1
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Theophall GG, Ramirez LMS, Premo A, Reverdatto S, Manigrasso MB, Yepuri G, Burz DS, Ramasamy R, Schmidt AM, Shekhtman A. Disruption of the productive encounter complex results in dysregulation of DIAPH1 activity. J Biol Chem 2023; 299:105342. [PMID: 37832872 PMCID: PMC10656230 DOI: 10.1016/j.jbc.2023.105342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/27/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
The diaphanous-related formin, Diaphanous 1 (DIAPH1), is required for the assembly of Filamentous (F)-actin structures. DIAPH1 is an intracellular effector of the receptor for advanced glycation end products (RAGE) and contributes to RAGE signaling and effects such as increased cell migration upon RAGE stimulation. Mutations in DIAPH1, including those in the basic "RRKR" motif of its autoregulatory domain, diaphanous autoinhibitory domain (DAD), are implicated in hearing loss, macrothrombocytopenia, and cardiovascular diseases. The solution structure of the complex between the N-terminal inhibitory domain, DID, and the C-terminal DAD, resolved by NMR spectroscopy shows only transient interactions between DID and the basic motif of DAD, resembling those found in encounter complexes. Cross-linking studies placed the RRKR motif into the negatively charged cavity of DID. Neutralizing the cavity resulted in a 5-fold decrease in the binding affinity and 4-fold decrease in the association rate constant of DAD for DID, indicating that the RRKR interactions with DID form a productive encounter complex. A DIAPH1 mutant containing a neutralized RRKR binding cavity shows excessive colocalization with actin and is unresponsive to RAGE stimulation. This is the first demonstration of a specific alteration of the surfaces responsible for productive encounter complexation with implications for human pathology.
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Affiliation(s)
- Gregory G Theophall
- Department of Chemistry, State University of New York at Albany, Albany, New York, USA
| | - Lisa M S Ramirez
- Department of Chemistry, State University of New York at Albany, Albany, New York, USA
| | - Aaron Premo
- Department of Chemistry, State University of New York at Albany, Albany, New York, USA
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany, Albany, New York, USA
| | - Michaele B Manigrasso
- Department of Medicine, Diabetes Research Program, New York University Grossman School of Medicine, New York, New York, USA
| | - Gautham Yepuri
- Department of Medicine, Diabetes Research Program, New York University Grossman School of Medicine, New York, New York, USA
| | - David S Burz
- Department of Chemistry, State University of New York at Albany, Albany, New York, USA
| | - Ravichandran Ramasamy
- Department of Medicine, Diabetes Research Program, New York University Grossman School of Medicine, New York, New York, USA
| | - Ann Marie Schmidt
- Department of Medicine, Diabetes Research Program, New York University Grossman School of Medicine, New York, New York, USA
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany, Albany, New York, USA.
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2
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Yepuri G, Ramirez LM, Theophall GG, Reverdatto SV, Quadri N, Hasan SN, Bu L, Thiagarajan D, Wilson R, Díez RL, Gugger PF, Mangar K, Narula N, Katz SD, Zhou B, Li H, Stotland AB, Gottlieb RA, Schmidt AM, Shekhtman A, Ramasamy R. DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress. Nat Commun 2023; 14:6900. [PMID: 37903764 PMCID: PMC10616211 DOI: 10.1038/s41467-023-42521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
Inter-organelle contact and communication between mitochondria and sarco/endoplasmic reticulum (SR/ER) maintain cellular homeostasis and are profoundly disturbed during tissue ischemia. We tested the hypothesis that the formin Diaphanous-1 (DIAPH1), which regulates actin dynamics, signal transduction and metabolic functions, contributes to these processes. We demonstrate that DIAPH1 interacts directly with Mitofusin-2 (MFN2) to shorten mitochondria-SR/ER distance, thereby enhancing mitochondria-ER contact in cells including cardiomyocytes, endothelial cells and macrophages. Solution structure studies affirm the interaction between the Diaphanous Inhibitory Domain and the cytosolic GTPase domain of MFN2. In male rodent and human cardiomyocytes, DIAPH1-MFN2 interaction regulates mitochondrial turnover, mitophagy, and oxidative stress. Introduction of synthetic linker construct, which shorten the mitochondria-SR/ER distance, mitigated the molecular and functional benefits of DIAPH1 silencing in ischemia. This work establishes fundamental roles for DIAPH1-MFN2 interaction in the regulation of mitochondria-SR/ER contact networks. We propose that targeting pathways that regulate DIAPH1-MFN2 interactions may facilitate recovery from tissue ischemia.
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Affiliation(s)
- Gautham Yepuri
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Lisa M Ramirez
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Gregory G Theophall
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Sergei V Reverdatto
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Nosirudeen Quadri
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Syed Nurul Hasan
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Lei Bu
- Department of Medicine, Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Devi Thiagarajan
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Robin Wilson
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Raquel López Díez
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Paul F Gugger
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Kaamashri Mangar
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Navneet Narula
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Stuart D Katz
- Department of Medicine, Leon H. Charney Division of Cardiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Boyan Zhou
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Huilin Li
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Aleksandr B Stotland
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Roberta A Gottlieb
- Department of Biomedical Sciences, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA
| | - Alexander Shekhtman
- Department of Chemistry, University of Albany, State University of New York, Albany, NY, 12222, USA
| | - Ravichandran Ramasamy
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, NYU Grossman School of Medicine, New York, New York, 10016, USA.
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3
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Yang Y, Glidden MD, Dhayalan B, Zaykov AN, Chen YS, Wickramasinghe NP, DiMarchi RD, Weiss MA. Peptide Model of the Mutant Proinsulin Syndrome. II. Nascent Structure and Biological Implications. Front Endocrinol (Lausanne) 2022; 13:821091. [PMID: 35299958 PMCID: PMC8922542 DOI: 10.3389/fendo.2022.821091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Toxic misfolding of proinsulin variants in β-cells defines a monogenic diabetes syndrome, designated mutant INS-gene induced diabetes of the young (MIDY). In our first study (previous article in this issue), we described a one-disulfide peptide model of a proinsulin folding intermediate and its use to study such variants. The mutations (LeuB15→Pro, LeuA16→Pro, and PheB24→Ser) probe residues conserved among vertebrate insulins. In this companion study, we describe 1H and 1H-13C NMR studies of the peptides; key NMR resonance assignments were verified by synthetic 13C-labeling. Parent spectra retain nativelike features in the neighborhood of the single disulfide bridge (cystine B19-A20), including secondary NMR chemical shifts and nonlocal nuclear Overhauser effects. This partial fold engages wild-type side chains LeuB15, LeuA16 and PheB24 at the nexus of nativelike α-helices α1 and α3 (as defined in native proinsulin) and flanking β-strand (residues B24-B26). The variant peptides exhibit successive structural perturbations in order: parent (most organized) > SerB24 >> ProA16 > ProB15 (least organized). The same order pertains to (a) overall α-helix content as probed by circular dichroism, (b) synthetic yields of corresponding three-disulfide insulin analogs, and (c) ER stress induced in cell culture by corresponding mutant proinsulins. These findings suggest that this and related peptide models will provide a general platform for classification of MIDY mutations based on molecular mechanisms by which nascent disulfide pairing is impaired. We propose that the syndrome's variable phenotypic spectrum-onsets ranging from the neonatal period to later in childhood or adolescence-reflects structural features of respective folding intermediates.
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Affiliation(s)
- Yanwu Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Michael D. Glidden
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Balamurugan Dhayalan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nalinda P. Wickramasinghe
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | | | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
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4
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Pijning AE, Butera D, Hogg PJ. Not one, but many forms of thrombosis proteins. J Thromb Haemost 2022; 20:285-292. [PMID: 34674369 DOI: 10.1111/jth.15567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/01/2022]
Abstract
The disulfide bond is a covalent bond formed between the sulfur atoms of two cysteine residues in proteins. Our understanding of the role of these ubiquitous bonds in protein function has changed dramatically over the past decade. Initially thought to be fully formed and inert in the native protein, we know now that both these assumptions are incorrect for many proteins. Here, we review recent evidence for production and function of multiple partially disulfide-bonded forms of plasma fibrinogen and platelet αIIbβ3 integrin. The disulfide bonds are not cleaved in these mature proteins but rather a significant fraction of the bonds never form during maturation of the protein. The resulting different covalent states influence the functioning of the protein. These findings change our concept of the native, functional protein.
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Affiliation(s)
- Aster E Pijning
- The Centenary Institute, University of Sydney, Camperdown, NSW, Australia
| | - Diego Butera
- The Centenary Institute, University of Sydney, Camperdown, NSW, Australia
| | - Philip J Hogg
- The Centenary Institute, University of Sydney, Camperdown, NSW, Australia
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5
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Manigrasso MB, Rabbani P, Egaña-Gorroño L, Quadri N, Frye L, Zhou B, Reverdatto S, Ramirez LS, Dansereau S, Pan J, Li H, D’Agati VD, Ramasamy R, DeVita RJ, Shekhtman A, Schmidt AM. Small-molecule antagonism of the interaction of the RAGE cytoplasmic domain with DIAPH1 reduces diabetic complications in mice. Sci Transl Med 2021; 13:eabf7084. [PMID: 34818060 PMCID: PMC8669775 DOI: 10.1126/scitranslmed.abf7084] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The macro- and microvascular complications of type 1 and 2 diabetes lead to increased disease severity and mortality. The receptor for advanced glycation end products (RAGE) can bind AGEs and multiple proinflammatory ligands that accumulate in diabetic tissues. Preclinical studies indicate that RAGE antagonists have beneficial effects on numerous complications of diabetes. However, these antagonists target the extracellular domains of RAGE, which bind distinct RAGE ligands at diverse sites in the immunoglobulin-like variable domain and two constant domains. The cytoplasmic tail of RAGE (ctRAGE) binds to the formin, Diaphanous-1 (DIAPH1), and this interaction is important for RAGE signaling. To comprehensively capture the breadth of RAGE signaling, we developed small-molecule antagonists of ctRAGE-DIAPH1 interaction, termed RAGE229. We demonstrated that RAGE229 is effective in suppressing RAGE-DIAPH1 binding, Förster resonance energy transfer, and biological activities in cellular assays. Using solution nuclear magnetic resonance spectroscopy, we defined the molecular underpinnings of the interaction of RAGE229 with RAGE. Through in vivo experimentation, we showed that RAGE229 assuaged short- and long-term complications of diabetes in both male and female mice, without lowering blood glucose concentrations. Last, the treatment with RAGE229 reduced plasma concentrations of TNF-α, IL-6, and CCL2/JE-MCP1 in diabetic mice, in parallel with reduced pathological and functional indices of diabetes-like kidney disease. Targeting ctRAGE-DIAPH1 interaction with RAGE229 mitigated diabetic complications in rodents by attenuating inflammatory signaling.
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Affiliation(s)
- Michaele B. Manigrasso
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU Langone Health, New York, NY 10016, USA
| | - Piul Rabbani
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Health, New York, NY 10016, USA
| | - Lander Egaña-Gorroño
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU Langone Health, New York, NY 10016, USA
| | - Nosirudeen Quadri
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU Langone Health, New York, NY 10016, USA
| | - Laura Frye
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU Langone Health, New York, NY 10016, USA
| | - Boyan Zhou
- Departments of Population Health (Biostatistics) and Environmental Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Lisa S. Ramirez
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Stephen Dansereau
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Jinhong Pan
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Huilin Li
- Departments of Population Health (Biostatistics) and Environmental Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Vivette D. D’Agati
- Department of Pathology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ravichandran Ramasamy
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU Langone Health, New York, NY 10016, USA
| | - Robert J. DeVita
- RJD Medicinal Chemistry and Drug Discovery Consulting LLC, Westfield, NJ 07091, USA
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany, Albany, NY 12222, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU Langone Health, New York, NY 10016, USA
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6
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Schroder RV, Cohen LS, Wang P, Arizala JD, Poget SF. Expression, Purification and Refolding of a Human Na V1.7 Voltage Sensing Domain with Native-like Toxin Binding Properties. Toxins (Basel) 2021; 13:toxins13100722. [PMID: 34679015 PMCID: PMC8541342 DOI: 10.3390/toxins13100722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/04/2021] [Accepted: 10/04/2021] [Indexed: 01/28/2023] Open
Abstract
The voltage-gated sodium channel NaV1.7 is an important target for drug development due to its role in pain perception. Recombinant expression of full-length channels and their use for biophysical characterization of interactions with potential drug candidates is challenging due to the protein size and complexity. To overcome this issue, we developed a protocol for the recombinant expression in E. coli and refolding into lipids of the isolated voltage sensing domain (VSD) of repeat II of NaV1.7, obtaining yields of about 2 mg of refolded VSD from 1 L bacterial cell culture. This VSD is known to be involved in the binding of a number of gating-modifier toxins, including the tarantula toxins ProTx-II and GpTx-I. Binding studies using microscale thermophoresis showed that recombinant refolded VSD binds both of these toxins with dissociation constants in the high nM range, and their relative binding affinities reflect the relative IC50 values of these toxins for full-channel inhibition. Additionally, we expressed mutant VSDs incorporating single amino acid substitutions that had previously been shown to affect the activity of ProTx-II on full channel. We found decreases in GpTx-I binding affinity for these mutants, consistent with a similar binding mechanism for GpTx-I as compared to that of ProTx-II. Therefore, this recombinant VSD captures many of the native interactions between NaV1.7 and tarantula gating-modifier toxins and represents a valuable tool for elucidating details of toxin binding and specificity that could help in the design of non-addictive pain medication acting through NaV1.7 inhibition.
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Affiliation(s)
- Ryan V. Schroder
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
- The Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Leah S. Cohen
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
| | - Ping Wang
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
| | - Joekeem D. Arizala
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
- The Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Sébastien F. Poget
- Department of Chemistry, College of Staten Island, University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA; (R.V.S.); (L.S.C.); (P.W.); (J.D.A.)
- The Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Correspondence:
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7
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Fibrinogen function achieved through multiple covalent states. Nat Commun 2020; 11:5468. [PMID: 33122656 PMCID: PMC7596563 DOI: 10.1038/s41467-020-19295-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 10/07/2020] [Indexed: 11/23/2022] Open
Abstract
Disulfide bonds link pairs of cysteine amino acids and their formation is assumed to be complete in the mature, functional protein. Here, we test this assumption by quantifying the redox state of disulfide bonds in the blood clotting protein fibrinogen. The disulfide status of fibrinogen from healthy human donor plasma and cultured human hepatocytes are measured using differential cysteine alkylation and mass spectrometry. This analysis identifies 13 disulfide bonds that are 10–50% reduced, indicating that fibrinogen is produced in multiple disulfide-bonded or covalent states. We further show that disulfides form upon fibrin polymerization and are required for a robust fibrin matrix that withstands the mechanical forces of flowing blood and resists premature fibrinolysis. The covalent states of fibrinogen are changed by fluid shear forces ex vivo and in vivo, indicating that the different states are dynamic. These findings demonstrate that fibrinogen exists and functions as multiple covalent forms. Disulfide bonds play critical roles in determining protein structure and function. Here, the authors show that fibrinogen exists in multiple disulfide-bonded states in human blood, and that these states change during fibrin polymerization and in response to fluid shear forces.
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8
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Naider F, Becker JM. A Paradigm for Peptide Hormone-GPCR Analyses. Molecules 2020; 25:E4272. [PMID: 32961885 PMCID: PMC7570734 DOI: 10.3390/molecules25184272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/14/2023] Open
Abstract
Work from our laboratories over the last 35 years that has focused on Ste2p, a G protein-coupled receptor (GPCR), and its tridecapeptide ligand α-factor is reviewed. Our work utilized the yeast Saccharomyces cerevisiae as a model system for understanding peptide-GPCR interactions. It explored the structure and function of synthetic α-factor analogs and biosynthetic receptor domains, as well as designed mutations of Ste2p. The results and conclusions are described using the nuclear magnetic resonance interrogation of synthetic Ste2p transmembrane domains (TMs), the fluorescence interrogation of agonist and antagonist binding, the biochemical crosslinking of peptide analogs to Ste2p, and the phenotypes of receptor mutants. We identified the ligand-binding domain in Ste2p, the functional assemblies of TMs, unexpected and interesting ligand analogs; gained insights into the bound α-factor structure; and unraveled the function and structures of various Ste2p domains, including the N-terminus, TMs, loops connecting the TMs, and the C-terminus. Our studies showed interactions between specific residues of Ste2p in an active state, but not resting state, and the effect of ligand activation on the dimerization of Ste2p. We show that, using a battery of different biochemical and genetic approaches, deep insight can be gained into the structure and conformational dynamics of GPCR-peptide interactions in the absence of a crystal structure.
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Affiliation(s)
- Fred Naider
- Department of Chemistry, College of Staten Island, CUNY, 2800 Victory Blvd, Staten Island, NY 10314, USA
| | - Jeffrey M. Becker
- Department of Microbiology, University of Tennessee, 610 Ken and Blaire Mossman Building, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
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9
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Szczepaniak J, Holmes P, Rajasekar K, Kaminska R, Samsudin F, Inns PG, Rassam P, Khalid S, Murray SM, Redfield C, Kleanthous C. The lipoprotein Pal stabilises the bacterial outer membrane during constriction by a mobilisation-and-capture mechanism. Nat Commun 2020; 11:1305. [PMID: 32161270 PMCID: PMC7066135 DOI: 10.1038/s41467-020-15083-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/13/2020] [Indexed: 11/24/2022] Open
Abstract
Coordination of outer membrane constriction with septation is critical to faithful division in Gram-negative bacteria and vital to the barrier function of the membrane. This coordination requires the recruitment of the peptidoglycan-binding outer-membrane lipoprotein Pal at division sites by the Tol system. Here, we show that Pal accumulation at Escherichia coli division sites is a consequence of three key functions of the Tol system. First, Tol mobilises Pal molecules in dividing cells, which otherwise diffuse very slowly due to their binding of the cell wall. Second, Tol actively captures mobilised Pal molecules and deposits them at the division septum. Third, the active capture mechanism is analogous to that used by the inner membrane protein TonB to dislodge the plug domains of outer membrane TonB-dependent nutrient transporters. We conclude that outer membrane constriction is coordinated with cell division by active mobilisation-and-capture of Pal at division septa by the Tol system.
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Affiliation(s)
| | - Peter Holmes
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Karthik Rajasekar
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Evotec SE, 112-114 Innovation Drive, Milton Park, Abingdon, OX14 4RZ, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Firdaus Samsudin
- Department of Chemistry, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | | | - Patrice Rassam
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- Laboratoire de Bioimagerie et Pathologie, UMR 7021, CNRS, Université de Strasbourg, Faculté de pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Syma Khalid
- Department of Chemistry, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, 35043, Marburg, Germany
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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10
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Oestringer BP, Bolivar JH, Claridge JK, Almanea L, Chipot C, Dehez F, Holzmann N, Schnell JR, Zitzmann N. Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features. Sci Rep 2019; 9:8383. [PMID: 31182749 PMCID: PMC6557816 DOI: 10.1038/s41598-019-44413-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022] Open
Abstract
The hepatitis C virus (HCV) viroporin p7 oligomerizes to form ion channels, which are required for the assembly and secretion of infectious viruses. The 63-amino acid p7 monomer has two putative transmembrane domains connected by a cytosolic loop, and has both N- and C- termini exposed to the endoplasmic reticulum (ER) lumen. NMR studies have indicated differences between p7 structures of distantly related HCV genotypes. A critical question is whether these differences arise from the high sequence variation between the different isolates and if so, how the divergent structures can support similar biological functions. Here, we present a side-by-side characterization of p7 derived from genotype 1b (isolate J4) in the detergent 6-cyclohexyl-1-hexylphosphocholine (Cyclofos-6) and p7 derived from genotype 5a (isolate EUH1480) in n-dodecylphosphocholine (DPC). The 5a isolate p7 in conditions previously associated with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility broadly like those of the monomeric 1b isolate p7. The largest differences occur at the start of the second transmembrane domain, which is destabilized in the 5a isolate. The results show a broad consensus among the p7 variants that have been studied under a range of different conditions and indicate that distantly related HCVs preserve key features of structure and dynamics.
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Affiliation(s)
- Benjamin P Oestringer
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RY, United Kingdom
| | - Juan H Bolivar
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Jolyon K Claridge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Latifah Almanea
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Chris Chipot
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois, 61801, United States
| | - François Dehez
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Nicole Holzmann
- Laboratoire International Associé CNRS-University of Illinois at Urbana Champaign, Université de Lorraine, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Jason R Schnell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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11
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Chiu J, Hogg PJ. Allosteric disulfides: Sophisticated molecular structures enabling flexible protein regulation. J Biol Chem 2019; 294:2949-2960. [PMID: 30635401 DOI: 10.1074/jbc.rev118.005604] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein disulfide bonds link pairs of cysteine residues in polypeptide chains. Many of these bonds serve a purely structural or energetic role, but a growing subset of cleavable disulfide bonds has been shown to control the function of the mature protein in which they reside. These allosteric disulfides and the factors that cleave these bonds are being identified across biological systems and life forms and have been shown to control hemostasis, the immune response, and viral infection in mammals. The discovery of these functional disulfides and a rationale for their facile nature has been aided by the emergence of a conformational signature for allosteric bonds. This post-translational modification mostly occurs extracellularly, making these chemical events prime drug targets. Indeed, a membrane-impermeable inhibitor of one of the cleaving factors is currently being trialed as an antithrombotic agent in cancer patients. Allosteric disulfides are firmly established as a sophisticated means by which a protein's shape and function can be altered; however, the full scope of this biological regulation will not be realized without new tools and techniques to study this regulation and innovative ways of targeting it.
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Affiliation(s)
- Joyce Chiu
- From the Centenary Institute, National Health and Medical Research Council Clinical Trials Centre, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Philip J Hogg
- From the Centenary Institute, National Health and Medical Research Council Clinical Trials Centre, Sydney Medical School, University of Sydney, Camperdown, New South Wales 2006, Australia
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12
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Szekely O, Armony G, Olsen GL, Bigman LS, Levy Y, Fass D, Frydman L. Identification and Rationalization of Kinetic Folding Intermediates for a Low-Density Lipoprotein Receptor Ligand-Binding Module. Biochemistry 2018; 57:4776-4787. [PMID: 29979586 DOI: 10.1021/acs.biochem.8b00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many mutations that cause familial hypercholesterolemia localize to ligand-binding domain 5 (LA5) of the low-density lipoprotein receptor, motivating investigation of the folding and misfolding of this small, disulfide-rich, calcium-binding domain. LA5 folding is known to involve non-native disulfide isomers, yet these folding intermediates have not been structurally characterized. To provide insight into these intermediates, we used nuclear magnetic resonance (NMR) to follow LA5 folding in real time. We demonstrate that misfolded or partially folded disulfide intermediates are indistinguishable from the unfolded state when focusing on the backbone NMR signals, which provide information on the formation of only the final, native state. However, 13C labeling of cysteine side chains differentiated transient intermediates from the unfolded and native states and reported on disulfide bond formation in real time. The cysteine pairings in a dominant intermediate were identified using 13C-edited three-dimensional NMR, and coarse-grained molecular dynamics simulations were used to investigate the preference of this disulfide set over other non-native arrangements. The transient population of LA5 species with particular non-native cysteine connectitivies during folding supports the conclusion that cysteine pairing is not random and that there is a bias toward certain structural ensembles during the folding process, even prior to the binding of calcium.
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Affiliation(s)
- Or Szekely
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gad Armony
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gregory Lars Olsen
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lavi S Bigman
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Yaakov Levy
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Deborah Fass
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
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13
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Mousa R, Lansky S, Shoham G, Metanis N. BPTI folding revisited: switching a disulfide into methylene thioacetal reveals a previously hidden path. Chem Sci 2018; 9:4814-4820. [PMID: 29910933 PMCID: PMC5982216 DOI: 10.1039/c8sc01110a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/01/2018] [Indexed: 01/07/2023] Open
Abstract
The folding mechanism of the model protein bovine pancreatic trypsin inhibitor was revisited. By switching the solvent exposed disulfide bond with methylene thioacetal we uncovered a hidden pathway in its folding mechanism. In addition, this moiety enhanced protein stability while fully maintaining the protein structure and biological function.
Bovine pancreatic trypsin inhibitor (BPTI) is a 58-residue protein that is stabilized by three disulfide bonds at positions 5–55, 14–38 and 30–51. Widely studied for about 50 years, BPTI represents a folding model for many disulfide-rich proteins. In the study described below, we replaced the solvent exposed 14–38 disulfide bond with a methylene thioacetal bridge in an attempt to arrest the folding pathway of the protein at its two well-known intermediates, N′ and N*. The modified protein was expected to be unable to undergo the rate-determining step in the widely accepted BPTI folding mechanism: the opening of the 14–38 disulfide bond followed by rearrangements that leads to the native state, N. Surprisingly, instead of halting BPTI folding at N′ and N*, we uncovered a hidden pathway involving a direct reaction between the N* intermediate and the oxidizing reagent glutathione (GSSG) to form the disulfide-mixed intermediate N*–SG, which spontaneously folds into N. On the other hand, N′ was unable to fold into N. In addition, we found that the methylene thioacetal bridge enhances BPTI stability while fully maintaining its structure and biological function. These findings suggest a general strategy for enhancing protein stability without compromising on function or structure, suggesting potential applications for future therapeutic protein production.
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Affiliation(s)
- Reem Mousa
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - Shifra Lansky
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - Gil Shoham
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - Norman Metanis
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
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14
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Ramirez L, Shekhtman A, Pande J. Nuclear Magnetic Resonance-Based Structural Characterization and Backbone Dynamics of Recombinant Bee Venom Melittin. Biochemistry 2018; 57:2775-2785. [PMID: 29668274 DOI: 10.1021/acs.biochem.8b00156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, there has been a resurgence of interest in melittin and its variants as their therapeutic potential has become increasingly evident. Melittin is a 26-residue peptide and a toxic component of honey bee venom. The versatility of melittin in interacting with various biological substrates, such as membranes, glycosaminoglycans, and a variety of proteins, has inspired a slew of studies that aim to improve our understanding of the structural basis of such interactions. However, these studies have largely focused on melittin solutions at high concentrations (>1 mM), even though melittin is generally effective at lower (micromolar) concentrations. Here we present high-resolution nuclear magnetic resonance studies in the lower-concentration regime using a novel method to produce isotope-labeled (15N and 13C) recombinant melittin. We provide residue-specific structural characterization of melittin in dilute aqueous solution and in 2,2,2-trifluoroethanol/water mixtures, which mimic melittin structure-function and interactions in aqueous and membrane-like environments, respectively. We find that the cis-trans isomerization of Pro14 is key to changes in the secondary structure of melittin. Thus, this study provides residue-specific structural information about melittin in the free state and in a model of the substrate-bound state. These results, taken together with published work from other laboratories, reveal the peptide's structural versatility that resembles that of intrinsically disordered proteins and peptides.
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Affiliation(s)
- Lisa Ramirez
- Department of Chemistry , University at Albany, State University of New York , Albany , New York 12222 , United States
| | - Alexander Shekhtman
- Department of Chemistry , University at Albany, State University of New York , Albany , New York 12222 , United States
| | - Jayanti Pande
- Department of Chemistry , University at Albany, State University of New York , Albany , New York 12222 , United States
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15
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Kukic P, Pustovalova Y, Camilloni C, Gianni S, Korzhnev DM, Vendruscolo M. Structural Characterization of the Early Events in the Nucleation–Condensation Mechanism in a Protein Folding Process. J Am Chem Soc 2017; 139:6899-6910. [DOI: 10.1021/jacs.7b01540] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Predrag Kukic
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Yulia Pustovalova
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Carlo Camilloni
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
- Technische Universität Mun̈chen Institute for Advanced Study & Department of Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Stefano Gianni
- Istituto
Pasteur - Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia
Molecolari del CNR, Dipartimento di Scienze Biochimiche “A.
Rossi Fanelli”, Sapienza Università di Roma, Rome 00185, Italy
| | - Dmitry M. Korzhnev
- Department
of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
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16
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Poms M, Ansorge P, Martinez-Gil L, Jurt S, Gottstein D, Fracchiolla KE, Cohen LS, Güntert P, Mingarro I, Naider F, Zerbe O. NMR Investigation of Structures of G-protein Coupled Receptor Folding Intermediates. J Biol Chem 2016; 291:27170-27186. [PMID: 27864365 DOI: 10.1074/jbc.m116.740985] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/03/2016] [Indexed: 11/06/2022] Open
Abstract
Folding of G-protein coupled receptors (GPCRs) according to the two-stage model (Popot, J. L., and Engelman, D. M. (1990) Biochemistry 29, 4031-4037) is postulated to proceed in 2 steps: partitioning of the polypeptide into the membrane followed by diffusion until native contacts are formed. Herein we investigate conformational preferences of fragments of the yeast Ste2p receptor using NMR. Constructs comprising the first, the first two, and the first three transmembrane (TM) segments, as well as a construct comprising TM1-TM2 covalently linked to TM7 were examined. We observed that the isolated TM1 does not form a stable helix nor does it integrate well into the micelle. TM1 is significantly stabilized upon interaction with TM2, forming a helical hairpin reported previously (Neumoin, A., Cohen, L. S., Arshava, B., Tantry, S., Becker, J. M., Zerbe, O., and Naider, F. (2009) Biophys. J. 96, 3187-3196), and in this case the protein integrates into the hydrophobic interior of the micelle. TM123 displays a strong tendency to oligomerize, but hydrogen exchange data reveal that the center of TM3 is solvent exposed. In all GPCRs so-far structurally characterized TM7 forms many contacts with TM1 and TM2. In our study TM127 integrates well into the hydrophobic environment, but TM7 does not stably pack against the remaining helices. Topology mapping in microsomal membranes also indicates that TM1 does not integrate in a membrane-spanning fashion, but that TM12, TM123, and TM127 adopt predominantly native-like topologies. The data from our study would be consistent with the retention of individual helices of incompletely synthesized GPCRs in the vicinity of the translocon until the complete receptor is released into the membrane interior.
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Affiliation(s)
- Martin Poms
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Philipp Ansorge
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Luis Martinez-Gil
- the Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, E-46100 Burjassot, Spain
| | - Simon Jurt
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Gottstein
- the Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Katrina E Fracchiolla
- the Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, New York 10314, the Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Leah S Cohen
- the Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, New York 10314, the Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Peter Güntert
- the Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,the Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Ismael Mingarro
- the Department of Biochemistry and Molecular Biology, ERI BioTecMed, University of Valencia, E-46100 Burjassot, Spain
| | - Fred Naider
- the Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, New York 10314, the Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Oliver Zerbe
- From the Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland,
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17
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Structural and Dynamic Features of F-recruitment Site Driven Substrate Phosphorylation by ERK2. Sci Rep 2015; 5:11127. [PMID: 26054059 PMCID: PMC4459106 DOI: 10.1038/srep11127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/18/2015] [Indexed: 02/07/2023] Open
Abstract
The F-recruitment site (FRS) of active ERK2 binds F-site (Phe-x-Phe-Pro) sequences found downstream of the Ser/Thr phospho-acceptor on cellular substrates. Here we apply NMR methods to analyze the interaction between active ERK2 (ppERK2), and a 13-residue F-site-bearing peptide substrate derived from its cellular target, the transcription factor Elk-1. Our results provide detailed insight into previously elusive structural and dynamic features of FRS/F-site interactions and FRS-driven substrate phosphorylation. We show that substrate F-site engagement significantly quenches slow dynamics involving the ppERK2 activation-loop and the FRS. We also demonstrate that the F-site phenylalanines make critical contacts with ppERK2, in contrast to the proline whose cis-trans isomerization has no significant effect on F-site recognition by the kinase FRS. Our results support a mechanism where phosphorylation of the disordered N-terminal phospho-acceptor is facilitated by its increased productive encounters with the ppERK2 active site due to docking of the proximal F-site at the kinase FRS.
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18
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Cobbert JD, DeMott C, Majumder S, Smith EA, Reverdatto S, Burz DS, McDonough KA, Shekhtman A. Caught in action: selecting peptide aptamers against intrinsically disordered proteins in live cells. Sci Rep 2015; 5:9402. [PMID: 25801767 PMCID: PMC4371151 DOI: 10.1038/srep09402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/03/2015] [Indexed: 11/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) or unstructured segments within proteins play an important role in cellular physiology and pathology. Low cellular concentration, multiple binding partners, frequent post-translational modifications and the presence of multiple conformations make it difficult to characterize IDP interactions in intact cells. We used peptide aptamers selected by using the yeast-two-hybrid scheme and in-cell NMR to identify high affinity binders to transiently structured IDP and unstructured segments at atomic resolution. Since both the selection and characterization of peptide aptamers take place inside the cell, only physiologically relevant conformations of IDPs are targeted. The method is validated by using peptide aptamers selected against the prokaryotic ubiquitin-like protein, Pup, of the mycobacterium proteasome. The selected aptamers bind to distinct sites on Pup and have vastly different effects on rescuing mycobacterial proteasome substrate and on the survival of the Bacille-Calmette-Guèrin, BCG, strain of M. bovis. This technology can be applied to study the elusive action of IDPs under near physiological conditions.
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Affiliation(s)
| | | | | | - Eric A Smith
- Wadsworth Center, NY State Department of Health, Albany, NY
| | | | - David S Burz
- Department of Chemistry, University at Albany, Albany, NY
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19
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Chen W, Cotten ML. Expression, purification, and micelle reconstitution of antimicrobial piscidin 1 and piscidin 3 for NMR studies. Protein Expr Purif 2014; 102:63-8. [PMID: 25131859 DOI: 10.1016/j.pep.2014.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 07/31/2014] [Accepted: 08/01/2014] [Indexed: 12/28/2022]
Abstract
Piscidin 1 and piscidin 3, which were discovered in the mast cells of hybrid striped sea bass, are homologous antimicrobial peptides that are active against drug-resistant bacteria. Piscidin 1, the more antimicrobial and hemolytic peptide, also has anti-HIV-1 and anti-cancer properties. To understand the reasons underlying the different biological activities of the two peptides and identify principles to design antimicrobial drugs with improved efficacy and lower toxicity, their atomic-level structures must be obtained under physiologically-relevant conditions. High-resolution backbone structures of both piscidins exist in the presence of hydrated phospholipid bilayers but full structures that include the side chains are missing. Here, the piscidins 1 and 3 genes were cloned into the TrpLE vector. The corresponding TrpLE-piscidin fusion partners were expressed in Escherichiacoli and recovered from inclusion bodies. Following steps that included Ni-NTA chromatography, cyanogen bromide cleavage of the fusion proteins, and reverse-phase HPLC, purified piscidins 1 and 3 were recovered in very good yield and characterized by NMR. High quality (15)N-(1)H HSQC spectra of piscidins 1 and 3 bound to SDS micelles were collected, demonstrating the feasibility of producing and purifying the isotopically-labeled piscidin peptides required to determine their full structures by multidimensional NMR spectroscopy.
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Affiliation(s)
- Wen Chen
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - Myriam L Cotten
- Department of Chemistry, Hamilton College, 198 College Hill Road, Clinton, NY 13323, United States.
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20
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Cohen LS, Fracchiolla KE, Becker J, Naider F. Invited review GPCR structural characterization: Using fragments as building blocks to determine a complete structure. Biopolymers 2014; 102:223-43. [DOI: 10.1002/bip.22490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Leah S. Cohen
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Katrina E. Fracchiolla
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Jeff Becker
- Department of Microbiology; University of Tennessee; Knoxville TN 37996
| | - Fred Naider
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
- Department of Biochemistry; The Graduate Center; CUNY NY 10016-4309
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21
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Endres NF, Das R, Smith AW, Arkhipov A, Kovacs E, Huang Y, Pelton JG, Shan Y, Shaw DE, Wemmer DE, Groves JT, Kuriyan J. Conformational coupling across the plasma membrane in activation of the EGF receptor. Cell 2013; 152:543-56. [PMID: 23374349 PMCID: PMC3718647 DOI: 10.1016/j.cell.2012.12.032] [Citation(s) in RCA: 376] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/28/2012] [Accepted: 12/11/2012] [Indexed: 01/01/2023]
Abstract
How the epidermal growth factor receptor (EGFR) activates is incompletely understood. The intracellular portion of the receptor is intrinsically active in solution, and to study its regulation, we measured autophosphorylation as a function of EGFR surface density in cells. Without EGF, intact EGFR escapes inhibition only at high surface densities. Although the transmembrane helix and the intracellular module together suffice for constitutive activity even at low densities, the intracellular module is inactivated when tethered on its own to the plasma membrane, and fluorescence cross-correlation shows that it fails to dimerize. NMR and functional data indicate that activation requires an N-terminal interaction between the transmembrane helices, which promotes an antiparallel interaction between juxtamembrane segments and release of inhibition by the membrane. We conclude that EGF binding removes steric constraints in the extracellular module, promoting activation through N-terminal association of the transmembrane helices.
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Affiliation(s)
- Nicholas F Endres
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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22
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Sharma P, Kaywan-Lutfi M, Krshnan L, Byrne EFX, Call MJ, Call ME. Production of disulfide-stabilized transmembrane peptide complexes for structural studies. J Vis Exp 2013:e50141. [PMID: 23486227 DOI: 10.3791/50141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Physical interactions among the lipid-embedded alpha-helical domains of membrane proteins play a crucial role in folding and assembly of membrane protein complexes and in dynamic processes such as transmembrane (TM) signaling and regulation of cell-surface protein levels. Understanding the structural features driving the association of particular sequences requires sophisticated biophysical and biochemical analyses of TM peptide complexes. However, the extreme hydrophobicity of TM domains makes them very difficult to manipulate using standard peptide chemistry techniques, and production of suitable study material often proves prohibitively challenging. Identifying conditions under which peptides can adopt stable helical conformations and form complexes spontaneously adds a further level of difficulty. Here we present a procedure for the production of homo- or hetero-dimeric TM peptide complexes from materials that are expressed in E. coli, thus allowing incorporation of stable isotope labels for nuclear magnetic resonance (NMR) or non-natural amino acids for other applications relatively inexpensively. The key innovation in this method is that TM complexes are produced and purified as covalently associated (disulfide-crosslinked) assemblies that can form stable, stoichiometric and homogeneous structures when reconstituted into detergent, lipid or other membrane-mimetic materials. We also present carefully optimized procedures for expression and purification that are equally applicable whether producing single TM domains or crosslinked complexes and provide advice for adapting these methods to new TM sequences.
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Affiliation(s)
- Pooja Sharma
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Australia
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23
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Potetinova Z, Tantry S, Cohen LS, Caroccia KE, Arshava B, Becker JM, Naider F. Large multiple transmembrane domain fragments of a G protein-coupled receptor: biosynthesis, purification, and biophysical studies. Biopolymers 2012; 98:485-500. [PMID: 23203693 PMCID: PMC3542537 DOI: 10.1002/bip.22122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 06/01/2012] [Accepted: 07/02/2012] [Indexed: 01/04/2023]
Abstract
To conduct biophysical analyses on large domains of GPCRs, multimilligram quantities of highly homogeneous proteins are necessary. This communication discusses the biosynthesis of four transmembrane and five transmembrane-containing fragments of Ste2p, a GPCR recognizing the Saccharomyces cerevisiae tridecapeptide pheromone α-factor. The target fragments contained the predicted four N-terminal Ste2p[G(31) -A(198) ] (4TMN), four C-terminal Ste2p[T(155) -L(340) ] (4TMC), or five C-terminal Ste2p[I(120) -L(340) ] (5TMC) transmembrane segments of Ste2p. 4TMN was expressed as a fusion protein using a modified pMMHa vector in L-arabinose-induced Escherichia coli BL21-AI, and cleaved with cyanogen bromide. 4TMC and 5TMC were obtained by direct expression using a pET21a vector in IPTG-induced E. coli BL21(DE3) cells. 4TMC and 5TMC were biosynthesized on a preparative scale, isolated in multimilligram amounts, characterized by MS and investigated by biophysical methods. CD spectroscopy indicated the expected highly α-helical content for 4TMC and 5TMC in membrane mimetic environments. Tryptophan fluorescence showed that 5TMC integrated into the nonpolar region of 1-stearoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) micelles. HSQC-TROSY investigations revealed that [(15) N]-labeled 5TMC in 50% trifluoroethanol-d(2) /H(2) O/0.05%-trifluoroacetic acid was stable enough to conduct long multidimensional NMR measurements. The entire Ste2p GPCR was not readily reconstituted from the first two and last five or first three and last four transmembrane domains.
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Affiliation(s)
- Zhanna Potetinova
- Department of Chemistry, College of Staten Island, The City University of New York, Staten Island, NY 10314, USA
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24
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Claridge JK, Schnell JR. Bacterial production and solution NMR studies of a viral membrane ion channel. Methods Mol Biol 2012; 831:165-79. [PMID: 22167674 DOI: 10.1007/978-1-61779-480-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Advances in solution nuclear magnetic resonance (NMR) methodology that enable studies of very large proteins have also paved the way for studies of membrane proteins that behave like large proteins due to the added weight of surfactants. Solution NMR has been used to determine the high-resolution structures of several small, membrane proteins dissolved in detergent micelles and small bicelles. However, the usual difficulties with membrane proteins in producing, purifying, and stabilizing the proteins away from native membranes remain, requiring intensive screening efforts. Low levels of heterologous expression can be the most detrimental aspect to studying membrane proteins. This is exacerbated for NMR studies because of the costs of isotopically enriched media. Thus, solution NMR studies have tended to focus on relatively small, membrane proteins that can be expressed into inclusion bodies and refolded. Here, we describe the methods used to produce, purify, and refold the proton channel M2 into detergent micelles, and the procedures used to determine chemical shift assignments and the atomic level structure of the closed form of the homotetrameric channel.
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25
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Rai V, Maldonado AY, Burz DS, Reverdatto S, Yan SF, Schmidt AM, Shekhtman A. Signal transduction in receptor for advanced glycation end products (RAGE): solution structure of C-terminal rage (ctRAGE) and its binding to mDia1. J Biol Chem 2011; 287:5133-44. [PMID: 22194616 DOI: 10.1074/jbc.m111.277731] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The receptor for advanced glycation end products (RAGE) is a multiligand cell surface macromolecule that plays a central role in the etiology of diabetes complications, inflammation, and neurodegeneration. The cytoplasmic domain of RAGE (C-terminal RAGE; ctRAGE) is critical for RAGE-dependent signal transduction. As the most membrane-proximal event, mDia1 binds to ctRAGE, and it is essential for RAGE ligand-stimulated phosphorylation of AKT and cell proliferation/migration. We show that ctRAGE contains an unusual α-turn that mediates the mDia1-ctRAGE interaction and is required for RAGE-dependent signaling. The results establish a novel mechanism through which an extracellular signal initiated by RAGE ligands regulates RAGE signaling in a manner requiring mDia1.
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Affiliation(s)
- Vivek Rai
- New York University Medical Center, New York, New York 10016, USA
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26
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Chang JY. Diverse pathways of oxidative folding of disulfide proteins: underlying causes and folding models. Biochemistry 2011; 50:3414-31. [PMID: 21410235 DOI: 10.1021/bi200131j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pathway of oxidative folding of disulfide proteins exhibits a high degree of diversity, which is manifested mainly by distinct structural heterogeneity and diverse rearrangement pathways of folding intermediates. During the past two decades, the scope of this diversity has widened through studies of more than 30 disulfide-rich proteins by various laboratories. A more comprehensive landscape of the mechanism of protein oxidative folding has emerged. This review will cover three themes. (1) Elaboration of the scope of diversity of disulfide folding pathways, including the two opposite extreme models, represented by bovine pancreatic trypsin inhibitor (BPTI) and hirudin. (2) Demonstration of experimental evidence accounting for the underlying mechanism of the folding diversity. (3) Discussion of the convergence between the extreme models of oxidative folding and models of conventional conformational folding (framework model, hydrophobic collapse model).
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Affiliation(s)
- Jui-Yoa Chang
- Research Center for Protein Chemistry, Institute of Molecular Medicine, Department of Biochemistry and Molecular Biology, Medical School, The University of Texas, Houston, 77030, USA.
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27
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Qureshi T, Goto NK. Contemporary methods in structure determination of membrane proteins by solution NMR. Top Curr Chem (Cham) 2011; 326:123-85. [PMID: 22160391 DOI: 10.1007/128_2011_306] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Integral membrane proteins are vital to life, being responsible for information and material exchange between a cell and its environment. Although high-resolution structural information is needed to understand how these functions are achieved, membrane proteins remain an under-represented subset of the protein structure databank. Solution NMR is increasingly demonstrating its ability to help address this knowledge shortfall, with the development of a diverse array of techniques to counter the challenges presented by membrane proteins. Here we document the advances that are helping to define solution NMR as an effective tool for membrane protein structure determination. Developments introduced over the last decade in the production of isotope-labeled samples, reconstitution of these samples into the growing selection of NMR-compatible membrane-mimetic systems, and the approaches used for the acquisition and application of structural restraints from these complexes are reviewed.
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Affiliation(s)
- Tabussom Qureshi
- Department of Chemistry, University of Ottawa, Ottawa, ON, Canada
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28
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Cohen LS, Becker JM, Naider F. Biosynthesis of peptide fragments of eukaryotic GPCRs in Escherichia coli by directing expression into inclusion bodies. J Pept Sci 2010; 16:213-8. [PMID: 20401922 DOI: 10.1002/psc.1222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Biosynthesis of peptides in heterologous systems is often a prerequisite to biophysical analyses. Large amounts of peptides, in particular portions of membrane proteins, are needed to optimize conditions for secondary and tertiary structure analysis. Chemical synthesis of these peptides is limited by their high hydrophobicity and also due to the need to incorporate isotopic labels for high resolution NMR analysis. In this protocol, we describe a method for the heterologous expression and purification of unlabeled and isotopically labeled peptide fragments of Ste2p, an integral membrane G protein-coupled receptor.
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Affiliation(s)
- Leah S Cohen
- Department of Chemistry, College of Staten Island, CUNY, Staten Island, NY 10314, USA
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29
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Ferrage F, Dutta K, Shekhtman A, Cowburn D. Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density. JOURNAL OF BIOMOLECULAR NMR 2010; 47:41-54. [PMID: 20372977 PMCID: PMC3637030 DOI: 10.1007/s10858-010-9409-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 03/10/2010] [Indexed: 05/02/2023]
Abstract
Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein-protein complexes.
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Affiliation(s)
| | | | | | - David Cowburn
- Corresponding author: David Cowburn, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, USA. Tel: 1 212 939 0660,
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30
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Wittlich M, Wiesehan K, Koenig BW, Willbold D. Expression, purification, and membrane reconstitution of a CD4 fragment comprising the transmembrane and cytoplasmic domains of the receptor. Protein Expr Purif 2007; 55:198-207. [PMID: 17613246 DOI: 10.1016/j.pep.2007.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 05/08/2007] [Accepted: 05/21/2007] [Indexed: 10/23/2022]
Abstract
The transmembrane glycoprotein CD4 plays a prominent role in the adaptive immune response. CD4 is displayed primarily on the surface of T helper cells, but also on subsets of memory and regulatory T lymphocytes, macrophages, and dendritic cells. Binding of the lymphocyte specific tyrosine kinase p56(lck) to the cytoplasmic domain of CD4 is crucial for antigen receptor-mediated signal transduction. The human immunodeficiency virus (HIV) utilizes CD4 as the main receptor for T cell invasion. The virus has developed multiple strategies for down-regulation of CD4 in infected cells. Physical interactions of viral proteins VpU and Nef with the cytoplasmic tail of CD4 initiate a cascade of events leading to degradation of CD4. Here we report heterologous expression and purification of a CD4 fragment comprising the transmembrane and cytoplasmic domains of human CD4. A synthetic gene encoding CD4 amino acid residues 372-433 and a protease cleavage site was cloned into the pTKK19xb/ub plasmid. The CD4 fragment was expressed in Escherichia coli C43(DE3) cells as a ubiquitin fusion with an N-terminal His-tag, isolated, released by PreScission proteolytic cleavage, and purified to homogeneity. Incorporation of the recombinant CD4 fragment in lipid membranes and physical interaction with the cytoplasmic domain of VpU was demonstrated by centrifugation assays followed by reversed phase chromatographic analysis of the composition of the proteoliposomes. A high resolution NMR spectrum of uniformly (15)N-labeled CD4 peptide in membrane simulating micelles proves the possibility of solution NMR studies of this CD4 fragment and of its molecular complexes.
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Affiliation(s)
- Marc Wittlich
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
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31
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Franzin CM, Gong XM, Thai K, Yu J, Marassi FM. NMR of membrane proteins in micelles and bilayers: the FXYD family proteins. Methods 2007; 41:398-408. [PMID: 17367712 PMCID: PMC2920895 DOI: 10.1016/j.ymeth.2006.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Revised: 08/10/2006] [Accepted: 08/15/2006] [Indexed: 11/25/2022] Open
Abstract
Determining the atomic resolution structures of membrane proteins is of particular interest in contemporary structural biology. Helical membrane proteins constitute one-third of the expressed proteins encoded in a genome, many drugs have membrane-bound proteins as their receptors, and mutations in membrane proteins result in human diseases. Although integral membrane proteins provide daunting technical challenges for all methods of protein structure determination, nuclear magnetic resonance (NMR) spectroscopy can be an extremely versatile and powerful method for determining their structures and characterizing their dynamics, in lipid environments that closely mimic the cell membranes. Once milligram amounts of isotopically labeled protein are expressed and purified, micelle samples can be prepared for solution NMR analysis, and lipid bilayer samples can be prepared for solid-state NMR analysis. The two approaches are complementary and can provide detailed structural and dynamic information. This paper describes the steps for membrane protein structure determination using solution and solid-state NMR. The methods for protein expression and purification, sample preparation and NMR experiments are described and illustrated with examples from the FXYD proteins, a family of regulatory subunits of the Na,K-ATPase.
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32
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Naider F. Synthesis, biosynthesis, and characterization of transmembrane domains of a G protein-coupled receptor. Methods Mol Biol 2007; 386:95-121. [PMID: 18604944 DOI: 10.1007/978-1-59745-430-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Peptide fragments have been widely used in biophysical studies on specific regions of integral membrane proteins. Because of their inherent insoluble nature and tendency to aggregate the preparation of such model peptides is challenging. We have developed synthetic and biosynthetic approaches to prepare peptides containing single and multiple domains of a G protein-coupled receptor. Both the synthetic and biosynthetic products can be isolated by reversed-phase high-performance liquid chromatography to near homogeneity. The biosynthetic product, a fusion protein, is processed by CNBr cleavage to yield the target peptide in various isotopic forms. The final peptides are studied by circular dichroism spectroscopy to determine their secondary structure under a variety of conditions.
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MESH Headings
- Amino Acid Sequence
- Chromatography, High Pressure Liquid/methods
- Circular Dichroism
- Cyanogen Bromide
- Drug Design
- Electrophoresis, Polyacrylamide Gel/methods
- Escherichia coli/genetics
- Models, Molecular
- Molecular Biology/methods
- Molecular Sequence Data
- Peptide Fragments/biosynthesis
- Peptide Fragments/chemical synthesis
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Plasmids/genetics
- Protein Engineering
- Protein Structure, Tertiary
- Receptors, G-Protein-Coupled/biosynthesis
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Receptors, Mating Factor/biosynthesis
- Receptors, Mating Factor/chemistry
- Receptors, Mating Factor/genetics
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Saccharomyces cerevisiae Proteins/biosynthesis
- Saccharomyces cerevisiae Proteins/chemical synthesis
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
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Affiliation(s)
- Fred Naider
- Department of Chemistry, College of Staten Island, NY, USA
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33
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Gong XM, Franzin CM, Thai K, Yu J, Marassi FM. Nuclear magnetic resonance structural studies of membrane proteins in micelles and bilayers. Methods Mol Biol 2007; 400:515-29. [PMID: 17951757 PMCID: PMC2918260 DOI: 10.1007/978-1-59745-519-0_35] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy enables determination of membrane protein structures in lipid environments, such as micelles and bilayers. This chapter outlines the steps for membrane-protein structure determination using solution NMR with micelle samples, and solid-state NMR with oriented lipid-bilayer samples. The methods for protein expression and purification, sample preparation, and NMR experiments are described and illustrated with examples from gamma and CHIF, two membrane proteins that function as regulatory subunits of the Na+- and K+-ATPase.
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34
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Englander J, Cohen L, Arshava B, Estephan R, Becker JM, Naider F. Selective labeling of a membrane peptide with 15N-amino acids using cells grown in rich medium. Biopolymers 2006; 84:508-18. [PMID: 16741986 DOI: 10.1002/bip.20546] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nuclear magnetic resonance spectra of membrane proteins containing multiple transmembrane helices have proven difficult to resolve due to the redundancy of aliphatic and Ser/Thr residues in transmembrane domains and the low chemical shift dispersity exhibited by residues in alpha-helical structures. Although (13)C- and (15)N-labeling are useful tools in the biophysical analysis of proteins, selective labeling of individual amino acids has been used to help elucidate more complete structures and to probe ligand-protein interactions. In general, selective labeling has been performed in Escherichia coli expression systems using minimal media supplemented with a single labeled amino acid and nineteen other unlabeled amino acids and/or by using auxotrophs for specific amino acids. Growth in minimal media often results in low yields of cells or expression products. We demonstrate a method in which one labeled amino acid is added to a rich medium. These conditions resulted in high expression (> or =100 mg/L) of a test fusion protein and milligram quantities of the selectively labeled membrane peptide after cyanogen bromide cleavage to release the peptide from the fusion protein. High levels of (15)N incorporation and acceptable levels of cross-labeling into other amino acid residues of the peptide were achieved. Growth in rich media is a simple and convenient alternative to growth in supplemented minimal media and is readily applicable to the expression of proteins selectively labeled with specific amino acids.
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Affiliation(s)
- Jacqueline Englander
- Department of Chemistry and the Macromolecular Assemblies Institute, The College of Staten Island of the City University of New York, Staten Island, NY 10314, USA
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35
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Call ME, Schnell JR, Xu C, Lutz RA, Chou JJ, Wucherpfennig KW. The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 2006; 127:355-68. [PMID: 17055436 PMCID: PMC3466601 DOI: 10.1016/j.cell.2006.08.044] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 07/23/2006] [Accepted: 08/11/2006] [Indexed: 11/29/2022]
Abstract
The T cell receptor (TCR) alphabeta heterodimer communicates ligand binding to the cell interior via noncovalently associated CD3gammaepsilon, CD3deltaepsilon, and zetazeta dimers. While structures of extracellular components of the TCR-CD3 complex are known, the transmembrane (TM) domains that mediate assembly have eluded structural characterization. Incorporation of the zetazeta signaling module is known to require one basic TCRalpha and two zetazeta aspartic acid TM residues. We report the NMR structure of the zetazeta(TM) dimer, a left-handed coiled coil with substantial polar contacts. Mutagenesis experiments demonstrate that three polar positions are critical for zetazeta dimerization and assembly with TCR. The two aspartic acids create a single structural unit at the zetazeta interface stabilized by extensive hydrogen bonding, and there is evidence for a structural water molecule (or molecules) within close proximity. This structural unit, representing only the second transmembrane dimer interface solved to date, serves as a paradigm for the assembly of all modules involved in TCR signaling.
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MESH Headings
- Amino Acid Sequence
- Aspartic Acid/chemistry
- Dimerization
- Humans
- Hydrogen Bonding
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis
- Nuclear Magnetic Resonance, Biomolecular
- Peptides/chemistry
- Peptides/metabolism
- Protein Binding
- Protein Conformation
- Protein Engineering
- Protein Structure, Tertiary
- Receptor-CD3 Complex, Antigen, T-Cell/chemistry
- Receptor-CD3 Complex, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
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Affiliation(s)
- Matthew E. Call
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason R. Schnell
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Chenqi Xu
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Regina A. Lutz
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - James J. Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kai W. Wucherpfennig
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
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36
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Ji H, Shekhtman A, Ghose R, McDonnell JM, Cowburn D. NMR determination that an extended BH3 motif of pro-apoptotic BID is specifically bound to BCL-XL. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S101-7. [PMID: 16826547 PMCID: PMC2365746 DOI: 10.1002/mrc.1856] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The BH3 motif of the pro-survival family of proteins, BCL, is also present in pro-apoptotic proteins like BID and BAX. Homo- and hetero-oligomerization interactions of the BH3 motif are generally recognized as the critical component of their apoptotic activities. In full-length BID, the putative hydrophobic binding surface of its BH3 motif is substantially occluded by intramolecular contacts, many of which are removed on BID's transformation to tBID by cleavage with caspase 8, required for tBID's pro-apoptotic action on mitochondria, thereby releasing cytochrome c.
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Affiliation(s)
| | | | | | | | - David Cowburn
- *Correspondence to: David Cowburn, The New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. E-mail:
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37
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Synthetic Approaches to Disulfide-free Circular Bovine Pancreatic Trypsin Inhibitor (c-BPTI) Analogues. Int J Pept Res Ther 2006. [DOI: 10.1007/s10989-006-9023-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Pazgier M, Lubkowski J. Expression and purification of recombinant human alpha-defensins in Escherichia coli. Protein Expr Purif 2006; 49:1-8. [PMID: 16839776 DOI: 10.1016/j.pep.2006.05.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 05/03/2006] [Accepted: 05/09/2006] [Indexed: 10/24/2022]
Abstract
Different strategies have been developed to produce small antimicrobial peptides (AMPs) using recombinant techniques. Up to now, all efforts to obtain larger quantities of active recombinant human alpha-defensins have been only moderately successful. Here we report an effective method of biosynthesis of human alpha-defensins (hNP-1 to hNP-3 and hD-5 and hD-6) in the Escherichia coli. All the peptides, expressed as insoluble fusions with the peptide encoded by a portion of E. coli tryptophan operon (trp DeltaLE 1413 polypeptide), were isolated from the inclusion bodies by immobilized metal affinity chromatography (IMAC) and separated from the fusion leader by chemical cleavage. Fully reduced peptides that were purified according to a straightforward protocol were subsequently folded, oxidized, and subjected to functional and structural analyses. With the exception of hD-6, all recombinant alpha-defensins exhibit expected anti-E. coli activity, as measured by the colony counting method. The method described in this report is a low-cost, efficient way of generating alpha-defensins in quantities ranging from milligrams to grams.
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Affiliation(s)
- Marzena Pazgier
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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39
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Collins ES, Wirmer J, Hirai K, Tachibana H, Segawa SI, Dobson CM, Schwalbe H. Characterisation of disulfide-bond dynamics in non-native states of lysozyme and its disulfide deletion mutants by NMR. Chembiochem 2006; 6:1619-27. [PMID: 16138305 DOI: 10.1002/cbic.200500196] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This report describes NMR-spectroscopic investigations of the conformational dynamics of disulfide bonds in hen-egg-white lysozyme substitution mutants. The following four systems have been investigated: 2SS(alpha), a lysozyme variant that contains C64A, C76A, C80A and C94A substitutions, was studied in water at pH 2 and 3.8 and in urea (8 M, pH 2); 2SS(beta) lysozyme, which has C6S, C30A, C115A and C127A substitutions, was studied in water (pH 2) and urea (8 M, pH 2). The NMR analysis of heteronuclear 15N-relaxation rates shows that the barrier to disulfide-bond isomerisation can vary substantially in different lysozyme mutants and depends on the residual structure present in these states. The investigations reveal cooperativity in the modulation of micro- to millisecond dynamics that is due to the presence of multiple disulfide bridges in lysozyme. Mutation of cysteines in one of the two structural domains substantially diminishes the barrier to rotational isomerisation in the other domain. However, the interactions between hydrophobic clusters within and across the domains remains intact.
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Affiliation(s)
- Emily S Collins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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40
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Chakraborty K, Shivakumar P, Raghothama S, Varadarajan R. NMR structural analysis of a peptide mimic of the bridging sheet of HIV-1 gp120 in methanol and water. Biochem J 2006; 390:573-81. [PMID: 15896194 PMCID: PMC1198937 DOI: 10.1042/bj20050442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
gp120 is a subunit of the Env (viral envelope protein) of HIV-1. The protein consists of inner and outer domains linked by a bridging sheet. Several gp120 residues that bind the neutralizing antibody 17b as well as the cellular co-receptor CCR5 (CC chemokine receptor 5), are located in the bridging sheet. Peptides that mimic the 17b-binding regions of gp120 would be useful potential immunogens for the generation of neutralizing antibodies against HIV-1. Towards this end, a 26-residue, four-stranded beta-sheet peptide was designed on the basis of the structure of the bridging sheet, and its structure was characterized in methanol by NMR. In methanol, amide and alpha-proton resonances were well resolved and dispersed. A number of interstrand NOEs (nuclear Overhauser effects) were observed, providing good evidence for multiple turn beta-hairpin structure. NOEs also provided good evidence for all Xxx-D-Pro bonds in the trans configuration and all three turns formed by a two residue D-Pro-Gly segment to be of type II' turn. The structure conforms well to the designed four-stranded beta-sheet structure. Approx. 20% of the peptide was estimated to adopt a folded conformation in water, as evidenced by CD spectroscopy. This was consistent with smaller, but still significant, downfield shifts of C(alpha)H protons relative to random-coil values. A second peptide was designed with two disulphide bonds to further constrain the peptide backbone. While structured in methanol, this peptide, like the previous one, also exhibits only partial structure formation in water, as evidenced by CD spectroscopy.
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Affiliation(s)
- Kausik Chakraborty
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - P. Shivakumar
- †Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - S. Raghothama
- †Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - Raghavan Varadarajan
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
- ‡Chemical Biology Unit, Jawaharlal Center for Advanced Scientific Research, Jakkur, P.O., Bangalore 560 004, India
- To whom correspondence should be sent at the Molecular Biophysics Unit address (email )
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41
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Zheng H, Zhao J, Sheng W, Xie XQ. A transmembrane helix-bundle from G-protein coupled receptor CB2: Biosynthesis, purification, and NMR characterization. Biopolymers 2006; 83:46-61. [PMID: 16634087 DOI: 10.1002/bip.20526] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cannabinoid receptor subtype 2 (CB2) is a member of the G-protein coupled receptor (GPCR) superfamily. As the relationship between structure and function for this receptor remains poorly understood, the present study was undertaken to characterize the structure of a segment including the first and second transmembrane helix (TM1 and TM2) domains of CB2. To accomplish this, a transmembrane double-helix bundle from this region was expressed, purified, and characterized by NMR. Milligrams of this hydrophobic fragment of the receptor were biosynthesized using a fusion protein overexpression strategy and purified by affinity chromatography combined with reverse phase HPLC. Chemical and enzymatic cleavage methods were implemented to remove the fusion tag. The resultant recombinant protein samples were analyzed and confirmed by HPLC, mass spectrometry, and circular dichroism (CD). The CD analyses of HPLC-purified protein in solution and in DPC micelle preparations suggested predominant alpha-helical structures under both conditions. The 13C/15N double-labeled protein CB2(27-101) was further verified and analyzed by NMR spectroscopy. Sequential assignment was accomplished for more than 80% of residues. The 15N HSQC NMR results show a clear chemical shift dispersion of the amide nitrogen-proton correlation indicative of a pure double-labeled polypeptide molecule. The results suggest that this method is capable of generating transmembrane helical bundles from GPCRs in quantity and purity sufficient for NMR and other biophysical studies. Therefore, the biosynthesis of GPCR transmembrane helix bundles represents a satisfactory alternative strategy to obtain and assemble NMR structures from recombinant "building blocks."
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Affiliation(s)
- HaiAn Zheng
- Department of Pharmaceutical and Pharmacological Sciences, College of Pharmacy, University of Houston, Houston, TX, 77204-5037, USA
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42
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Li X, Hood RJ, Wedemeyer WJ, Watson JT. Characterization of peptide folding nuclei by hydrogen/deuterium exchange-mass spectrometry. Protein Sci 2005; 14:1922-8. [PMID: 15987911 PMCID: PMC2253355 DOI: 10.1110/ps.051458905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Covalently linked pairs of well-chosen peptides can be good model systems for protein folding studies because they can adopt stable secondary, side-chain, and tertiary structure under certain conditions. We demonstrate a method for characterizing the structure in such peptide pairs by hydrogen/deuterium exchange of individual amide groups analyzed by collision-induced dissociation tandem mass spectrometry, in concert with circular dichroism spectroscopy. We apply the method to two peptides (and their three possible pairs) from bovine pancreatic trypsin inhibitor to address specific hypotheses regarding the stabilization of local secondary structure by long-range interactions.
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Affiliation(s)
- Xue Li
- Departments of Chemistry, Michigan State University, East Lansing, 48824, USA
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43
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Zheng H, Zhao J, Wang S, Lin CM, Chen T, Jones DH, Ma C, Opella S, Xie XQ. Biosynthesis and purification of a hydrophobic peptide from transmembrane domains of G-protein-coupled CB2 receptor. ACTA ACUST UNITED AC 2005; 65:450-8. [PMID: 15813893 DOI: 10.1111/j.1399-3011.2005.00239.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A major challenge for the structural study of the seven-transmembrane G-protein-coupled receptors is to obtain a sufficient amount of purified protein at the milligram level, which is required for either nuclear magnetic resonance (NMR) spectroscopy or X-ray crystallography. In order to develop a high-yield and cost-effective method, and also to obtain preliminary structural information for the computer modeling of the three-dimensional receptor structural model, a highly hydrophobic peptide from human cannabinoid subtype 2 receptor CB2(65-101), was chosen to develop high-yield membrane protein expression and purification methods. The peptide included the second transmembrane helix with the associated loop regions of the CB2 receptor. It was over-expressed in Escherichia coli, with a modified TrpDelta LE1413 (TrpLE) leading fusion sequence and a nine-histidine tag, and was then separated and purified from the tag in a preparative scale. An experimental protocol for the chemical cleavage of membrane protein fragment was developed using cyanogen bromide to remove the TrpLE tag from the hydrophobic fusion protein. In addition, protein uniformly labeled with isotopic 15N was obtained by expression in 15N-enriched minimum media. The developed and optimized preparation scheme of expression, cleavage, and purification provided a sufficient amount of peptide for NMR structure analysis and other biophysical studies that will be reported elsewhere. The process of fusion protein cleavage following purification was monitored by high-performance liquid chromatography (HPLC) and mass spectrometry (MS), and the final sample was validated by MS and circular dichroism experiments.
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Affiliation(s)
- H Zheng
- Department of Pharmaceutical & Pharmacological Sciences, College of Pharmacy, University of Houston, Houston, TX 77204-5037, USA
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44
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Thai K, Choi J, Franzin CM, Marassi FM. Bcl-XL as a fusion protein for the high-level expression of membrane-associated proteins. Protein Sci 2005; 14:948-55. [PMID: 15741345 PMCID: PMC2253446 DOI: 10.1110/ps.041244305] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
An Escherichia coli plasmid vector for the high-level expression of hydrophobic membrane proteins is described. The plasmid, pBCL, directs the expression of a target polypeptide fused to the C terminus of a mutant form of the anti-apoptotic Bcl-2 family protein, Bcl-XL, where the hydrophobic C terminus has been deleted, and Met residues have been mutated to Leu to facilitate CNBr cleavage after a single Met inserted at the beginning of the target sequence. Fusion protein expression is in inclusion bodies, simplifying the protein purification steps. Here we report the high-level production of PLM, a membrane protein that is a member of the FXYD family of tissue-specific and physiological-state-specific auxiliary subunits of the Na,K-ATPase, expressed abundantly in heart and skeletal muscle. We demonstrate that milligram quantities of pure, isotopically labeled protein can be obtained easily and in little time with this system.
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Affiliation(s)
- Khang Thai
- The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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45
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De Angelis AA, Jones DH, Grant CV, Park SH, Mesleh MF, Opella SJ. NMR experiments on aligned samples of membrane proteins. Methods Enzymol 2005; 394:350-82. [PMID: 15808228 DOI: 10.1016/s0076-6879(05)94014-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
NMR methods can be used to determine the structures of membrane proteins. Lipids can be chosen so that protein-containing micelles, bicelles, or bilayers are available as samples. All three types of samples can be aligned weakly or strongly, depending on their rotational correlation time. Solution NMR methods can be used with weakly aligned micelle and small bicelle samples. Solid-state NMR methods can be used with mechanically aligned bilayer and magnetically aligned bicelle samples.
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Affiliation(s)
- A A De Angelis
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093, USA
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46
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Bulaj G, Koehn RE, Goldenberg DP. Alteration of the disulfide-coupled folding pathway of BPTI by circular permutation. Protein Sci 2004; 13:1182-96. [PMID: 15096625 PMCID: PMC2286756 DOI: 10.1110/ps.03563704] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The kinetics of disulfide-coupled folding and unfolding of four circularly permuted forms of bovine pancreatic trypsin inhibitor (BPTI) were studied and compared with previously published results for both wild-type BPTI and a cyclized form. Each of the permuted proteins was found to be less stable than either the wild-type or circular proteins, by 3-8 kcal/mole. These stability differences were used to estimate effective concentrations of the chain termini in the native proteins, which were 1 mM for the wild-type protein and 2.5 to 4000 M for the permuted forms. The circular permutations increased the rates of unfolding and caused a variety of effects on the kinetics of refolding. For two of the proteins, the rates of a direct disulfide-formation pathway were dramatically increased, making this process as fast or faster than the competing disulfide rearrangement mechanism that predominates in the folding of the wild-type protein. These two permutations break the covalent connectivity among the beta-strands of the native protein, and removal of these constraints appears to facilitate direct formation and reduction of nearby disulfides that are buried in the folded structure. The effects on folding kinetics and mechanism do not appear to be correlated with relative contact order, a measure of overall topological complexity. These observations are consistent with the results of other recent experimental and computational studies suggesting that circular permutation may generally influence folding mechanisms by favoring or disfavoring specific interactions that promote alternative pathways, rather than through effects on the overall topology of the native protein.
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Affiliation(s)
- Grzegorz Bulaj
- Department of Biology, University of Utah, Salt Lake City, Utah 84112-0840, USA
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47
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Xie XQ, Zhao J, Zheng H. Expression, purification, and isotope labeling of cannabinoid CB2 receptor fragment, CB2180–233. Protein Expr Purif 2004; 38:61-8. [PMID: 15477083 DOI: 10.1016/j.pep.2004.07.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Revised: 07/29/2004] [Indexed: 11/18/2022]
Abstract
To develop an approach to obtain milligram quantities of purified isotope-labeled seven transmembrane G-protein coupled cannabinoid (CB) receptor for NMR structural analysis, we chose a truncated CB receptor fragment, CB2(180-233), spanning from the fifth transmembrane domain (TM5) to the associated loop regions of cannabinoid CB2 receptor. This highly hydrophobic membrane protein fragment was pursued for developmental studies of membrane proteins through expression and purification in Escherichia coli. The target peptide was cloned and over-expressed in a preparative scale as a fusion protein with a modified TrpDeltaLE1413 (TrpLE) leader sequence and a nine-histidine tag at its N-terminal. An experimental protocol for enzyme cleavage was developed by using Factor Xa to remove the TrpLE tag from the fusion protein. A purification process was also established using a nickel affinity column and reverse-phase HPLC, and then monitored by SDS-PAGE and MS. This expression level is one of the highest reported for a G-protein coupled receptor and fragments in E. Coli, and provided a sufficient amount of purified protein for further biophysical studies.
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Affiliation(s)
- Xiang-Qun Xie
- Department of Pharmaceutical and Pharmacological Sciences, College of Pharmacy, University of Houston, TX 77247-5037, USA.
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48
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Gong XM, Choi J, Franzin CM, Zhai D, Reed JC, Marassi FM. Conformation of membrane-associated proapoptotic tBid. J Biol Chem 2004; 279:28954-60. [PMID: 15123718 PMCID: PMC3033194 DOI: 10.1074/jbc.m403490200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proapoptotic Bcl-2 family protein Bid is cleaved by caspase-8 to release the C-terminal fragment tBid, which translocates to the outer mitochondrial membrane and induces massive cytochrome c release and cell death. In this study, we have characterized the conformation of tBid in lipid membrane environments, using NMR and CD spectroscopy with lipid micelle and lipid bilayer samples. In micelles, tBid adopts a unique helical conformation, and the solution NMR (1)H/(15)N HSQC spectra have a single well resolved resonance for each of the protein amide sites. In lipid bilayers, tBid associates with the membrane with its helices parallel to the membrane surface and without trans-membrane helix insertion, and the solid-state NMR (1)H/(15)N polarization inversion with spin exchange at the magic angle spectrum has all of the amide resonances centered at (15)N chemical shift (70-90 ppm) and (1)H-(15)N dipolar coupling (0-5 kHz) frequencies associated with NH bonds parallel to the bilayer surface, with no intensity at frequencies associated with NH bonds in trans-membrane helices. Thus, the cytotoxic activity of tBid at mitochondria may be similar to that observed for antibiotic polypeptides, which bind to the surface of bacterial membranes as amphipathic helices and destabilize the bilayer structure, promoting the leakage of cell contents.
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Affiliation(s)
| | | | | | | | | | - Francesca M. Marassi
- To whom correspondence should be addressed: The Burnham Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037. Tel.: 858-713-6282; Fax: 858-713-6268;
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49
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Franzin CM, Choi J, Zhai D, Reed JC, Marassi FM. Structural studies of apoptosis and ion transport regulatory proteins in membranes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2004; 42:172-179. [PMID: 14745797 PMCID: PMC3033199 DOI: 10.1002/mrc.1322] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Solid-state NMR spectroscopy is being used to determine the structures of membrane proteins involved in the regulation of apoptosis and ion transport. The Bcl-2 family includes pro- and anti-apoptotic proteins that play a major regulatory role in mitochondrion-dependent apoptosis or programmed cell death. The NMR data obtained for (15)N-labeled anti-apoptotic Bcl-xL in lipid bilayers are consistent with membrane association through insertion of the two central hydrophobic alpha-helices that are also required for channel formation and cytoprotective activity. The FXYD family proteins regulate ion flux across membranes, through interaction with the Na(+), K(+)-ATPase, in tissues that perform fluid and solute transport or that are electrically excitable. We have expressed and purified three FXYD family members, Mat8 (mammary tumor protein), CHIF (channel-inducing factor) and PLM (phospholemman), for structure determination by NMR in lipids. The solid-state NMR spectra of Bcl-2 and FXYD proteins, in uniaxially oriented lipid bilayers, give the first view of their membrane-associated architectures.
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Affiliation(s)
| | | | | | | | - Francesca M. Marassi
- Correspondence to: Francesca M. Marassi, The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.
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50
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Naider F, Estephan R, Englander J, Suresh Babu VV, Arevalo E, Samples K, Becker JM. Sexual conjugation in yeast: A paradigm to study G-protein-coupled receptor domain structure. Biopolymers 2004; 76:119-28. [PMID: 15054892 DOI: 10.1002/bip.10567] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The yeast Saccharomyces cerevisiae undergoes cell fusion during sexual conjugation to form diploid cells. The haploids participating in this process signal each other through secreted peptide-mating factors (alpha-factor and a-factor) that are recognized by G-protein-coupled receptors. The receptor (Ste2p) recognizing the tridecapeptide alpha-factor is used as a model system in our laboratory to understand various aspects of peptide-receptor interactions and receptor structure. Using chemical procedures we have synthesized peptides corresponding to the seven transmembrane domains of Ste2p and studied their structures in membrane mimetic environments. Extension of these studies requires preparation of longer fragments of Ste2p. This article discusses strategies used in our laboratory to prepare peptides containing multiple domains of Ste2p. Data are presented on the use of chemical synthesis, biosynthesis, and native chemical ligation. Using biosynthetic approaches fusion proteins have been expressed that contain single receptor domains, two transmembrane domains connected by the contiguous loop, and the tail connected to the seventh transmembrane domain. Tens of milligrams of fusion protein were obtained per liter, and multimilligram quantities of the isotopically labeled target peptides were isolated using such biosynthetic approaches. Initial circular dichroism results on a chemically synthesized 64-residue peptide containing a portion of the cytosolic tail and the complete seventh transmembrane domain showed that the tail portion and the hydrophobic core of this peptide maintained individual conformational preferences. Moreover, this peptide could be studied at near millimolar concentrations in the presence of micelles and did not aggregate under these conditions. Thus, these constructs can be investigated using high-resolution nuclear magnetic resonance techniques, and the cytosolic tail of Ste2p can be used as a hydrophilic template to improve solubility of transmembrane peptides for structural analysis.
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Affiliation(s)
- Fred Naider
- Department of Chemistry, The College of Staten Island of The City University of New York, Staten Island, NY 10314, USA.
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