1
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Ilie IM, Caflisch A. Antibody binding increases the flexibility of the prion protein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140827. [PMID: 35931365 DOI: 10.1016/j.bbapap.2022.140827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/29/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Prion diseases are associated with the conversion of the cellular prion protein (PrP) into a pathogenic conformer (PrPSc). A proposed therapeutic approach to avoid the pathogenic transformation is to develop antibodies that bind to PrP and stabilize its structure. POM1 and POM6 are two monoclonal antibodies that bind the globular domain of PrP and have different biological responses, i.e., trigger neurotoxicity mimicking prion infections (POM1) or prevent neurotoxicity (POM6). The crystal structures of PrP in complex with the two antibodies show similar epitopes which seems inconsistent with the opposite phenotypes. Here, we investigate the influence of the POM1 and POM6 antibodies on the flexibility of the mouse PrP by molecular dynamics simulations. The simulations reveal that the POM6/PrP interface is less stable than the POM1/PrP interface, ascribable to localized polar mismatches at the interface, despite the former complex having a larger epitope than the latter. In the presence of any of the two antibodies, the flexibility of the globular domain increases everywhere except for the β1-α1 loop in the POM1/PrP complex which suggests the involvement of this loop in the pathological conversion. The secondary structure of PrP is preserved whereas the polar interactions involving residues Glu146, Arg156 and Arg208 are modified upon antibody binding.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
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2
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A conformational switch controlling the toxicity of the prion protein. Nat Struct Mol Biol 2022; 29:831-840. [PMID: 35948768 PMCID: PMC9371974 DOI: 10.1038/s41594-022-00814-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/06/2022] [Indexed: 11/08/2022]
Abstract
Prion infections cause conformational changes of the cellular prion protein (PrPC) and lead to progressive neurological impairment. Here we show that toxic, prion-mimetic ligands induce an intramolecular R208-H140 hydrogen bond ('H-latch'), altering the flexibility of the α2-α3 and β2-α2 loops of PrPC. Expression of a PrP2Cys mutant mimicking the H-latch was constitutively toxic, whereas a PrPR207A mutant unable to form the H-latch conferred resistance to prion infection. High-affinity ligands that prevented H-latch induction repressed prion-related neurodegeneration in organotypic cerebellar cultures. We then selected phage-displayed ligands binding wild-type PrPC, but not PrP2Cys. These binders depopulated H-latched conformers and conferred protection against prion toxicity. Finally, brain-specific expression of an antibody rationally designed to prevent H-latch formation prolonged the life of prion-infected mice despite unhampered prion propagation, confirming that the H-latch is an important reporter of prion neurotoxicity.
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3
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Ilie IM, Bacci M, Vitalis A, Caflisch A. Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophys J 2022; 121:2813-2825. [PMID: 35672948 DOI: 10.1016/j.bpj.2022.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/20/2022] [Accepted: 06/01/2022] [Indexed: 11/18/2022] Open
Abstract
Misfolding of the cellular prion protein (PrPC) is associated with lethal neurodegeneration. PrPC consists of a flexible tail (residues 23-123) and a globular domain (residues 124-231) whose C-terminal end is anchored to the cell membrane. The neurotoxic antibody POM1 and the innocuous antibody POM6 recognize the globular domain. Experimental evidence indicates that POM1 binding to PrPC emulates the influence on PrPC of the misfolded prion protein (PrPSc) while the binding of POM6 has the opposite biological response. Little is known about the potential interactions between flexible tail, globular domain, and the membrane. Here, we used atomistic simulations to investigate how these interactions are modulated by the binding of the Fab fragments of POM1 and POM6 to PrPC and by interstitial sequence truncations to the flexible tail. The simulations show that the binding of the antibodies restricts the range of orientations of the globular domain with respect to the membrane and decreases the distance between tail and membrane. Five of the six sequence truncations influence only marginally this distance and the contact patterns between tail and globular domain. The only exception is a truncation coupled to a charge inversion mutation of four N-terminal residues, which increases the distance of the flexible tail from the membrane. The interactions of the flexible tail and globular domain are modulated differently by the two antibodies.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Marco Bacci
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich, Switzerland.
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4
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Novel quaternary structures of the human prion protein globular domain. Biochimie 2021; 191:118-125. [PMID: 34517052 DOI: 10.1016/j.biochi.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
Prion disease is caused by the misfolding of the cellular prion protein, PrPC, into a self-templating conformer, PrPSc. Nuclear magnetic resonance (NMR) and X-ray crystallography revealed the 3D structure of the globular domain of PrPC and the possibility of its dimerization via an interchain disulfide bridge that forms due to domain swap or by non-covalent association of two monomers. On the contrary, PrPSc is composed by a complex and heterogeneous ensemble of poorly defined conformations and quaternary arrangements that are related to different patterns of neurotoxicity. Targeting PrPC with molecules that stabilize the native conformation of its globular domain emerged as a promising approach to develop anti-prion therapies. One of the advantages of this approach is employing structure-based drug discovery methods to PrPC. Thus, it is essential to expand our structural knowledge about PrPC as much as possible to aid such drug discovery efforts. In this work, we report a crystallographic structure of the globular domain of human PrPC that shows a novel dimeric form and a novel oligomeric arrangement. We use molecular dynamics simulations to explore its structural dynamics and stability and discuss potential implications of these new quaternary structures to the conversion process.
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5
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Bergasa-Caceres F, Rabitz HA. Identification of Two Early Folding Stage Prion Non-Local Contacts Suggested to Serve as Key Steps in Directing the Final Fold to Be Either Native or Pathogenic. Int J Mol Sci 2021; 22:ijms22168619. [PMID: 34445324 PMCID: PMC8395309 DOI: 10.3390/ijms22168619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
The initial steps of the folding pathway of the C-terminal domain of the murine prion protein mPrP(90–231) are predicted based on the sequential collapse model (SCM). A non-local dominant contact is found to form between the connecting region between helix 1 and β-sheet 1 and the C-terminal region of helix 3. This non-local contact nucleates the most populated molten globule-like intermediate along the folding pathway. A less stable early non-local contact between segments 120–124 and 179–183, located in the middle of helix 2, promotes the formation of a less populated molten globule-like intermediate. The formation of the dominant non-local contact constitutes an example of the postulated Nature’s Shortcut to the prion protein collapse into the native structure. The possible role of the less populated molten globule-like intermediate is explored as the potential initiation point for the folding for three pathogenic mutants (T182A, I214V, and Q211P in mouse prion numbering) of the prion protein.
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6
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Abskharon R, Wang F, Wohlkonig A, Ruan J, Soror S, Giachin G, Pardon E, Zou W, Legname G, Ma J, Steyaert J. Structural evidence for the critical role of the prion protein hydrophobic region in forming an infectious prion. PLoS Pathog 2019; 15:e1008139. [PMID: 31815959 PMCID: PMC6922452 DOI: 10.1371/journal.ppat.1008139] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 12/19/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022] Open
Abstract
Prion or PrPSc is the proteinaceous infectious agent causing prion diseases in various mammalian species. Despite decades of research, the structural basis for PrPSc formation and prion infectivity remains elusive. To understand the role of the hydrophobic region in forming infectious prion at the molecular level, we report X-ray crystal structures of mouse (Mo) prion protein (PrP) (residues 89-230) in complex with a nanobody (Nb484). Using the recombinant prion propagation system, we show that the binding of Nb484 to the hydrophobic region of MoPrP efficiently inhibits the propagation of proteinase K resistant PrPSc and prion infectivity. In addition, when added to cultured mouse brain slices in high concentrations, Nb484 exhibits no neurotoxicity, which is drastically different from other neurotoxic anti-PrP antibodies, suggesting that the Nb484 can be a potential therapeutic agent against prion disease. In summary, our data provides the first structure-function evidence supporting a crucial role of the hydrophobic region of PrP in forming an infectious prion.
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Affiliation(s)
- Romany Abskharon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
- National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt
| | - Fei Wang
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
- * E-mail: (FW); (JM); (JS)
| | - Alexandre Wohlkonig
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
| | - Juxin Ruan
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
| | - Sameh Soror
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
- Center of Excellence, Helwan Structural Biology Research, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Gabriele Giachin
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
| | - Wenquan Zou
- Departments of Pathology and Neurology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Jiyan Ma
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, United States of America
- * E-mail: (FW); (JM); (JS)
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- VIB-VUB Center for Structural Biology, Vlaams Instituut Biotechnologie (VIB), Brussels, Belgium
- * E-mail: (FW); (JM); (JS)
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7
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Baral PK, Yin J, Aguzzi A, James MNG. Transition of the prion protein from a structured cellular form (PrP C ) to the infectious scrapie agent (PrP Sc ). Protein Sci 2019; 28:2055-2063. [PMID: 31583788 DOI: 10.1002/pro.3735] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 11/07/2022]
Abstract
Prion diseases in mammals are caused by a conformational transition of the cellular prion protein from its native conformation (PrPC ) to a pathological isoform called "prion protein scrapie" (PrPSc ). A molecular level of understanding of this conformational transition will be helpful in unveiling the disease etiology. Experimental structural biological techniques (NMR and X-ray crystallography) have been used to unravel the atomic level structural information for the prion and its binding partners. More than one hundred three-dimensional structures of the mammalian prions have been deposited in the protein databank. Structural studies on the prion protein and its structural transitions will deepen our understanding of the molecular basis of prion pathogenesis and will provide valuable guidance for future structure-based drug discovery endeavors.
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Affiliation(s)
- Pravas K Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jiang Yin
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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8
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Purro SA, Mead S, Khalili-Shirazi A, Nicoll AJ, Collinge J. Reply to: Intrinsic Toxicity of Antibodies to the Globular Domain of the Prion Protein. Biol Psychiatry 2018; 84:e53-e54. [PMID: 29752071 DOI: 10.1016/j.biopsych.2018.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Silvia A Purro
- Medical Research Council Prion Unit, Institute of Prion Diseases, University College London, London, United Kingdom
| | - Simon Mead
- Medical Research Council Prion Unit, Institute of Prion Diseases, University College London, London, United Kingdom
| | - Azadeh Khalili-Shirazi
- Medical Research Council Prion Unit, Institute of Prion Diseases, University College London, London, United Kingdom
| | - Andrew J Nicoll
- Medical Research Council Prion Unit, Institute of Prion Diseases, University College London, London, United Kingdom.
| | - John Collinge
- Medical Research Council Prion Unit, Institute of Prion Diseases, University College London, London, United Kingdom.
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9
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A bispecific immunotweezer prevents soluble PrP oligomers and abolishes prion toxicity. PLoS Pathog 2018; 14:e1007335. [PMID: 30273408 PMCID: PMC6181439 DOI: 10.1371/journal.ppat.1007335] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 10/11/2018] [Accepted: 09/13/2018] [Indexed: 11/28/2022] Open
Abstract
Antibodies to the prion protein, PrP, represent a promising therapeutic approach against prion diseases but the neurotoxicity of certain anti-PrP antibodies has caused concern. Here we describe scPOM-bi, a bispecific antibody designed to function as a molecular prion tweezer. scPOM-bi combines the complementarity-determining regions of the neurotoxic antibody POM1 and the neuroprotective POM2, which bind the globular domain (GD) and flexible tail (FT) respectively. We found that scPOM-bi confers protection to prion-infected organotypic cerebellar slices even when prion pathology is already conspicuous. Moreover, scPOM-bi prevents the formation of soluble oligomers that correlate with neurotoxic PrP species. Simultaneous targeting of both GD and FT was more effective than concomitant treatment with the individual molecules or targeting the tail alone, possibly by preventing the GD from entering a toxic-prone state. We conclude that simultaneous binding of the GD and flexible tail of PrP results in strong protection from prion neurotoxicity and may represent a promising strategy for anti-prion immunotherapy. Antibody immunotherapy is considered a viable strategy against prion disease. We previously showed that antibodies against the so-called globular domain of Prion Protein (PrP) can cause PrP dependent neurotoxicity; this does not happen for antibodies against the flexible tail of PrP, which therefore ought to be preferred for therapy. Here we show that simultaneous targeting of both globular domain and flexible tail by a bispecific, combination of a toxic and a non-toxic antibody, results in stronger protection against prion toxicity, even if the bispecific is administered when prion pathology is already conspicuous. We hypothesize that neurotoxicity arises from binding to specific “toxicity triggering sites” in the globular domain. We designed our bispecific with two aims: i) occupying one such site and preventing prion or other factors from docking to it and ii) binding to the flexible tail to engage the region of PrP necessary for neurotoxicity. We also show that neurotoxic antibodies cause the formation of soluble PrP oligomers that cause toxicity on PrP expressing cell lines; these are not formed in the presence of prion protective antibodies. We suggest that these soluble species might play a role in prion toxicity, similarly to what is generally agreed to happen in other neurodegenerative disorders.
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10
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Abstract
Three decades after the discovery of prions as the cause of Creutzfeldt-Jakob disease and other transmissible spongiform encephalopathies, we are still nowhere close to finding an effective therapy. Numerous pharmacological interventions have attempted to target various stages of disease progression, yet none has significantly ameliorated the course of disease. We still lack a mechanistic understanding of how the prions damage the brain, and this situation results in a dearth of validated pharmacological targets. In this review, we discuss the attempts to interfere with the replication of prions and to enhance their clearance. We also trace some of the possibilities to identify novel targets that may arise with increasing insights into prion biology.
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Affiliation(s)
- Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, CH-8091 Zürich, Switzerland;
| | - Asvin K K Lakkaraju
- Institute of Neuropathology, University of Zurich, CH-8091 Zürich, Switzerland;
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, CH-8091 Zürich, Switzerland;
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11
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Ma B, Zhao J, Nussinov R. Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1860:2672-81. [PMID: 27266343 PMCID: PMC5610039 DOI: 10.1016/j.bbagen.2016.05.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/05/2016] [Accepted: 05/31/2016] [Indexed: 11/27/2022]
Abstract
BACKGROUND The dominant feature in neurodegenerative diseases is protein aggregations that lead to neuronal loss. Immunotherapies using antibodies or antibody fragments to target the aggregations are a highly perused approach. The molecular mechanisms underlying the amyloid-based immunotherapy are complex. Deciphering the properties of amyloidogenic proteins responsible for these diseases is essential to obtain insights into antibody recognition of the amyloid antigens. SCOPE OF REVIEW We systematically explore all available crystal structures of antibody-amyloid complexes related to neurodegenerative diseases, including antibodies that recognize the Aβ peptide, tau protein, prion protein, alpha-synuclein, huntingtin protein (mHTT), and polyglutamine. MAJOR CONCLUSIONS We found that antibodies mostly use the conformational selection mechanism to recognize the highly flexible amyloid antigens. In particular, solanezumab bound to Aβ12-28 tripeptide motif conformation (F19F20A21), which is shared with the Aβ42 fibril. This motif, which is trapped by the antibody, may provide the missing link in amyloid formation. Water molecules often bridge between the antibody and amyloid, contributing to the recognition. GENERAL SIGNIFICANCE This paper provides the structural basis for antibody recognition of amyloidogenic proteins. The analysis and discussion of known structures are expected to help in the design and optimization of antibodies in neurodegenerative diseases. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States.
| | - Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States; Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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12
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Reimann RR, Sonati T, Hornemann S, Herrmann US, Arand M, Hawke S, Aguzzi A. Differential Toxicity of Antibodies to the Prion Protein. PLoS Pathog 2016; 12:e1005401. [PMID: 26821311 PMCID: PMC4731068 DOI: 10.1371/journal.ppat.1005401] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/22/2015] [Indexed: 11/25/2022] Open
Abstract
Antibodies against the prion protein PrPC can antagonize prion replication and neuroinvasion, and therefore hold promise as possible therapeutics against prion diseases. However, the safety profile of such antibodies is controversial. It was originally reported that the monoclonal antibody D13 exhibits strong target-related toxicity, yet a subsequent study contradicted these findings. We have reported that several antibodies against certain epitopes of PrPC, including antibody POM1, are profoundly neurotoxic, yet antibody ICSM18, with an epitope that overlaps with POM1, was reported to be innocuous when injected into mouse brains. In order to clarify this confusing situation, we assessed the neurotoxicity of antibodies D13 and ICSM18 with dose-escalation studies using diffusion-weighted magnetic resonance imaging and various histological techniques. We report that both D13 and ICSM18 induce rapid, dose-dependent, on-target neurotoxicity. We conclude that antibodies directed to this region may not be suitable as therapeutics. No such toxicity was found when antibodies against the flexible tail of PrPC were administered. Any attempt at immunotherapy or immunoprophylaxis of prion diseases should account for these potential untoward effects.
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Affiliation(s)
- Regina R. Reimann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Tiziana Sonati
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Uli S. Herrmann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Michael Arand
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Simon Hawke
- Vascular Immunology Laboratory, Department of Pathology, University of Sydney, Camperdown, Australia
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
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13
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Baral PK, Swayampakula M, Aguzzi A, James MNG. X-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins. J Struct Biol 2015; 192:37-47. [PMID: 26320075 DOI: 10.1016/j.jsb.2015.08.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/17/2015] [Accepted: 08/25/2015] [Indexed: 02/03/2023]
Abstract
Misfolded prion proteins are the cause of neurodegenerative diseases that affect many mammalian species, including humans. Transmission of the prion diseases poses a considerable public-health risk as a specific prion disease such as bovine spongiform encephalopathy can be transferred to humans and other mammalian species upon contaminant exposure. The underlying mechanism of prion propagation and the species barriers that control cross species transmission has been investigated quite extensively. So far a number of prion strains have been characterized and those have been intimately linked to species-specific infectivity and other pathophysiological manifestations. These strains are encoded by a protein-only agent, and have a high degree of sequence identity across mammalian species. The molecular events that lead to strain differentiation remain elusive. In order to contribute to the understanding of strain differentiation, we have determined the crystal structures of the globular, folded domains of four prion proteins (cow, deer, elk and Syrian hamster) bound to the POM1 antibody fragment Fab. Although the overall structural folds of the mammalian prion proteins remains extremely similar, there are several local structural variations observed in the misfolding-initiator motifs. In additional molecular dynamics simulation studies on these several prion proteins reveal differences in the local fluctuations and imply that these differences have possible roles in the unfolding of the globular domains. These local variations in the structured domains perpetuate diverse patterns of prion misfolding and possibly facilitate the strain selection and adaptation.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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14
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Wang X, McGovern G, Zhang Y, Wang F, Zha L, Jeffrey M, Ma J. Intraperitoneal Infection of Wild-Type Mice with Synthetically Generated Mammalian Prion. PLoS Pathog 2015; 11:e1004958. [PMID: 26136122 PMCID: PMC4489884 DOI: 10.1371/journal.ppat.1004958] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 05/14/2015] [Indexed: 11/23/2022] Open
Abstract
The prion hypothesis postulates that the infectious agent in transmissible spongiform encephalopathies (TSEs) is an unorthodox protein conformation based agent. Recent successes in generating mammalian prions in vitro with bacterially expressed recombinant prion protein provide strong support for the hypothesis. However, whether the pathogenic properties of synthetically generated prion (rec-Prion) recapitulate those of naturally occurring prions remains unresolved. Using end-point titration assay, we showed that the in vitro prepared rec-Prions have infectious titers of around 104 LD50 / μg. In addition, intraperitoneal (i.p.) inoculation of wild-type mice with rec-Prion caused prion disease with an average survival time of 210 – 220 days post inoculation. Detailed pathological analyses revealed that the nature of rec-Prion induced lesions, including spongiform change, disease specific prion protein accumulation (PrP-d) and the PrP-d dissemination amongst lymphoid and peripheral nervous system tissues, the route and mechanisms of neuroinvasion were all typical of classical rodent prions. Our results revealed that, similar to naturally occurring prions, the rec-Prion has a titratable infectivity and is capable of causing prion disease via routes other than direct intra-cerebral challenge. More importantly, our results established that the rec-Prion caused disease is pathogenically and pathologically identical to naturally occurring contagious TSEs, supporting the concept that a conformationally altered protein agent is responsible for the infectivity in TSEs. The transmissible spongiform encephalopathies (TSEs) are a group of infectious neurodegenerative diseases affecting both humans and animals. The prion hypothesis postulates that prions are protein conformation based infectious agents responsible for TSE infectivity. Prions have been synthetically generated in vitro, but it remains unclear whether the properties of synthetically generated prion are the same as those of TSE agents and whether the disease caused by synthetically generated prion is identical to naturally occurring TSEs. In this study, we demonstrated that similar to the classical TSE agents, the synthetically generated prion has a titratable infectivity and is able to cause prion disease in wild-type mice via routes other than direct intra-cerebral inoculation. More importantly, we showed that the synthetically generated prion induced pathological changes, including the dissemination of disease-specific prion protein accumulation and the route and mechanism of neuroinvasion, were all typical of classical TSEs. These results demonstrate the similarity of synthetically generated prion to the infectious agent in TSEs, providing strong evidence supporting the prion hypothesis.
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Affiliation(s)
- Xinhe Wang
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio, United States of America
| | - Gillian McGovern
- Animal and Plant Health Agency, Lasswade Laboratory, Pentlands Science Park, Penicuik, Midlothian, Scotland
| | - Yi Zhang
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio, United States of America
- Key Laboratory of Brain Functional Genomics (East China Normal University), Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics (East China Normal University), School of Life Sciences, East China Normal University, Shanghai, China
| | - Fei Wang
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio, United States of America
| | - Liang Zha
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio, United States of America
| | - Martin Jeffrey
- Animal and Plant Health Agency, Lasswade Laboratory, Pentlands Science Park, Penicuik, Midlothian, Scotland
| | - Jiyan Ma
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, United States of America
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, Ohio, United States of America
- Key Laboratory of Brain Functional Genomics (East China Normal University), Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics (East China Normal University), School of Life Sciences, East China Normal University, Shanghai, China
- * E-mail:
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15
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Herrmann US, Sonati T, Falsig J, Reimann RR, Dametto P, O’Connor T, Li B, Lau A, Hornemann S, Sorce S, Wagner U, Sanoudou D, Aguzzi A. Prion infections and anti-PrP antibodies trigger converging neurotoxic pathways. PLoS Pathog 2015; 11:e1004662. [PMID: 25710374 PMCID: PMC4339193 DOI: 10.1371/journal.ppat.1004662] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 01/06/2015] [Indexed: 02/08/2023] Open
Abstract
Prions induce lethal neurodegeneration and consist of PrPSc, an aggregated conformer of the cellular prion protein PrPC. Antibody-derived ligands to the globular domain of PrPC (collectively termed GDL) are also neurotoxic. Here we show that GDL and prion infections activate the same pathways. Firstly, both GDL and prion infection of cerebellar organotypic cultured slices (COCS) induced the production of reactive oxygen species (ROS). Accordingly, ROS scavenging, which counteracts GDL toxicity in vitro and in vivo, prolonged the lifespan of prion-infected mice and protected prion-infected COCS from neurodegeneration. Instead, neither glutamate receptor antagonists nor inhibitors of endoplasmic reticulum calcium channels abolished neurotoxicity in either model. Secondly, antibodies against the flexible tail (FT) of PrPC reduced neurotoxicity in both GDL-exposed and prion-infected COCS, suggesting that the FT executes toxicity in both paradigms. Thirdly, the PERK pathway of the unfolded protein response was activated in both models. Finally, 80% of transcriptionally downregulated genes overlapped between prion-infected and GDL-treated COCS. We conclude that GDL mimic the interaction of PrPSc with PrPC, thereby triggering the downstream events characteristic of prion infection. Prion diseases are a group of infectious, invariably fatal neurodegenerative diseases. Progress in developing therapeutics is slow, partly because animal models of prion diseases require stringent biosafety and are very slow. We recently found that treatment of cerebellar slices with antibodies targeting the globular domain (GD ligands) of the prion protein (PrP) is neurotoxic. Here we compared this model to prion infection, and describe striking similarities. Both models involved the production of reactive oxygen species, and antioxidants could reverse the toxicity in cerebellar slices and even prolong the survival time of prion-infected mice. Antibodies targeting the flexible tail of PrP that prevent toxicity of GD ligands reduced the toxicity induced by prions. Endoplasmic reticulum stress, which is involved in prion toxicity, is also found in GD-ligand induced neurotoxicity. Finally, changes of gene expression were similar in both models. We conclude that prion infection and GD ligands use converging neurotoxic pathways. Because GD ligands induce toxicity within days rather than months and do not pose biosafety hazards, they may represent a powerful tool for furthering our understanding of prion pathogenesis and also for the discovery of antiprion drugs.
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Affiliation(s)
- Uli S. Herrmann
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Tiziana Sonati
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Jeppe Falsig
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Regina R. Reimann
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Paolo Dametto
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Tracy O’Connor
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Bei Li
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Agnes Lau
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Silvia Sorce
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
| | - Uli Wagner
- Institute of Surgical Pathology, University Hospital of Zurich, Zurich, Switzerland
| | - Despina Sanoudou
- Department of Pharmacology, Medical School, University of Athens, Athens, Greece
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital of Zurich, Zurich, Switzerland
- * E-mail:
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16
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Rasmussen J, Gilroyed BH, Reuter T, Dudas S, Neumann NF, Balachandran A, Kav NNV, Graham C, Czub S, McAllister TA. Can plants serve as a vector for prions causing chronic wasting disease? Prion 2015; 8:136-42. [PMID: 24509640 DOI: 10.4161/pri.27963] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prions, the causative agent of chronic wasting disease (CWD) enter the environment through shedding of bodily fluids and carcass decay, posing a disease risk as a result of their environmental persistence. Plants have the ability to take up large organic particles, including whole proteins, and microbes. This study used wheat (Triticum aestivum L.) to investigate the uptake of infectious CWD prions into roots and their transport into aerial tissues. The roots of intact wheat plants were exposed to infectious prions (PrP(TSE)) for 24 h in three replicate studies with PrP(TSE) in protein extracts being detected by western blot, IDEXX and Bio-Rad diagnostic tests. Recombinant prion protein (PrP(C)) bound to roots, but was not detected in the stem or leaves. Protease-digested CWD prions (PrP(TSE)) in elk brain homogenate interacted with root tissue, but were not detected in the stem. This suggests wheat was unable to transport sufficient PrP(TSE) from the roots to the stem to be detectable by the methods employed. Undigested PrP(TSE) did not associate with roots. The present study suggests that if prions are transported from the roots to the stems it is at levels that are below those that are detectable by western blot, IDEXX or Bio-Rad diagnostic kits.
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17
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Hadži S, Ondračka A, Jerala R, Hafner‐Bratkovič I. Pathological mutations H187R and E196K facilitate subdomain separation and prion protein conversion by destabilization of the native structure. FASEB J 2014; 29:882-93. [DOI: 10.1096/fj.14-255646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- San Hadži
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
| | - Andrej Ondračka
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
| | - Roman Jerala
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
- EN‐FIST Centre of ExcellenceLjubljanaSlovenia
| | - Iva Hafner‐Bratkovič
- Department of BiotechnologyNational Institute of ChemistryLjubljanaSlovenia
- EN‐FIST Centre of ExcellenceLjubljanaSlovenia
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18
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Zhang Y, Wang F, Wang X, Zhang Z, Xu Y, Yu G, Yuan C, Ma J. Comparison of 2 synthetically generated recombinant prions. Prion 2014; 8:28669. [PMID: 24721728 PMCID: PMC4189893 DOI: 10.4161/pri.28669] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prion is a protein-conformation-based infectious agent causing fatal neurodegenerative diseases in humans and animals. Our previous studies revealed that in the presence of cofactors, infectious prions can be synthetically generated in vitro with bacterially expressed recombinant prion protein (PrP). Once initiated, the recombinant prion is able to propagate indefinitely via serial protein misfolding cyclic amplification (sPMCA). In this study, we compared 2 separately initiated recombinant prions. Our results showed that these 2 recombinant prions had distinct biochemical properties and caused different patterns of spongiosis and PrP deposition in inoculated mice. Our findings indicate that various recombinant prions can be initiated in vitro and potential reasons for this variability are discussed.
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Affiliation(s)
- Yi Zhang
- Key Laboratory of Brain Functional Genomics; Ministry of Education; Shanghai Key Laboratory of Brain Functional Genomics; School of Life Sciences; East China Normal University; Shanghai, PR China; Department of Molecular and Cellular Biochemistry; Ohio State University; Columbus, OH USA
| | - Fei Wang
- Department of Molecular and Cellular Biochemistry; Ohio State University; Columbus, OH USA
| | - Xinhe Wang
- Department of Molecular and Cellular Biochemistry; Ohio State University; Columbus, OH USA
| | - Zhihong Zhang
- Key Laboratory of Brain Functional Genomics; Ministry of Education; Shanghai Key Laboratory of Brain Functional Genomics; School of Life Sciences; East China Normal University; Shanghai, PR China
| | - Yuanyuan Xu
- Key Laboratory of Brain Functional Genomics; Ministry of Education; Shanghai Key Laboratory of Brain Functional Genomics; School of Life Sciences; East China Normal University; Shanghai, PR China
| | - Guohua Yu
- Key Laboratory of Brain Functional Genomics; Ministry of Education; Shanghai Key Laboratory of Brain Functional Genomics; School of Life Sciences; East China Normal University; Shanghai, PR China
| | - Chonggang Yuan
- Key Laboratory of Brain Functional Genomics; Ministry of Education; Shanghai Key Laboratory of Brain Functional Genomics; School of Life Sciences; East China Normal University; Shanghai, PR China
| | - Jiyan Ma
- Key Laboratory of Brain Functional Genomics; Ministry of Education; Shanghai Key Laboratory of Brain Functional Genomics; School of Life Sciences; East China Normal University; Shanghai, PR China; Department of Molecular and Cellular Biochemistry; Ohio State University; Columbus, OH USA
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19
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Baral PK, Swayampakula M, Rout MK, Kav NNV, Spyracopoulos L, Aguzzi A, James MNG. Structural basis of prion inhibition by phenothiazine compounds. Structure 2013; 22:291-303. [PMID: 24373770 DOI: 10.1016/j.str.2013.11.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/10/2023]
Abstract
Conformational transitions of the cellular form of the prion protein, PrP(C), into an infectious isoform, PrP(Sc), are considered to be central events in the progression of fatal neurodegenerative diseases known as transmissible spongiform encephalopathies. Tricyclic phenothiazine compounds exhibit antiprion activity; however, the underlying molecular mechanism of PrP(Sc) inhibition remains elusive. We report the molecular structures of two phenothiazine compounds, promazine and chlorpromazine bound to a binding pocket formed at the intersection of the structured and the unstructured domains of the mouse prion protein. Promazine binding induces structural rearrangement of the unstructured region proximal to β1, through the formation of a "hydrophobic anchor." We demonstrate that these molecules, promazine in particular, allosterically stabilize the misfolding initiator-motifs such as the C terminus of α2, the α2-α3 loop, as well as the polymorphic β2-α2 loop. Hence, the stabilization effects of the phenothiazine derivatives on initiator-motifs induce a PrP(C) isoform that potentially resists oligomerization.
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Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Manoj Kumar Rout
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Adriano Aguzzi
- Department of Pathology, Institute of Neuropathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Michael N G James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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20
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Timmes AG, Moore RA, Fischer ER, Priola SA. Recombinant prion protein refolded with lipid and RNA has the biochemical hallmarks of a prion but lacks in vivo infectivity. PLoS One 2013; 8:e71081. [PMID: 23936256 PMCID: PMC3728029 DOI: 10.1371/journal.pone.0071081] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/24/2013] [Indexed: 11/21/2022] Open
Abstract
During prion infection, the normal, protease-sensitive conformation of prion protein (PrPC) is converted via seeded polymerization to an abnormal, infectious conformation with greatly increased protease-resistance (PrPSc). In vitro, protein misfolding cyclic amplification (PMCA) uses PrPSc in prion-infected brain homogenates as an initiating seed to convert PrPC and trigger the self-propagation of PrPSc over many cycles of amplification. While PMCA reactions produce high levels of protease-resistant PrP, the infectious titer is often lower than that of brain-derived PrPSc. More recently, PMCA techniques using bacterially derived recombinant PrP (rPrP) in the presence of lipid and RNA but in the absence of any starting PrPSc seed have been used to generate infectious prions that cause disease in wild-type mice with relatively short incubation times. These data suggest that lipid and/or RNA act as cofactors to facilitate the de novo formation of high levels of prion infectivity. Using rPrP purified by two different techniques, we generated a self-propagating protease-resistant rPrP molecule that, regardless of the amount of RNA and lipid used, had a molecular mass, protease resistance and insolubility similar to that of PrPSc. However, we were unable to detect prion infectivity in any of our reactions using either cell-culture or animal bioassays. These results demonstrate that the ability to self-propagate into a protease-resistant insoluble conformer is not unique to infectious PrP molecules. They suggest that the presence of RNA and lipid cofactors may facilitate the spontaneous refolding of PrP into an infectious form while also allowing the de novo formation of self-propagating, but non-infectious, rPrP-res.
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Affiliation(s)
- Andrew G. Timmes
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Roger A. Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Elizabeth R. Fischer
- Electron Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
| | - Suzette A. Priola
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Disease, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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21
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Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. PLoS One 2013; 8:e67051. [PMID: 23869206 PMCID: PMC3712014 DOI: 10.1371/journal.pone.0067051] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones), oligooxopiperazines, oligo-peptoids, -peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org). This work helps address the peptidomimetic community's need for an automated and expandable modeling tool for noncanonical backbones.
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Affiliation(s)
- Kevin Drew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - P. Douglas Renfrew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Timothy W. Craven
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Glenn L. Butterfoss
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Fang-Chieh Chou
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Brooke N. Bullock
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Andrew Watkins
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Jason W. Labonte
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Michael Pacella
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Krishna Praneeth Kilambi
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Andrew Leaver-Fay
- Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Brian Kuhlman
- Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Philip Bradley
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, United States of America
- * E-mail:
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22
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Swayampakula M, Baral PK, Aguzzi A, Kav NNV, James MNG. The crystal structure of an octapeptide repeat of the prion protein in complex with a Fab fragment of the POM2 antibody. Protein Sci 2013; 22:893-903. [PMID: 23629842 DOI: 10.1002/pro.2270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 11/09/2022]
Abstract
Prion diseases are progressive, infectious neurodegenerative disorders caused primarily by the misfolding of the cellular prion protein (PrP(c)) into an insoluble, protease-resistant, aggregated isoform termed PrP(sc). In native conditions, PrP(c) has a structured C-terminal domain and a highly flexible N-terminal domain. A part of this N-terminal domain consists of 4-5 repeats of an unusual glycine-rich, eight amino acids long peptide known as the octapeptide repeat (OR) domain. In this article, we successfully report the first crystal structure of an OR of PrP(c) bound to the Fab fragment of the POM2 antibody. The structure was solved at a resolution of 2.3 Å by molecular replacement. Although several studies have previously predicted a β-turn-like structure of the unbound ORs, our structure shows an extended conformation of the OR when bound to a molecule of the POM2 Fab indicating that the bound Fab disrupts any putative native β turn conformation of the ORs. Encouraging results from several recent studies have shown that administering small molecule ligands or antibodies targeting the OR domain of PrP result in arresting the progress of peripheral prion infections both in ex vivo and in in vivo models. This makes the structural study of the interactions of POM2 Fab with the OR domain very important as it would help us to design smaller and tighter binding OR ligands.
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Affiliation(s)
- Mridula Swayampakula
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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