1
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Yuan Z, Qu Z, Duan B, Wang T, Xu J, Xia B. Is amyloid fibrillation related to 3D domain swapping for the C-terminal domain of SARS-CoV main protease? Int J Biol Macromol 2021; 197:68-76. [PMID: 34953805 PMCID: PMC8694786 DOI: 10.1016/j.ijbiomac.2021.12.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/02/2021] [Accepted: 12/12/2021] [Indexed: 12/02/2022]
Abstract
The C-terminal domain of SARS-CoV main protease (Mpro-C) can form 3D domain-swapped dimer by exchanging the α1-helices fully buried inside the protein hydrophobic core, under non-denaturing conditions. Here, we report that Mpro-C can also form amyloid fibrils under the 3D domain-swappable conditions in vitro, and the fibrils are not formed through runaway/propagated domain swapping. It is found that there are positive correlations between the rates of domain swapping dimerization and amyloid fibrillation at different temperatures, and for different mutants. However, some Mpro-C mutants incapable of 3D domain swapping can still form amyloid fibrils, indicating that 3D domain swapping is not essential for amyloid fibrillation. Furthermore, NMR H/D exchange data and molecular dynamics simulation results suggest that the protofibril core region tends to unpack at the early stage of 3D domain swapping, so that the amyloid fibrillation can proceed during the 3D domain swapping process. We propose that 3D domain swapping makes it possible for the unpacking of the amyloidogenic fragment of the protein and thus accelerates the amyloid fibrillation process kinetically, which explains the well-documented correlations between amyloid fibrillation and 3D domain swapping observed in many proteins.
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Affiliation(s)
- Zhiliang Yuan
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhi Qu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bo Duan
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tianyi Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiajun Xu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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2
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High-resolution structure and strain comparison of infectious mammalian prions. Mol Cell 2021; 81:4540-4551.e6. [PMID: 34433091 DOI: 10.1016/j.molcel.2021.08.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/29/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022]
Abstract
Within the extensive range of self-propagating pathologic protein aggregates of mammals, prions are the most clearly infectious (e.g., ∼109 lethal doses per milligram). The structures of such lethal assemblies of PrP molecules have been poorly understood. Here we report a near-atomic core structure of a brain-derived, fully infectious prion (263K strain). Cryo-electron microscopy showed amyloid fibrils assembled with parallel in-register intermolecular β sheets. Each monomer provides one rung of the ordered fibril core, with N-linked glycans and glycolipid anchors projecting outward. Thus, single monomers form the templating surface for incoming monomers at fibril ends, where prion growth occurs. Comparison to another prion strain (aRML) revealed major differences in fibril morphology but, like 263K, an asymmetric fibril cross-section without paired protofilaments. These findings provide structural insights into prion propagation, strains, species barriers, and membrane pathogenesis. This structure also helps frame considerations of factors influencing the relative transmissibility of other pathologic amyloids.
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3
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Bustamante A, Rivera R, Floor M, Babul J, Baez M. Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein. Biophys J 2021; 120:4809-4818. [PMID: 34555362 PMCID: PMC8595740 DOI: 10.1016/j.bpj.2021.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/15/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Domain swapping is a mechanism of protein oligomerization by which two or more subunits exchange structural elements to generate an intertwined complex. Numerous studies support a diversity of swapping mechanisms in which structural elements can be exchanged at different stages of the folding pathway of a subunit. Here, we used single-molecule optical tweezers technique to analyze the swapping mechanism of the forkhead DNA-binding domain of human transcription factor FoxP1. FoxP1 populates folded monomers in equilibrium with a swapped dimer. We generated a fusion protein linking two FoxP1 domains in tandem to obtain repetitive mechanical folding and unfolding trajectories. Thus, by stretching the same molecule several times, we detected either the independent folding of each domain or the elusive swapping step between domains. We found that a swapped dimer can be formed directly from fully or mostly folded monomer. In this situation, the interaction between the monomers in route to the domain-swapped dimer is the rate-limiting step. This approach is a useful strategy to test the different proposed domain swapping mechanisms for proteins with relevant physiological functions.
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Affiliation(s)
- Andres Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Rodrigo Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Martin Floor
- Bioinformatics and Medical Statistics Group, Faculty of Science and Technology, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain; Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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4
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Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping. Int J Mol Sci 2021; 22:ijms221910296. [PMID: 34638644 PMCID: PMC8508939 DOI: 10.3390/ijms221910296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/18/2023] Open
Abstract
The association of two or more proteins to adopt a quaternary complex is one of the most widespread mechanisms by which protein function is modulated. In this scenario, three-dimensional domain swapping (3D-DS) constitutes one plausible pathway for the evolution of protein oligomerization that exploits readily available intramolecular contacts to be established in an intermolecular fashion. However, analysis of the oligomerization kinetics and thermodynamics of most extant 3D-DS proteins shows its dependence on protein unfolding, obscuring the elucidation of the emergence of 3D-DS during evolution, its occurrence under physiological conditions, and its biological relevance. Here, we describe the human FoxP subfamily of transcription factors as a feasible model to study the evolution of 3D-DS, due to their significantly faster dissociation and dimerization kinetics and lower dissociation constants in comparison to most 3D-DS models. Through the biophysical and functional characterization of FoxP proteins, relevant structural aspects highlighting the evolutionary adaptations of these proteins to enable efficient 3D-DS have been ascertained. Most biophysical studies on FoxP suggest that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling its fast oligomerization under physiological conditions. Moreover, comparison of biophysical parameters between human FoxP proteins in the context of their minute sequence differences suggests differential evolutionary strategies to favor homoassociation and presages the possibility of heteroassociations, with direct impacts in their gene regulation function.
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5
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Palaniappan C, Narayanan RC, Sekar K. Mutation-Dependent Refolding of Prion Protein Unveils Amyloidogenic-Related Structural Ramifications: Insights from Molecular Dynamics Simulations. ACS Chem Neurosci 2021; 12:2810-2819. [PMID: 34296847 DOI: 10.1021/acschemneuro.1c00142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The main focus of prion structural biology studies is to understand the molecular basis of prion diseases caused by misfolding, and aggregation of the cellular prion protein PrPC remains elusive. Several genetic mutations are linked with human prion diseases and driven by the conformational conversion of PrPC to the toxic PrPSc. The main goal of this study is to gain a better insight into the molecular effect of disease-associated V210I mutation on this process by molecular dynamics simulations. This inherited mutation elicited copious structural changes in the β1-α1-β2 subdomain, including an unfolding of a helix α1 and the elongation of the β-sheet. These unusual structural changes likely appeared to detach the β1-α1-β2 subdomain from the α2-α3 core, an early misfolding event necessary for the conformational conversion of PrPC to PrPSc. Ultimately, the unfolded α1 and its prior β1-α1 loop further engaged with unrestrained conformational dynamics and were widely considered as amyloidogenic-inducing traits. Furthermore, the resulting folding intermediate possesses a highly unstable β1-α1-β2 subdomain, thereby enhancing the aggregation of misfolded PrPC through intermolecular interactions between frequently refolding regions. Briefly, these remarkable changes as seen in the mutant β1-α1-β2 subdomain are consistent with previous experimental results and thus provide a molecular basis of PrPC misfolding associated with the conformational conversion of PrPC to PrPSc.
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Affiliation(s)
| | - Rahul C. Narayanan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
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6
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Wang W, Ventura S. Prion domains as a driving force for the assembly of functional nanomaterials. Prion 2020; 14:170-179. [PMID: 32597308 PMCID: PMC7518758 DOI: 10.1080/19336896.2020.1785659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/06/2023] Open
Abstract
Amyloids display a highly ordered fibrillar structure. Many of these assemblies appear associated with human disease. However, the controllable, stable, tunable, and robust nature of amyloid fibrils can be exploited to build up remarkable nanomaterials with a wide range of applications in biomedicine and biotechnology. Functional prions constitute a particular class of amyloids. These transmissible proteins exhibit a modular architecture, with a disordered prion domain responsible for the assembly and one or more globular domains that account for the activity. Importantly, the original globular protein can be replaced with any protein of interest, without compromising the fibrillation potential. These genetic fusions form fibrils in which the globular domain remains folded, rendering functional nanostructures. However, in some cases, steric hindrance restricts the activity of these fibrils. This limitation can be solved by dissecting prion domains into shorter sequences that keep their self-assembling properties while allowing better access to the active protein in the fibrillar state. In this review, we will discuss the properties of prion-like functional nanomaterials and the amazing applications of these biocompatible fibrillar arrangements.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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7
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Reidenbach AG, Mesleh MF, Casalena D, Vallabh SM, Dahlin JL, Leed AJ, Chan AI, Usanov DL, Yehl JB, Lemke CT, Campbell AJ, Shah RN, Shrestha OK, Sacher JR, Rangel VL, Moroco JA, Sathappa M, Nonato MC, Nguyen KT, Wright SK, Liu DR, Wagner FF, Kaushik VK, Auld DS, Schreiber SL, Minikel EV. Multimodal small-molecule screening for human prion protein binders. J Biol Chem 2020; 295:13516-13531. [PMID: 32723867 PMCID: PMC7521658 DOI: 10.1074/jbc.ra120.014905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19F-observed and saturation transfer difference (STD) NMR spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, and in silico screening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (Kd > 1 mm), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. Whereas orthogonal binder discovery methods could yield high-affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.
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Affiliation(s)
- Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dominick Casalena
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Sonia M Vallabh
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Jayme L Dahlin
- Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alison J Leed
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alix I Chan
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dmitry L Usanov
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jenna B Yehl
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher T Lemke
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Arthur J Campbell
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rishi N Shah
- Undergraduate Research Opportunities Program (UROP), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Om K Shrestha
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Joshua R Sacher
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Victor L Rangel
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jamie A Moroco
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Murugappan Sathappa
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Kong T Nguyen
- Artificial Intelligence Molecular Screen (AIMS) Awards Program, Atomwise, San Francisco, California, USA
| | - S Kirk Wright
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - David R Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Florence F Wagner
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Douglas S Auld
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Vallabh Minikel
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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8
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Di Natale C, La Manna S, Avitabile C, Florio D, Morelli G, Netti PA, Marasco D. Engineered β-hairpin scaffolds from human prion protein regions: Structural and functional investigations of aggregates. Bioorg Chem 2020; 96:103594. [PMID: 31991323 DOI: 10.1016/j.bioorg.2020.103594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 12/16/2022]
Abstract
The investigation of conformational features of regions of amyloidogenic proteins are of great interest to deepen the structural changes and consequent self-aggregation mechanisms at the basis of many neurodegenerative diseases. Here we explore the effect of β-hairpin inducing motifs on regions of prion protein covering strands S1 and S2. In detail, we unveiled the structural and functional features of two model chimeric peptides in which natural sequences are covalently linked together by two dipeptides (l-Pro-Gly and d-Pro-Gly) that are known to differently enhance β-hairpin conformations but both containing N- and the C-terminal aromatic cap motifs to further improve interactions between natural strands. Spectroscopic investigations at solution state indicate that primary assemblies of the monomers of both constructs follow different aggregativemechanisms during the self-assembly: these distinctions, evidenced by CD and ThT emission spectroscopies, reflect into great morphological differences of nanostructures and suggest that rigid β-hairpin conformations greatly limit amyloid-like fibrillogenesis. Overall data confirm the important role exerted by the β-structure of regions S1 and S2 during the aggregation process and lead to speculate to its persistence even in unfolding conditions.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Concetta Avitabile
- Institute of Biostructures and Bioimaging (IBB), National Research Council, Via Mezzocannone 16, 80134 Naples, Italy
| | - Daniele Florio
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy; Task force di Ateneo"METODOLOGIE ANALITICHE PER LA SALVAGUARDIA DEI BENI CULTURALI" MASBC, University of Naples "Federico II", Italy.
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9
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Mondal B, Reddy G. A Transient Intermediate Populated in Prion Folding Leads to Domain Swapping. Biochemistry 2019; 59:114-124. [DOI: 10.1021/acs.biochem.9b00621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Balaka Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka India, 560012
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka India, 560012
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10
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Wang W, Navarro S, Azizyan RA, Baño-Polo M, Esperante SA, Kajava AV, Ventura S. Prion soft amyloid core driven self-assembly of globular proteins into bioactive nanofibrils. NANOSCALE 2019; 11:12680-12694. [PMID: 31237592 DOI: 10.1039/c9nr01755k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Amyloids have been exploited to build amazing bioactive materials. In most cases, short synthetic peptides constitute the functional components of such materials. The controlled assembly of globular proteins into active amyloid nanofibrils is still challenging, because the formation of amyloids implies a conformational conversion towards a β-sheet-rich structure, with a concomitant loss of the native fold and the inactivation of the protein. There is, however, a remarkable exception to this rule: yeast prions. They are singular proteins able to switch between a soluble and an amyloid state. In both states, the structure of their globular domains remains essentially intact. The transit between these two conformations is encoded in prion domains (PrDs): long and disordered sequences to which the active globular domains are appended. PrDs are much larger than typical self-assembling peptides. This seriously limits their use for nanotechnological applications. We have recently shown that these domains contain soft amyloid cores (SACs) that suffice to nucleate their self-assembly reaction. Here we genetically fused a model SAC with different globular proteins. We demonstrate that this very short sequence acts as a minimalist PrD, driving the selective and slow assembly of the initially soluble fusion proteins into amyloid fibrils in which the globular proteins retain their native structure and display high activity. Overall, we provide here a novel, modular and straightforward strategy to build active protein-based nanomaterials at a preparative scale.
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Affiliation(s)
- Weiqiang Wang
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Rafayel A Azizyan
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France
| | - Manuel Baño-Polo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Sebastian A Esperante
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, 34293 Montpellier, Cedex 5, France
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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11
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Sengupta I, Udgaonkar J. Monitoring site-specific conformational changes in real-time reveals a misfolding mechanism of the prion protein. eLife 2019; 8:44698. [PMID: 31232689 PMCID: PMC6590988 DOI: 10.7554/elife.44698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 06/11/2019] [Indexed: 11/25/2022] Open
Abstract
During pathological aggregation, proteins undergo remarkable conformational re-arrangements to anomalously assemble into a heterogeneous collection of misfolded multimers, ranging from soluble oligomers to insoluble amyloid fibrils. Inspired by fluorescence resonance energy transfer (FRET) measurements of protein folding, an experimental strategy to study site-specific misfolding kinetics during aggregation, by effectively suppressing contributions from inter-molecular FRET, is described. Specifically, the kinetics of conformational changes across different secondary and tertiary structural segments of the mouse prion protein (moPrP) were monitored independently, after the monomeric units transformed into large oligomers OL, which subsequently disaggregated reversibly into small oligomers OS at pH 4. The sequence segments spanning helices α2 and α3 underwent a compaction during the formation of OL and elongation into β-sheets during the formation of OS. The β1-α1-β2 and α2-α3 subdomains were separated, and the helix α1 was unfolded to varying extents in both OL and OS.
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Affiliation(s)
- Ishita Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Jayant Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
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12
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Sang JC, Lee JE, Dear AJ, De S, Meisl G, Thackray AM, Bujdoso R, Knowles TPJ, Klenerman D. Direct observation of prion protein oligomer formation reveals an aggregation mechanism with multiple conformationally distinct species. Chem Sci 2019; 10:4588-4597. [PMID: 31123569 PMCID: PMC6492631 DOI: 10.1039/c8sc05627g] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
The aggregation of the prion protein (PrP) plays a key role in the development of prion diseases. In the past decade, a similar process has been associated with other proteins, such as Aβ, tau, and α-synuclein, which participate in other neurodegenerative diseases. It is increasingly recognized that the small oligomeric species of aggregates can play an important role in the development of prion diseases. However, determining the nature of the oligomers formed during the aggregation process has been experimentally difficult due to the lack of suitable methods capable of the detection and characterization of the low level of oligomers that may form. To address this problem, we have utilized single-aggregate methods to study the early events associated with aggregation of recombinant murine PrP in vitro to approach the bona fide process in vivo. PrP aggregation resulted in the formation of thioflavin T (ThT)-inactive and ThT-active species of oligomers. The ThT-active oligomers undergo conversion from a Proteinase K (PK)-sensitive to PK-resistant conformer, from which mature fibrils can eventually emerge. Overall, our results show that single-aggregate methods can provide structural and mechanistic insights into PrP aggregation, identify the potential species that mediates cytotoxicity, and reveal that a range of distinct oligomeric species with different properties is formed during prion protein aggregation.
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Affiliation(s)
- Jason C Sang
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Ji-Eun Lee
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Alexander J Dear
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Suman De
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Alana M Thackray
- Department of Veterinary Medicine , University of Cambridge , Madingley Road , Cambridge , CB3 0ES , UK
| | - Raymond Bujdoso
- Department of Veterinary Medicine , University of Cambridge , Madingley Road , Cambridge , CB3 0ES , UK
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - David Klenerman
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
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13
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Goluguri RR, Sen S, Udgaonkar J. Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein. eLife 2019; 8:e44766. [PMID: 31025940 PMCID: PMC6516828 DOI: 10.7554/elife.44766] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/25/2019] [Indexed: 12/29/2022] Open
Abstract
Protein aggregation appears to originate from partially unfolded conformations that are sampled through stochastic fluctuations of the native protein. It has been a challenge to characterize these fluctuations, under native like conditions. Here, the conformational dynamics of the full-length (23-231) mouse prion protein were studied under native conditions, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS). The slowest fluctuations could be associated with the folding of the unfolded state to an intermediate state, by the use of microsecond mixing experiments. The two faster fluctuations observed by PET-FCS, could be attributed to fluctuations within the native state ensemble. The addition of salt, which is known to initiate the aggregation of the protein, resulted in an enhancement in the time scale of fluctuations in the core of the protein. The results indicate the importance of native state dynamics in initiating the aggregation of proteins.
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Affiliation(s)
- Rama Reddy Goluguri
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Sreemantee Sen
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Jayant Udgaonkar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
- Indian Institute of Science Education and ResearchPuneIndia
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14
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Iglesias V, Paladin L, Juan-Blanco T, Pallarès I, Aloy P, Tosatto SCE, Ventura S. In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases. Front Physiol 2019; 10:314. [PMID: 30971948 PMCID: PMC6445884 DOI: 10.3389/fphys.2019.00314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Prion-like behavior has been in the spotlight since it was first associated with the onset of mammalian neurodegenerative diseases. However, a growing body of evidence suggests that this mechanism could be behind the regulation of processes such as transcription and translation in multiple species. Here, we perform a stringent computational survey to identify prion-like proteins in the human proteome. We detected 242 candidate polypeptides and computationally assessed their function, protein–protein interaction networks, tissular expression, and their link to disease. Human prion-like proteins constitute a subset of modular polypeptides broadly expressed across different cell types and tissues, significantly associated with disease, embedded in highly connected interaction networks, and involved in the flow of genetic information in the cell. Our analysis suggests that these proteins might play a relevant role not only in neurological disorders, but also in different types of cancer and viral infections.
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Affiliation(s)
- Valentin Iglesias
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Teresa Juan-Blanco
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Patrick Aloy
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy.,CNR Institute of Neuroscience, Padua, Italy
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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15
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Abstract
The cellular prion protein, PrPC, is a small, cell surface glycoprotein with a function that is currently somewhat ill defined. It is also the key molecule involved in the family of neurodegenerative disorders called transmissible spongiform encephalopathies, which are also known as prion diseases. The misfolding of PrPC to a conformationally altered isoform, designated PrPTSE, is the main molecular process involved in pathogenesis and appears to precede many other pathologic and clinical manifestations of disease, including neuronal loss, astrogliosis, and cognitive loss. PrPTSE is also believed to be the major component of the infectious "prion," the agent responsible for disease transmission, and preparations of this protein can cause prion disease when inoculated into a naïve host. Thus, understanding the biochemical and biophysical properties of both PrPC and PrPTSE, and ultimately the mechanisms of their interconversion, is critical if we are to understand prion disease biology. Although entire books could be devoted to research pertaining to the protein, herein we briefly review the state of knowledge of prion biochemistry, including consideration of prion protein structure, function, misfolding, and dysfunction.
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Affiliation(s)
- Andrew C Gill
- School of Chemistry, Joseph Banks Laboratories, University of Lincoln, Lincoln, United Kingdom; Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom.
| | - Andrew R Castle
- Division of Neurobiology, The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom
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16
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Wang LJ, Gu XD, Yu GH, Shen L, Ji HF. Different effects of lipid on conformational conversion of chicken and murine prion proteins. Vet Microbiol 2018; 224:1-7. [PMID: 30269782 DOI: 10.1016/j.vetmic.2018.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/09/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Prion diseases are characterized by the conformational conversion of the cellular prion protein (PrPC) to the pathogenic isoform (PrPSc). Lipids have been found to interact with PrPC and contribute to the efficient formation of PrPSc. Non-mammalian PrPs are not readily to undergo the conversion process into an infectious isoform, yet the effect of lipid on the conformational conversion of non-mammalian PrPC remains to be explored. Herein, the effects of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) on full-length recombinant chicken PrP (ChPrP) 24-249 and murine PrP (MoPrP) 23-230 were investigated. Firstly, it was found that in the presence of chemical denaturant, POPG remarkably inhibited MoPrP amyloid fibril growth, while had slight effect on that of ChPrP as estimated by amyloid fibril growth and transmissible electronic microscope assays. Secondly, under physiological condition, POPG induced conformation changes in both MoPrP and ChPrP using Thioflavin T (ThT) fluorescence, circular dichroism, proteinase K digestion and transmission electron microscopy assays. With a POPG:PrP molar ratio of 30:1, the ThT fluorescence of MoPrP was found to be lower than that of ChPrP, however, the POPG-induced MoPrP had higher β-sheet content and was more proteinase K-resistant than POPG-induced ChPrP. In summary, the present results suggested that the effects of POPG on conformational conversion of MoPrP and ChPrP were different under both denaturation and physiological conditions.
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Affiliation(s)
- Li-Juan Wang
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China
| | - Xiao-Dan Gu
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China
| | - Guo-Hua Yu
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, School of Life Sciences, Longyan University, Longyan 364012, China
| | - Liang Shen
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China.
| | - Hong-Fang Ji
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China.
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17
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Taguchi Y, Lu L, Marrero-Winkens C, Otaki H, Nishida N, Schatzl HM. Disulfide-crosslink scanning reveals prion-induced conformational changes and prion strain-specific structures of the pathological prion protein PrP Sc. J Biol Chem 2018; 293:12730-12740. [PMID: 29934306 PMCID: PMC6102138 DOI: 10.1074/jbc.ra117.001633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/15/2018] [Indexed: 11/06/2022] Open
Abstract
Prions are composed solely of the pathological isoform (PrPSc) of the normal cellular prion protein (PrPC). Identification of different PrPSc structures is crucially important for understanding prion biology because the pathogenic properties of prions are hypothesized to be encoded in the structures of PrPSc However, these structures remain yet to be identified, because of the incompatibility of PrPSc with conventional high-resolution structural analysis methods. Previously, we reported that the region between the first and the second α-helix (H1∼H2) of PrPC might cooperate with the more C-terminal side region for efficient interactions with PrPSc From this starting point, we created a series of PrP variants with two cysteine substitutions (C;C-PrP) forming a disulfide-crosslink between H1∼H2 and the distal region of the third helix (Ctrm). We then assessed the conversion capabilities of the C;C-PrP variants in N2a cells infected with mouse-adapted scrapie prions (22L-ScN2a). Specifically, Cys substitutions at residues 165, 166, or 168 in H1∼H2 were combined with cysteine scanning along Ctrm residues 220-229. We found that C;C-PrPs are expressed normally with glycosylation patterns and subcellular localization similar to WT PrP, albeit differing in expression levels. Interestingly, some C;C-PrPs converted to protease-resistant isoforms in the 22L-ScN2a cells, but not in Fukuoka1 prion-infected cells. Crosslink patterns of convertible C;C-PrPs indicated a positional change of H1∼H2 toward Ctrm in PrPSc-induced conformational conversion. Given the properties of the C;C-PrPs reported here, we propose that these PrP variants may be useful tools for investigating prion strain-specific structures and structure-phenotype relationships of PrPSc.
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Affiliation(s)
- Yuzuru Taguchi
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; Department of Molecular Microbiology and Immunology, Division of Cellular and Molecular Biology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan.
| | - Li Lu
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; Calgary Prion Research Unit, University of Calgary, Calgary, Alberta, Canada
| | - Cristobal Marrero-Winkens
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; Calgary Prion Research Unit, University of Calgary, Calgary, Alberta, Canada
| | - Hiroki Otaki
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Division of Cellular and Molecular Biology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Hermann M Schatzl
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; Calgary Prion Research Unit, University of Calgary, Calgary, Alberta, Canada.
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18
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Baral PK, Swayampakula M, Aguzzi A, James MNG. Structural characterization of
POM
6 Fab and mouse prion protein complex identifies key regions for prions conformational conversion. FEBS J 2018; 285:1701-1714. [DOI: 10.1111/febs.14438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/02/2018] [Accepted: 03/16/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Pravas Kumar Baral
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
| | - Mridula Swayampakula
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
| | - Adriano Aguzzi
- Institute of Neuropathology University of Zurich Switzerland
| | - Michael N. G. James
- Department of Biochemistry Faculty of Medicine and Dentistry University of Alberta Edmonton Canada
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19
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Three-Dimensional Domain Swapping Changes the Folding Mechanism of the Forkhead Domain of FoxP1. Biophys J 2017; 110:2349-2360. [PMID: 27276253 DOI: 10.1016/j.bpj.2016.04.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/04/2016] [Accepted: 04/27/2016] [Indexed: 11/20/2022] Open
Abstract
The forkhead family of transcription factors (Fox) controls gene transcription during key processes such as regulation of metabolism, embryogenesis, and immunity. Structurally, Fox proteins feature a conserved DNA-binding domain known as forkhead. Interestingly, solved forkhead structures of members from the P subfamily (FoxP) show that they can oligomerize by three-dimensional domain swapping, whereby structural elements are exchanged between adjacent subunits, leading to an intertwined dimer. Recent evidence has largely stressed the biological relevance of domain swapping in FoxP, as several disease-causing mutations have been related to impairment of this process. Here, we explore the equilibrium folding and binding mechanism of the forkhead domain of wild-type FoxP1, and of two mutants that hinder DNA-binding (R53H) and domain swapping (A39P), using size-exclusion chromatography, circular dichroism, and hydrogen-deuterium exchange mass spectrometry. Our results show that domain swapping of FoxP1 occurs at micromolar protein concentrations within hours of incubation and is energetically favored, in contrast to classical domain-swapping proteins. Also, DNA-binding mutations do not significantly affect domain swapping. Remarkably, equilibrium unfolding of dimeric FoxP1 follows a three-state N2 ↔ 2I ↔ 2U folding mechanism in which dimer dissociation into a monomeric intermediate precedes protein unfolding, in contrast to the typical two-state model described for most domain-swapping proteins, whereas the A39P mutant follows a two-state N ↔ U folding mechanism consistent with the second transition observed for dimeric FoxP1. Also, the free-energy change of the N ↔ U in A39P FoxP1 is ∼2 kcal⋅mol(-1) larger than the I ↔ U transition of both wild-type and R53H FoxP1. Finally, hydrogen-deuterium exchange mass spectrometry reveals that the intermediate strongly resembles the native state. Our results suggest that domain swapping in FoxP1 is at least partially linked to monomer folding stability and follows an unusual three-state folding mechanism, which might proceed via transient structural changes rather than requiring complete protein unfolding as do most domain-swapping proteins.
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20
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Cheng CJ, Koldsø H, Van der Kamp MW, Schiøtt B, Daggett V. Simulations of membrane-bound diglycosylated human prion protein reveal potential protective mechanisms against misfolding. J Neurochem 2017; 142:171-182. [PMID: 28407243 DOI: 10.1111/jnc.14044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/06/2023]
Abstract
Prion diseases are associated with the misfolding of the prion protein (PrP) from its normal cellular form (PrPC ) to its infectious scrapie form (PrPSc ). Post-translational modifications in PrP in vivo can play an important role in modulating the process of misfolding. To gain more insight into the effects of post-translational modifications in PrP structure and dynamics and to test the hypothesis that such modifications can interact with the protein, we have performed molecular dynamics simulations of diglycosylated human PrPC bound to a lipid bilayer via a glycophosphatidylinositol anchor. Multiple simulations were performed at three different pH ranges to explore pH effects on structure and dynamics. In contrast to simulations of protein-only PrPC , no large effects were observed upon lowering the pH of the system. The protein tilted toward the membrane surface in all of the simulations and the putative PrPSc oligomerization sites became inaccessible, thereby offering a possible protective mechanism against PrPSc -induced misfolding of PrPC .
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Affiliation(s)
- Chin Jung Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Heidi Koldsø
- Department of Bioengineering, University of Washington, Seattle, Washington, USA.,Department of Chemistry, inSPIN and iNANO Centers, Aarhus University, Aarhus C, Denmark
| | - Marc W Van der Kamp
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Birgit Schiøtt
- Department of Chemistry, inSPIN and iNANO Centers, Aarhus University, Aarhus C, Denmark
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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21
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Linden R. The Biological Function of the Prion Protein: A Cell Surface Scaffold of Signaling Modules. Front Mol Neurosci 2017; 10:77. [PMID: 28373833 PMCID: PMC5357658 DOI: 10.3389/fnmol.2017.00077] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/06/2017] [Indexed: 12/18/2022] Open
Abstract
The prion glycoprotein (PrPC) is mostly located at the cell surface, tethered to the plasma membrane through a glycosyl-phosphatydil inositol (GPI) anchor. Misfolding of PrPC is associated with the transmissible spongiform encephalopathies (TSEs), whereas its normal conformer serves as a receptor for oligomers of the β-amyloid peptide, which play a major role in the pathogenesis of Alzheimer’s Disease (AD). PrPC is highly expressed in both the nervous and immune systems, as well as in other organs, but its functions are controversial. Extensive experimental work disclosed multiple physiological roles of PrPC at the molecular, cellular and systemic levels, affecting the homeostasis of copper, neuroprotection, stem cell renewal and memory mechanisms, among others. Often each such process has been heralded as the bona fide function of PrPC, despite restricted attention paid to a selected phenotypic trait, associated with either modulation of gene expression or to the engagement of PrPC with a single ligand. In contrast, the GPI-anchored prion protein was shown to bind several extracellular and transmembrane ligands, which are required to endow that protein with the ability to play various roles in transmembrane signal transduction. In addition, differing sets of those ligands are available in cell type- and context-dependent scenarios. To account for such properties, we proposed that PrPC serves as a dynamic platform for the assembly of signaling modules at the cell surface, with widespread consequences for both physiology and behavior. The current review advances the hypothesis that the biological function of the prion protein is that of a cell surface scaffold protein, based on the striking similarities of its functional properties with those of scaffold proteins involved in the organization of intracellular signal transduction pathways. Those properties are: the ability to recruit spatially restricted sets of binding molecules involved in specific signaling; mediation of the crosstalk of signaling pathways; reciprocal allosteric regulation with binding partners; compartmentalized responses; dependence of signaling properties upon posttranslational modification; and stoichiometric requirements and/or oligomerization-dependent impact on signaling. The scaffold concept may contribute to novel approaches to the development of effective treatments to hitherto incurable neurodegenerative diseases, through informed modulation of prion protein-ligand interactions.
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Affiliation(s)
- Rafael Linden
- Laboratory of Neurogenesis, Institute of Biophysics, Federal University of Rio de Janeiro Rio de Janeiro, Brazil
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22
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Small Molecule-Induced Domain Swapping as a Mechanism for Controlling Protein Function and Assembly. Sci Rep 2017; 7:44388. [PMID: 28287617 PMCID: PMC5347425 DOI: 10.1038/srep44388] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/07/2017] [Indexed: 12/22/2022] Open
Abstract
Domain swapping is the process by which identical proteins exchange reciprocal segments to generate dimers. Here we introduce induced domain swapping (INDOS) as a mechanism for regulating protein function. INDOS employs a modular design consisting of the fusion of two proteins: a recognition protein that binds a triggering molecule, and a target protein that undergoes a domain swap in response to binding of the triggering ligand. The recognition protein (FK506 binding protein) is inserted into functionally-inactivated point mutants of two target proteins (staphylococcal nuclease and ribose binding protein). Binding of FK506 to the FKBP domain causes the target domain to first unfold, then refold via domain swap. The inactivating mutations become ‘swapped out’ in the dimer, increasing nuclease and ribose binding activities by 100-fold and 15-fold, respectively, restoring them to near wild-type values. INDOS is intended to convert an arbitrary protein into a functional switch, and is the first example of rational design in which a small molecule is used to trigger protein domain swapping and subsequent activation of biological function.
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23
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Moulick R, Udgaonkar JB. Identification and Structural Characterization of the Precursor Conformation of the Prion Protein which Directly Initiates Misfolding and Oligomerization. J Mol Biol 2017; 429:886-899. [DOI: 10.1016/j.jmb.2017.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
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24
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Taguchi Y, Nishida N. Secondary-structure prediction revisited: Theoretical β-sheet propensity and coil propensity represent structures of amyloids and aid in elucidating phenomena involved in interspecies transmission of prions. PLoS One 2017; 12:e0171974. [PMID: 28199368 PMCID: PMC5310760 DOI: 10.1371/journal.pone.0171974] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/27/2017] [Indexed: 01/18/2023] Open
Abstract
Prions are unique infectious agents, consisting solely of abnormally-folded prion protein (PrPSc). However, they possess virus-like features, including strain diversity, the ability to adapt to new hosts and to be altered evolutionarily. Because prions lack genetic material (DNA and RNA), these biological phenomena have been attributed to the structural properties of PrPSc. Therefore, many structural models of the structure of PrPSc have been proposed based on the limited structural information available, regardless of the incompatibility with high-resolution structural analysis. Recently hypothesized models consist solely of β-sheets and intervening loops/kinks; i.e. parallel in-register β-sheet and β-solenoid models. Owing to the relative simplicity of these structural models of PrPSc, we hypothesized that numerical conversion of the primary structures with a relevant algorithm would enable quantitative comparison between PrPs of distinct primary structures. We therefore used the theoretical values of β-sheet (Pβ) and random-coil (Pc) propensity calculated by secondary structure prediction with a neural network, to analyze interspecies transmission of prions. By reviewing experiments in the literature, we ascertained the biological relevance of Pβ and Pc and found that these classical parameters surprisingly carry substantial information of amyloid structures. We also demonstrated how these parameters could aid in interpreting and explaining phenomena in interspecies transmissions. Our approach can lead to the development of a versatile tool for investigating not only prions but also other amyloids.
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Affiliation(s)
- Yuzuru Taguchi
- Division of Cellular and Molecular Biology, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, JAPAN
- * E-mail:
| | - Noriyuki Nishida
- Division of Cellular and Molecular Biology, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, JAPAN
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25
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Munoz-Montesino C, Sizun C, Moudjou M, Herzog L, Reine F, Igel-Egalon A, Barbereau C, Chapuis J, Ciric D, Laude H, Béringue V, Rezaei H, Dron M. A stretch of residues within the protease-resistant core is not necessary for prion structure and infectivity. Prion 2017; 11:25-30. [PMID: 28281924 DOI: 10.1080/19336896.2016.1274851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mapping out regions of PrP influencing prion conversion remains a challenging issue complicated by the lack of prion structure. The portion of PrP associated with infectivity contains the α-helical domain of the correctly folded protein and turns into a β-sheet-rich insoluble core in prions. Deletions performed so far inside this segment essentially prevented the conversion. Recently we found that deletion of the last C-terminal residues of the helix H2 was fully compatible with prion conversion in the RK13-ovPrP cell culture model, using 3 different infecting strains. This was in agreement with preservation of the overall PrPC structure even after removal of up to one-third of this helix. Prions with internal deletion were infectious for cells and mice expressing the wild-type PrP and they retained prion strain-specific characteristics. We thus identified a piece of the prion domain that is neither necessary for the conformational transition of PrPC nor for the formation of a stable prion structure.
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Affiliation(s)
| | - Christina Sizun
- b Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay , Gif-sur-Yvette , France
| | | | - Laetitia Herzog
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Fabienne Reine
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | | | | | - Jérôme Chapuis
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Danica Ciric
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Hubert Laude
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | | | - Human Rezaei
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Michel Dron
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
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26
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Kovač V, Hafner-Bratkovič I, Čurin Šerbec V. Anchorless forms of prion protein - Impact of truncation on structure destabilization and prion protein conversion. Biochem Biophys Res Commun 2016; 481:1-6. [PMID: 27836542 DOI: 10.1016/j.bbrc.2016.11.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
Abstract
Prion diseases are a group of fatal neurodegenerative diseases caused by scrapie form of prion protein, PrPSc. Prion protein (PrP) is bound to the cell via glycophosphatidylinositol (GPI) anchor. The role of GPI anchor in PrPSc replication and propagation remains unclear. It has been shown that anchorless and truncated PrP accelerate the formation and propagation of prions in vivo and further increases the risk for transmission of prion diseases among species. To explain the role of anchorless forms of PrP in the development of prion diseases, we have prepared five C-terminal PrP truncated variants, determined their thermodynamic properties and analyzed the kinetics of conversion into amyloid fibrils. According to our results thermodynamic and kinetic properties are affected both by pH and truncation. We have shown that the shortest variant was the most destabilized and converted faster than other variants in acidic pH. Other variants converted with longer lag time of fibrillization than WT despite comparable or even decreased stability in acidic pH. Our results indicate that even the change in length for 1 amino acid residue can have a profound effect on in vitro conversion.
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Affiliation(s)
- Valerija Kovač
- Department for the Production of Diagnostic Reagents and Research & R&D Service, Blood Transfusion Centre of Slovenia, Šlajmerjeva 6, SI-1000, Ljubljana, Slovenia
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, 1000, Ljubljana, Slovenia
| | - Vladka Čurin Šerbec
- Department for the Production of Diagnostic Reagents and Research & R&D Service, Blood Transfusion Centre of Slovenia, Šlajmerjeva 6, SI-1000, Ljubljana, Slovenia.
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Fagagnini A, Montioli R, Caloiu A, Ribó M, Laurents DV, Gotte G. Extensive deamidation of RNase A inhibits its oligomerization through 3D domain swapping. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:76-87. [PMID: 27783927 DOI: 10.1016/j.bbapap.2016.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/03/2016] [Accepted: 10/20/2016] [Indexed: 12/27/2022]
Abstract
Bovine pancreatic ribonuclease A (RNase A) is the monomeric prototype of the so-called secretory 'pancreatic-type' RNase super-family. Like the naturally domain-swapped dimeric bovine seminal variant, BS-RNase, and its glycosylated RNase B isoform, RNase A forms N- and C-terminal 3D domain-swapped oligomers after lyophilization from acid solutions, or if subjected to thermal denaturation at high protein concentration. All mentioned RNases can undergo deamidation at Asn67, forming Asp or isoAsp derivatives that modify the protein net charge and consequently its enzymatic activity. In addition, deamidation slightly affects RNase B self-association through the 3D domain swapping (3D-DS) mechanism. We report here the influence of extensive deamidation on RNase A tendency to oligomerize through 3D-DS. In particular, deamidation of Asn67 alone slightly decreases the propensity of the protein to oligomerize, with the Asp derivative being less affected than the isoAsp one. Contrarily, the additional Asp and/or isoAsp conversion of residues other than N67 almost nullifies RNase A oligomerization capability. In addition, Gln deamidation, although less kinetically favorable, may affect RNase A self-association. Using 2D and 3D NMR we identified the Asn/Gln residues most prone to undergo deamidation. Together with CD spectroscopy, NMR also indicates that poly-deamidated RNase A generally maintains its native tertiary structure. Again, we investigated in silico the effect of the residues undergoing deamidation on RNase A dimers structures. Finally, the effect of deamidation on RNase A oligomerization is discussed in comparison with studies on deamidation-prone proteins involved in amyloid formation.
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Affiliation(s)
- Andrea Fagagnini
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Riccardo Montioli
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Andra Caloiu
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, 17071, y Institut d'Investigació Biomèdica de Girona Josep Trueta, (IdIBGi), Girona, Spain
| | - Douglas V Laurents
- Instituto de Quimica Fisica "Rocasolano" (C.S.I.C.), Serrano 119, E-28006 Madrid, Spain
| | - Giovanni Gotte
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
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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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29
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Chamachi NG, Chakrabarty S. Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization. J Phys Chem B 2016; 120:7332-45. [DOI: 10.1021/acs.jpcb.6b03690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Neharika G. Chamachi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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30
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Generating Bona Fide Mammalian Prions with Internal Deletions. J Virol 2016; 90:6963-6975. [PMID: 27226369 DOI: 10.1128/jvi.00555-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 05/14/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Mammalian prions are PrP proteins with altered structures causing transmissible fatal neurodegenerative diseases. They are self-perpetuating through formation of beta-sheet-rich assemblies that seed conformational change of cellular PrP. Pathological PrP usually forms an insoluble protease-resistant core exhibiting beta-sheet structures but no more alpha-helical content, loosing the three alpha-helices contained in the correctly folded PrP. The lack of a high-resolution prion structure makes it difficult to understand the dynamics of conversion and to identify elements of the protein involved in this process. To determine whether completeness of residues within the protease-resistant domain is required for prions, we performed serial deletions in the helix H2 C terminus of ovine PrP, since this region has previously shown some tolerance to sequence changes without preventing prion replication. Deletions of either four or five residues essentially preserved the overall PrP structure and mutant PrP expressed in RK13 cells were efficiently converted into bona fide prions upon challenge by three different prion strains. Remarkably, deletions in PrP facilitated the replication of two strains that otherwise do not replicate in this cellular context. Prions with internal deletion were self-propagating and de novo infectious for naive homologous and wild-type PrP-expressing cells. Moreover, they caused transmissible spongiform encephalopathies in mice, with similar biochemical signatures and neuropathologies other than the original strains. Prion convertibility and transfer of strain-specific information are thus preserved despite shortening of an alpha-helix in PrP and removal of residues within prions. These findings provide new insights into sequence/structure/infectivity relationship for prions. IMPORTANCE Prions are misfolded PrP proteins that convert the normal protein into a replicate of their own abnormal form. They are responsible for invariably fatal neurodegenerative disorders. Other aggregation-prone proteins appear to have a prion-like mode of expansion in brains, such as in Alzheimer's or Parkinson's diseases. To date, the resolution of prion structure remains elusive. Thus, to genetically define the landscape of regions critical for prion conversion, we tested the effect of short deletions. We found that, surprisingly, removal of a portion of PrP, the C terminus of alpha-helix H2, did not hamper prion formation but generated infectious agents with an internal deletion that showed characteristics essentially similar to those of original infecting strains. Thus, we demonstrate that completeness of the residues inside prions is not necessary for maintaining infectivity and the main strain-specific information, while reporting one of the few if not the only bona fide prions with an internal deletion.
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Saijo E, Hughson AG, Raymond GJ, Suzuki A, Horiuchi M, Caughey B. PrPSc-Specific Antibody Reveals C-Terminal Conformational Differences between Prion Strains. J Virol 2016; 90:4905-4913. [PMID: 26937029 PMCID: PMC4859706 DOI: 10.1128/jvi.00088-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/19/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Understanding the structure of PrP(Sc) and its strain variation has been one of the major challenges in prion disease biology. To study the strain-dependent conformations of PrP(Sc), we purified proteinase-resistant PrP(Sc) (PrP(RES)) from mouse brains with three different murine-adapted scrapie strains (Chandler, 22L, and Me7) and systematically tested the accessibility of epitopes of a wide range of anti-PrP and anti-PrP(Sc) specific antibodies by indirect enzyme-linked immunosorbent assay (ELISA). We found that epitopes of most anti-PrP antibodies were hidden in the folded structure of PrP(RES), even though these epitopes are revealed with guanidine denaturation. However, reactivities to a PrP(Sc)-specific conformational C-terminal antibody showed significant differences among the three different prion strains. Our results provide evidence for strain-dependent conformational variation near the C termini of molecules within PrP(Sc) multimers. IMPORTANCE It has long been apparent that prion strains can have different conformations near the N terminus of the PrP(Sc) protease-resistant core. Here, we show that a C-terminal conformational PrP(Sc)-specific antibody reacts differently to three murine-adapted scrapie strains. These results suggest, in turn, that conformational differences in the C terminus of PrP(Sc) also contribute to the phenotypic distinction between prion strains.
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Affiliation(s)
- Eri Saijo
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Andrew G Hughson
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Gregory J Raymond
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Akio Suzuki
- Laboratory of Veterinary Hygiene, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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Nagel-Steger L, Owen MC, Strodel B. An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations. Chembiochem 2016; 17:657-76. [PMID: 26910367 DOI: 10.1002/cbic.201500623] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 12/27/2022]
Abstract
The deposition of amyloid in brain tissue in the context of neurodegenerative diseases involves the formation of intermediate species-termed oligomers-of lower molecular mass and with structures that deviate from those of mature amyloid fibrils. Because these oligomers are thought to be primarily responsible for the subsequent disease pathogenesis, the elucidation of their structure is of enormous interest. Nevertheless, because of the high aggregation propensity and the polydispersity of oligomeric species formed by the proteins or peptides in question, the preparation of appropriate samples for high-resolution structural methods has proven to be rather difficult. This is why theoretical approaches have been of particular importance in gaining insights into possible oligomeric structures for some time. Only recently has it been possible to achieve some progress with regard to the experimentally based structural characterization of defined oligomeric species. Here we discuss how theory and experiment are used to determine oligomer structures and what can be done to improve the integration of the two disciplines.
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Affiliation(s)
- Luitgard Nagel-Steger
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany
| | - Michael C Owen
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany.
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33
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Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Arch Biochem Biophys 2016; 602:116-126. [PMID: 26924596 DOI: 10.1016/j.abb.2016.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.
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34
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Wodak SJ, Malevanets A, MacKinnon SS. The Landscape of Intertwined Associations in Homooligomeric Proteins. Biophys J 2015; 109:1087-100. [PMID: 26340815 DOI: 10.1016/j.bpj.2015.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/06/2015] [Accepted: 08/03/2015] [Indexed: 01/22/2023] Open
Abstract
We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different categories of intertwined associations in known protein structures, their assembly modes, the properties of their interfaces, and their structural plasticity. Furthermore, the current body of knowledge on the so-called three-dimensional domain-swapped systems is reexamined in the context of the wider landscape of intertwined homooligomers, with a particular focus on the mechanistic aspects that underpin intertwined self-association processes in proteins. Insights gained from this integrated overview into the physical and biological roles of intertwining are highlighted.
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Affiliation(s)
- Shoshana J Wodak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; VIB Structural Biology Research Center, Brussels, Belgium.
| | | | - Stephen S MacKinnon
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Cyclica, Inc., Toronto, Ontario, Canada
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35
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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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36
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Liebold J, Winter R, Golbik R, Hause G, Parthier C, Schwarz E. Conformational stability of the RNP domain controls fibril formation of PABPN1. Protein Sci 2015; 24:1789-99. [PMID: 26267866 DOI: 10.1002/pro.2769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 11/07/2022]
Abstract
The disease oculopharyngeal muscular dystrophy is caused by alanine codon trinucleotide expansions in the N-terminal segment of the nuclear poly(A) binding protein PABPN1. As histochemical features of the disease, intranuclear inclusions of PABPN1 have been reported. Whereas the purified N-terminal domain of PABPN1 forms fibrils in an alanine-dependent way, fibril formation of the full-length protein occurs also in the absence of alanines. Here, we addressed the question whether the stability of the RNP domain or domain swapping within the RNP domain may add to fibril formation. A variant of full-length PABPN1 with a stabilizing disulfide bond at position 185/201 in the RNP domain fibrillized in a redox-sensitive manner suggesting that the integrity of the RNP domain may contribute to fibril formation. Thermodynamic analysis of the isolated wild-type and the disulfide-linked RNP domain showed two state unfolding/refolding characteristics without detectable intermediates. Quantification of the thermodynamic stability of the mutant RNP domain pointed to an inverse correlation between fibril formation of full-length PABPN1 and the stability of the RNP domain.
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Affiliation(s)
- Jens Liebold
- Department of Protein Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University, Halle Wittenberg, 06120, Halle, Germany
| | - Reno Winter
- Department of Protein Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University, Halle Wittenberg, 06120, Halle, Germany
| | - Ralph Golbik
- Department of Virology, Institute of Biochemistry and Biotechnology, Martin Luther University, Halle Wittenberg, 06120, Halle, Germany
| | - Gerd Hause
- Biocenter, Martin Luther University, Halle Wittenberg, 06120, Halle, Germany
| | - Christoph Parthier
- Department of Physical Biotechnology, Institute of Biochemistry and Biotechnology, Martin Luther University, Halle Wittenberg, 06120, Halle, Germany
| | - Elisabeth Schwarz
- Department of Protein Biochemistry, Institute of Biochemistry and Biotechnology, Martin Luther University, Halle Wittenberg, 06120, Halle, Germany
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37
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Wong SH, King CY. Amino Acid Proximities in Two Sup35 Prion Strains Revealed by Chemical Cross-linking. J Biol Chem 2015; 290:25062-71. [PMID: 26265470 DOI: 10.1074/jbc.m115.676379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/26/2022] Open
Abstract
Strains of the yeast prion [PSI] are different folding patterns of the same Sup35 protein, which stacks up periodically to form a prion fiber. Chemical cross-linking is employed here to probe different fiber structures assembled with a mutant Sup35 fragment. The photo-reactive cross-linker, p-benzoyl-l-phenylalanine (pBpa), was biosynthetically incorporated into bacterially prepared recombinant Sup(1-61)-GFP, containing the first 61 residues of Sup35, followed by the green fluorescent protein. Four methionine substitutions and two alanine substitutions were introduced at fixed positions in Sup(1-61) to allow cyanogen bromide cleavage to facilitate subsequent mass spectrometry analysis. Amyloid fibers of pBpa and Met/Ala-substituted Sup(1-61)-GFP were nucleated from purified yeast prion particles of two different strains, namely VK and VL, and shown to faithfully transmit specific strain characteristics to yeast expressing the wild type Sup35 protein. Intra- and intermolecular cross-linking were distinguished by tandem mass spectrometry analysis on fibers seeded from solutions containing equal amounts of (14)N- and (15)N-labeled protein. Fibers propagating the VL strain type exhibited intra- and intermolecular cross-linking between amino acid residues 3 and 28, as well as intra- and intermolecular linking between 32 and 55. Inter- and intramolecular cross-linking between residues 32 and 55 were detected in fibers propagating the VK strain type. Adjacencies of amino acid residues in space revealed by cross-linking were used to constrain possible chain folds of different [PSI] strains.
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Affiliation(s)
- Shenq-Huey Wong
- From the Molecular Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan and the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Yen King
- the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
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38
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Davis PJ, Holmes D, Waltho JP, Staniforth RA. Limited Proteolysis Reveals That Amyloids from the 3D Domain-Swapping Cystatin B Have a Non-Native β-Sheet Topology. J Mol Biol 2015; 427:2418-2434. [DOI: 10.1016/j.jmb.2015.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/08/2015] [Accepted: 05/15/2015] [Indexed: 01/21/2023]
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39
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Yuan Z, Yang L, Chen B, Zhu T, Hassan MF, Yin X, Zhou X, Zhao D. Protein misfolding cyclic amplification induces the conversion of recombinant prion protein to PrP oligomers causing neuronal apoptosis. J Neurochem 2015; 133:722-9. [DOI: 10.1111/jnc.13098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/12/2015] [Accepted: 03/15/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Zhen Yuan
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Lifeng Yang
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Baian Chen
- Department of Laboratory Animal Science; School of Basic Medical Science; Capital Medical University; Beijing China
| | - Ting Zhu
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Mohammad Farooque Hassan
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Xiaomin Yin
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Xiangmei Zhou
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
| | - Deming Zhao
- State Key Laboratories for Agrobiotechnology; Key Lab of Animal Epidemiology and Zoonosis; Ministry of Agriculture; National Animal Transmissible Spongiform Encephalopathy Laboratory; College of Veterinary Medicine; China Agricultural University; Beijing China
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40
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Nagao S, Ueda M, Osuka H, Komori H, Kamikubo H, Kataoka M, Higuchi Y, Hirota S. Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551: structural insights into domain swapping of cytochrome c family proteins. PLoS One 2015; 10:e0123653. [PMID: 25853415 PMCID: PMC4390240 DOI: 10.1371/journal.pone.0123653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/23/2015] [Indexed: 02/06/2023] Open
Abstract
Cytochrome c (cyt c) family proteins, such as horse cyt c, Pseudomonas aeruginosa cytochrome c551 (PA cyt c551), and Hydrogenobacter thermophilus cytochrome c552 (HT cyt c552), have been used as model proteins to study the relationship between the protein structure and folding process. We have shown in the past that horse cyt c forms oligomers by domain swapping its C-terminal helix, perturbing the Met–heme coordination significantly compared to the monomer. HT cyt c552 forms dimers by domain swapping the region containing the N-terminal α-helix and heme, where the heme axial His and Met ligands belong to different protomers. Herein, we show that PA cyt c551 also forms domain-swapped dimers by swapping the region containing the N-terminal α-helix and heme. The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping. The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins. These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.
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Affiliation(s)
- Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916–5 Takayama, Ikoma, Nara 630–0192, Japan
| | - Mariko Ueda
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916–5 Takayama, Ikoma, Nara 630–0192, Japan
| | - Hisao Osuka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916–5 Takayama, Ikoma, Nara 630–0192, Japan
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678–1297, Japan
| | - Hirofumi Komori
- Faculty of Education, Kagawa University, 1–1 Saiwai-cho, Takamatsu, Kagawa 760–8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679–5148, Japan
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916–5 Takayama, Ikoma, Nara 630–0192, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916–5 Takayama, Ikoma, Nara 630–0192, Japan
| | - Yoshiki Higuchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678–1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679–5148, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916–5 Takayama, Ikoma, Nara 630–0192, Japan
- * E-mail:
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Cheng CJ, Daggett V. Different misfolding mechanisms converge on common conformational changes: human prion protein pathogenic mutants Y218N and E196K. Prion 2015; 8:125-35. [PMID: 24509603 DOI: 10.4161/pri.27807] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Prion diseases are caused by misfolding and aggregation of the prion protein (PrP). Pathogenic mutations such as Y218N and E196K are known to cause Gerstmann-Sträussler-Scheinker syndrome and Creutzfeldt-Jakob disease, respectively. Here we describe molecular dynamics simulations of these mutant proteins to better characterize the detailed conformational effects of these sequence substitutions. Our results indicate that the mutations disrupt the wild-type native PrP(C) structure and cause misfolding. Y218N reduced hydrophobic packing around the X-loop (residues 165-171), and E196K abolished an important wild-type salt bridge. While differences in the mutation site led PrP mutants to misfold along different pathways, we observed multiple traits of misfolding that were common to both mutants. Common traits of misfolding included: 1) detachment of the short helix (HA) from the PrP core; 2) exposure of side chain F198; and 3) formation of a nonnative strand at the N-terminus. The effect of the E196K mutation directly abolished the wild-type salt bridge E196-R156, which further destabilized the F198 hydrophobic pocket and HA. The Y218N mutation propagated its effect by increasing the HB-HC interhelical angle, which in turn disrupted the packing around F198. Furthermore, a nonnative contact formed between E221 and S132 on the S1-HA loop, which offered a direct mechanism for disrupting the hydrophobic packing between the S1-HA loop and HC. While there were common misfolding features shared between Y218N and E196K, the differences in the orientation of HB and HC and the X-loop conformation might provide a structural basis for identifying different prion strains.
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Electrostatic effects in the folding of the SH3 domain of the c-Src tyrosine kinase: pH-dependence in 3D-domain swapping and amyloid formation. PLoS One 2014; 9:e113224. [PMID: 25490095 PMCID: PMC4260792 DOI: 10.1371/journal.pone.0113224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/20/2014] [Indexed: 11/19/2022] Open
Abstract
The SH3 domain of the c-Src tyrosine kinase (c-Src-SH3) aggregates to form intertwined dimers and amyloid fibrils at mild acid pHs. In this work, we show that a single mutation of residue Gln128 of this SH3 domain has a significant effect on: (i) its thermal stability; and (ii) its propensity to form amyloid fibrils. The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH, while Gln128Lys and Gln128Arg mutants do not form these aggregates under any of the conditions assayed. We have also solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6522 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P212121, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. Analysis of these crystallographic structures shows that the residue at position 128 is connected to Glu106 at the diverging β-turn through a cluster of water molecules. Changes in this hydrogen-bond network lead to the displacement of the c-Src-SH3 distal loop, resulting also in conformational changes of Leu100 that might be related to the binding of proline rich motifs. Our findings show that electrostatic interactions and solvation of residues close to the folding nucleation site of the c-Src-SH3 domain might play an important role during the folding reaction and the amyloid fibril formation.
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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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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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45
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Roucou X. Regulation of PrP(C) signaling and processing by dimerization. Front Cell Dev Biol 2014; 2:57. [PMID: 25364762 PMCID: PMC4207009 DOI: 10.3389/fcell.2014.00057] [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] [Received: 08/04/2014] [Accepted: 09/19/2014] [Indexed: 12/15/2022] Open
Abstract
The cellular prion protein (PrPC) is a glycosylphosphatidylinositol (GPI)-anchored protein present at the cell surface. PrPC N-terminal moiety is intrinsically disordered and is able to interact with a variety of ligands. Physiological ligands have neurotrophic activity, whilst others, including protein toxic oligomers, have neurotoxic functions. These two opposite activities involve different interacting partners and result from different PrPC-activated signaling pathways. Remarkably, PrPC may be inactivated either by physiological endoproteolysis and release of the N-terminal domain, or by ectodomain shedding. Ligand-induced PrPC dimerization or enforced dimerization of PrPC indicate that PrPC dimerization represents an important molecular switch for both intracellular signaling and inactivation by the release of PrPC N-terminal domain or shedding. In this review, we summarize evidence that cell surface receptor activity of PrPC is finely regulated by dimerization.
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Affiliation(s)
- Xavier Roucou
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke Sherbrooke, QC, Canada
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46
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Groveman BR, Dolan MA, Taubner LM, Kraus A, Wickner RB, Caughey B. Parallel in-register intermolecular β-sheet architectures for prion-seeded prion protein (PrP) amyloids. J Biol Chem 2014; 289:24129-42. [PMID: 25028516 DOI: 10.1074/jbc.m114.578344] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structures of the infectious form of prion protein (e.g. PrP(Sc) or PrP-Scrapie) remain poorly defined. The prevalent structural models of PrP(Sc) retain most of the native α-helices of the normal, noninfectious prion protein, cellular prion protein (PrP(C)), but evidence is accumulating that these helices are absent in PrP(Sc) amyloid. Moreover, recombinant PrP(C) can form amyloid fibrils in vitro that have parallel in-register intermolecular β-sheet architectures in the domains originally occupied by helices 2 and 3. Here, we provide solid-state NMR evidence that the latter is also true of initially prion-seeded recombinant PrP amyloids formed in the absence of denaturants. These results, in the context of a primarily β-sheet structure, led us to build detailed models of PrP amyloid based on parallel in-register architectures, fibrillar shapes and dimensions, and other available experimentally derived conformational constraints. Molecular dynamics simulations of PrP(90-231) octameric segments suggested that such linear fibrils, which are consistent with many features of PrP(Sc) fibrils, can have stable parallel in-register β-sheet cores. These simulations revealed that the C-terminal residues ∼124-227 more readily adopt stable tightly packed structures than the N-terminal residues ∼90-123 in the absence of cofactors. Variations in the placement of turns and loops that link the β-sheets could give rise to distinct prion strains capable of faithful template-driven propagation. Moreover, our modeling suggests that single PrP monomers can comprise the entire cross-section of fibrils that have previously been assumed to be pairs of laterally associated protofilaments. Together, these insights provide a new basis for deciphering mammalian prion structures.
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Affiliation(s)
- Bradley R Groveman
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
| | - Michael A Dolan
- the Computational Biology Section, Bioinformatics and Computational Biosciences Branch, NIAID, and
| | - Lara M Taubner
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
| | - Allison Kraus
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
| | - Reed B Wickner
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Byron Caughey
- From the Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840 and
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47
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Vieira TCRG, Cordeiro Y, Caughey B, Silva JL. Heparin binding confers prion stability and impairs its aggregation. FASEB J 2014; 28:2667-76. [PMID: 24648544 DOI: 10.1096/fj.13-246777] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The conversion of the prion protein (PrP) into scrapie PrP (PrP(Sc)) is a central event in prion diseases. Several molecules work as cofactors in the conversion process, including glycosaminoglycans (GAGs). GAGs exhibit a paradoxical effect, as they convert PrP into protease-resistant PrP (PrP-res) but also exert protective activity. We compared the stability and aggregation propensity of PrP and the heparin-PrP complex through the application of different in vitro aggregation approaches, including real-time quaking-induced conversion (RT-QuIC). Transmissible spongiform encephalopathy-associated forms from mouse and hamster brain homogenates were used to seed RT-QuIC-induced fibrillization. In our study, interaction between heparin and cellular PrP (PrP(C)) increased thermal PrP stability, leading to an 8-fold decrease in temperature-induced aggregation. The interaction of low-molecular-weight heparin (LMWHep) with the PrP N- or C-terminal domain affected not only the extent of PrP fibrillization but also its kinetics, lowering the reaction rate constant from 1.04 to 0.29 s(-1) and increasing the lag phase from 12 to 19 h in RT-QuIC experiments. Our findings explain the protective effect of heparin in different models of prion and prion-like neurodegenerative diseases and establish the groundwork for the development of therapeutic strategies based on GAGs.
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Affiliation(s)
- Tuane C R G Vieira
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica Leopoldo De Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, and
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; and
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, Hamilton, Montana, USA
| | - Jerson L Silva
- Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Instituto de Bioquímica Médica Leopoldo De Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, and
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48
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Cheng CJ, Daggett V. Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH. Biomolecules 2014; 4:181-201. [PMID: 24970211 PMCID: PMC4030982 DOI: 10.3390/biom4010181] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/07/2014] [Accepted: 02/09/2014] [Indexed: 12/24/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE), or mad cow disease, is a fatal neurodegenerative disease that is transmissible to humans and that is currently incurable. BSE is caused by the prion protein (PrP), which adopts two conformers; PrPC is the native innocuous form, which is α-helix rich; and PrPSc is the β-sheet rich misfolded form, which is infectious and forms neurotoxic species. Acidic pH induces the conversion of PrPC to PrPSc. We have performed molecular dynamics simulations of bovine PrP at various pH regimes. An acidic pH environment induced conformational changes that were not observed in neutral pH simulations. Putative misfolded structures, with nonnative β-strands formed in the flexible N-terminal domain, were found in acidic pH simulations. Two distinct pathways were observed for the formation of nonnative β-strands: at low pH, hydrophobic contacts with M129 nucleated the nonnative β-strand; at mid-pH, polar contacts involving Q168 and D178 facilitated the formation of a hairpin at the flexible N-terminus. These mid- and low pH simulations capture the process of nonnative β-strand formation, thereby improving our understanding of how PrPC misfolds into the β-sheet rich PrPSc and how pH factors into the process.
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Affiliation(s)
- Chin Jung Cheng
- Department of Bioengineering, University of Washington, Seattle WA 98195-5013, USA.
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle WA 98195-5013, USA.
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49
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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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50
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Thakkar SV, Sahni N, Joshi SB, Kerwin BA, He F, Volkin DB, Middaugh CR. Understanding the relevance of local conformational stability and dynamics to the aggregation propensity of an IgG1 and IgG2 monoclonal antibodies. Protein Sci 2013; 22:1295-305. [PMID: 23893936 DOI: 10.1002/pro.2316] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/27/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022]
Abstract
Aggregation of monoclonal antibodies is often a multi-step process involving structural alterations in monomeric proteins and subsequent formation of soluble or insoluble oligomers. The role of local conformational stability and dynamics of native and/or partially altered structures in determining the aggregation propensity of monoclonal antibodies, however, is not well understood. Here, we investigate the role of conformational stability and dynamics of regions with distinct solvent exposure in determining the aggregation propensity of an IgG1 and IgG2 monoclonal antibody. The temperatures employed span the pre-unfolding range (10-40°C) and the onset temperatures (T onset ) for exposure of apolar residues (≈ 50°C), alterations in secondary structures (≈ 60°C) and initiation of visible aggregate formation (≈ 60°C). Solvent-exposed regions were found to precede solvent-shielded regions in an initiation of aggregation for both proteins. Such a process was observed upon alterations in overall tertiary structure while retaining the secondary structures in both the proteins. In addition, a greater dynamic nature of solvent-shielded regions in potential intermediates of IgG1 and the improved conformational stability increased its resistance to aggregation when compared to IgG2. These results suggest that local conformational stability and fluctuations of partially altered structures can influence the aggregation propensity of immunoglobulins.
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Affiliation(s)
- Santosh V Thakkar
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, USA
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