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DMSO-Induced Unfolding of the Antifungal Disulfide Protein PAF and Its Inactive Variant: A Combined NMR and DSC Study. Int J Mol Sci 2023; 24:ijms24021208. [PMID: 36674720 PMCID: PMC9864379 DOI: 10.3390/ijms24021208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
PAF and related antifungal proteins are promising antimicrobial agents. They have highly stable folds around room temperature due to the presence of 3-4 disulfide bonds. However, unfolded states persist and contribute to the thermal equilibrium in aqueous solution, and low-populated states might influence their biological impact. To explore such equilibria during dimethyl sulfoxide (DMSO)-induced chemical unfolding, we studied PAF and its inactive variant PAFD19S using nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC). According to the NMR monitoring at 310 K, the folded structures disappear above 80 v/v% DMSO concentration, while the unfolding is completely reversible. Evaluation of a few resolved peaks from viscosity-compensated 15N-1H HSQC spectra of PAF yielded ∆G = 23 ± 7 kJ/M as the average value for NMR unfolding enthalpy. The NMR-based structures of PAF and the mutant in 50 v/v% DMSO/H2O mixtures were more similar in the mixed solvents then they were in water. The 15N NMR relaxation dynamics in the same mixtures verified the rigid backbones of the NMR-visible fractions of the proteins; still, enhanced dynamics around the termini and some loops were observed. DSC monitoring of the Tm melting point showed parabolic dependence on the DMSO molar fraction and suggested that PAF is more stable than the inactive PAFD19S. The DSC experiments were irreversible due to the applied broad temperature range, but still suggestive of the endothermic unfolding of PAF.
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2
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Li H, Zhang Y, Huang Y, Cao D, Wang S. Dissolution-enhanced emission of 1,3,6,8-tetrakis( p-benzoic acid)pyrene for selectively detecting protamine and “on-to-on” heparin detection in water. NEW J CHEM 2022. [DOI: 10.1039/d1nj03946f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A small molecule TBAPy was used as a turn-on fluorescent probe to selectively detect protamine and heparin based on the dissolution-enhanced emission (DEE) phenomenon.
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Affiliation(s)
- Hongtao Li
- State Key Laboratory of Organic–Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yuting Zhang
- State Key Laboratory of Organic–Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yan Huang
- State Key Laboratory of Organic–Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Dapeng Cao
- State Key Laboratory of Organic–Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Shitao Wang
- State Key Laboratory of Organic–Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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Admane N, Srivastava A, Jamal S, Kundu B, Grover A. Protective Effects of a Neurohypophyseal Hormone Analogue on Prion Aggregation, Cellular Internalization, and Toxicity. ACS Chem Neurosci 2020; 11:2422-2430. [PMID: 31407881 DOI: 10.1021/acschemneuro.9b00299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Herein, we report novel neuroprotective activity of the neurohypophyseal hormone analogue desmopressin (DDAVP) against toxic conformations of human prion protein. Systematic analysis using biophysical techniques in conjunction with surface plasmon resonance, high-end microscopy, conformational antibodies, and cell-based assays demonstrated DDAVP's specific binding and potent antiaggregating effects on prion protein (rPrPres). In addition to subjugating conformational conversion of rPrPres into oligomeric forms, DDAVP also exhibits potent fibril modulatory effects. It eventually ameliorated neuronal toxicity of rPrPres oligomers by significantly reducing their cellular internalization. Molecular dynamics simulations showed that DDAVP prevents β-sheet transitions in the N-terminal amyloidogenic region of prion and induces antagonistic mobilities in its α2-α3 and β2-α2 loop regions. Collectively, our data proposes DDAVP as a new structural motif for rational drug discovery against prion diseases.
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Affiliation(s)
- Nikita Admane
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Ankit Srivastava
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Salma Jamal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
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4
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Moulick R, Goluguri RR, Udgaonkar JB. Ruggedness in the Free Energy Landscape Dictates Misfolding of the Prion Protein. J Mol Biol 2019; 431:807-824. [DOI: 10.1016/j.jmb.2018.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/15/2018] [Accepted: 12/16/2018] [Indexed: 12/12/2022]
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5
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Sinha D, Mondal R, Mahapa A, Sau K, Chattopadhyaya R, Sau S. A staphylococcal anti-sigma factor possesses a single-domain, carries different denaturant-sensitive regions and unfolds via two intermediates. PLoS One 2018; 13:e0195416. [PMID: 29621342 PMCID: PMC5886543 DOI: 10.1371/journal.pone.0195416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/21/2018] [Indexed: 11/26/2022] Open
Abstract
RsbW, an anti-sigma factor possessing kinase activity, is expressed by many Gram-positive bacteria including Staphylococcus aureus. To obtain clues about the domain structure and the folding-unfolding mechanism of RsbW, we have elaborately studied rRsbW, a recombinant S. aureus RsbW. Sequence analysis of the protein fragments, generated by the limited proteolysis of rRsbW, has proposed it to be a single-domain protein. The unfolding of rRsbW in the presence of GdnCl or urea was completely reversible in nature and occurred through the formation of at least two intermediates. The structure, shape, and the surface hydrophobicity of no intermediate completely matches with those of other intermediates or the native rRsbW. Interestingly, one of the intermediates, formed in the presence of less GdnCl concentrations, has a molten globule-like structure. Conversely, all of the intermediates, like native rRsbW, exist as dimers in aqueous solution. The putative molten globule and the urea-generated intermediates also have retained some kinase activity. Additionally, the putative ATP binding site/catalytic site of rRsbW shows higher denaturant sensitivity than the tentative dimerization region of this enzyme.
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Affiliation(s)
- Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Rajkrishna Mondal
- Department of Biotechnology, Nagaland University, Dimapur, Nagaland, India
| | - Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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6
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Mercer RCC, Daude N, Dorosh L, Fu ZL, Mays CE, Gapeshina H, Wohlgemuth SL, Acevedo-Morantes CY, Yang J, Cashman NR, Coulthart MB, Pearson DM, Joseph JT, Wille H, Safar JG, Jansen GH, Stepanova M, Sykes BD, Westaway D. A novel Gerstmann-Sträussler-Scheinker disease mutation defines a precursor for amyloidogenic 8 kDa PrP fragments and reveals N-terminal structural changes shared by other GSS alleles. PLoS Pathog 2018; 14:e1006826. [PMID: 29338055 PMCID: PMC5786331 DOI: 10.1371/journal.ppat.1006826] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 01/26/2018] [Accepted: 12/18/2017] [Indexed: 11/29/2022] Open
Abstract
To explore pathogenesis in a young Gerstmann-Sträussler-Scheinker Disease (GSS) patient, the corresponding mutation, an eight-residue duplication in the hydrophobic region (HR), was inserted into the wild type mouse PrP gene. Transgenic (Tg) mouse lines expressing this mutation (Tg.HRdup) developed spontaneous neurologic syndromes and brain extracts hastened disease in low-expressor Tg.HRdup mice, suggesting de novo formation of prions. While Tg.HRdup mice exhibited spongiform change, PrP aggregates and the anticipated GSS hallmark of a proteinase K (PK)-resistant 8 kDa fragment deriving from the center of PrP, the LGGLGGYV insertion also imparted alterations in PrP's unstructured N-terminus, resulting in a 16 kDa species following thermolysin exposure. This species comprises a plausible precursor to the 8 kDa PK-resistant fragment and its detection in adolescent Tg.HRdup mice suggests that an early start to accumulation could account for early disease of the index case. A 16 kDa thermolysin-resistant signature was also found in GSS patients with P102L, A117V, H187R and F198S alleles and has coordinates similar to GSS stop codon mutations. Our data suggest a novel shared pathway of GSS pathogenesis that is fundamentally distinct from that producing structural alterations in the C-terminus of PrP, as observed in other prion diseases such as Creutzfeldt-Jakob Disease and scrapie. Prion diseases can be sporadic, infectious or genetic. The central event of all prion diseases is the structural conversion of the cellular prion protein (PrPC) to its disease associated conformer, PrPSc. Gerstmann-Sträussler-Scheinker Disease (GSS) is a genetic prion disease presenting as a multi-systemic neurological syndrome. A novel mutation, an eight amino acid insertion, was discovered in a young GSS patient. We created transgenic mice expressing this mutation and found that they recapitulate key features of the disease; namely PrP deposition in the brain and a low molecular weight proteinase K (PK) resistant internal PrP fragment. While structural investigations did not reveal a gross alteration in the conformation of this mutant PrP, the insertion lying at the boundary of the globular domain causes alterations in the unstructured amino terminal portion of the protein such that it becomes resistant to digestion by the enzyme thermolysin. We demonstrate by kinetic analysis and sequential digestion that this novel thermolysin resistant species is a precursor to the pathognomonic PK resistant fragment. Analysis of samples from other GSS patients revealed this same signature, suggesting a common molecular pathway.
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Affiliation(s)
- Robert C. C. Mercer
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Medicine (Neurology), University of Alberta, Edmonton, Alberta, Canada
| | - Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Lyudmyla Dorosh
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Ze-Lin Fu
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Charles E. Mays
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Hristina Gapeshina
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Serene L. Wohlgemuth
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | | | - Jing Yang
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Neil R. Cashman
- Brain Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael B. Coulthart
- Canadian Creutzfeldt-Jakob Disease Surveillance System, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Dawn M. Pearson
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Jeffrey T. Joseph
- Hotchkiss Brain Institute and Calgary Laboratory Services, University of Calgary, Calgary, Alberta, Canada
| | - Holger Wille
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jiri G. Safar
- Departments of Pathology and Neurology, School of Medicine Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gerard H. Jansen
- Canadian Creutzfeldt-Jakob Disease Surveillance System, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
- Division of Anatomical Pathology, University of Ottawa, Ottawa, Ontario, Canada
| | - Maria Stepanova
- National Research Council of Canada, Edmonton, Alberta, Canada
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Brian D. Sykes
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Department of Medicine (Neurology), University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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7
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In Vitro Approach To Identify Key Amino Acids in Low Susceptibility of Rabbit Prion Protein to Misfolding. J Virol 2017; 91:JVI.01543-17. [PMID: 28978705 DOI: 10.1128/jvi.01543-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/22/2017] [Indexed: 01/10/2023] Open
Abstract
Prion diseases, or transmissible spongiform encephalopathies (TSEs), are a group of rare progressive neurodegenerative disorders caused by an abnormally folded prion protein (PrPSc). This is capable of transforming the normal cellular prion protein (PrPC) into new infectious PrPSc Interspecies prion transmissibility studies performed by experimental challenge and the outbreak of bovine spongiform encephalopathy that occurred in the late 1980s and 1990s showed that while some species (sheep, mice, and cats) are readily susceptible to TSEs, others are apparently resistant (rabbits, dogs, and horses) to the same agent. To study the mechanisms of low susceptibility to TSEs of certain species, the mouse-rabbit transmission barrier was used as a model. To identify which specific amino acid residues determine high or low susceptibility to PrPSc propagation, protein misfolding cyclic amplification (PMCA), which mimics PrPC-to-PrPSc conversion with accelerated kinetics, was used. This allowed amino acid substitutions in rabbit PrP and accurate analysis of misfolding propensities. Wild-type rabbit recombinant PrP could not be misfolded into a protease-resistant self-propagating isoform in vitro despite seeding with at least 12 different infectious prions from diverse origins. Therefore, rabbit recombinant PrP mutants were designed to contain every single amino acid substitution that distinguishes rabbit recombinant PrP from mouse recombinant PrP. Key amino acid residue substitutions were identified that make rabbit recombinant PrP susceptible to misfolding, and using these, protease-resistant misfolded recombinant rabbit PrP was generated. Additional studies characterized the mechanisms by which these critical amino acid residue substitutions increased the misfolding susceptibility of rabbit PrP.IMPORTANCE Prion disorders are invariably fatal, untreatable diseases typically associated with long incubation periods and characteristic spongiform changes associated with neuronal loss in the brain. Development of any treatment or preventative measure is dependent upon a detailed understanding of the pathogenesis of these diseases, and understanding the mechanism by which certain species appear to be resistant to TSEs is critical. Rabbits are highly resistant to naturally acquired TSEs, and even under experimental conditions, induction of clinical disease is not easy. Using recombinant rabbit PrP as a model, this study describes critical molecular determinants that confer this high resistance to transmissible spongiform encephalopathies.
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8
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Malevanets A, Chong PA, Hansen DF, Rizk P, Sun Y, Lin H, Muhandiram R, Chakrabartty A, Kay LE, Forman-Kay JD, Wodak SJ. Interplay of buried histidine protonation and protein stability in prion misfolding. Sci Rep 2017; 7:882. [PMID: 28408762 PMCID: PMC5429843 DOI: 10.1038/s41598-017-00954-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/20/2017] [Indexed: 12/03/2022] Open
Abstract
Misofolding of mammalian prion proteins (PrP) is believed to be the cause of a group of rare and fatal neurodegenerative diseases. Despite intense scrutiny however, the mechanism of the misfolding reaction remains unclear. We perform nuclear Magnetic Resonance and thermodynamic stability measurements on the C-terminal domains (residues 90–231) of two PrP variants exhibiting different pH-induced susceptibilities to aggregation: the susceptible hamster prion (GHaPrP) and its less susceptible rabbit homolog (RaPrP). The pKa of histidines in these domains are determined from titration experiments, and proton-exchange rates are measured at pH 5 and pH 7. A single buried highly conserved histidine, H187/H186 in GHaPrP/RaPrP, exhibited a markedly down shifted pKa ~5 for both proteins. However, noticeably larger pH-induced shifts in exchange rates occur for GHaPrP versus RaPrP. Analysis of the data indicates that protonation of the buried histidine destabilizes both PrP variants, but produces a more drastic effect in the less stable GHaPrP. This interpretation is supported by urea denaturation experiments performed on both PrP variants at neutral and low pH, and correlates with the difference in disease susceptibility of the two species, as expected from the documented linkage between destabilization of the folded state and formation of misfolded and aggregated species.
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Affiliation(s)
- Anatoly Malevanets
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada
| | - P Andrew Chong
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - D Flemming Hansen
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,University College London, Division of Biosciences, London, WC1E 6BT, UK
| | - Paul Rizk
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yulong Sun
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Hong Lin
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada
| | - Ranjith Muhandiram
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Avi Chakrabartty
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Lewis E Kay
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Julie D Forman-Kay
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Shoshana J Wodak
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1A8, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,VIB Structural Biology Research Center, VUB, Pleinlaan 2, 1050, Brussels, Belgium.
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9
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Moulick R, Udgaonkar JB. Identification and Structural Characterization of the Precursor Conformation of the Prion Protein which Directly Initiates Misfolding and Oligomerization. J Mol Biol 2017; 429:886-899. [DOI: 10.1016/j.jmb.2017.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
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10
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The structural and functional effects of the familial hypertrophic cardiomyopathy-linked cardiac troponin C mutation, L29Q. J Mol Cell Cardiol 2015; 87:257-69. [PMID: 26341255 PMCID: PMC4640586 DOI: 10.1016/j.yjmcc.2015.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/09/2015] [Accepted: 08/23/2015] [Indexed: 01/02/2023]
Abstract
Familial hypertrophic cardiomyopathy (FHC) is characterized by severe abnormal cardiac muscle growth. The traditional view of disease progression in FHC is that an increase in the Ca2 +-sensitivity of cardiac muscle contraction ultimately leads to pathogenic myocardial remodeling, though recent studies suggest this may be an oversimplification. For example, FHC may be developed through altered signaling that prevents downstream regulation of contraction. The mutation L29Q, found in the Ca2 +-binding regulatory protein in heart muscle, cardiac troponin C (cTnC), has been linked to cardiac hypertrophy. However, reports on the functional effects of this mutation are conflicting, and our goal was to combine in vitro and in situ structural and functional data to elucidate its mechanism of action. We used nuclear magnetic resonance and circular dichroism to solve the structure and characterize the backbone dynamics and stability of the regulatory domain of cTnC with the L29Q mutation. The overall structure and dynamics of cTnC were unperturbed, although a slight rearrangement of site 1, an increase in backbone flexibility, and a small decrease in protein stability were observed. The structure and function of cTnC was also assessed in demembranated ventricular trabeculae using fluorescence for in situ structure. L29Q reduced the cooperativity of the Ca2 +-dependent structural change in cTnC in trabeculae under basal conditions and abolished the effect of force-generating myosin cross-bridges on this structural change. These effects could contribute to the pathogenesis of this mutation. The cTnC L29Q mutation causes a small change in the NMR structure of site 1 in cTnC. L29Q reduces the cooperativity of Ca2 +-dependent structural changes in cTnC in situ. L29Q removes the impact of force-generating myosin heads on cTnC structural changes.
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11
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Yuan Z, Yang L, Chen B, Zhu T, Hassan MF, Yin X, Zhou X, Zhao D. Protein misfolding cyclic amplification induces the conversion of recombinant prion protein to PrP oligomers causing neuronal apoptosis. J Neurochem 2015; 133:722-9. [DOI: 10.1111/jnc.13098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/12/2015] [Accepted: 03/15/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Zhen Yuan
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Lifeng Yang
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Baian Chen
- Department of Laboratory Animal Science; School of Basic Medical Science; Capital Medical University; Beijing China
| | - Ting Zhu
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Mohammad Farooque Hassan
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Xiaomin Yin
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Xiangmei Zhou
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Deming Zhao
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
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12
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Moulick R, Udgaonkar JB. Thermodynamic characterization of the unfolding of the prion protein. Biophys J 2014; 106:410-20. [PMID: 24461016 DOI: 10.1016/j.bpj.2013.11.4491] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 11/15/2013] [Accepted: 11/27/2013] [Indexed: 12/16/2022] Open
Abstract
The prion protein appears to be unusually susceptible to conformational change, and unlike nearly all other proteins, it can easily be made to convert to alternative misfolded conformations. To understand the basis of this structural plasticity, a detailed thermodynamic characterization of two variants of the mouse prion protein (moPrP), the full-length moPrP (23-231) and the structured C-terminal domain, moPrP (121-231), has been carried out. All thermodynamic parameters governing unfolding, including the changes in enthalpy, entropy, free energy, and heat capacity, were found to be identical for the two protein variants. The N-terminal domain remains unstructured and does not interact with the C-terminal domain in the full-length protein at pH 4. Moreover, the enthalpy and entropy of unfolding of moPrP (121-231) are similar in magnitude to values reported for other proteins of similar size. However, the protein has an unusually high native-state heat capacity, and consequently, the change in heat capacity upon unfolding is much lower than that expected for a protein of similar size. It appears, therefore, that the native state of the prion protein undergoes substantial fluctuations in enthalpy and hence, in structure.
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Affiliation(s)
- Roumita Moulick
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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13
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Honda RP, Yamaguchi KI, Kuwata K. Acid-induced molten globule state of a prion protein: crucial role of Strand 1-Helix 1-Strand 2 segment. J Biol Chem 2014; 289:30355-30363. [PMID: 25217639 DOI: 10.1074/jbc.m114.559450] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conversion of a cellular prion protein (PrP(C)) to its pathogenic isoform (PrP(Sc)) is a critical event in the pathogenesis of prion diseases. Pathogenic conversion is usually associated with the oligomerization process; therefore, the conformational characteristics of the pre-oligomer state may provide insights into the conversion process. Previous studies indicate that PrP(C) is prone to oligomer formation at low pH, but the conformation of the pre-oligomer state remains unknown. In this study, we systematically analyzed the acid-induced conformational changes of PrP(C) and discovered a unique acid-induced molten globule state at pH 2.0 termed the "A-state." We characterized the structure of the A-state using far/near-UV CD, 1-anilino-8-naphthalene sulfonate fluorescence, size exclusion chromatography, and NMR. Deuterium exchange experiments with NMR detection revealed its first unique structure ever reported thus far; i.e. the Strand 1-Helix 1-Strand 2 segment at the N terminus was preferentially unfolded, whereas the Helix 2-Helix 3 segment at the C terminus remained marginally stable. This conformational change could be triggered by the protonation of Asp(144), Asp(147), and Glu(196), followed by disruption of key salt bridges in PrP(C). Moreover, the initial population of the A-state at low pH (pH 2.0-5.0) was well correlated with the rate of the β-rich oligomer formation, suggesting that the A-state is the pre-oligomer state. Thus, the specific conformation of the A-state would provide crucial insights into the mechanisms of oligomerization and further pathogenic conversion as well as facilitating the design of novel medical chaperones for treating prion diseases.
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Affiliation(s)
- Ryo P Honda
- School of Medicine and Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Kei-Ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Kazuo Kuwata
- School of Medicine and Gifu University, Yanagido 1-1, Gifu 501-1193, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan; Department of Gene and Development, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan and.
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14
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Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins. J Theor Biol 2013; 342:70-82. [PMID: 24184221 DOI: 10.1016/j.jtbi.2013.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 08/25/2013] [Accepted: 10/09/2013] [Indexed: 12/27/2022]
Abstract
Prion diseases, traditionally referred to as transmissible spongiform encephalopathies (TSEs), are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep and goats, bovine spongiform encephalopathy (BSE or mad-cow disease) in cattle, chronic wasting disease in deer and elk, and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)), and the conversion of PrP(C) to PrP(Sc) is believed to involve conformational change from a predominantly α-helical protein to one rich in β-sheet structure. Such a conformational change may be amenable to study by molecular dynamics (MD) techniques. For rabbits, classical studies show that they have a low susceptibility to be infected by PrP(Sc), but recently it was reported that rabbit prions can be generated through saPMCA (serial automated Protein Misfolding Cyclic Amplification) in vitro and the rabbit prion is infectious and transmissible. In this paper, we first do a detailed survey on the research advances of rabbit prion protein (RaPrP) and then we perform MD simulations on the NMR and X-ray molecular structures of rabbit prion protein wild-type and mutants. The survey shows to us that rabbits were not challenged directly in vivo with other known prion strains and the saPMCA result did not pass the test of the known BSE strain of cattle. Thus, we might still look rabbits as a prion resistant species. MD results indicate that the three α-helices of the wild-type are stable under the neutral pH environment (but under low pH environment the three α-helices have been unfolded into β-sheets), and the three α-helices of the mutants (I214V and S173N) are unfolded into rich β-sheet structures under the same pH environment. In addition, we found an interesting result that the salt bridges such as ASP201-ARG155, ASP177-ARG163 contribute greatly to the structural stability of RaPrP.
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15
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Jetha NN, Semenchenko V, Wishart DS, Cashman NR, Marziali A. Nanopore analysis of wild-type and mutant prion protein (PrP(C)): single molecule discrimination and PrP(C) kinetics. PLoS One 2013; 8:e54982. [PMID: 23393562 PMCID: PMC3564863 DOI: 10.1371/journal.pone.0054982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/18/2012] [Indexed: 11/19/2022] Open
Abstract
Prion diseases are fatal neurodegenerative diseases associated with the conversion of cellular prion protein (PrP(C)) in the central nervous system into the infectious isoform (PrP(Sc)). The mechanics of conversion are almost entirely unknown, with understanding stymied by the lack of an atomic-level structure for PrP(Sc). A number of pathogenic PrP(C) mutants exist that are characterized by an increased propensity for conversion into PrP(Sc) and that differ from wild-type by only a single amino-acid point mutation in their primary structure. These mutations are known to perturb the stability and conformational dynamics of the protein. Understanding of how this occurs may provide insight into the mechanism of PrP(C) conversion. In this work we sought to explore wild-type and pathogenic mutant prion protein structure and dynamics by analysis of the current fluctuations through an organic α-hemolysin nanometer-scale pore (nanopore) in which a single prion protein has been captured electrophoretically. In doing this, we find that wild-type and D178N mutant PrP(C), (a PrP(C) mutant associated with both Fatal Familial Insomnia and Creutzfeldt-Jakob disease), exhibit easily distinguishable current signatures and kinetics inside the pore and we further demonstrate, with the use of Hidden Markov Model signal processing, accurate discrimination between these two proteins at the single molecule level based on the kinetics of a single PrP(C) capture event. Moreover, we present a four-state model to describe wild-type PrP(C) kinetics in the pore as a first step in our investigation on characterizing the differences in kinetics and conformational dynamics between wild-type and D178N mutant PrP(C). These results demonstrate the potential of nanopore analysis for highly sensitive, real-time protein and small molecule detection based on single molecule kinetics inside a nanopore, and show the utility of this technique as an assay to probe differences in stability between wild-type and mutant prion proteins at the single molecule level.
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Affiliation(s)
- Nahid N Jetha
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada.
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16
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Cortez LM, Kumar J, Renault L, Young HS, Sim VL. Mouse prion protein polymorphism Phe-108/Val-189 affects the kinetics of fibril formation and the response to seeding: evidence for a two-step nucleation polymerization mechanism. J Biol Chem 2013; 288:4772-81. [PMID: 23283973 DOI: 10.1074/jbc.m112.414581] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Prion diseases are fatal neurodegenerative disorders associated with the polymerization of the cellular form of prion protein (PrP(C)) into an amyloidogenic β-sheet infectious form (PrP(Sc)). The sequence of host PrP is the major determinant of host prion disease susceptibility. In mice, the presence of allele a (Prnp(a), encoding the polymorphism Leu-108/Thr-189) or b (Prnp(b), Phe-108/Val-189) is associated with short or long incubation times, respectively, following infection with PrP(Sc). The molecular bases linking PrP sequence, infection susceptibility, and convertibility of PrP(C) into PrP(Sc) remain unclear. Here we show that recombinant PrP(a) and PrP(b) aggregate and respond to seeding differently in vitro. Our kinetic studies reveal differences during the nucleation phase of the aggregation process, where PrP(b) exhibits a longer lag phase that cannot be completely eliminated by seeding the reaction with preformed fibrils. Additionally, PrP(b) is more prone to propagate features of the seeds, as demonstrated by conformational stability and electron microscopy studies of the formed fibrils. We propose a model of polymerization to explain how the polymorphisms at positions 108 and 189 produce the phenotypes seen in vivo. This model also provides insight into phenomena such as species barrier and prion strain generation, two phenomena also influenced by the primary structure of PrP.
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Affiliation(s)
- Leonardo M Cortez
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
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Hasegawa K, Mohri S, Yokoyama T. Comparison of the local structural stabilities of mammalian prion protein (PrP) by fragment molecular orbital calculations. Prion 2012; 7:185-91. [PMID: 23232497 PMCID: PMC3609128 DOI: 10.4161/pri.23122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE), a member of the prion diseases, is a fatal neurodegenerative disorder suspected to be caused by a malfunction of prion protein (PrP). Although BSE prions have been reported to be transmitted to a wide range of animal species, dogs and hamsters are known to be BSE-resistant animals. Analysis of canine and hamster PrP could elucidate the molecular mechanisms supporting the species barriers to BSE prion transmission. The structural stability of 6 mammalian PrPs, including human, cattle, mouse, hamster, dog and cat, was analyzed. We then evaluated intramolecular interactions in PrP by fragment molecular orbital (FMO) calculations. Despite similar backbone structures, the PrP side-chain orientations differed among the animal species examined. The pair interaction energies between secondary structural elements in the PrPs varied considerably, indicating that the local structural stabilities of PrP varied among the different animal species. Principal component analysis (PCA) demonstrated that different local structural stability exists in bovine PrP compared with the PrP of other animal species examined. The results of the present study suggest that differences in local structural stabilities between canine and bovine PrP link diversity in susceptibility to BSE prion infection.
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Vrentas CE, Onstot S, Nicholson EM. A comparative analysis of rapid methods for purification and refolding of recombinant bovine prion protein. Protein Expr Purif 2012; 82:380-8. [PMID: 22381461 DOI: 10.1016/j.pep.2012.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/09/2012] [Accepted: 02/10/2012] [Indexed: 11/28/2022]
Abstract
Bacterially-produced recombinant prion protein (rPrP) is a frequently used model system for the study of the properties of wild-type and mutant prion proteins by biochemical and biophysical approaches. A range of approaches have been developed for the purification and refolding of untagged rPrP expressed as inclusion bodies in Escherichia coli, including refolding by dialysis and simultaneous on-column purification and refolding. In order to perform a higher-throughput analysis of different rPrP proteins, an approach that produces highly pure rPrP with a minimum of purification steps and a high yield per liter of induced bacterial culture is desired. Here, we directly compare purification approaches for untagged bovine rPrP as adapted to rapid, small-scale formats useful for higher-throughput studies. An analysis of protein yield, purity, oxidation, and refolding revealed significant differences between preparative methods as adapted to the small-scale format, and based on these findings we provide recommendations for future purifications. We also describe the utility of a sensitive commercial kit for thiol analysis of these preparations, the pH dependence of dimer formation during refolding of bovine rPrP, and bovine rPrP binding to cobalt affinity resin.
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Affiliation(s)
- Catherine E Vrentas
- Virus and Prion Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, 1920 Dayton Ave., Ames, IA 50010, USA
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