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Chatterjee S, Salimi A, Lee JY. Unraveling the Histidine Tautomerism Effect on the Initial Stages of Prion Misfolding: New Insights from a Computational Perspective. ACS Chem Neurosci 2021; 12:3203-3213. [PMID: 34382391 DOI: 10.1021/acschemneuro.1c00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The aggregation and structural conversion of normal prion peptide (PrPC) into the pathogenic scrapie form (PrPSc), which can act as a seed to enhance prion amyloid fiber formation, is believed to be a crucial event in prionopathies. Previous research suggests that the prion monomer may play an important role in oligomer generation during disease pathogenesis. In the present study, extensive replica-exchange molecular dynamics (REMD) simulations were conducted to explore the conformational characteristics of the huPrP (125-160) monomer under the histidine tautomerism effect. Investigating the structural characteristics and fibrilization process is challenging because two histidine tautomers [Nε2-H (ε) and Nδ1-H (δ)] can occur in the open neutral state. Molecular dynamics (MD) simulation outcomes have shown that the toxic εδ and δδ isomer (containing several and broader local minima) had the highest α-helix structures, with contents of 21.11% and 21.01%, respectively, and may have a strong influence on the organizational behavior of a monomeric prion. The amino acids aspartate 20 (D20)-asparagine 29 (N29) and isoleucine 15 (I15)-histidine 16 (H16), D20-arginine 27 (R27) as well as N29 formed α-helix with the highest probabilities in the δδ and εδ isomer, accordingly. On the basis of our findings, we propose the histidine tautomerization hypothesis as a new prion accumulation mechanism, which may exist to induce the formation of prion accumulates. Overall, our tautomerism hypothesis constitutes a promising perspective for enhancing understanding of prion disease pathobiology and may help in the design of a good inhibitor.
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Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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2
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Kumari A, Muthu SA, Prakash P, Ahmad B. Herbalome of Chandraprabha vati, a polyherbal formulation of Ayurveda prevents fibrillation of lysozyme by stabilizing aggregation-prone intermediate state. Int J Biol Macromol 2020; 148:102-109. [DOI: 10.1016/j.ijbiomac.2020.01.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/09/2020] [Accepted: 01/12/2020] [Indexed: 10/25/2022]
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3
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Sabareesan AT, Udgaonkar JB. Pathogenic Mutations within the Disordered Palindromic Region of the Prion Protein Induce Structure Therein and Accelerate the Formation of Misfolded Oligomers. J Mol Biol 2016; 428:3935-3947. [PMID: 27545411 DOI: 10.1016/j.jmb.2016.08.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/11/2022]
Abstract
Little is understood about how the intrinsically disordered N-terminal region (NTR) of the prion protein modulates its misfolding and aggregation, which lead to prion disease. In this study, two pathogenic mutations, G113V and A116V, in the palindromic region of the NTR are shown to have no effect on the structure, stability, or dynamics of native mouse prion protein (moPrP) but nevertheless accelerate misfolding and oligomerization. For wild-type moPrP, misfolding and oligomerization appear to occur concurrently, while for both mutant variants, oligomerization is shown to precede misfolding. Kinetic hydrogen-deuterium exchange-mass spectrometry experiments show that sequence segment 89-132 from the NTR becomes structured, albeit weakly, during the oligomerization of both mutant variants. Importantly, this structure formation occurs prior to structural conversion in the C-terminal domain and appears to be the reason that the formation of misfolded oligomers is accelerated by the pathogenic mutations.
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Affiliation(s)
- A T Sabareesan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.
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4
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Fonseca-Ornelas L, Zweckstetter M. The protonation state of histidine 111 regulates the aggregation of the evolutionary most conserved region of the human prion protein. Protein Sci 2016; 25:1563-7. [PMID: 27184108 DOI: 10.1002/pro.2947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/13/2016] [Indexed: 12/18/2022]
Abstract
In a group of neurodegenerative diseases, collectively termed transmissible spongiform encephalopathies, the prion protein aggregates into β-sheet rich amyloid-like deposits. Because amyloid structure has been connected to different prion strains and cellular toxicity, it is important to obtain insight into the structural properties of prion fibrils. Using a combination of solution NMR spectroscopy, thioflavin-T fluorescence and electron microscopy we here show that within amyloid fibrils of a peptide containing residues 108-143 of the human prion protein [humPrP (108-143)]-the evolutionary most conserved part of the prion protein - residue H111 and S135 are in close spatial proximity and their interaction is critical for fibrillization. We further show that residues H111 and H140 share the same microenvironment in the unfolded, monomeric state of the peptide, but not in the fibrillar form. While protonation of H140 has little influence on fibrillization of humPrP (108-143), a positive charge at position 111 blocks the conformational change, which is necessary for amyloid formation of humPrP (108-143). Our study thus highlights the importance of protonation of histidine residues for protein aggregation and suggests point mutations to probe the structure of infectious prion particles.
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Affiliation(s)
- Luis Fonseca-Ornelas
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Markus Zweckstetter
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany.,German Center for Neurodegenerative Diseases (DZNE), Von Siebold-Str. 3a, Göttingen, 37075, Germany.,Department of Neurology, University Medical Center Göttingen, University of Göttingen, Am Waldweg 33, Göttingen, 37073, Germany
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6
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Structural and dynamic properties of the human prion protein. Biophys J 2014; 106:1152-63. [PMID: 24606939 DOI: 10.1016/j.bpj.2013.12.053] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 12/11/2013] [Accepted: 12/26/2013] [Indexed: 11/23/2022] Open
Abstract
Prion diseases involve the conformational conversion of the cellular prion protein (PrP(C)) to its misfolded pathogenic form (PrP(Sc)). To better understand the structural mechanism of this conversion, we performed extensive all-atom, explicit-solvent molecular-dynamics simulations for three structures of the wild-type human PrP (huPrP) at different pH values and temperatures. Residue 129 is polymorphic, being either Met or Val. Two of the three structures have Met in position 129 and the other has Val. Lowering the pH or raising the temperature induced large conformational changes of the C-terminal globular domain and increased exposure of its hydrophobic core. In some simulations, HA and its preceding S1-HA loop underwent large displacements. The C-terminus of HB was unstable and sometimes partially unfolded. Two hydrophobic residues, Phe-198 and Met-134, frequently became exposed to solvent. These conformational changes became more dramatic at lower pH or higher temperature. Furthermore, Tyr-169 and the S2-HB loop, or the X-loop, were different in the starting structures but converged to common conformations in the simulations for the Met-129, but not the Val-129, protein. α-Strands and β-strands formed in the initially unstructured N-terminus. α-Strand propensity in the N-terminus was different between the Met-129 and Val129 proteins, but β-strand propensity was similar. This study reveals detailed structural and dynamic properties of huPrP, providing insight into the mechanism of the conversion of PrP(C) to PrP(Sc).
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7
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Singh J, Udgaonkar JB. Dissection of Conformational Conversion Events during Prion Amyloid Fibril Formation Using Hydrogen Exchange and Mass Spectrometry. J Mol Biol 2013; 425:3510-21. [DOI: 10.1016/j.jmb.2013.06.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/10/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
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8
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Polyproline-II Helix in Proteins: Structure and Function. J Mol Biol 2013; 425:2100-32. [DOI: 10.1016/j.jmb.2013.03.018] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/28/2013] [Accepted: 03/11/2013] [Indexed: 12/31/2022]
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9
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De Simone A, Stanzione F, Marasco D, Vitagliano L, Esposito L. The intrinsic stability of the human prion β-sheet region investigated by molecular dynamics. J Biomol Struct Dyn 2013; 31:441-52. [DOI: 10.1080/07391102.2012.703070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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10
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Lu Y, Wei G, Derreumaux P. Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations. J Chem Phys 2012; 137:025101. [PMID: 22803563 DOI: 10.1063/1.4732761] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Characterizing the early formed oligomeric intermediates of amyloid peptides is of particular interest due to their links with neurodegenerative diseases. Here we study the NNQQ peptide, known to display parallel β-strands in amyloid fibrils by x-ray microcrystallography, and investigate the structural, thermodynamical, and dynamical properties of 20 NNQQ peptides using molecular dynamics and replica exchange molecular dynamics simulations coupled to a coarse-grained force field. All simulations are initiated from randomized and fully dispersed monomeric conformations. Our simulations reveal that the phase transition is characterized by a change in the oligomer and β-sheet size distributions and the percentage of mixed parallel/antiparallel β-strands when the sheets are formed. At all temperatures, however, the fraction of parallel β-strands remains low, though there are many association/fragmentation events. This work and a growing body of computational studies provide strong evidence that the critical nucleus goes beyond 20 chains and reordering of the β-strands occurs in larger oligomers.
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Affiliation(s)
- Yan Lu
- State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
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11
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Skora L, Zweckstetter M. Determination of amyloid core structure using chemical shifts. Protein Sci 2012; 21:1948-53. [PMID: 23033250 DOI: 10.1002/pro.2170] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 12/18/2022]
Abstract
Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.
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Affiliation(s)
- Lukasz Skora
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, Germany
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12
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Chebaro Y, Pasquali S, Derreumaux P. The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins. J Phys Chem B 2012; 116:8741-52. [DOI: 10.1021/jp301665f] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique,
CNRS UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique,
13 rue Pierre et Marie Curie, 75005 Paris
| | - Samuela Pasquali
- Laboratoire de Biochimie Théorique,
CNRS UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique,
13 rue Pierre et Marie Curie, 75005 Paris
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique,
CNRS UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique,
13 rue Pierre et Marie Curie, 75005 Paris
- Institut Universitaire de France, 103 Bvd Saint-Michel, Paris 75005, France
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Camilloni C, Schaal D, Schweimer K, Schwarzinger S, De Simone A. Energy landscape of the prion protein helix 1 probed by metadynamics and NMR. Biophys J 2012; 102:158-67. [PMID: 22225810 DOI: 10.1016/j.bpj.2011.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/30/2011] [Accepted: 12/05/2011] [Indexed: 11/30/2022] Open
Abstract
The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecular simulations of metadynamics and NMR measurements to study heterogeneous states of proteins and peptides. In this way, we determined the structural ensemble and free-energy landscape of the highly dynamic helix 1 of the prion protein (PrP-H1), whose misfolding and aggregation are intimately connected to a group of neurodegenerative disorders known as transmissible spongiform encephalopathies. Our combined approach allowed us to dissect the factors that govern the conformational states of PrP-H1 in solution, and the implications of these factors for prion protein misfolding and aggregation. The results underline the importance of adopting novel integrated approaches that take advantage of experiments and theory to achieve a comprehensive characterization of the structure and dynamics of biological macromolecules.
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Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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Thakur AK, Srivastava AK, Srinivas V, Chary KVR, Rao CM. Copper alters aggregation behavior of prion protein and induces novel interactions between its N- and C-terminal regions. J Biol Chem 2011; 286:38533-38545. [PMID: 21900252 DOI: 10.1074/jbc.m111.265645] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Copper is reported to promote and prevent aggregation of prion protein. Conformational and functional consequences of Cu(2+)-binding to prion protein (PrP) are not well understood largely because most of the Cu(2+)-binding studies have been performed on fragments and truncated variants of the prion protein. In this context, we set out to investigate the conformational consequences of Cu(2+)-binding to full-length prion protein (PrP) by isothermal calorimetry, NMR, and small angle x-ray scattering. In this study, we report altered aggregation behavior of full-length PrP upon binding to Cu(2+). At physiological temperature, Cu(2+) did not promote aggregation suggesting that Cu(2+) may not play a role in the aggregation of PrP at physiological temperature (37 °C). However, Cu(2+)-bound PrP aggregated at lower temperatures. This temperature-dependent process is reversible. Our results show two novel intra-protein interactions upon Cu(2+)-binding. The N-terminal region (residues 90-120 that contain the site His-96/His-111) becomes proximal to helix-1 (residues 144-147) and its nearby loop region (residues 139-143), which may be important in preventing amyloid fibril formation in the presence of Cu(2+). In addition, we observed another novel interaction between the N-terminal region comprising the octapeptide repeats (residues 60-91) and helix-2 (residues 174-185) of PrP. Small angle x-ray scattering studies of full-length PrP show significant compactness upon Cu(2+)-binding. Our results demonstrate novel long range inter-domain interactions of the N- and C-terminal regions of PrP upon Cu(2+)-binding, which might have physiological significance.
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Affiliation(s)
- Abhay Kumar Thakur
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India
| | - Atul Kumar Srivastava
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Volety Srinivas
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India
| | - Kandala Venkata Ramana Chary
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Chintalagiri Mohan Rao
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India.
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Wagoner VA, Cheon M, Chang I, Hall CK. Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides. Proteins 2011; 79:2132-45. [PMID: 21557317 DOI: 10.1002/prot.23034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 01/26/2011] [Accepted: 02/11/2011] [Indexed: 11/11/2022]
Abstract
We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113-120 (AGAAAAGA) and the mouse prion protein MoPrP 111-120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)(4) , A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well-ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures.
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Affiliation(s)
- Victoria A Wagoner
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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Gerum C, Silvers R, Wirmer-Bartoschek J, Schwalbe H. Unfolded-state structure and dynamics influence the fibril formation of human prion protein. Angew Chem Int Ed Engl 2010; 48:9452-6. [PMID: 19882604 DOI: 10.1002/anie.200903771] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christian Gerum
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-Universität, 60438 Frankfurt, Germany
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Abstract
The crucial event in the development of transmissible spongiform encephalopathies (TSEs) is the conformational change of a host-encoded membrane protein - the cellular PrPC - into a disease associated, fibril-forming isoform PrPSc. This conformational transition from the α-helix-rich cellular form into the mainly β-sheet containing counterpart initiates an ‘autocatalytic’ reaction which leads to the accumulation of amyloid fibrils in the central nervous system (CNS) and to neurodegeneration, a hallmark of TSEs. The exact molecular mechanisms which lead to the conformational change are still unknown. It also remains to be brought to light how a polypeptide chain can adopt at least two stable conformations. This review focuses on structural aspects of the prion protein with regard to protein-protein interactions and the initiation of prion protein misfolding. It therefore highlights parts of the protein which might play a notable role in the conformational transition from PrPC to PrPSc and consequently in inducing a fatal chain reaction of protein misfolding. Furthermore, features of different proteins, which are able to adopt insoluble fibrillar states under certain circumstances, are compared to PrP in an attempt to understand the unique characteristics of prion diseases.
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Affiliation(s)
- L Kupfer
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
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Rigter A, Priem J, Timmers-Parohi D, Langeveld JPM, van Zijderveld FG, Bossers A. Prion protein self-peptides modulate prion interactions and conversion. BMC BIOCHEMISTRY 2009; 10:29. [PMID: 19943977 PMCID: PMC2789745 DOI: 10.1186/1471-2091-10-29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 11/30/2009] [Indexed: 12/30/2022]
Abstract
Background Molecular mechanisms underlying prion agent replication, converting host-encoded cellular prion protein (PrPC) into the scrapie associated isoform (PrPSc), are poorly understood. Selective self-interaction between PrP molecules forms a basis underlying the observed differences of the PrPC into PrPSc conversion process (agent replication). The importance of previously peptide-scanning mapped ovine PrP self-interaction domains on this conversion was investigated by studying the ability of six of these ovine PrP based peptides to modulate two processes; PrP self-interaction and conversion. Results Three peptides (octarepeat, binding domain 2 -and C-terminal) were capable of inhibiting self-interaction of PrP in a solid-phase PrP peptide array. Three peptides (N-terminal, binding domain 2, and amyloidogenic motif) modulated prion conversion when added before or after initiation of the prion protein misfolding cyclic amplification (PMCA) reaction using brain homogenates. The C-terminal peptides (core region and C-terminal) only affected conversion (increased PrPres formation) when added before mixing PrPC and PrPSc, whereas the octarepeat peptide only affected conversion when added after this mixing. Conclusion This study identified the putative PrP core binding domain that facilitates the PrPC-PrPSc interaction (not conversion), corroborating evidence that the region of PrP containing this domain is important in the species-barrier and/or scrapie susceptibility. The octarepeats can be involved in PrPC-PrPSc stabilization, whereas the N-terminal glycosaminoglycan binding motif and the amyloidogenic motif indirectly affected conversion. Binding domain 2 and the C-terminal domain are directly implicated in PrPC self-interaction during the conversion process and may prove to be prime targets in new therapeutic strategy development, potentially retaining PrPC function. These results emphasize the importance of probable PrPC-PrPC and required PrPC-PrPSc interactions during PrP conversion. All interactions are probably part of the complex process in which polymorphisms and species barriers affect TSE transmission and susceptibility.
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Affiliation(s)
- Alan Rigter
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen UR, Lelystad, 8200 AB, the Netherlands.
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Gerum C, Silvers R, Wirmer-Bartoschek J, Schwalbe H. Unfolded-State Structure and Dynamics Influence the Fibril Formation of Human Prion Protein. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903771] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Saracino GA, Villa A, Moro G, Cosentino U, Salmona M. Spontaneous β-helical fold in prion protein: The case of PrP(82-146). Proteins 2009; 75:964-76. [DOI: 10.1002/prot.22306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Chebaro Y, Derreumaux P. The Conversion of Helix H2 to β-Sheet Is Accelerated in the Monomer and Dimer of the Prion Protein upon T183A Mutation. J Phys Chem B 2009; 113:6942-8. [DOI: 10.1021/jp900334s] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico Chimique et Université Paris Diderot-Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico Chimique et Université Paris Diderot-Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
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22
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Bąk D, Cutting GR, Milewski M. The CFTR-derived peptides as a model of sequence-specific protein aggregation. Cell Mol Biol Lett 2007; 12:435-47. [PMID: 17361366 PMCID: PMC6275903 DOI: 10.2478/s11658-007-0014-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 01/26/2007] [Indexed: 12/02/2022] Open
Abstract
Protein aggregation is a hallmark of a growing group of pathologies known as conformational diseases. Although many native or mutated proteins are able to form aggregates, the exact amino acid sequences involved in the process of aggregation are known only in a few cases. Hence, there is a need for different model systems to expand our knowledge in this area. The so-called ag region was previously found to cause the aggregation of the C-terminal fragment of the cystic fibrosis transmembrane conductance regulator (CFTR). To investigate whether this specific amino acid sequence is able to induce protein aggregation irrespective of the amino acid context, we altered its position within the CFTR-derived C-terminal peptide and analyzed the localization of such modified peptides in transfected mammalian cells. Insertion of the ag region into a different amino acid background affected not only the overall level of intracellular protein aggregation, but also the morphology and subcellular localization of aggregates, suggesting that sequences other than the ag region can substantially influence the peptide’s behavior. Also, the introduction of a short dipeptide (His-Arg) motif, a crucial component of the ag region, into different locations within the C-terminus of CFTR lead to changes in the aggregation pattern that were less striking, although still statistically significant. Thus, our results indicate that even subtle alterations within the aggregating peptide can affect many different aspects of the aggregation process.
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Affiliation(s)
- Daniel Bąk
- Laboratory of Cell Biology, Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland.
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De Simone A, Zagari A, Derreumaux P. Structural and hydration properties of the partially unfolded states of the prion protein. Biophys J 2007; 93:1284-92. [PMID: 17483173 PMCID: PMC1929054 DOI: 10.1529/biophysj.107.108613] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Misfolding and aggregation of the prion protein (PrP) is responsible for the development of transmissible spongiform encephalopathies (TSE). To gain insights into possible aggregation-prone intermediate states, we construct the free energy surface of the C-terminal globular domain of the PrP from enhanced sampling of replica exchange molecular dynamics. This cellular domain is characterized by three helices H1-H3 and a small beta-sheet. In agreement with experimental studies, the partially unfolded states display a stable core built from the central portions of helices H2 and H3 and a high mobility of helix H1 from the core. Among all identified conformational basins, a marginally populated state appears to be a very good candidate for aggregation. This intermediate is stabilized by four TSE-sensitive key interactions, displays a longer helix H1 with both a dry and solvated surface, and is featured by a significant detachment of helix H1 from the PrP-core.
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Affiliation(s)
- Alfonso De Simone
- Dipartimento delle Scienze Biologiche, Sezione Biostrutture and CNISM, Università di Napoli Federico II, I-80134 Naples, Italy.
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DeMarco ML, Daggett V. Molecular Mechanism for Low pH Triggered Misfolding of the Human Prion Protein†. Biochemistry 2007; 46:3045-54. [PMID: 17315950 DOI: 10.1021/bi0619066] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational changes in the prion protein cause transmissible spongiform encephalopathies, also referred to as prion diseases. In its native state, the prion protein is innocuous (PrPC), but it can misfold into a neurotoxic and infectious isoform (PrPSc). The full-length cellular form of the prion protein consists of residues 23-230, with over half of the sequence belonging to the unstructured N-terminal domain and the remaining residues forming a small globular domain. During misfolding and aggregation, portions of both the structured and unstructured domains are incorporated into the aggregates. After limited proteolysis by proteinase K, the most abundant fragment from brain-derived prion fibrils is a 141-residue fragment composed of residues 90-230. Here we describe simulations of this fragment of the human prion protein at low pH, which triggers misfolding, and at neutral pH as a control. The simulations, in agreement with experiment, show that this biologically and pathologically relevant prion construct is stable and native-like at neutral pH. In contrast, at low pH the prion protein is destabilized via disruption of critical long-range salt bridges. In one of the low pH simulations this destabilization resulted in a conformational transition to a PrPSc-like isoform consistent with our previous simulations of a smaller construct.
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Affiliation(s)
- Mari L DeMarco
- Department of Medicinal Chemistry, Biomolecular Structure and Design Program, University of Washington, Seattle, Washington 98195-7610, USA
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Oboznaya MB, Gilch S, Titova MA, Koroev DO, Volkova TD, Volpina OM, Schätzl HM. Antibodies to a Nonconjugated Prion Protein Peptide 95-123 Interfere with PrP Sc Propagation in Prion-Infected Cells. Cell Mol Neurobiol 2007; 27:271-84. [PMID: 17205391 DOI: 10.1007/s10571-006-9108-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 06/23/2006] [Indexed: 11/29/2022]
Abstract
1. Vaccination-induced anti-prion protein antibodies are presently regarded as a promising approach toward treatment of prion diseases. Here, we investigated the ability of five peptides corresponding to three different regions of the bovine prion protein (PrP) to elicit antibodies interfering with PrP(Sc) propagation in prion-infected cells.2. Rabbits were immunized with free nonconjugated peptides. Obtained immune sera were tested in enzyme-linked immunosorbent assay (ELISA) and immunoblot for their binding to recombinant PrP and cell-derived pathogenic isoform (PrP(Sc)) and normal prion protein (PrP(c)), respectively. Sera positive in all tests were chosen for PrP(Sc) inhibition studies in cell culture.3. All peptides induced anti-peptide antibodies, most of them reacting with recombinant PrP. Moreover, addition of the serum specific to peptide 95-123 led to a transient reduction of PrP(Sc) levels in persistently prion-infected cells.4. Thus, anti-PrP antibodies interfering with PrP(Sc) propagation were induced with a prion protein peptide nonconjugated to a protein carrier. These results point to the potential application of the nonconjugated peptide 95-123 for the treatment of prion diseases.
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Affiliation(s)
- Maria B Oboznaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997, GSP Moscow, Russia,
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DeMarco ML, Silveira J, Caughey B, Daggett V. Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models. Biochemistry 2006; 45:15573-82. [PMID: 17176078 DOI: 10.1021/bi0612723] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Decades after the prion protein was implicated in transmissible spongiform encephalopathies, the structure of its toxic isoform and its mechanism of toxicity remain unknown. By gathering available experimental data, albeit low resolution, a few pieces of the prion puzzle can be put in place. Currently, there are two fundamentally different models of a prion protofibril. One has its building blocks derived from a molecular dynamics simulation of the prion protein under amyloidogenic conditions, termed the spiral model. The other model was constructed by threading a portion of the prion sequence through a beta-helical structure from the Protein Data Bank. Here we compare and contrast these models with respect to all of the available experimental information, including electron micrographs, symmetries, secondary structure, oligomerization interfaces, enzymatic digestion, epitope exposure, and disaggregation profiles. Much of this information was not available when the two models were introduced. Overall, we find that the spiral model is consistent with all of the experimental results. In contrast, it is difficult to reconcile several of the experimental observables with the beta-helix model. While the experimental constraints are of low resolution, in bringing together the previously disconnected experiments, we have developed a clearer picture of prion aggregates. Both the improved characterization of prion aggregates and the existing atomic models can be used to devise further experiments to better elucidate the misfolding pathway and the structure of prion protofibrils.
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Affiliation(s)
- Mari L DeMarco
- Department of Medicinal Chemistry, Biomolecular Structure and Design Program, University of Washington, Seattle, Washington 98195-7610, USA
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