1 as exhibiting high affinity for all six mATG8 proteins. Using peptide truncation studies, we found that both N- and C-terminal acidic residues, as well as the C-terminal Cys residue of the TP53INP1 LIR peptide, are required for its high-affinity binding to LC3A and LC3B, whereas binding to the GABARAP subfamily proteins was facilitated by residues either N-terminal or C-terminal to the core motif. Finally, we used NMR chemical shift perturbation analysis to gain molecular insights into these findings. Collectively, our results may aid in the development of molecules that selectively disrupt specific mATG8-LIR interactions to dissect the biological roles of the six mATG8 homologs for potential therapeutic applications.
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Affiliation(s)
- Jennifer M Atkinson
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Yansheng Ye
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Melat T Gebru
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Qiang Liu
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Shouhao Zhou
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Megan M Young
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Yoshinori Takahashi
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260
| | - Fang Tian
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033
| | - Hong-Gang Wang
- Department of Pediatrics, Penn State College of Medicine, Hershey, Pennsylvania 17033
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18
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Kam A, Loo S, Dutta B, Sze SK, Tam JP. Plant-derived mitochondria-targeting cysteine-rich peptide modulates cellular bioenergetics. J Biol Chem 2019; 294:4000-4011. [PMID: 30674551 DOI: 10.1074/jbc.ra118.006693] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are attractive therapeutic targets for developing agents to delay age-related frailty and diseases. However, few promising leads have been identified from natural products. Previously, we identified roseltide rT1, a hyperstable 27-residue cysteine-rich peptide from Hibiscus sabdariffa, as a knottin-type neutrophil elastase inhibitor. Here, we show that roseltide rT1 is also a cell-penetrating, mitochondria-targeting peptide that increases ATP production. Results from flow cytometry, live-cell imaging, pulldown assays, and genetically-modified cell lines supported that roseltide rT1 enters cells via glycosaminoglycan-dependent endocytosis, and enters the mitochondria through TOM20, a mitochondrial protein import receptor. We further showed that roseltide rT1 increases cellular ATP production via mitochondrial membrane hyperpolarization. Using biotinylated roseltide rT1 for target identification and proteomic analysis, we showed that human mitochondrial membrane ATP synthase subunit O is an intramitochondrial target. Collectively, these data support our discovery that roseltide rT1 is a first-in-class mitochondria-targeting, cysteine-rich peptide with potentials to be developed into tools to further our understanding of mitochrondria-related diseases.
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Affiliation(s)
- Antony Kam
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Shining Loo
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Bamaprasad Dutta
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Siu Kwan Sze
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - James P Tam
- From the School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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19
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Spiliotopoulos A, Blokpoel Ferreras L, Densham RM, Caulton SG, Maddison BC, Morris JR, Dixon JE, Gough KC, Dreveny I. Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11. J Biol Chem 2019; 294:424-436. [PMID: 30373771 PMCID: PMC6333900 DOI: 10.1074/jbc.ra118.004469] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/11/2018] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) reverse ubiquitination and regulate virtually all cellular processes. Defined noncatalytic domains in USP4 and USP15 are known to interact with E3 ligases and substrate recruitment factors. No such interactions have been reported for these domains in the paralog USP11, a key regulator of DNA double-strand break repair by homologous recombination. We hypothesized that USP11 domains adjacent to its protease domain harbor unique peptide-binding sites. Here, using a next-generation phage display (NGPD) strategy, combining phage display library screening with next-generation sequencing, we discovered unique USP11-interacting peptide motifs. Isothermal titration calorimetry disclosed that the highest affinity peptides (KD of ∼10 μm) exhibit exclusive selectivity for USP11 over USP4 and USP15 in vitro Furthermore, a crystal structure of a USP11-peptide complex revealed a previously unknown binding site in USP11's noncatalytic ubiquitin-like (UBL) region. This site interacted with a helical motif and is absent in USP4 and USP15. Reporter assays using USP11-WT versus a binding pocket-deficient double mutant disclosed that this binding site modulates USP11's function in homologous recombination-mediated DNA repair. The highest affinity USP11 peptide binder fused to a cellular delivery sequence induced significant nuclear localization and cell cycle arrest in S phase, affecting the viability of different mammalian cell lines. The USP11 peptide ligands and the paralog-specific functional site in USP11 identified here provide a framework for the development of new biochemical tools and therapeutic agents. We propose that an NGPD-based strategy for identifying interacting peptides may be applied also to other cellular targets.
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Affiliation(s)
- Anastasios Spiliotopoulos
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
- the School of Veterinary Medicine and Science, Sutton Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD
| | - Lia Blokpoel Ferreras
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Ruth M Densham
- the Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham B15 2TT, and
| | - Simon G Caulton
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Ben C Maddison
- ADAS, School of Veterinary Medicine and Science, Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Joanna R Morris
- the Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham B15 2TT, and
| | - James E Dixon
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD
| | - Kevin C Gough
- the School of Veterinary Medicine and Science, Sutton Bonington Campus, College Road, Sutton Bonington, Leicestershire LE12 5RD,
| | - Ingrid Dreveny
- From the Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD,
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20
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Haugaard-Kedström LM, Lee HS, Jones MV, Song A, Rathod V, Hossain MA, Bathgate RAD, Rosengren KJ. Binding conformation and determinants of a single-chain peptide antagonist at the relaxin-3 receptor RXFP3. J Biol Chem 2018; 293:15765-15776. [PMID: 30131342 DOI: 10.1074/jbc.ra118.002611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
The neuropeptide relaxin-3 and its receptor relaxin family peptide receptor-3 (RXFP3) play key roles in modulating behavior such as memory and learning, food intake, and reward seeking. A linear relaxin-3 antagonist (R3 B1-22R) based on a modified and truncated relaxin-3 B-chain was recently developed. R3 B1-22R is unstructured in solution; thus, the binding conformation and determinants of receptor binding are unclear. Here, we have designed, chemically synthesized, and pharmacologically characterized more than 60 analogues of R3 B1-22R to develop an extensive understanding of its structure-activity relationships. We show that the key driver for affinity is the nonnative C-terminal Arg23 Additional contributors to binding include amino acid residues that are important also for relaxin-3 binding, including Arg12, Ile15, and Ile19 Intriguingly, amino acid residues that are not exposed in native relaxin-3, including Phe14 and Ala17, also interact with RXFP3. We show that R3 B1-22R has a propensity to form a helical structure, and modifications that support a helical conformation are functionally well-tolerated, whereas helix breakers such as proline residues disrupt binding. These data suggest that the peptide adopts a helical conformation, like relaxin-3, upon binding to RXFP3, but that its smaller size allows it to penetrate deeper into the orthosteric binding site, creating more extensive contacts with the receptor.
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Affiliation(s)
- Linda M Haugaard-Kedström
- From the Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.,the Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark, and
| | - Han Siean Lee
- From the Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maryon V Jones
- From the Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Angela Song
- From the Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Vishaal Rathod
- From the Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Ross A D Bathgate
- the Florey Institute of Neuroscience and Mental Health, .,Department of Biochemistry and Molecular Biology, University of Melbourne, Victoria 3010, Australia
| | - K Johan Rosengren
- From the Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia,
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21
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Martínez-Florensa M, Català C, Velasco-de Andrés M, Cañadas O, Fraile-Ágreda V, Casadó-Llombart S, Armiger-Borràs N, Consuegra-Fernández M, Casals C, Lozano F. Conserved Bacterial-Binding Peptides of the Scavenger-Like Human Lymphocyte Receptor CD6 Protect From Mouse Experimental Sepsis. Front Immunol 2018; 9:627. [PMID: 29706953 PMCID: PMC5906529 DOI: 10.3389/fimmu.2018.00627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/13/2018] [Indexed: 01/01/2023] Open
Abstract
Sepsis is an unmet clinical need constituting one of the most important causes of death worldwide, a fact aggravated by the appearance of multidrug resistant strains due to indiscriminate use of antibiotics. Host innate immune receptors involved in pathogen-associated molecular patterns (PAMPs) recognition represent a source of broad-spectrum therapies alternative or adjunctive to antibiotics. Among the few members of the ancient and highly conserved scavenger receptor cysteine-rich superfamily (SRCR-SF) sharing bacterial-binding properties there is CD6, a lymphocyte-specific surface receptor. Here, we analyze the bacterial-binding properties of three conserved short peptides (11-mer) mapping at extracellular SRCR domains of human CD6 (CD6.PD1, GTVEVRLEASW; CD6.PD2 GRVEMLEHGEW; and CD6.PD3, GQVEVHFRGVW). All peptides show high binding affinity for PAMPs from Gram-negative (lipopolysaccharide; Kd from 3.5 to 3,000 nM) and Gram-positive (lipoteichoic acid; Kd from 36 to 680 nM) bacteria. The CD6.PD3 peptide possesses broad bacterial-agglutination properties and improved survival of mice undergoing polymicrobial sepsis in a dose- and time-dependent manner. Accordingly, CD6.PD3 triggers a decrease in serum levels of both pro-inflammatory cytokines and bacterial load. Interestingly, CD6.PD3 shows additive survival effects on septic mice when combined with Imipenem/Cilastatin. These results illustrate the therapeutic potential of peptides retaining the bacterial-binding properties of native CD6.
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Affiliation(s)
- Mario Martínez-Florensa
- Immunoreceptors of the Innate and Adaptive System, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Cristina Català
- Immunoreceptors of the Innate and Adaptive System, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - María Velasco-de Andrés
- Immunoreceptors of the Innate and Adaptive System, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Olga Cañadas
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Departmento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid, Spain
| | - Víctor Fraile-Ágreda
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Departmento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid, Spain
| | - Sergi Casadó-Llombart
- Immunoreceptors of the Innate and Adaptive System, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Noelia Armiger-Borràs
- Immunoreceptors of the Innate and Adaptive System, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marta Consuegra-Fernández
- Immunoreceptors of the Innate and Adaptive System, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Cristina Casals
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Departmento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid, Spain
| | - Francisco Lozano
- Immunoreceptors of the Innate and Adaptive System, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clínic de Barcelona, Barcelona, Spain.,Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
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22
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Davis TA, Holland LA. Peptide Probe for Multiwalled Carbon Nanotubes: Electrophoretic Assessment of the Binding Interface and Evaluation of Surface Functionalization. ACS Appl Mater Interfaces 2018; 10:11311-11318. [PMID: 29468871 DOI: 10.1021/acsami.8b00022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Noncovalent interactions of peptides and proteins with carbon nanotubes play a key role in sensing, dispersion, and biocompatibility. Advances in these areas require that the forces which contribute to physical adsorption are understood in order that the carbon nanotubes present a degree of functionalization appropriate to the desired application. Affinity analyses of peptides are employed to evaluate the role of tryptophan and arginine residues in physical adsorption to carboxylated multiwalled carbon nanotubes. Peptides containing arginine and tryptophan, WR(W) n, are used with affinity capillary electrophoresis to identify factors that lead to the formation of peptide-carbon nanotube complexes. The effects of changing the amino acid composition and residue length are evaluated by measuring dissociation constants. Electrostatic interactions contribute significantly to complexation, with the strongest interaction observed using the peptide WRWWWW and carboxylated carbon nanotube. Stronger interaction is observed when the tryptophan content is successively increased as follows: WR(W)4 > WR(W)3 > WR(W)2 > WRW > WR. However, as observed with polytryptophan (W5, W4, W3, and W2), removing the arginine residue significantly reduces the interaction with carbon nanotubes. Increasing the arginine content to WRWWRW does not improve binding, whereas replacing the arginine residue in WRWWWW with lysine (WKWWWW) reveals that lysine also contributes to surface adsorption, but not as effectively as arginine. These observations are used to guide a search of the primary sequence of lysozyme to identify short regions in the peptide that contain a single cationic residue and two aromatic residues. One candidate peptide sequence (WMCLAKW) from this search is analyzed by capillary electrophoresis. The dissociation constant of carboxylated multiwalled carbon nanotubes is measured for the peptide, WMCLAKW, to demonstrate the utility of affinity capillary electrophoresis analysis.
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Affiliation(s)
- Tyler A Davis
- C. Eugene Bennett Department of Chemistry , West Virginia University , Morgantown , West Virginia 26506 , United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry , West Virginia University , Morgantown , West Virginia 26506 , United States
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23
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Krotee P, Griner SL, Sawaya MR, Cascio D, Rodriguez JA, Shi D, Philipp S, Murray K, Saelices L, Lee J, Seidler P, Glabe CG, Jiang L, Gonen T, Eisenberg DS. Common fibrillar spines of amyloid-β and human islet amyloid polypeptide revealed by microelectron diffraction and structure-based inhibitors. J Biol Chem 2017; 293:2888-2902. [PMID: 29282295 DOI: 10.1074/jbc.m117.806109] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/18/2017] [Indexed: 01/21/2023] Open
Abstract
Amyloid-β (Aβ) and human islet amyloid polypeptide (hIAPP) aggregate to form amyloid fibrils that deposit in tissues and are associated with Alzheimer's disease (AD) and type II diabetes (T2D), respectively. Individuals with T2D have an increased risk of developing AD, and conversely, AD patients have an increased risk of developing T2D. Evidence suggests that this link between AD and T2D might originate from a structural similarity between aggregates of Aβ and hIAPP. Using the cryoEM method microelectron diffraction, we determined the atomic structures of 11-residue segments from both Aβ and hIAPP, termed Aβ(24-34) WT and hIAPP(19-29) S20G, with 64% sequence similarity. We observed a high degree of structural similarity between their backbone atoms (0.96-Å root mean square deviation). Moreover, fibrils of these segments induced amyloid formation through self- and cross-seeding. Furthermore, inhibitors designed for one segment showed cross-efficacy for full-length Aβ and hIAPP and reduced cytotoxicity of both proteins, although by apparently blocking different cytotoxic mechanisms. The similarity of the atomic structures of Aβ(24-34) WT and hIAPP(19-29) S20G offers a molecular model for cross-seeding between Aβ and hIAPP.
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Affiliation(s)
- Pascal Krotee
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Sarah L Griner
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Duilio Cascio
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Jose A Rodriguez
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Dan Shi
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147
| | - Stephan Philipp
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - Kevin Murray
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Lorena Saelices
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Ji Lee
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Paul Seidler
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Charles G Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697; Biochemistry Department, Faculty of Science and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Lin Jiang
- Department of Neurology, Molecular Biology Institute, and Brain Research Institute (BRI), David Geffen School of Medicine, UCLA, Los Angeles, California, 90095
| | - Tamir Gonen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia 20147
| | - David S Eisenberg
- Howard Hughes Medical Institute, UCLA-United States Department of Energy (DOE) Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095.
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24
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Lee S, Devamani T, Song HD, Sandhu M, Larsen A, Sommese R, Jain A, Vaidehi N, Sivaramakrishnan S. Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα. J Biol Chem 2017; 292:16300-16309. [PMID: 28821615 PMCID: PMC5625059 DOI: 10.1074/jbc.m117.804781] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/04/2017] [Indexed: 11/06/2022] Open
Abstract
Protein kinase Cα (PKCα) belongs to the family of AGC kinases that phosphorylate multiple peptide substrates. Although the consensus sequence motif has been identified and used to explain substrate specificity for PKCα, it does not inform the structural basis of substrate-binding and kinase activity for diverse substrates phosphorylated by this kinase. The transient, dynamic, and unstructured nature of this protein-protein interaction has limited structural mapping of kinase-substrate interfaces. Here, using multiscale MD simulation-based predictions and FRET sensor-based experiments, we investigated the conformational dynamics of the kinase-substrate interface. We found that the binding strength of the kinase-substrate interaction is primarily determined by long-range columbic interactions between basic (Arg/Lys) residues located N-terminally to the phosphorylated Ser/Thr residues in the substrate and by an acidic patch in the kinase catalytic domain. Kinase activity stemmed from conformational flexibility in the region C-terminal to the phosphorylated Ser/Thr residues. Flexibility of the substrate-kinase interaction enabled an Arg/Lys two to three amino acids C-terminal to the phosphorylated Ser/Thr to prime a catalytically active conformation, facilitating phosphoryl transfer to the substrate. The structural mechanisms determining substrate binding and catalytic activity formed the basis of diverse binding affinities and kinase activities of PKCα for 14 substrates with varying degrees of sequence conservation. Our findings provide insight into the dynamic properties of the kinase-substrate interaction that govern substrate binding and turnover. Moreover, this study establishes a modeling and experimental method to elucidate the structural dynamics underlying substrate selectivity among eukaryotic kinases.
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Affiliation(s)
- Sangbae Lee
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Titu Devamani
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, and
| | - Hyun Deok Song
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Manbir Sandhu
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Adrien Larsen
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Ruth Sommese
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, and
| | - Abhinandan Jain
- the Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109
| | - Nagarajan Vaidehi
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010,
| | - Sivaraj Sivaramakrishnan
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, and
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25
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Bakou M, Hille K, Kracklauer M, Spanopoulou A, Frost CV, Malideli E, Yan LM, Caporale A, Zacharias M, Kapurniotu A. Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly. J Biol Chem 2017; 292:14587-14602. [PMID: 28684415 DOI: 10.1074/jbc.m117.774893] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 07/02/2017] [Indexed: 12/28/2022] Open
Abstract
The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions.
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Affiliation(s)
- Maria Bakou
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Kathleen Hille
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Michael Kracklauer
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Anna Spanopoulou
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Christina V Frost
- the Physik Department, Technische Universität München, D-85748 Garching, Germany
| | - Eleni Malideli
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Li-Mei Yan
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Andrea Caporale
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Martin Zacharias
- the Physik Department, Technische Universität München, D-85748 Garching, Germany
| | - Aphrodite Kapurniotu
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
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26
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Liu Y, Qin S, Lei M, Tempel W, Zhang Y, Loppnau P, Li Y, Min J. Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1. J Biol Chem 2017; 292:5655-5664. [PMID: 28223359 DOI: 10.1074/jbc.m116.768374] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/16/2017] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSDγ) in complex with an H3 peptide suggests that recognition of H3 by CSDγ to some extent resembles CSD-PXVXL interaction. Nevertheless, the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1β CSD-PXVXL complexes. We consequently generalize the historical CSD-PXVXL interaction model and expand the search scope for additional CSD binding partners.
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Affiliation(s)
- Yanli Liu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Su Qin
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Ming Lei
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Wolfram Tempel
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yuzhe Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yanjun Li
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Jinrong Min
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and .,the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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27
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Remesh SG, Andreatta M, Ying G, Kaever T, Nielsen M, McMurtrey C, Hildebrand W, Peters B, Zajonc DM. Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT. J Biol Chem 2017; 292:5262-5270. [PMID: 28179428 DOI: 10.1074/jbc.m117.776542] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Peptide antigen presentation by major histocompatibility complex (MHC) class I proteins initiates CD8+ T cell-mediated immunity against pathogens and cancers. MHC I molecules typically bind peptides with 9 amino acids in length with both ends tucked inside the major A and F binding pockets. It has been known for a while that longer peptides can also bind by either bulging out of the groove in the middle of the peptide or by binding in a zigzag fashion inside the groove. In a recent study, we identified an alternative binding conformation of naturally occurring peptides from Toxoplasma gondii bound by HLA-A*02:01. These peptides were extended at the C terminus (PΩ) and contained charged amino acids not more than 3 residues after the anchor amino acid at PΩ, which enabled them to open the F pocket and expose their C-terminal extension into the solvent. Here, we show that the mechanism of F pocket opening is dictated by the charge of the first charged amino acid found within the extension. Although positively charged amino acids result in the Tyr-84 swing, amino acids that are negatively charged induce a not previously described Lys-146 lift. Furthermore, we demonstrate that the peptides with alternative binding modes have properties that fit very poorly to the conventional MHC class I pathway and suggest they are presented via alternative means, potentially including cross-presentation via the MHC class II pathway.
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Affiliation(s)
| | - Massimo Andreatta
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Argentina
| | - Ge Ying
- From the Division for Cell Biology and
| | - Thomas Kaever
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Argentina.,Center for Biological Sequence Analysis, Department of Bio and Health Informatics, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Curtis McMurtrey
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104.,Pure MHC LLC, Austin, Texas 78229, and
| | - William Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104.,Pure MHC LLC, Austin, Texas 78229, and
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Dirk M Zajonc
- From the Division for Cell Biology and .,Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
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28
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Charpentier TH, Waldo GL, Lowery-Gionta EG, Krajewski K, Strahl BD, Kash TL, Harden TK, Sondek J. Potent and Selective Peptide-based Inhibition of the G Protein Gαq. J Biol Chem 2016; 291:25608-25616. [PMID: 27742837 DOI: 10.1074/jbc.m116.740407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 10/13/2016] [Indexed: 11/06/2022] Open
Abstract
In contrast to G protein-coupled receptors, for which chemical and peptidic inhibitors have been extensively explored, few compounds are available that directly modulate heterotrimeric G proteins. Active Gαq binds its two major classes of effectors, the phospholipase C (PLC)-β isozymes and Rho guanine nucleotide exchange factors (RhoGEFs) related to Trio, in a strikingly similar fashion: a continuous helix-turn-helix of the effectors engages Gαq within its canonical binding site consisting of a groove formed between switch II and helix α3. This information was exploited to synthesize peptides that bound active Gαq in vitro with affinities similar to full-length effectors and directly competed with effectors for engagement of Gαq A representative peptide was specific for active Gαq because it did not bind inactive Gαq or other classes of active Gα subunits and did not inhibit the activation of PLC-β3 by Gβ1γ2 In contrast, the peptide robustly prevented activation of PLC-β3 or p63RhoGEF by Gαq; it also prevented G protein-coupled receptor-promoted neuronal depolarization downstream of Gαq in the mouse prefrontal cortex. Moreover, a genetically encoded form of this peptide flanked by fluorescent proteins inhibited Gαq-dependent activation of PLC-β3 at least as effectively as a dominant-negative form of full-length PLC-β3. These attributes suggest that related, cell-penetrating peptides should effectively inhibit active Gαq in cells and that these and genetically encoded sequences may find application as molecular probes, drug leads, and biosensors to monitor the spatiotemporal activation of Gαq in cells.
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Affiliation(s)
- Thomas H Charpentier
- From the Departments of Pharmacology and.,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | | | | | - Krzysztof Krajewski
- Biochemistry and Biophysics.,High-Throughput Peptide Synthesis and Array Facility, and
| | - Brian D Strahl
- Biochemistry and Biophysics.,High-Throughput Peptide Synthesis and Array Facility, and
| | | | | | - John Sondek
- From the Departments of Pharmacology and .,Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599.,Biochemistry and Biophysics
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29
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Murray B, Pearson CS, Aranjo A, Cherupalla D, Belfort G. Mechanism of Four de Novo Designed Antimicrobial Peptides. J Biol Chem 2016; 291:25706-25715. [PMID: 27738105 DOI: 10.1074/jbc.m116.733816] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/11/2016] [Indexed: 11/06/2022] Open
Abstract
As pathogenic bacteria become resistant to traditional antibiotics, alternate approaches such as designing and testing new potent selective antimicrobial peptides (AMP) are increasingly attractive. However, whereas much is known regarding the relationship between the AMP sequence and potency, less research has focused on developing links between AMP properties, such as design and structure, with mechanisms. Here we use four natural AMPs of varying known secondary structures and mechanisms of lipid bilayer disruption as controls to determine the mechanisms of four rationally designed AMPs with similar secondary structures and rearranged amino acid sequences. Using a Quartz Crystal Microbalance with Dissipation, we were able to differentiate between molecular models of AMP actions such as barrel-stave pore formation, toroidal pore formation, and peptide insertion mechanisms by quantifying differential frequencies throughout an oscillating supported lipid bilayer. Barrel-stave pores were identified by uniform frequency modulation, whereas toroidal pores possessed characteristic changes in oscillation frequency throughout the bilayer. The resulting modes of action demonstrate that rearrangement of an amino acid sequence of the AMP resulted in identical overall mechanisms, and that a given secondary structure did not necessarily predict mechanism. Also, increased mass addition to Gram-positive mimetic membranes from AMP disruption corresponded with lower minimum inhibitory concentrations against the Gram-positive Staphylococcus aureus.
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Affiliation(s)
- Brian Murray
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - C Seth Pearson
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Alexa Aranjo
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Dinesh Cherupalla
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Georges Belfort
- From the Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
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30
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Johansson E, Hansen JL, Hansen AMK, Shaw AC, Becker P, Schäffer L, Reedtz-Runge S. Type II Turn of Receptor-bound Salmon Calcitonin Revealed by X-ray Crystallography. J Biol Chem 2016; 291:13689-98. [PMID: 27189946 DOI: 10.1074/jbc.m116.726034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Indexed: 12/20/2022] Open
Abstract
Calcitonin is a peptide hormone consisting of 32 amino acid residues and the calcitonin receptor is a Class B G protein-coupled receptor (GPCR). The crystal structure of the human calcitonin receptor ectodomain (CTR ECD) in complex with a truncated analogue of salmon calcitonin ([BrPhe(22)]sCT(8-32)) has been determined to 2.1-Å resolution. Parallel analysis of a series of peptide ligands showed that the rank order of binding of the CTR ECD is identical to the rank order of binding of the full-length CTR, confirming the structural integrity and relevance of the isolated CTR ECD. The structure of the CTR ECD is similar to other Class B GPCRs and the ligand binding site is similar to the binding site of the homologous receptors for the calcitonin gene-related peptide (CGRP) and adrenomedulin (AM) recently published (Booe, J. M., Walker, C. S., Barwell, J., Kuteyi, G., Simms, J., Jamaluddin, M. A., Warner, M. L., Bill, R. M., Harris, P. W., Brimble, M. A., Poyner, D. R., Hay, D. L., and Pioszak, A. A. (2015) Mol. Cell 58, 1040-1052). Interestingly the receptor-bound structure of the ligand [BrPhe(22)]sCT(8-32) differs from the receptor-bound structure of the homologous ligands CGRP and AM. They all adopt an extended conformation followed by a C-terminal β turn, however, [BrPhe(22)]sCT(8-32) adopts a type II turn (Gly(28)-Thr(31)), whereas CGRP and AM adopt type I turns. Our results suggest that a type II turn is the preferred conformation of calcitonin, whereas a type I turn is the preferred conformation of peptides that require RAMPs; CGRP, AM, and amylin. In addition the structure provides a detailed molecular explanation and hypothesis regarding ligand binding properties of CTR and the amylin receptors.
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Affiliation(s)
- Eva Johansson
- From Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | | | | | | | - Peter Becker
- From Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - Lauge Schäffer
- From Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
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31
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Yang D, de Graaf C, Yang L, Song G, Dai A, Cai X, Feng Y, Reedtz-Runge S, Hanson MA, Yang H, Jiang H, Stevens RC, Wang MW. Structural Determinants of Binding the Seven-transmembrane Domain of the Glucagon-like Peptide-1 Receptor (GLP-1R). J Biol Chem 2016; 291:12991-3004. [PMID: 27059958 DOI: 10.1074/jbc.m116.721977] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Indexed: 12/25/2022] Open
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) belongs to the secretin-like (class B) family of G protein-coupled receptors. Members of the class B family are distinguished by their large extracellular domain, which works cooperatively with the canonical seven-transmembrane (7TM) helical domain to signal in response to binding of various peptide hormones. We have combined structure-based site-specific mutational studies with molecular dynamics simulations of a full-length model of GLP-1R bound to multiple peptide ligand variants. Despite the high sequence similarity between GLP-1R and its closest structural homologue, the glucagon receptor (GCGR), nearly half of the 62 stably expressed mutants affected GLP-1R in a different manner than the corresponding mutants in GCGR. The molecular dynamics simulations of wild-type and mutant GLP-1R·ligand complexes provided molecular insights into GLP-1R-specific recognition mechanisms for the N terminus of GLP-1 by residues in the 7TM pocket and explained how glucagon-mimicking GLP-1 mutants restored binding affinity for (GCGR-mimicking) GLP-1R mutants. Structural analysis of the simulations suggested that peptide ligand binding mode variations in the 7TM binding pocket are facilitated by movement of the extracellular domain relative to the 7TM bundle. These differences in binding modes may account for the pharmacological differences between GLP-1 peptide variants.
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Affiliation(s)
- Dehua Yang
- From The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Shanghai 201203, China
| | - Chris de Graaf
- the Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Linlin Yang
- the Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Gaojie Song
- the iHuman Institute, ShanghaiTech University, 99 Haike Road, Shanghai 201203, China
| | - Antao Dai
- From The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Shanghai 201203, China
| | - Xiaoqing Cai
- From The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Shanghai 201203, China
| | - Yang Feng
- From The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Shanghai 201203, China
| | - Steffen Reedtz-Runge
- the Department of Protein Structure, Novo Nordisk, Novo Nordisk Park, Malov 2760, Denmark
| | | | - Huaiyu Yang
- the Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- the Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Raymond C Stevens
- the iHuman Institute, ShanghaiTech University, 99 Haike Road, Shanghai 201203, China, the Bridge Institute, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California 90089, and
| | - Ming-Wei Wang
- From The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Shanghai 201203, China, the School of Pharmacy, Fudan University, 826 Zhang Heng Road, Shanghai 201203, China
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32
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Niu YY, Yang Y, Liu Y, Huang LD, Yang XN, Fan YZ, Cheng XY, Cao P, Hu YM, Li L, Lu XY, Tian Y, Yu Y. Exploration of the Peptide Recognition of an Amiloride-sensitive FMRFamide Peptide-gated Sodium Channel. J Biol Chem 2016; 291:7571-82. [PMID: 26867576 DOI: 10.1074/jbc.m115.710251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Indexed: 12/22/2022] Open
Abstract
FMRFamide (Phe-Met-Arg-Phe-NH2)-activated sodium channel (FaNaC) is an amiloride-sensitive sodium channel activated by endogenous tetrapeptide in invertebrates, and belongs to the epithelial sodium channel/degenerin (ENaC/DEG) superfamily. The ENaC/DEG superfamily differs markedly in its means of activation, such as spontaneously opening or gating by mechanical stimuli or tissue acidosis. Recently, it has been observed that a number of ENaC/DEG channels can be activated by small molecules or peptides, indicating that the ligand-gating may be an important feature of this superfamily. The peptide ligand control of the channel gating might be an ancient ligand-gating feature in this superfamily. Therefore, studying the peptide recognition of FaNaC channels would advance our understanding of the ligand-gating properties of this superfamily of ion channels. Here we demonstrate that Tyr-131, Asn-134, Asp-154, and Ile-160, located in the putative upper finger domain ofHelix aspersaFaNaC (HaFaNaC) channels, are key residues for peptide recognition of this ion channel. Two HaFaNaC specific-insertion motifs among the ENaC/DEG superfamily, residing at the putative α4-α5 linker of the upper thumb domain and the α6-α7 linker of the upper knuckle domain, are also essential for the peptide recognition of HaFaNaC channels. Chemical modifications and double mutant cycle analysis further indicated that those two specific inserts and key residues in the upper finger domain together participate in peptide recognition of HaFaNaC channels. This ligand recognition site is distinct from that of acid-sensing ion channels (ASICs) by a longer distance between the recognition site and the channel gate, carrying useful information about the ligand gating and the evolution of the trimeric ENaC/DEG superfamily of ion channels.
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Affiliation(s)
- You-Ya Niu
- From the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China, Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Yang
- Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yan Liu
- Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Li-Dong Huang
- Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Na Yang
- From the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China, Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ying-Zhe Fan
- Putuo District Center Hospital, Shanghai University of Chinese Traditional Medicine, Shanghai, 200062, China
| | - Xiao-Yang Cheng
- Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Peng Cao
- Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China, and Laboratory of Cellular and Molecular Biology, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing 210028, China
| | - You-Min Hu
- Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lingyong Li
- Department of Anesthesiology and Perioperative Medicine, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Xiang-Yang Lu
- From the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Yun Tian
- From the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China,
| | - Ye Yu
- From the College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China, Institute of Medical Sciences and Departments of Pharmacology and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China,
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33
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Garrido-Urbani S, Garg P, Ghossoub R, Arnold R, Lembo F, Sundell GN, Kim PM, Lopez M, Zimmermann P, Sidhu SS, Ivarsson Y. Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. FEBS Lett 2016; 590:3-12. [PMID: 26787460 PMCID: PMC4819696 DOI: 10.1002/1873-3468.12037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/29/2015] [Indexed: 11/10/2022]
Abstract
Syntenin has crucial roles in cell adhesion, cell migration and synaptic transmission. Its closely linked postsynaptic density-95, discs large 1, zonula occludens-1 (PDZ) domains typically interact with C-terminal ligands. We profile syntenin PDZ1-2 through proteomic peptide phage display (ProP-PD) using a library that displays C-terminal regions of the human proteome. The protein recognizes a broad range of peptides, with a preference for hydrophobic motifs and has a tendency to recognize cryptic internal ligands. We validate the interaction with nectin-1 through orthogonal assays. The study demonstrates the power of ProP-PD as a complementary approach to uncover interactions of potential biological relevance.
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Affiliation(s)
- Sarah Garrido-Urbani
- Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille University, Centre National de la Recherche Scientifique UMR7258, Marseille, France
| | - Pankaj Garg
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada.,Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Rania Ghossoub
- Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille University, Centre National de la Recherche Scientifique UMR7258, Marseille, France
| | - Roland Arnold
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Frédérique Lembo
- Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille University, Centre National de la Recherche Scientifique UMR7258, Marseille, France
| | | | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Marc Lopez
- Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille University, Centre National de la Recherche Scientifique UMR7258, Marseille, France
| | - Pascale Zimmermann
- Inserm U1068, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille University, Centre National de la Recherche Scientifique UMR7258, Marseille, France.,Department of Human Genetics, KU Leuven, Belgium
| | - Sachdev S Sidhu
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada.,Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Sweden
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Mourier G, Salinas M, Kessler P, Stura EA, Leblanc M, Tepshi L, Besson T, Diochot S, Baron A, Douguet D, Lingueglia E, Servent D. Mambalgin-1 Pain-relieving Peptide, Stepwise Solid-phase Synthesis, Crystal Structure, and Functional Domain for Acid-sensing Ion Channel 1a Inhibition. J Biol Chem 2015; 291:2616-29. [PMID: 26680001 DOI: 10.1074/jbc.m115.702373] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Indexed: 01/04/2023] Open
Abstract
Mambalgins are peptides isolated from mamba venom that specifically inhibit a set of acid-sensing ion channels (ASICs) to relieve pain. We show here the first full stepwise solid phase peptide synthesis of mambalgin-1 and confirm the biological activity of the synthetic toxin both in vitro and in vivo. We also report the determination of its three-dimensional crystal structure showing differences with previously described NMR structures. Finally, the functional domain by which the toxin inhibits ASIC1a channels was identified in its loop II and more precisely in the face containing Phe-27, Leu-32, and Leu-34 residues. Moreover, proximity between Leu-32 in mambalgin-1 and Phe-350 in rASIC1a was proposed from double mutant cycle analysis. These data provide information on the structure and on the pharmacophore for ASIC channel inhibition by mambalgins that could have therapeutic value against pain and probably other neurological disorders.
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Affiliation(s)
- Gilles Mourier
- From the Commissariat à l'Energie Atomique, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette
| | - Miguel Salinas
- the CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, the Université de Nice Sophia Antipolis, and the LabEx Ion Channel Science and Therapeutics, UMR 7275, 06560 Valbonne, France
| | - Pascal Kessler
- From the Commissariat à l'Energie Atomique, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette
| | - Enrico A Stura
- From the Commissariat à l'Energie Atomique, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette
| | - Mathieu Leblanc
- From the Commissariat à l'Energie Atomique, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette
| | - Livia Tepshi
- From the Commissariat à l'Energie Atomique, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette
| | - Thomas Besson
- the CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, the Université de Nice Sophia Antipolis, and the LabEx Ion Channel Science and Therapeutics, UMR 7275, 06560 Valbonne, France
| | - Sylvie Diochot
- the CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, the Université de Nice Sophia Antipolis, and the LabEx Ion Channel Science and Therapeutics, UMR 7275, 06560 Valbonne, France
| | - Anne Baron
- the CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, the Université de Nice Sophia Antipolis, and the LabEx Ion Channel Science and Therapeutics, UMR 7275, 06560 Valbonne, France
| | - Dominique Douguet
- the CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, the Université de Nice Sophia Antipolis, and
| | - Eric Lingueglia
- the CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, the Université de Nice Sophia Antipolis, and the LabEx Ion Channel Science and Therapeutics, UMR 7275, 06560 Valbonne, France
| | - Denis Servent
- From the Commissariat à l'Energie Atomique, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette,
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35
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Mattera R, Guardia CM, Sidhu SS, Bonifacino JS. Bivalent Motif-Ear Interactions Mediate the Association of the Accessory Protein Tepsin with the AP-4 Adaptor Complex. J Biol Chem 2015; 290:30736-49. [PMID: 26542808 DOI: 10.1074/jbc.m115.683409] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 01/11/2023] Open
Abstract
The heterotetrameric (ϵ-β4-μ4-σ4) complex adaptor protein 4 (AP-4) is a component of a non-clathrin coat involved in protein sorting at the trans-Golgi network (TGN). Considerable interest in this complex has arisen from the recent discovery that mutations in each of its four subunits are the cause of a congenital intellectual disability and movement disorder in humans. Despite its physiological importance, the structure and function of this coat remain poorly understood. To investigate the assembly of the AP-4 coat, we dissected the determinants of interaction of AP-4 with its only known accessory protein, the ENTH/VHS-domain-containing protein tepsin. Using a variety of protein interaction assays, we found that tepsin comprises two phylogenetically conserved peptide motifs, [GS]LFXG[ML]X[LV] and S[AV]F[SA]FLN, within its C-terminal unstructured region, which interact with the C-terminal ear (or appendage) domains of the β4 and ϵ subunits of AP-4, respectively. Structure-based mutational analyses mapped the binding site for the [GS]LFXG[ML]X[LV] motif to a conserved, hydrophobic surface on the β4-ear platform fold. Both peptide-ear interactions are required for efficient association of tepsin with AP-4, and for recruitment of tepsin to the TGN. The bivalency of the interactions increases the avidity of tepsin for AP-4 and may enable cross-linking of multiple AP-4 heterotetramers, thus contributing to the assembly of the AP-4 coat. In addition to revealing critical aspects of this coat, our findings extend the paradigm of peptide-ear interactions, previously established for clathrin-AP-1/AP-2 coats, to a non-clathrin coat.
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Affiliation(s)
- Rafael Mattera
- From the Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Carlos M Guardia
- From the Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Juan S Bonifacino
- From the Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 and
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36
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Saelices L, Johnson LM, Liang WY, Sawaya MR, Cascio D, Ruchala P, Whitelegge J, Jiang L, Riek R, Eisenberg DS. Uncovering the Mechanism of Aggregation of Human Transthyretin. J Biol Chem 2015; 290:28932-43. [PMID: 26459562 PMCID: PMC4661406 DOI: 10.1074/jbc.m115.659912] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Indexed: 11/06/2022] Open
Abstract
The tetrameric thyroxine transport protein transthyretin (TTR) forms amyloid fibrils upon dissociation and monomer unfolding. The aggregation of transthyretin has been reported as the cause of the life-threatening transthyretin amyloidosis. The standard treatment of familial cases of TTR amyloidosis has been liver transplantation. Although aggregation-preventing strategies involving ligands are known, understanding the mechanism of TTR aggregation can lead to additional inhibition approaches. Several models of TTR amyloid fibrils have been proposed, but the segments that drive aggregation of the protein have remained unknown. Here we identify β-strands F and H as necessary for TTR aggregation. Based on the crystal structures of these segments, we designed two non-natural peptide inhibitors that block aggregation. This work provides the first characterization of peptide inhibitors for TTR aggregation, establishing a novel therapeutic strategy.
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Affiliation(s)
- Lorena Saelices
- From the Department of Biological Chemistry, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095-1570, Swiss Federal Institute of Technology in Zürich (ETH), Physical Chemistry, ETH Hönggerberg, 8093 Zürich, Switzerland, and
| | - Lisa M Johnson
- From the Department of Biological Chemistry, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095-1570
| | - Wilson Y Liang
- From the Department of Biological Chemistry, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095-1570
| | - Michael R Sawaya
- From the Department of Biological Chemistry, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095-1570
| | - Duilio Cascio
- From the Department of Biological Chemistry, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095-1570
| | - Piotr Ruchala
- the Department of Psychiatry and Biobehavioral Sciences, UCLA and The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90024
| | - Julian Whitelegge
- the Department of Psychiatry and Biobehavioral Sciences, UCLA and The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, Los Angeles, California 90024
| | - Lin Jiang
- From the Department of Biological Chemistry, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095-1570
| | - Roland Riek
- Swiss Federal Institute of Technology in Zürich (ETH), Physical Chemistry, ETH Hönggerberg, 8093 Zürich, Switzerland, and
| | - David S Eisenberg
- From the Department of Biological Chemistry, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095-1570,
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37
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Wang H, Jin H, Rapraeger AC. Syndecan-1 and Syndecan-4 Capture Epidermal Growth Factor Receptor Family Members and the α3β1 Integrin Via Binding Sites in Their Ectodomains: NOVEL SYNSTATINS PREVENT KINASE CAPTURE AND INHIBIT α6β4-INTEGRIN-DEPENDENT EPITHELIAL CELL MOTILITY. J Biol Chem 2015; 290:26103-13. [PMID: 26350464 DOI: 10.1074/jbc.m115.679084] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Indexed: 11/06/2022] Open
Abstract
The α6β4 integrin is known to associate with receptor tyrosine kinases when engaged in epithelial wound healing and in carcinoma invasion and survival. Prior work has shown that HER2 associates with α6β4 integrin and syndecan-1 (Sdc1), in which Sdc1 engages the cytoplasmic domain of the β4 integrin subunit allowing HER2-dependent motility and carcinoma cell survival. In contrast, EGFR associates with Sdc4 and the α6β4 integrin, and EGFR-dependent motility depends on cytoplasmic engagement of β4 integrin with Sdc4. However, how HER2 and EGFR assimilate into a complex with the syndecans and integrin, and why kinase capture is syndecan-specific has remained unknown. In the present study, we demonstrate that HER2 is captured via a site, comprised of amino acids 210-240, in the extracellular domain of human Sdc1, and EGFR is captured via an extracellular site comprised of amino acids 87-131 in human Sdc4. Binding assays using purified recombinant proteins demonstrate that the interaction between the EGFR family members and the syndecans is direct. The α3β1 integrin, which is responsible for the motility of the cells, is captured at these sites as well. Peptides based on the interaction motifs in Sdc1 and Sdc4, called synstatins (SSTN210-240 and SSTN87-131) competitively displace the receptor tyrosine kinase and α3β1 integrin from the syndecan with an IC50 of 100-300 nm. The syndecans remain anchored to the α6β4 integrin via its cytoplasmic domain, but the activation of cell motility is disrupted. These novel SSTN peptides are potential therapeutics for carcinomas that depend on these HER2- and EGFR-coupled mechanisms for their invasion and survival.
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Affiliation(s)
| | | | - Alan C Rapraeger
- From the Department of Human Oncology and the University of Wisconsin Carbone Cancer Center, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, Wisconsin 53705
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38
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Kenealey J, Subramanian P, Comitato A, Bullock J, Keehan L, Polato F, Hoover D, Marigo V, Becerra SP. Small Retinoprotective Peptides Reveal a Receptor-binding Region on Pigment Epithelium-derived Factor. J Biol Chem 2015; 290:25241-53. [PMID: 26304116 DOI: 10.1074/jbc.m115.645846] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 11/06/2022] Open
Abstract
The cytoprotective effects of pigment epithelium-derived factor (PEDF) require interactions between an as of a yet undefined region with a distinct ectodomain on the PEDF receptor (PEDF-R). Here we characterized the area in PEDF that interacts with PEDF-R to promote photoreceptor survival. Molecular docking studies suggested that the ligand binding site of PEDF-R interacts with the neurotrophic region of PEDF (44-mer, positions 78-121). Binding assays demonstrated that PEDF-R bound the 44-mer peptide. Moreover, peptide P1 from the PEDF-R ectodomain had affinity for the 44-mer and a shorter fragment within it, 17-mer (positions 98-114). Single residue substitutions to alanine along the 17-mer sequence were designed and tested for binding and biological activity. Altered 17-mer[R99A] did not bind to the P1 peptide, whereas 17-mer[H105A] had higher affinity than the unmodified 17-mer. Peptides 17-mer, 17-mer[H105A], and 44-mer exhibited cytoprotective effects in cultured retina R28 cells. Intravitreal injections of these peptides and PEDF in the rd1 mouse model of retinal degeneration decreased the numbers of dying photoreceptors, 17-mer[H105A] being most effective. The blocking peptide P1 hindered their protective effects both in retina cells and in vivo. Thus, in addition to demonstrating that the region composed of positions 98-114 of PEDF contains critical residues for PEDF-R interaction that mediates survival effects, the findings reveal distinct small PEDF fragments with neurotrophic effects on photoreceptors.
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Affiliation(s)
| | | | - Antonella Comitato
- the Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy, and
| | - Jeanee Bullock
- From the National Eye Institute and the Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, D. C. 20057
| | | | | | - David Hoover
- the Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892
| | - Valeria Marigo
- the Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy, and
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39
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Nata T, Basheer A, Cocchi F, van Besien R, Massoud R, Jacobson S, Azimi N, Tagaya Y. Targeting the binding interface on a shared receptor subunit of a cytokine family enables the inhibition of multiple member cytokines with selectable target spectrum. J Biol Chem 2015; 290:22338-51. [PMID: 26183780 DOI: 10.1074/jbc.m115.661074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Indexed: 02/04/2023] Open
Abstract
The common γ molecule (γc) is a shared signaling receptor subunit used by six γc-cytokines. These cytokines play crucial roles in the differentiation of the mature immune system and are involved in many human diseases. Moreover, recent studies suggest that multiple γc-cytokines are pathogenically involved in a single disease, thus making the shared γc-molecule a logical target for therapeutic intervention. However, the current therapeutic strategies seem to lack options to treat such cases, partly because of the lack of appropriate neutralizing antibodies recognizing the γc and, more importantly, because of the inherent and practical limitations in the use of monoclonal antibodies. By targeting the binding interface of the γc and cytokines, we successfully designed peptides that not only inhibit multiple γc-cytokines but with a selectable target spectrum. Notably, the lead peptide inhibited three γc-cytokines without affecting the other three or non-γc-cytokines. Biological and mutational analyses of our peptide provide new insights to our current understanding on the structural aspect of the binding of γc-cytokines the γc-molecule. Furthermore, we provide evidence that our peptide, when conjugated to polyethylene glycol to gain stability in vivo, efficiently blocks the action of one of the target cytokines in animal models. Collectively, our technology can be expanded to target various combinations of γc-cytokines and thereby will provide a novel strategy to the current anti-cytokine therapies against immune, inflammatory, and malignant diseases.
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Affiliation(s)
- Toshie Nata
- From the Cell Biology Laboratory, Division of Basic Science, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | | | - Fiorenza Cocchi
- From the Cell Biology Laboratory, Division of Basic Science, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Richard van Besien
- From the Cell Biology Laboratory, Division of Basic Science, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Raya Massoud
- the Section of Neuroimmunology, NINDS, National Institutes of Health, Bethesda, Maryland 20890
| | - Steven Jacobson
- the Section of Neuroimmunology, NINDS, National Institutes of Health, Bethesda, Maryland 20890
| | | | - Yutaka Tagaya
- From the Cell Biology Laboratory, Division of Basic Science, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201,
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40
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Hampe L, Radjainia M, Xu C, Harris PWR, Bashiri G, Goldstone DC, Brimble MA, Wang Y, Mitra AK. Regulation and Quality Control of Adiponectin Assembly by Endoplasmic Reticulum Chaperone ERp44. J Biol Chem 2015; 290:18111-18123. [PMID: 26060250 DOI: 10.1074/jbc.m115.663088] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 01/09/2023] Open
Abstract
Adiponectin, a collagenous hormone secreted abundantly from adipocytes, possesses potent antidiabetic and anti-inflammatory properties. Mediated by the conserved Cys(39) located in the variable region of the N terminus, the trimeric (low molecular weight (LMW)) adiponectin subunit assembles into different higher order complexes, e.g. hexamers (middle molecular weight (MMW)) and 12-18-mers (high molecular weight (HMW)), the latter being mostly responsible for the insulin-sensitizing activity of adiponectin. The endoplasmic reticulum (ER) chaperone ERp44 retains adiponectin in the early secretory compartment and tightly controls the oxidative state of Cys(39) and the oligomerization of adiponectin. Using cellular and in vitro assays, we show that ERp44 specifically recognizes the LMW and MMW forms but not the HMW form. Our binding assays with short peptide mimetics of adiponectin suggest that ERp44 intercepts and converts the pool of fully oxidized LMW and MMW adiponectin, but not the HMW form, into reduced trimeric precursors. These ERp44-bound precursors in the cis-Golgi may be transported back to the ER and released to enhance the population of adiponectin intermediates with appropriate oxidative state for HMW assembly, thereby underpinning the process of ERp44 quality control.
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Affiliation(s)
- Lutz Hampe
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Mazdak Radjainia
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Cheng Xu
- State Key Laboratory of Pharmaceutical Biotechnology and Department of Pharmacology and Pharmacy, The University of Hong Kong, 999007 Hong Kong, China
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand; Institute for Innovation in Biotechnology, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Ghader Bashiri
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - David C Goldstone
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand; Institute for Innovation in Biotechnology, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Yu Wang
- State Key Laboratory of Pharmaceutical Biotechnology and Department of Pharmacology and Pharmacy, The University of Hong Kong, 999007 Hong Kong, China
| | - Alok K Mitra
- School of Biological Science, The University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.
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41
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Latham JA, Iavarone AT, Barr I, Juthani PV, Klinman JP. PqqD is a novel peptide chaperone that forms a ternary complex with the radical S-adenosylmethionine protein PqqE in the pyrroloquinoline quinone biosynthetic pathway. J Biol Chem 2015; 290:12908-18. [PMID: 25817994 DOI: 10.1074/jbc.m115.646521] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 11/06/2022] Open
Abstract
Pyrroloquinoline quinone (PQQ) is a product of a ribosomally synthesized and post-translationally modified pathway consisting of five conserved genes, pqqA-E. PqqE is a radical S-adenosylmethionine (RS) protein with a C-terminal SPASM domain, and is proposed to catalyze the formation of a carbon-carbon bond between the glutamate and tyrosine side chains of the peptide substrate PqqA. PqqD is a 10-kDa protein with an unknown function, but is essential for PQQ production. Recently, in Klebsiella pneumoniae (Kp), PqqD and PqqE were shown to interact; however, the stoichiometry and KD were not obtained. Here, we show that the PqqE and PqqD interaction transcends species, also occurring in Methylobacterium extorquens AM1 (Me). The stoichiometry of the MePqqD and MePqqE interaction is 1:1 and the KD, determined by surface plasmon resonance spectroscopy (SPR), was found to be ∼12 μm. Moreover, using SPR and isothermal calorimetry techniques, we establish for the first time that MePqqD binds MePqqA tightly (KD ∼200 nm). The formation of a ternary MePqqA-D-E complex was captured by native mass spectrometry and the KD for the MePqqAD-MePqqE interaction was found to be ∼5 μm. Finally, using a bioinformatic analysis, we found that PqqD orthologues are associated with the RS-SPASM family of proteins (subtilosin, pyrroloquinoline quinone, anaerobic sulfatase maturating enzyme, and mycofactocin), all of which modify either peptides or proteins. In conclusion, we propose that PqqD is a novel peptide chaperone and that PqqD orthologues may play a similar role in peptide modification pathways that use an RS-SPASM protein.
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Affiliation(s)
- John A Latham
- From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Anthony T Iavarone
- From the Departments of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Ian Barr
- From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Prerak V Juthani
- From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Judith P Klinman
- From the Departments of Chemistry and Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
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