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Jheng CP, Lee CI. Combination of structure-based virtual screening, molecular docking and molecular dynamics approaches for the discovery of anti-prion fibril flavonoids. Front Mol Biosci 2023; 9:1088733. [PMID: 36685276 PMCID: PMC9849400 DOI: 10.3389/fmolb.2022.1088733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Prion diseases are a group of rare neurodegenerative diseases caused by the structural conversion of cellular prion into Scrapie prion resulting aggregated fibrils. Therapy of prion diseases has been developed for several decades, especially drug designs based on the structure of prion monomers. Unfortunately, none of the designed anti-prion drugs function well clinically. To fight against prion fibrils, a drug design based on the precise structure of mammalian prion fibrils is highly required. Fortunately, based on the advantage of newly advanced cryo-electron microscopy (cryo-EM) in the deconvolution of large complexes, three prion fibril structures were resolved in the last 2 years. Based on the cryo-EM solved prion fibril structures, we are able to find some molecules fighting against prion fibrils. Quercetin, one flavonoid molecule in the polyphenol group, has been found to disaggregate the prion fibrils in vitro. In this study, we performed the molecular docking and molecular dynamics simulation on quercetin-like molecules possessing pharmacological properties to evaluate the anti-prion ability of tested molecules. As a result, four quercetin-like molecules interact with prion fibril and decrease the β-strand content by converting some β-strands into loop and helical structures to disintegrate the existing fibril structure. The results of this study are significant in the treatment of prion diseases, and the approaches used in this study are applicable to other amyloid diseases.
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Affiliation(s)
- Cheng-Ping Jheng
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan
| | - Cheng-I Lee
- Department of Biomedical Sciences, National Chung Cheng University, Chia-Yi, Taiwan,Center for Nano Bio-Detections, National Chung Cheng University, Chia-Yi, Taiwan,Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Chia-Yi, Taiwan,*Correspondence: Cheng-I Lee,
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2
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Silva CJ. Chronic Wasting Disease (CWD) in Cervids and the Consequences of a Mutable Protein Conformation. ACS OMEGA 2022; 7:12474-12492. [PMID: 35465121 PMCID: PMC9022204 DOI: 10.1021/acsomega.2c00155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/18/2022] [Indexed: 05/15/2023]
Abstract
Chronic wasting disease (CWD) is a prion disease of cervids (deer, elk, moose, etc.). It spreads readily from CWD-contaminated environments and among wild cervids. As of 2022, North American CWD has been found in 29 states, four Canadian provinces and South Korea. The Scandinavian form of CWD originated independently. Prions propagate their pathology by inducing a natively expressed prion protein (PrPC) to adopt the prion conformation (PrPSc). PrPC and PrPSc differ solely in their conformation. Like other prion diseases, transmissible CWD prions can arise spontaneously. The CWD prions can respond to selection pressures resulting in the emergence of new strain phenotypes. Annually, 11.5 million Americans hunt and harvest nearly 6 million deer, indicating that CWD is a potential threat to an important American food source. No tested CWD strain has been shown to be zoonotic. However, this may not be true for emerging strains. Should a zoonotic CWD strain emerge, it could adversely impact the hunting economy and game meat consumers.
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Affiliation(s)
- Christopher J. Silva
- Produce Safety & Microbiology
Research Unit, Western Regional Research Center, Agricultural Research
Service, United States Department of Agriculture, Albany, California 94710, United States of America
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3
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Yang W, Kim BS, Muniyappan S, Lee YH, Kim JH, Yu W. Aggregation-Prone Structural Ensembles of Transthyretin Collected With Regression Analysis for NMR Chemical Shift. Front Mol Biosci 2021; 8:766830. [PMID: 34746240 PMCID: PMC8568061 DOI: 10.3389/fmolb.2021.766830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
Monomer dissociation and subsequent misfolding of the transthyretin (TTR) is one of the most critical causative factors of TTR amyloidosis. TTR amyloidosis causes several human diseases, such as senile systemic amyloidosis and familial amyloid cardiomyopathy/polyneuropathy; therefore, it is important to understand the molecular details of the structural deformation and aggregation mechanisms of TTR. However, such molecular characteristics are still elusive because of the complicated structural heterogeneity of TTR and its highly sensitive nature to various environmental factors. Several nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) studies of TTR variants have recently reported evidence of transient aggregation-prone structural states of TTR. According to these studies, the stability of the DAGH β-sheet, one of the two main β-sheets in TTR, is a crucial determinant of the TTR amyloidosis mechanism. In addition, its conformational perturbation and possible involvement of nearby structural motifs facilitates TTR aggregation. This study proposes aggregation-prone structural ensembles of TTR obtained by MD simulation with enhanced sampling and a multiple linear regression approach. This method provides plausible structural models that are composed of ensemble structures consistent with NMR chemical shift data. This study validated the ensemble models with experimental data obtained from circular dichroism (CD) spectroscopy and NMR order parameter analysis. In addition, our results suggest that the structural deformation of the DAGH β-sheet and the AB loop regions may correlate with the manifestation of the aggregation-prone conformational states of TTR. In summary, our method employing MD techniques to extend the structural ensembles from NMR experimental data analysis may provide new opportunities to investigate various transient yet important structural states of amyloidogenic proteins.
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Affiliation(s)
- Wonjin Yang
- Department of Brain and Cognitive Sciences, DGIST, Daegu, South Korea
| | - Beom Soo Kim
- Department of Brain and Cognitive Sciences, DGIST, Daegu, South Korea
| | | | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, South Korea.,Department of Bio-analytical Science, University of Science and Technology, Daejeon, South Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea.,Research Headquarters, Korea Brain Research Institute, Daegu, South Korea
| | - Jin Hae Kim
- Department of New Biology, DGIST, Daegu, South Korea
| | - Wookyung Yu
- Department of Brain and Cognitive Sciences, DGIST, Daegu, South Korea.,Core Protein Resources Center, DGIST, Daegu, South Korea
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4
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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: 114] [Impact Index Per Article: 38.0] [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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5
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Wang LQ, Zhao K, Yuan HY, Li XN, Dang HB, Ma Y, Wang Q, Wang C, Sun Y, Chen J, Li D, Zhang D, Yin P, Liu C, Liang Y. Genetic prion disease-related mutation E196K displays a novel amyloid fibril structure revealed by cryo-EM. SCIENCE ADVANCES 2021; 7:eabg9676. [PMID: 34516876 PMCID: PMC8442898 DOI: 10.1126/sciadv.abg9676] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Prion diseases are caused by the conformational conversion of prion protein (PrP). Forty-two different mutations were identified in human PrP, leading to genetic prion diseases with distinct clinical syndromes. Here, we report the cryo–electron microscopy structure of an amyloid fibril formed by full-length human PrP with E196K mutation, a genetic Creutzfeldt-Jakob disease–related mutation. This mutation disrupts key interactions in the wild-type PrP fibril, forming an amyloid fibril with a conformation distinct from the wild-type PrP fibril and hamster brain–derived prion fibril. The E196K fibril consists of two protofibrils. Each subunit forms five β strands stabilized by a disulfide bond and an unusual hydrophilic cavity stabilized by a salt bridge. Four pairs of amino acids from opposing subunits form four salt bridges to stabilize the zigzag interface of the two protofibrils. Our results provide structural evidences of the diverse prion strains and highlight the importance of familial mutations in inducing different strains.
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Affiliation(s)
- Li-Qiang Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kun Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Han-Ye Yuan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiang-Ning Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hai-Bin Dang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yeyang Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Chen Wang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Sun
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dan Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yi Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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7
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Kamali-Jamil R, Vázquez-Fernández E, Tancowny B, Rathod V, Amidian S, Wang X, Tang X, Fang A, Senatore A, Hornemann S, Dudas S, Aguzzi A, Young HS, Wille H. The ultrastructure of infectious L-type bovine spongiform encephalopathy prions constrains molecular models. PLoS Pathog 2021; 17:e1009628. [PMID: 34061899 PMCID: PMC8195424 DOI: 10.1371/journal.ppat.1009628] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/11/2021] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE) is a prion disease of cattle that is caused by the misfolding of the cellular prion protein (PrPC) into an infectious conformation (PrPSc). PrPC is a predominantly α-helical membrane protein that misfolds into a β-sheet rich, infectious state, which has a high propensity to self-assemble into amyloid fibrils. Three strains of BSE prions can cause prion disease in cattle, including classical BSE (C-type) and two atypical strains, named L-type and H-type BSE. To date, there is no detailed information available about the structure of any of the infectious BSE prion strains. In this study, we purified L-type BSE prions from transgenic mouse brains and investigated their biochemical and ultrastructural characteristics using electron microscopy, image processing, and immunogold labeling techniques. By using phosphotungstate anions (PTA) to precipitate PrPSc combined with sucrose gradient centrifugation, a high yield of proteinase K-resistant BSE amyloid fibrils was obtained. A morphological examination using electron microscopy, two-dimensional class averages, and three-dimensional reconstructions revealed two structural classes of L-type BSE amyloid fibrils; fibrils that consisted of two protofilaments with a central gap and an average width of 22.5 nm and one-protofilament fibrils that were 10.6 nm wide. The one-protofilament fibrils were found to be more abundant compared to the thicker two-protofilament fibrils. Both fibrillar assemblies were successfully decorated with monoclonal antibodies against N- and C-terminal epitopes of PrP using immunogold-labeling techniques, confirming the presence of polypeptides that span residues 100-110 to 227-237. The fact that the one-protofilament fibrils contain both N- and C-terminal PrP epitopes constrains molecular models for the structure of the infectious conformer in favour of a compact four-rung β-solenoid fold.
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Affiliation(s)
- Razieh Kamali-Jamil
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Ester Vázquez-Fernández
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Brian Tancowny
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Vineet Rathod
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Xiongyao Wang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Xinli Tang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew Fang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Assunta Senatore
- Institute of Neuropathology, University of Zürich, Zürich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University of Zürich, Zürich, Switzerland
| | - Sandor Dudas
- Canadian BSE Reference Laboratory, Canadian Food Inspection Agency, Lethbridge Laboratory, Lethbridge, Alberta, Canada
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zürich, Zürich, Switzerland
| | - Howard S. Young
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, Canada
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Noor A, Zafar S, Zerr I. Neurodegenerative Proteinopathies in the Proteoform Spectrum-Tools and Challenges. Int J Mol Sci 2021; 22:1085. [PMID: 33499319 PMCID: PMC7865347 DOI: 10.3390/ijms22031085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
Proteinopathy refers to a group of disorders defined by depositions of amyloids within living tissue. Neurodegenerative proteinopathies, including Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease, and others, constitute a large fraction of these disorders. Amyloids are highly insoluble, ordered, stable, beta-sheet rich proteins. The emerging theory about the pathophysiology of neurodegenerative proteinopathies suggests that the primary amyloid-forming proteins, also known as the prion-like proteins, may exist as multiple proteoforms that contribute differentially towards the disease prognosis. It is therefore necessary to resolve these disorders on the level of proteoforms rather than the proteome. The transient and hydrophobic nature of amyloid-forming proteins and the minor post-translational alterations that lead to the formation of proteoforms require the use of highly sensitive and specialized techniques. Several conventional techniques, like gel electrophoresis and conventional mass spectrometry, have been modified to accommodate the proteoform theory and prion-like proteins. Several new ones, like imaging mass spectrometry, have also emerged. This review aims to discuss the proteoform theory of neurodegenerative disorders along with the utility of these proteomic techniques for the study of highly insoluble proteins and their associated proteoforms.
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Affiliation(s)
- Aneeqa Noor
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Saima Zafar
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Bolan Road, H-12, 44000 Islamabad, Pakistan
| | - Inga Zerr
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
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