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Lee CH, Saw JE, Chen EHL, Wang CH, Uchihashi T, Chen RPY. The Positively Charged Cluster in the N-terminal Disordered Region may Affect Prion Protein Misfolding: Cryo-EM Structure of Hamster PrP(23-144) Fibrils. J Mol Biol 2024; 436:168576. [PMID: 38641239 DOI: 10.1016/j.jmb.2024.168576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
Prions, the misfolding form of prion proteins, are contagious proteinaceous macromolecules. Recent studies have shown that infectious prion fibrils formed in the brain and non-infectious fibrils formed from recombinant prion protein in a partially denaturing condition have distinct structures. The amyloid core of the in vitro-prepared non-infectious fibrils starts at about residue 160, while that of infectious prion fibrils formed in the brain involves a longer sequence (residues ∼90-230) of structural conversion. The C-terminal truncated prion protein PrP(23-144) can form infectious fibrils under certain conditions and cause disease in animals. In this study, we used cryogenic electron microscopy (cryo-EM) to resolve the structure of hamster sHaPrP(23-144) fibrils prepared at pH 3.7. This 2.88 Å cryo-EM structure has an amyloid core covering residues 94-144. It comprises two protofilaments, each containing five β-strands arranged as a long hairpin plus an N-terminal β-strand. This N-terminal β-strand resides in a positively charged cluster region (named PCC2; sequence 96-111), which interacts with the turn region of the opposite protofilaments' hairpin to stabilize the fibril structure. Interestingly, this sHaPrP(23-144) fibril structure differs from a recently reported structure formed by the human or mouse counterpart at pH 6.5. Moreover, sHaPrP(23-144) fibrils have many structural features in common with infectious prions. Whether this structure is infectious remains to be determined. More importantly, the sHaPrP(23-144) structure is different from the sHaPrP(108-144) fibrils prepared in the same fibrillization buffer, indicating that the N-terminal disordered region, possibly the positively charged cluster, influences the misfolding pathway of the prion protein.
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Affiliation(s)
- Chih-Hsuan Lee
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei 115, Taiwan
| | - Jing-Ee Saw
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei 106, Taiwan
| | - Eric H-L Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei 115, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei 115, Taiwan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya 464-8602, Japan; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya 464-8602, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd, Taipei 106, Taiwan; Neuroscience Program of Academia Sinica, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei 115, Taiwan.
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Ziaunys M, Mikalauskaite K, Krasauskas L, Smirnovas V. Conformation-Specific Association of Prion Protein Amyloid Aggregates with Tau Protein Monomers. Int J Mol Sci 2023; 24:ijms24119277. [PMID: 37298227 DOI: 10.3390/ijms24119277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Protein aggregation into amyloid fibrils is associated with several amyloidoses, including neurodegenerative Alzheimer's and Parkinson's diseases. Despite years of research and numerous studies, the process is still not fully understood, which significantly impedes the search for cures of amyloid-related disorders. Recently, there has been an increase in reports of amyloidogenic protein cross-interactions during the fibril formation process, which further complicates the already intricate process of amyloid aggregation. One of these reports displayed an interaction involving Tau and prion proteins, which prompted a need for further investigation into the matter. In this work, we generated five populations of conformationally distinct prion protein amyloid fibrils and examined their interaction with Tau proteins. We observed that there was a conformation-specific association between Tau monomers and prion protein fibrils, which increased the aggregate self-association and amyloidophilic dye binding capacity. We also determined that the interaction did not induce the formation of Tau protein amyloid aggregates, but rather caused their electrostatic adsorption to the prion protein fibril surface.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Lukas Krasauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
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Zhang T, Pan Y, Kandapal S, Sun X, Xu B. Following the Aggregation of Human Prion Protein on Heparin Functionalized Gold Surface in Real Time. ACS APPLIED BIO MATERIALS 2022; 5:5457-5464. [PMID: 36228282 DOI: 10.1021/acsabm.2c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The aggregation of the prion protein (PrP) plays a key role in the development of prion diseases and is believed to be an autocatalytic process with a very high kinetic barrier. Intensive studies have focused on overcoming the kinetic barriers under extremely nonphysiological in vitro conditions by altering the pH of PrP solution on solid surfaces, such as gold, mica, and a lipid bilayer. Importantly, sulfated glycosaminoglycans (GAGs), including heparin, were found to be associated with PrP misfolding and aggregation, suggesting GAGs have catalytic roles in PrP aggregation processes. However, the exact role and details of GAGs in the PrP aggregation are not clear and need a thorough perusal. Here, we investigate the PrP aggregation process on a heparin functionalized gold surface by in situ, real-time monitoring of the atomic scale details of the whole aggregation process by single molecule atomic force microscopy (AFM), combining simultaneous topographic and recognition (TREC) imaging and single molecule force spectroscopy (SMFS). We observed the whole aggregation process for full-length human recombinant PrP (23-231) aggregation on the heparin modified gold surface, from the formation of oligomers, to the assembly of protofibrils and short fibers, and the formation of elongated mature fibers. Heparin is found to promote the PrP aggregation by facilitating the formation of oligomers during the early nucleation stage.
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Affiliation(s)
- Tong Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Yangang Pan
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Sneha Kandapal
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Xin Sun
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
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Chen EHL, Kao HW, Lee CH, Huang JYC, Wu KP, Chen RPY. 2.2 Å Cryo-EM Tetra-Protofilament Structure of the Hamster Prion 108-144 Fibril Reveals an Ordered Water Channel in the Center. J Am Chem Soc 2022; 144:13888-13894. [PMID: 35857020 DOI: 10.1021/jacs.2c05479] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based on the gold-standard Fourier shell correlation (FSC) curve. The fibril has a novel architecture that has never been found in other amyloid fibrils. Each fibril is assembled by four protofilaments (PFs) and has an ordered water channel in the center. Each protofilament contains three β-strands (125-130, 133-135, and 138-141) arranged in an "R"-shaped construct. The structural data indicate that these three β-strand segments are the most amyloidogenic region of the prion peptide/protein and might be the site of nucleation during fibrillization under conditions without denaturants.
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Affiliation(s)
- Eric H-L Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan
| | - Hsi-Wen Kao
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan
| | - Chih-Hsuan Lee
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Jessica Y C Huang
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.,Neuroscience Program of Academia Sinica, Academia Sinica, No. 128, Section 2, Academia Road, Nankang, Taipei 115, Taiwan
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Chu BK, Tsai R, Hung C, Kuo Y, Chen EH, Chiang Y, Chan SI, Chen RP. Location of the cross‐β structure in prion fibrils: A search by seeding and electron spin resonance spectroscopy. Protein Sci 2022; 31:e4326. [DOI: 10.1002/pro.4326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Brett K.‐Y. Chu
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - Ruei‐Fong Tsai
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Chien‐Lun Hung
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Yun‐Hsuan Kuo
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Eric H.‐L. Chen
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
| | - Yun‐Wei Chiang
- Department of Chemistry National Tsing Hua University Hsinchu Taiwan
| | - Sunney I. Chan
- Department of Chemistry National Taiwan University Taipei Taiwan
- Institute of Chemistry Academia Sinica Taipei Taiwan
| | - Rita P.‐Y. Chen
- Institute of Biological Chemistry Academia Sinica Taipei Taiwan
- Institute of Biochemical Sciences National Taiwan University Taipei Taiwan
- Neuroscience Program of Academia Sinica Academia Sinica Taipei Taiwan
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