1
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Pal S, Udgaonkar JB. Slow Misfolding of a Molten Globule form of a Mutant Prion Protein Variant into a β-rich Dimer. J Mol Biol 2024; 436:168736. [PMID: 39097185 DOI: 10.1016/j.jmb.2024.168736] [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: 05/27/2024] [Revised: 07/13/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Misfolding of the prion protein is linked to multiple neurodegenerative diseases. A better understanding of the process requires the identification and structural characterization of intermediate conformations via which misfolding proceeds. In this study, three conserved aromatic residues (Tyr168, Phe174, and Tyr217) located in the C-terminal domain of mouse PrP (wt moPrP) were mutated to Ala. The resultant mutant protein, 3A moPrP, is shown to adopt a molten globule (MG)-like native conformation. Hydrogen-deuterium exchange studies coupled with mass spectrometry revealed that for 3A moPrP, the free energy gap between the MG-like native conformation and misfolding-prone partially unfolded forms is reduced. Consequently, 3A moPrP misfolds in native conditions even in the absence of salt, unlike wt moPrP, which requires the addition of salt to misfold. 3A moPrP misfolds to a β-rich dimer in the absence of salt, which can rapidly form an oligomer upon the addition of salt. In the presence of salt, 3A moPrP misfolds to a β-rich oligomer about a thousand-fold faster than wt moPrP. Importantly, the misfolded structure of the dimer is similar to that of the salt-induced oligomer. Misfolding to oligomer seems to be induced at the level of the dimeric unit by monomer-monomer association, and the oligomer grows by accretion of misfolded dimeric units. Additionally, it is shown that the conserved aromatic residues collectively stabilize not only monomeric protein, but also the structural core of the β-rich oligomers. Finally, it is also shown that 3A moPrP misfolds much faster to amyloid-fibrils than does the wt protein.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research Pune, Pune 411008, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research Pune, Pune 411008, India.
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2
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Zheng L, Shi S, Sun X, Lu M, Liao Y, Zhu S, Zhang H, Pan Z, Fang P, Zeng Z, Li H, Li Z, Xue W, Zhu F. MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Brief Bioinform 2024; 25:bbae006. [PMID: 38305456 PMCID: PMC10835750 DOI: 10.1093/bib/bbae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled 'MoDAFold' was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.
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Affiliation(s)
- Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Shuiyang Shi
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xiuna Sun
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
| | - Yang Liao
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Sisi Zhu
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Pan Fang
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhenyu Zeng
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Honglin Li
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhaorong Li
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Industry Solutions Research and Development, Alibaba Cloud Computing, Hangzhou 330110, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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3
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Pal S, Udgaonkar JB. Mutations of evolutionarily conserved aromatic residues suggest that misfolding of the mouse prion protein may commence in multiple ways. J Neurochem 2023; 167:696-710. [PMID: 37941487 DOI: 10.1111/jnc.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
The misfolding of the mammalian prion protein from its α-helix rich cellular isoform to its β-sheet rich infectious isoform is associated with several neurodegenerative diseases. The determination of the structural mechanism by which misfolding commences, still remains an unsolved problem. In the current study, native-state hydrogen exchange coupled with mass spectrometry has revealed that the N state of the mouse prion protein (moPrP) at pH 4 is in dynamic equilibrium with multiple partially unfolded forms (PUFs) capable of initiating misfolding. Mutation of three evolutionarily conserved aromatic residues, Tyr168, Phe174, and Tyr217 present at the interface of the β2-α2 loop and the C-terminal end of α3 in the structured C-terminal domain of moPrP significantly destabilize the native state (N) of the protein. They also reduce the free energy differences between the N state and two PUFs identified as PUF1 and PUF2**. It is shown that PUF2** in which the β2-α2 loop and the C-terminal end of α3 are disordered, has the same stability as the previously identified PUF2*, but to have a very different structure. Misfolding can commence from both PUF1 and PUF2**, as it can from PUF2*. Hence, misfolding can commence and proceed in multiple ways from structurally distinct precursor conformations. The increased extents to which PUF1 and PUF2** are populated at equilibrium in the case of the mutant variants, greatly accelerate their misfolding. The results suggest that the three aromatic residues may have been evolutionarily selected to impede the misfolding of moPrP.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research Pune, Pune, India
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4
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Mollica L, Giachin G. Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. J Chem Inf Model 2022; 63:531-545. [PMID: 36580661 PMCID: PMC9875307 DOI: 10.1021/acs.jcim.2c01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Immunotherapy using antibodies to target the aggregation of flexible proteins holds promise for therapeutic interventions in neurodegenerative diseases caused by protein misfolding. Prions or PrPSc, the causal agents of transmissible spongiform encephalopathies (TSE), represent a model target for immunotherapies as TSE are prototypical protein misfolding diseases. The X-ray crystal structure of the wild-type (WT) human prion protein (HuPrP) bound to a camelid antibody fragment, denoted as Nanobody 484 (Nb484), has been previously solved. Nb484 was found to inhibit prion aggregation in vitro through a unique mechanism of structural stabilization of two disordered epitopes, that is, the palindromic motif (residues 113-120) and the β2-α2 loop region (residues 164-185). The study of the structural basis for antibody recognition of flexible proteins requires appropriate sampling techniques for the identification of conformational states occurring in disordered epitopes. To elucidate the Nb484-HuPrP recognition mechanisms, here we applied molecular dynamics (MD) simulations complemented with available NMR and X-ray crystallography data collected on the WT HuPrP to describe the conformational spaces occurring on HuPrP prior to Nb484 binding. We observe the experimentally determined binding competent conformations within the ensembles of pre-existing conformational states in solution before binding. We also described the Nb484 recognition mechanisms in two HuPrP carrying a polymorphism (E219K) and a TSE-causing mutation (V210I). Our hybrid approaches allow the identification of dynamic conformational landscapes existing on HuPrP and highly characterized by molecular disorder to identify physiologically relevant and druggable transitions.
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Affiliation(s)
- Luca Mollica
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, 20090 Milan, Italy,
| | - Gabriele Giachin
- Department
of Chemical Sciences (DiSC), University
of Padua, 35131 Padova, Italy,
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5
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Halder P, Mitra P. Human prion protein: exploring the thermodynamic stability and structural dynamics of its pathogenic mutants. J Biomol Struct Dyn 2022; 40:11274-11290. [PMID: 34338141 DOI: 10.1080/07391102.2021.1957715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Human familial prion diseases are known to be associated with different single-point mutants of the gene coding for prion protein with a primary focus at several locations of the globular domain. We have identified 12 different single-point pathogenic mutants of human prion protein (HuPrP) with the help of extensive perturbations/mutation technique at multiple locations of HuPrP sequence related to potentiality towards conformational disorders. Among these, some of the mutants include pathogenic variants that corroborate well with the literature reported proteins while majority include some unique single-point mutants that are either not explicitly studied early or studied for variants with different residues at the specific position. Primarily, our study sheds light on the unfolding mechanism of the above mentioned mutants in depth. Besides, we could identify some mutants under investigation that demonstrates not only unfolding of the helical structures but also extension and generation of the β-sheet structures and or simultaneously have highly exposed hydrophobic surface which is assumed to be linked with the production of aggregate/fibril structures of the prion protein. Among the identified mutants, Q212E needs special attention due to its maximum exposure of hydrophobic core towards solvent and E200Q is found to be important due to its maximum extent of β-content. We are also able to identify different respective structural conformations of the proteins according to their degree of structural unfolding and those conformations can be extracted and further studied in detail. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Puspita Halder
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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6
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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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7
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Xiao K, Zhou W, Gao LP, Wu YZ, Wang Y, Chen C, Gao C, Shi Q, Dong XP. Clinical and Laboratory Features of Three Rare Chinese V210I gCJD Patients. Pathogens 2020; 9:pathogens9100800. [PMID: 32998248 PMCID: PMC7601525 DOI: 10.3390/pathogens9100800] [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: 09/02/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 11/16/2022] Open
Abstract
Genetic human prion diseases are a group of inherited encephalopathies directly associated with different mutations in PrP-encoding gene PRNP, including more than 50 different mutations worldwide. Some genotypes of mutations show ethno-correlation, and among them, genetic Creutzfeldt-Jacob disease (gCJD) with V210I mutation is frequent in European countries but rare in East Asia. Here, we comparatively analyzed the clinical and laboratory features of three Chinese patients with V210I mutant identified via the Chinese National CJD Surveillance System (CNS-CJD) in 2019. Two cases were Han Chinese and one was Hui Chinese, without blood kinship. The onset ages of three cases were 69, 64, and 59 years old, respectively. The clinical features of V210I gCJD were similar to sporadic CJD (sCJD), displaying typical clinical symptoms and signs, except that Case 3 did not show myoclonic movement. All three cases displayed sCJD-associated abnormalities on MRI and positive CSF 14-3-3, while two cases recorded typical EEG abnormalities. Only one case was positive in CSF real-time quaking-induced conversion (RT-QuIC). Appearances of mutism in three cases were relatively fast, with the intervals of 30 to 50 days after onset. Family history was not reported in all three cases. Those V210I gCJD cases are rare in China, and probably the first three in East Asia.
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Affiliation(s)
- Kang Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
| | - Wei Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
| | - Li-Ping Gao
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
| | - Yue-Zhang Wu
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
| | - Yuan Wang
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
| | - Cao Chen
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chen Gao
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
| | - Qi Shi
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
- China Academy of Chinese Medical Sciences, Dongzhimeinei, South Rd 16, Beijing 100700, China
- Correspondence: (Q.S.); (X.-P.D.); Fax: +86-10-58900815 (X.-P.D.)
| | - Xiao-Ping Dong
- State Key Laboratory for Infectious Disease Prevention and Control, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China; (K.X.); (W.Z.); (L.-P.G.); (Y.-Z.W.); (Y.W.); (C.C.); (C.G.)
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310027, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- China Academy of Chinese Medical Sciences, Dongzhimeinei, South Rd 16, Beijing 100700, China
- Center for Global Public Health, Chinese Center for Disease Control and Prevention, Chang-Bai Rd 155, Beijing 102206, China
- Correspondence: (Q.S.); (X.-P.D.); Fax: +86-10-58900815 (X.-P.D.)
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8
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Shida T, Kamatari YO, Yoda T, Yamaguchi Y, Feig M, Ohhashi Y, Sugita Y, Kuwata K, Tanaka M. Short disordered protein segment regulates cross-species transmission of a yeast prion. Nat Chem Biol 2020; 16:756-765. [PMID: 32284601 DOI: 10.1038/s41589-020-0516-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Soluble prion proteins contingently encounter foreign prion aggregates, leading to cross-species prion transmission. However, how its efficiency is regulated by structural fluctuation of the host soluble prion protein remains unsolved. In the present study, through the use of two distantly related yeast prion Sup35 proteins, we found that a specific conformation of a short disordered segment governs interspecies prion transmissibility. Using a multidisciplinary approach including high-resolution NMR and molecular dynamics simulation, we identified critical residues within this segment that allow interspecies prion transmission in vitro and in vivo, by locally altering dynamics and conformation of soluble prion proteins. Remarkably, subtle conformational differences caused by a methylene group between asparagine and glutamine sufficed to change the short segment structure and substantially modulate the cross-seeding activity. Thus, our findings uncover how conformational dynamics of the short segment in the host prion protein impacts cross-species prion transmission. More broadly, our study provides mechanistic insights into cross-seeding between heterologous proteins.
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Affiliation(s)
- Toshinobu Shida
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan
| | - Yuji O Kamatari
- Life Science Research Center, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan.,Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan.,RIKEN-Max Planck Joint Research Center, Wako, Japan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yumiko Ohhashi
- Graduate School of Science, Kobe University, Kobe, Japan.,Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Motomasa Tanaka
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan. .,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan.
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9
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Piazza M, Prior TW, Khalsa PS, Appleby B. A case report of genetic prion disease with two different PRNP variants. Mol Genet Genomic Med 2020; 8:e1134. [PMID: 31953922 PMCID: PMC7057106 DOI: 10.1002/mgg3.1134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/08/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
Background Prion diseases are a group of lethal neurodegenerative conditions that occur when the normal, cellular form of the prion protein (PrPC) is converted into an abnormal, scrapie, form of the protein (PrPSc). Disease may be caused by genetic, infectious, or sporadic etiologies. The genetic form of prion disease comprises~10%–15% of all cases. Prion disease is typically inherited in an autosomal dominant manner. The low incidence of disease makes it highly unlikely that a patient would have two different pathogenic variants. However, we recently identified a case in which the patient did have two pathogenic PRNP variants and presented with an atypical phenotype. Methods The patient was evaluated at the Washington Hospital Healthcare System in Fremont, CA. The clinical information for this case report was obtained retrospectively. Variants in the PRNP were identified by polymerase chain reaction (PCR) amplification of exon two of the gene followed by bi‐directional sequence analysis. To determine the phase of the identified variants, a restriction enzyme digestion was utilized, followed by sequence analysis of the products. Cerebral spinal fluid (CSF) was analyzed for surrogate markers of prion disease, 14–3–3 and Tau proteins. CSF real‐time quaking‐induced conversion (RT‐QuIC) assays were also performed. Results The patient was a compound heterozygote for the well‐characterized c.628G>A (p.Val210Ile) variant and the rare octapeptide deletion of two repeats [c.202_249del48 (p.P68_Q83del)]. Clinically, the patient presented with an early onset demyelinating peripheral neuropathy, followed by later onset cognitive symptoms. Conclusion This presentation is reminiscent of prion protein knockout mice whose predominate symptom, due to complete loss of PrP, was late‐onset peripheral neuropathy. To our knowledge this is the first case reported of a patient with prion disease who had two different pathogenic variants in PRNP.
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Affiliation(s)
- Megan Piazza
- Center for Human Genetics Laboratory, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Thomas W Prior
- Center for Human Genetics Laboratory, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Prabhjot S Khalsa
- Fremont Neurology Medical Associates, Fremont, CA, USA.,Washington Hospital Healthcare System, Fremont, CA, USA.,University of California Davis, Davis, CA, USA
| | - Brian Appleby
- National Prion Disease Pathology Surveillance Center, Case Western Reserve University, Cleveland, OH, USA
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10
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Lee J, Chang I, Yu W. Atomic insights into the effects of pathological mutants through the disruption of hydrophobic core in the prion protein. Sci Rep 2019; 9:19144. [PMID: 31844149 PMCID: PMC6915724 DOI: 10.1038/s41598-019-55661-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Destabilization of prion protein induces a conformational change from normal prion protein (PrPC) to abnormal prion protein (PrPSC). Hydrophobic interaction is the main driving force for protein folding, and critically affects the stability and solvability. To examine the importance of the hydrophobic core in the PrP, we chose six amino acids (V176, V180, T183, V210, I215, and Y218) that make up the hydrophobic core at the middle of the H2-H3 bundle. A few pathological mutants of these amino acids have been reported, such as V176G, V180I, T183A, V210I, I215V, and Y218N. We focused on how these pathologic mutations affect the hydrophobic core and thermostability of PrP. For this, we ran a temperature-based replica-exchange molecular dynamics (T-REMD) simulation, with a cumulative simulation time of 28 μs, for extensive ensemble sampling. From the T-REMD ensemble, we calculated the protein folding free energy difference between wild-type and mutant PrP using the thermodynamic integration (TI) method. Our results showed that pathological mutants V176G, T183A, I215V, and Y218N decrease the PrP stability. At the atomic level, we examined the change in pair-wise hydrophobic interactions from valine-valine to valine-isoleucine (and vice versa), which is induced by mutation V180I, V210I (I215V) at the 180th-210th (176th-215th) pair. Finally, we investigated the importance of the π-stacking between Y218 and F175.
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Affiliation(s)
- Juhwan Lee
- Center for Proteome Biophysics, DGIST, Daegu, 42988, Korea.
- Department of Emerging Material Sciences, DGIST, Daegu, 42988, Korea.
- Core Protein Resources Center, DGIST, Daegu, 42988, Korea.
- Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea.
| | - Iksoo Chang
- Center for Proteome Biophysics, DGIST, Daegu, 42988, Korea
- Core Protein Resources Center, DGIST, Daegu, 42988, Korea
- Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea
| | - Wookyung Yu
- Core Protein Resources Center, DGIST, Daegu, 42988, Korea.
- Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea.
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 42988, Korea.
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11
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Chandrasekaran P, Santosh Kumar C, Rangachari K, Sekar K. Disassociation of β1-α1-β2 from the α2-α3 domain of prion protein (PrP) is a prerequisite for the conformational conversion of PrPC into PrPSc: Driven by the free energy landscape. Int J Biol Macromol 2019; 136:368-376. [DOI: 10.1016/j.ijbiomac.2019.06.099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/29/2019] [Accepted: 06/13/2019] [Indexed: 12/16/2022]
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12
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Harrathi C, Fernández-Borges N, Eraña H, Elezgarai SR, Venegas V, Charco JM, Castilla J. Insights into the Bidirectional Properties of the Sheep-Deer Prion Transmission Barrier. Mol Neurobiol 2018; 56:5287-5303. [PMID: 30592012 PMCID: PMC6614146 DOI: 10.1007/s12035-018-1443-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023]
Abstract
The large chronic wasting disease (CWD)-affected cervid population in the USA and Canada, and the risk of the disease being transmitted to humans through intermediate species, is a highly worrying issue that is still poorly understood. In this case, recombinant protein misfolding cyclic amplification was used to determine, in vitro, the relevance of each individual amino acid on cross-species prion transmission. Others and we have found that the β2-α2 loop is a key modulator of transmission barriers between species and markedly influences infection by sheep scrapie, bovine spongiform encephalopathy (BSE), or elk CWD. Amino acids that differentiate ovine and deer normal host prion protein (PrPC) and associated with structural rigidity of the loop β2-α2 (S173N, N177T) appear to confer resistance to some prion diseases. However, addition of methionine at codon 208 together with the previously described rigid loop substitutions seems to hide a key in this species barrier, as it makes sheep recombinant prion protein highly susceptible to CWD-induced misfolding. These studies indicate that interspecies prion transmission is not only governed just by the β2-α2 loop amino acid sequence but also by its interactions with the α3-helix as shown by substitution I208M. Transmissible spongiform encephalopathies, characterized by long incubation periods and spongiform changes associated with neuronal loss in the brain, have been described in several mammalian species appearing either naturally (scrapie in sheep and goats, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids, Creutzfeldt-Jakob disease in humans) or by experimental transmission studies (scrapie in mice and hamsters). Much of the pathogenesis of the prion diseases has been determined in the last 40 years, such as the etiological agent or the fact that prions occur as different strains that show distinct biological and physicochemical properties. However, there are many unanswered questions regarding the strain phenomenon and interspecies transmissibility. To assess the risk of interspecies transmission between scrapie and chronic wasting disease, an in vitro prion propagation method has been used. This technique allows to predict the amino acids preventing the transmission between sheep and deer prion diseases.
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Affiliation(s)
- Chafik Harrathi
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | | | - Hasier Eraña
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Saioa R Elezgarai
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Vanessa Venegas
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Jorge M Charco
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Parque tecnológico de Bizkaia, 48160, Derio, Bizkaia, Spain. .,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Bizkaia, Spain.
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13
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Kakuda K, Yamaguchi KI, Kuwata K, Honda R. A valine-to-lysine substitution at position 210 induces structural conversion of prion protein into a β-sheet rich oligomer. Biochem Biophys Res Commun 2018; 506:81-86. [PMID: 30336980 DOI: 10.1016/j.bbrc.2018.10.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/12/2018] [Indexed: 12/18/2022]
Abstract
Prion diseases are fatal neurodegenerative diseases associated with structural conversion of α-helical prion protein (PrP) into its β-sheet rich isoform (PrPSc). Previous genetic analyses have indicated that several amino acid residues involved in the hydrophobic core of PrP (such as V180, F198, and V210) play a critical role in the development of prion diseases. To understand how these hydrophobic residues would contribute to the α-to-β conversion process of PrP, we substituted the V210 residue with bulkier (V210F, V210I, and V210L), smaller (V210A), and charged amino acids (V210K) and characterized its effects. Interestingly, although most of the mutations had little or no effect on the biochemical properties of PrP, the V210K mutation induced structural conversion of PrP into a β-structure. The β-inducing effect was prominent and observed even under a physiological condition (i.e., in the absence of denaturant, acidic pH, reducing agent, and high temperature) in contrast to the disease-associated mutations in the PrP gene. We also examined structural features of V210K PrP using guanidine-hydrochloride unfolding, dynamic light scattering, 8-anilino-1-naphthalene sulfonate fluorescence, and electron microscopy, and revealed that V210K PrP assembles into a non-fibrillar β-rich oligomer. Thus, the α-to-β conversion can be induced by introduction of a charged residue into the hydrophobic core, which provide novel insight into the structural dynamics of PrP.
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Affiliation(s)
- Kyosuke Kakuda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Kei-Ichi Yamaguchi
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan; Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, 501-1193, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, 501-1193, Japan.
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14
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Zheng Z, Zhang M, Wang Y, Ma R, Guo C, Feng L, Wu J, Yao H, Lin D. Structural basis for the complete resistance of the human prion protein mutant G127V to prion disease. Sci Rep 2018; 8:13211. [PMID: 30181558 PMCID: PMC6123418 DOI: 10.1038/s41598-018-31394-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 08/08/2018] [Indexed: 12/20/2022] Open
Abstract
Prion diseases are caused by the propagation of misfolded cellular prion proteins (PrPs). A completely prion disease-resistant genotype, V127M129, has been identified in Papua New Guinea and verified in transgenic mice. To disclose the structural basis of the disease-resistant effect of the G127V mutant, we determined and compared the structural and dynamic features of the G127V-mutated human PrP (residues 91-231) and the wild-type PrP in solution. HuPrP(G127V) contains α1, α2 and α3 helices and a stretch-strand (SS) pattern comprising residues Tyr128-Gly131 (SS1) and Val161-Arg164 (SS2), with extending atomic distances between the SS1 and SS2 strands, and a structural rearrangement of the Tyr128 side chain due to steric hindrance of the larger hydrophobic side chain of Val127. The extended α1 helix gets closer to the α2 and α3 helices. NMR dynamics analysis revealed that Tyr128, Gly131 and Tyr163 underwent significant conformational exchanges. Molecular dynamics simulations suggest that HuPrP(G127V) prevents the formation of stable β-sheets and dimers. Unique structural and dynamic features potentially inhibit the conformational conversion of the G127V mutant. This work is beneficial for understanding the molecular mechanisms underlying the complete resistance of the G127V mutant to prion disease and for developing new therapeutics for prion disease.
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Affiliation(s)
- Zhen Zheng
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Meilan Zhang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yongheng Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Rongsheng Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Chenyun Guo
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Liubin Feng
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jihui Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Hongwei Yao
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Donghai Lin
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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15
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Kovač V, Čurin Šerbec V. Prion Proteins Without the Glycophosphatidylinositol Anchor: Potential Biomarkers in Neurodegenerative Diseases. Biomark Insights 2018; 13:1177271918756648. [PMID: 29449775 PMCID: PMC5808966 DOI: 10.1177/1177271918756648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/23/2017] [Indexed: 01/17/2023] Open
Abstract
Prion protein (PrP) is a biomolecule that is involved in neuronal signaling, myelinization, and the development of neurodegenerative diseases. In the cell, PrP is shed by the ADAM10 protease. This process generates PrP molecules that lack glycophosphatidylinositol anchor, and these molecules incorporate into toxic aggregates and neutralize toxic oligomers. Due to this dual role, these molecules are important biomarkers for neurodegenerative diseases. In this review, we present shed PrP as a potential biomarker, with a focus on PrP226*, which may be the main biomarker for predicting neurodegenerative diseases in humans.
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Affiliation(s)
- Valerija Kovač
- Department for the Production of Diagnostic Reagents and Research, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
| | - Vladka Čurin Šerbec
- Department for the Production of Diagnostic Reagents and Research, Blood Transfusion Centre of Slovenia, Ljubljana, Slovenia
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16
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Bagyinszky E, Giau VV, Youn YC, An SSA, Kim S. Characterization of mutations in PRNP (prion) gene and their possible roles in neurodegenerative diseases. Neuropsychiatr Dis Treat 2018; 14:2067-2085. [PMID: 30147320 PMCID: PMC6097508 DOI: 10.2147/ndt.s165445] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abnormal prion proteins are responsible for several fatal neurodegenerative diseases in humans and in animals, including Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker disease, and fatal familial insomnia. Genetics is important in prion diseases, but in the most cases, cause of diseases remained unknown. Several mutations were found to be causative for prion disorders, and the effect of mutations may be heterogeneous. In addition, different prion mutations were suggested to play a possible role in additional phenotypes, such as Alzheimer's type pathology, spongiform encephalopathy, or frontotemporal dementia. Pathogenic nature of several prion mutations remained unclear, such as M129V and E219K. These two polymorphic sites were suggested as either risk factors for different disorders, such as Alzheimer's disease (AD), variant CJD, or protease-sensitive prionopathy, and they can also be disease-modifying factors. Pathological overlap may also be possible with AD or progressive dementia, and several patients with prion mutations were initially diagnosed with AD. This review also introduces briefly the diagnosis of prion diseases and the issues with their diagnosis. Since prion diseases have quite heterogeneous phenotypes, a complex analysis, a combination of genetic screening, cerebrospinal fluid biomarker analysis and imaging technologies could improve the early disease diagnosis.
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Affiliation(s)
- Eva Bagyinszky
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, Gyeonggi-do, South Korea,
| | - Vo Van Giau
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, Gyeonggi-do, South Korea,
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Seong Soo A An
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, Gyeonggi-do, South Korea,
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine & Neurocognitive Behavior Center, Seoul National University Bundang Hospital, Seongnam, South Korea
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17
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Identification of novel fluorescent probes preventing PrP Sc replication in prion diseases. Eur J Med Chem 2017; 127:859-873. [DOI: 10.1016/j.ejmech.2016.10.064] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/31/2016] [Indexed: 12/11/2022]
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18
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Kovač V, Zupančič B, Ilc G, Plavec J, Čurin Šerbec V. Truncated prion protein PrP226* - A structural view on its role in amyloid disease. Biochem Biophys Res Commun 2017; 484:45-50. [PMID: 28109886 DOI: 10.1016/j.bbrc.2017.01.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
Abstract
In the brain of patients with transmissible spongiform encephalopathies, besides PrPSc aggregates, deposition of truncated PrP molecules was described. Jansen et al. reported two clinical cases with deposition of C-terminally truncated PrP, one of them ending with Tyr226. We have previously described the discovery of monoclonal antibody V5B2 that selectively recognizes this version of the prion protein, which we called PrP226*. Using monoclonal antibody V5B2 we showed that accumulation of PrP226* is characteristic for most types of human and animal TSEs. Its distribution correlates to the distribution of PrPSc aggregates. To gain insight into the structural basis of its presence and distribution in PrP aggregates, we have determined the NMR structure of recombinant PrP226*. The structure of the protein consists of a disordered N-terminal part (residues 90-125) and a structured C-terminal part (residues 126-226). The C-terminal segment consists of four α-helices and a short antiparallel β-sheet. Our model predicts a break in the C-terminal helix and reorganized hydrophobic interactions between helix α3 and β2-α2 loop due to the shorter C-terminus. The structural model gives information on the possible role of the protein in the development of amyloid disease and can serve as a foundation to develop tools for prevention and treatment of prion diseases.
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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.
| | - Blaž Zupančič
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, Dunajska 156, SI-1001 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, Dunajska 156, SI-1001 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-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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19
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Biljan I, Ilc G, Plavec J. Analysis of Prion Protein Structure Using Nuclear Magnetic Resonance Spectroscopy. Methods Mol Biol 2017; 1658:35-49. [PMID: 28861781 DOI: 10.1007/978-1-4939-7244-9_4] [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: 01/19/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful experimental tool for obtaining information on three-dimensional (3D) structures of proteins at atomic resolution. In inherited forms of prion diseases, misfolding of cellular prion protein, PrPC, into its pathological form, PrPSc, is caused by mutations in the human prion protein gene (PRNP). Understanding of the earliest stages of the conformational changes leading to spontaneous generation of prions in inherited forms of prion diseases may benefit from detailed structural analysis of different human (Hu) PrP variants. Here, we describe the protocol for structure determination of HuPrP variants by NMR spectroscopy in solution that consists of preparation of NMR samples, acquisition of NMR data, NMR resonance assignments, and structure calculation.
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Affiliation(s)
- Ivana Biljan
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, 10000, Zagreb, Croatia
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia. .,EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia. .,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000, Ljubljana, Slovenia.
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20
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Understanding the Effect of Disease-Related Mutations on Human Prion Protein Structure: Insights From NMR Spectroscopy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:83-103. [DOI: 10.1016/bs.pmbts.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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21
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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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22
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Yu Y, Yu Z, Zheng Z, Wang H, Wu X, Guo C, Lin D. Distinct effects of mutations on biophysical properties of human prion protein monomers and oligomers. Acta Biochim Biophys Sin (Shanghai) 2016; 48:1016-1025. [PMID: 27649893 DOI: 10.1093/abbs/gmw094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/15/2016] [Indexed: 02/05/2023] Open
Abstract
Prion diseases are a group of fatal neurodegenerative illnesses, resulting from the conformational conversion of the cellular prion protein (PrPC) into a misfolded form (PrPSc). The formation of neurotoxic soluble prion protein oligomer (PrPO) is regarded as a key step in the development of prion diseases. About 10%-15% of human prion diseases are caused by mutations in the prion protein gene; however, the underlying molecular mechanisms remain unclear. In the present work, we compared the biophysical properties of wild-type (WT) human prion protein 91-231 (WT HuPrP91-231) and its disease-associated variants (P105L, D178N, V203I, and Q212P) using several biophysical techniques. In comparison with WT HuPrPC, the Q212P and D178N variants possessed greatly increased conversion propensities of PrPC into PrPO, while the V203I variant had dramatically decreased conversion propensity. The P105L variant displayed a similar conversion propensity to WT HuPrPC Guanidine hydrochloride-induced unfolding experiments ranked the thermodynamic stabilities of these proteins as Q212P < D178N < WT ≈ P105L < V203I. It was thus suggested that the conversion propensities of the prion proteins are closely associated with their thermodynamic stabilities. Furthermore, structural comparison illustrated that Q212P, D178N, and V203I variants underwent larger structural changes compared with WT HuPrPC, while the P105L variant adopted a similar structure to the WT HuPrPC The mutation-induced structural perturbations might change the thermodynamic stabilities of the HuPrPC variants, and correspondingly alter the conversion propensities for these prion proteins. Our results extend the mechanistic understanding of prion pathogenesis, and lay the basis for the prevention and treatment of prion diseases.
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Affiliation(s)
- Yuanhui Yu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ziyao Yu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Zheng
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Huilin Wang
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xueji Wu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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23
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Chandrasekaran P, Rajasekaran R. Detailed computational analysis revealed mutation V210I on PrP induced conformational conversion on β2–α2 loop and α2–α3. MOLECULAR BIOSYSTEMS 2016; 12:3223-33. [DOI: 10.1039/c6mb00342g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of fatal transmissible spongiform encephalopathies (TSE) is associated with the conformational conversion of the normal cellular prion protein, PrPC, into its pathogenic isoform, PrPSc.
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Affiliation(s)
- P. Chandrasekaran
- Computational Biology Lab
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore 632 014
| | - R. Rajasekaran
- Computational Biology Lab
- Department of Biotechnology
- School of Biosciences and Technology
- VIT University
- Vellore 632 014
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24
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Moda F, T. Le TN, Aulić S, Bistaffa E, Campagnani I, Virgilio T, Indaco A, Palamara L, Andréoletti O, Tagliavini F, Legname G. Synthetic prions with novel strain-specified properties. PLoS Pathog 2015; 11:e1005354. [PMID: 26720726 PMCID: PMC4699842 DOI: 10.1371/journal.ppat.1005354] [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: 07/23/2015] [Accepted: 11/30/2015] [Indexed: 01/10/2023] Open
Abstract
Prions are infectious proteins that possess multiple self-propagating structures. The information for strains and structural specific barriers appears to be contained exclusively in the folding of the pathological isoform, PrPSc. Many recent studies determined that de novo prion strains could be generated in vitro from the structural conversion of recombinant (rec) prion protein (PrP) into amyloidal structures. Our aim was to elucidate the conformational diversity of pathological recPrP amyloids and their biological activities, as well as to gain novel insights in characterizing molecular events involved in mammalian prion conversion and propagation. To this end we generated infectious materials that possess different conformational structures. Our methodology for the prion conversion of recPrP required only purified rec full-length mouse (Mo) PrP and common chemicals. Neither infected brain extracts nor amplified PrPSc were used. Following two different in vitro protocols recMoPrP converted to amyloid fibrils without any seeding factor. Mouse hypothalamic GT1 and neuroblastoma N2a cell lines were infected with these amyloid preparations as fast screening methodology to characterize the infectious materials. Remarkably, a large number of amyloid preparations were able to induce the conformational change of endogenous PrPC to harbor several distinctive proteinase-resistant PrP forms. One such preparation was characterized in vivo habouring a synthetic prion with novel strain specified neuropathological and biochemical properties. Prions are infectious proteins capable of acquiring multiple self-propagating structures. The information for strains and structural specific barriers appears to be contained exclusively in the folding of the pathological isoform, designated as PrPSc. During propagation, disease-associated conformer PrPSc coerces the physiological form, denoted as PrPC, to adopt the pathological isoform conformation. We describe here the generation of an array of infectious materials with different structural, morphological, biochemical and cell biological characteristics. After producing purified recombinant prion protein of the wild-type mouse full-length sequence in Escherichia coli, we polymerized the protein into various amyloid fibril conformations based on different amyloid preparations. We also applied a build-in methodology for screening amyloid preparations and generate infectious materials using an amyloid-infected cell culture assay. Some of the amyloid fibrils preparations were able to efficiently amplify in PMCA (Protein Misfolding Cyclic Amplification), and to induce endogenous PrPC to convert into PrPSc in both murine hypothalamic GT1 and neuroblastoma N2a cell lines. One such protocol lead to the generation of a novel synthetic prion strain in mice.
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Affiliation(s)
- Fabio Moda
- Unit of Neuropathology and Neurology 5, IRCCS Foundation Carlo Besta Neurological Institute, Milano, Italy
| | - Thanh-Nhat T. Le
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Ital,y
| | - Suzana Aulić
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Ital,y
| | - Edoardo Bistaffa
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Ital,y
| | - Ilaria Campagnani
- Unit of Neuropathology and Neurology 5, IRCCS Foundation Carlo Besta Neurological Institute, Milano, Italy
| | - Tommaso Virgilio
- Unit of Neuropathology and Neurology 5, IRCCS Foundation Carlo Besta Neurological Institute, Milano, Italy
| | - Antonio Indaco
- Unit of Neuropathology and Neurology 5, IRCCS Foundation Carlo Besta Neurological Institute, Milano, Italy
| | - Luisa Palamara
- Unit of Neuropathology and Neurology 5, IRCCS Foundation Carlo Besta Neurological Institute, Milano, Italy
| | - Olivier Andréoletti
- UMR INRA-ENVT, Physiopathologie Infectieuse et Parasitaire des Ruminants, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Fabrizio Tagliavini
- Unit of Neuropathology and Neurology 5, IRCCS Foundation Carlo Besta Neurological Institute, Milano, Italy
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Ital,y
- ELETTRA Laboratory, Sincrotrone Trieste S.C.p.A, Basovizza, Trieste, Italy
- * E-mail:
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Safdar M, Junejo Y, Arman K, Abasıyanık MF. Rapid bovine and caprine species identification in ruminant feeds by duplex real-time PCR melting curve analysis using EvaGreen fluorescence dye. Mol Biotechnol 2015; 56:770-6. [PMID: 24770990 DOI: 10.1007/s12033-014-9756-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A duplex real-time PCR assay with melting curve analysis, using the EvaGreen fluorescence dye, was developed for rapid and reliable identification of bovine and caprine in ruminant feeds. The method merges the use of bovine (Bos taurus) and caprine (Capra hircus) specific primers that amplify small fragments (bovine 96 bp and caprine 142 bp) of the mitochondrial 16S rRNA and 12S rRNA genes, respectively. DNA was isolated from heat-treated meats (133 °C/3 bar for 20 min) mixtures of bovine and caprine and was used to optimize the assay. Gene products of caprine and bovine produced two distinct melting peaks simultaneously at 82 and 86.8 °C, respectively. Duplex analysis of the reference samples showed that the detection limit of the assay was 0.003 % for bovine and 0.005 % for caprine species. The aim of this study was to develop a duplex real-time PCR assay followed by a melt curve step for sensitive, rapid, specific, and cost-effective detection of bovine and caprine species based on the amplicon melting peak in ruminant feeds to prevent Transmissible Spongiform Encephalopathies.
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Affiliation(s)
- M Safdar
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey,
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The influence of PRNP polymorphisms on human prion disease susceptibility: an update. Acta Neuropathol 2015; 130:159-70. [PMID: 26022925 DOI: 10.1007/s00401-015-1447-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/15/2015] [Accepted: 05/16/2015] [Indexed: 02/04/2023]
Abstract
Two normally occurring polymorphisms of the human PRNP gene, methionine (M)/valine (V) at codon 129 and glutamic acid (E)/lysine (K) at codon 219, can affect the susceptibility to prion diseases. It has long been recognized that 129M/M homozygotes are overrepresented in sporadic Creutzfeldt-Jakob disease (CJD) patients and variant CJD patients, whereas 219E/K heterozygotes are absent in sporadic CJD patients. In addition to these pioneering findings, recent progress in experimental transmission studies and worldwide surveillance of prion diseases have identified novel relationships between the PRNP polymorphisms and the prion disease susceptibility. For example, although 219E/K heterozygosity confers resistance against the development of sporadic CJD, this genotype is not entirely protective against acquired forms (iatrogenic CJD and variant CJD) or genetic forms (genetic CJD and Gerstmann-Sträussler-Scheinker syndrome) of prion diseases. In addition, 129M/V heterozygotes predispose to genetic CJD caused by a pathogenic PRNP mutation at codon 180. These findings show that the effects of the PRNP polymorphisms may be more complicated than previously thought. This review aims to summarize recent advances in our knowledge about the influence of the PRNP polymorphisms on the prion disease susceptibility.
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Kraus A, Anson KJ, Raymond LD, Martens C, Groveman BR, Dorward DW, Caughey B. Prion Protein Prolines 102 and 105 and the Surrounding Lysine Cluster Impede Amyloid Formation. J Biol Chem 2015; 290:21510-22. [PMID: 26175152 DOI: 10.1074/jbc.m115.665844] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Indexed: 11/06/2022] Open
Abstract
Human prion diseases can have acquired, sporadic, or genetic origins, each of which results in the conversion of prion protein (PrP) to transmissible, pathological forms. The genetic prion disease Gerstmann-Straussler-Scheinker syndrome can arise from point mutations of prolines 102 or 105. However, the structural effects of these two prolines, and mutations thereof, on PrP misfolding are not well understood. Here, we provide evidence that individual mutations of Pro-102 or Pro-105 to noncyclic aliphatic residues such as the Gerstmann-Straussler-Scheinker-linked leucines can promote the in vitro formation of PrP amyloid with extended protease-resistant cores reminiscent of infectious prions. This effect was enhanced by additional charge-neutralizing mutations of four nearby lysine residues comprising the so-called central lysine cluster. Substitution of these proline and lysine residues accelerated PrP conversion such that spontaneous amyloid formation was no longer slower than scrapie-seeded amyloid formation. Thus, Pro-102 and Pro-105, as well as the lysines in the central lysine cluster, impede amyloid formation by PrP, implicating these residues as key structural modulators in the conversion of PrP to disease-associated types of amyloid.
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Affiliation(s)
- Allison Kraus
- From the Laboratory of Persistent Viral Diseases and
| | | | | | - Craig Martens
- Research Technologies Branch, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840
| | | | - David W Dorward
- Research Technologies Branch, Rocky Mountain Laboratories, NIAID, National Institutes of Health, Hamilton, Montana 59840
| | - Byron Caughey
- From the Laboratory of Persistent Viral Diseases and
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Abstract
It was reported that buffalo is a low susceptibility species resisting to transmissible spongiform encephalopathies (TSEs) (same as rabbits, horses, and dogs). TSEs, also called prion diseases, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species (except for rabbits, dogs, horses, and buffalo), manifesting as scrapie in sheep and goats; bovine spongiform encephalopathy (BSE or "mad-cow" disease) in cattle; chronic wasting disease in deer and elk; and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and Kulu in humans etc. In molecular structures, these neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)), predominantly with α-helices, into insoluble abnormally folded infectious prions (PrP(Sc)), rich in β-sheets. In this article, we studied the molecular structure and structural dynamics of buffalo PrP(C) (BufPrP(C)), in order to understand the reason why buffalo is resistant to prion diseases. We first did molecular modeling of a homology structure constructed by one mutation at residue 143 from the NMR structure of bovine and cattle PrP(124-227); immediately we found that for BufPrP(C)(124-227), there are five hydrogen bonds (HBs) at Asn143, but at this position, bovine/cattle do not have such HBs. Same as that of rabbits, dogs, or horses, our molecular dynamics studies also revealed there is a strong salt bridge (SB) ASP178-ARG164 (O-N) keeping the β2-α2 loop linked in buffalo. We also found there is a very strong HB SER170-TYR218 linking this loop with the C-terminal end of α-helix H3. Other information, such as (i) there is a very strong SB HIS187-ARG156 (N-O) linking α-helices H2 and H1 (if mutation H187R is made at position 187, then the hydrophobic core of PrP(C) will be exposed (L.H. Zhong (2010). Exposure of hydrophobic core in human prion protein pathogenic mutant H187R. Journal of Biomolecular Structure and Dynamics 28(3), 355-361)), (ii) at D178, there is a HB Y169-D178 and a polar contact R164-D178 for BufPrP(C) instead of a polar contact Q168-D178 for bovine PrP(C) (C.J. Cheng, & V. Daggett. (2014). Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH. Biomolecules 4(1), 181-201), (iii) BufPrP(C) owns three 310 helices at 125-127, 152-156, and in the β2-α2 loop, respectively, and (iv) in the β2-α2 loop, there is a strong π-π stacking and a strong π-cation F175-Y169-R164.(N)NH2, has been discovered.
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Affiliation(s)
- Jiapu Zhang
- a Molecular Model Discovery Laboratory, Faculty of Science, Engineering & Technology, Department of Chemistry & Biotechnology , Swinburne University of Technology , Hawthorn Campus, Hawthorn , Victoria 3122 , Australia.,b Faculty of Science, Graduate School of Sciences, Information Technology and Engineering & Centre of Informatics and Applied Optimisation , The Federation University Australia , Mount Helen Campus, Mount Helen, Ballarat , Victoria 3353 , Australia
| | - Feng Wang
- a Molecular Model Discovery Laboratory, Faculty of Science, Engineering & Technology, Department of Chemistry & Biotechnology , Swinburne University of Technology , Hawthorn Campus, Hawthorn , Victoria 3122 , Australia
| | - Subhojyoti Chatterjee
- a Molecular Model Discovery Laboratory, Faculty of Science, Engineering & Technology, Department of Chemistry & Biotechnology , Swinburne University of Technology , Hawthorn Campus, Hawthorn , Victoria 3122 , Australia
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Feng B, Wang Z, Liu T, Jin R, Wang S, Wang W, Xiao G, Zhou Z. Methionine oxidation accelerates the aggregation and enhances the neurotoxicity of the D178N variant of the human prion protein. Biochim Biophys Acta Mol Basis Dis 2014; 1842:2345-56. [PMID: 25281825 DOI: 10.1016/j.bbadis.2014.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/27/2014] [Accepted: 09/24/2014] [Indexed: 12/30/2022]
Abstract
The D178N mutation of the prion protein (PrP) results in the hereditary prion disease fatal familial insomnia (FFI). Little is known regarding the effects of methionine oxidation on the pathogenesis of D178N-associated FFI. In the present study, we found that the D178N variant was more susceptible to oxidation than wild-type PrP, as indicated by reverse-phase high performance liquid chromatography (RP-HPLC) and mass spectrometry (MS) analysis. Circular dichroism (CD), differential scanning calorimetry (DSC), thioflavin T (ThT) binding assay studies demonstrated that methionine oxidation decreased the structural stability of the D178N variant, and the oxidized D178N variant exhibited a greater propensity to form β-sheet-rich oligomers and aggregates. Moreover, these aggregates of oxidized D178N PrP were more resistant to proteinase K (PK) digestion. Additionally, using fluorescence confocal microscopy, we detected a high degree of aggregation in D178N-transfected Neuro-2a (N2a) cells after treatment with hydrogen peroxide (H2O2). Furthermore, the oxidation and consequent aggregation of the D178N variant induced greater apoptosis of N2a cells, as monitored using flow cytometry. Collectively, these observations suggest that methionine oxidation accelerates the aggregation and enhances the neurotoxicity of the D178N variant, possibly providing direct evidence to link the pathogenesis of D178N-associated FFI with methionine oxidation.
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Affiliation(s)
- Boya Feng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Zonglin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Ting Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Rui Jin
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Shaobo Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Wei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
| | - Zheng Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
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Abskharon RNN, Giachin G, Wohlkonig A, Soror SH, Pardon E, Legname G, Steyaert J. Probing the N-terminal β-sheet conversion in the crystal structure of the human prion protein bound to a nanobody. J Am Chem Soc 2014; 136:937-44. [PMID: 24400836 DOI: 10.1021/ja407527p] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prions are fatal neurodegenerative transmissible agents causing several incurable illnesses in humans and animals. Prion diseases are caused by the structural conversion of the cellular prion protein, PrP(C), into its misfolded oligomeric form, known as prion or PrP(Sc). The canonical human PrP(C) (HuPrP) fold features an unstructured N-terminal part (residues 23-124) and a well-defined C-terminal globular domain (residues 125-231). Compelling evidence indicates that an evolutionary N-terminal conserved motif AGAAAAGA (residues 113-120) plays an important role in the conversion to PrP(Sc). The intrinsic flexibility of the N-terminal has hampered efforts to obtain detailed atomic information on the structural features of this palindromic region. In this study, we crystallized the full-length HuPrP in complex with a nanobody (Nb484) that inhibits prion propagation. In the complex, the prion protein is unstructured from residue 23 to 116. The palindromic motif adopts a stable and fully extended configuration to form a three-stranded antiparallel β-sheet with the β1 and β2 strands, demonstrating that the full-length HuPrP(C) can adopt a more elaborate β0-β1-α1-β2-α2-α3 structural organization than the canonical β1-α1-β2-α2-α3 prion-like fold. From this structure, it appears that the palindromic motif mediates β-enrichment in the PrP(C) monomer as one of the early events in the conversion of PrP(C) into PrP(Sc).
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Affiliation(s)
- Romany N N Abskharon
- Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
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Prion protein misfolding, strains, and neurotoxicity: an update from studies on Mammalian prions. Int J Cell Biol 2013; 2013:910314. [PMID: 24454379 PMCID: PMC3884631 DOI: 10.1155/2013/910314] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 11/10/2013] [Accepted: 11/11/2013] [Indexed: 11/17/2022] Open
Abstract
Prion diseases, also known as transmissible spongiform encephalopathies (TSEs), are a group of fatal neurodegenerative disorders affecting humans and other mammalian species. The central event in TSE pathogenesis is the conformational conversion of the cellular prion protein, PrPC, into the aggregate, β-sheet rich, amyloidogenic form, PrPSc. Increasing evidence indicates that distinct PrPSc conformers, forming distinct ordered aggregates, can encipher the phenotypic TSE variants related to prion strains. Prion strains are TSE isolates that, after inoculation into syngenic hosts, cause disease with distinct characteristics, such as incubation period, pattern of PrPSc distribution, and regional severity of histopathological changes in the brain. In analogy with other amyloid forming proteins, PrPSc toxicity is thought to derive from the existence of various intermediate structures prior to the amyloid fiber formation and/or their specific interaction with membranes. The latter appears particularly relevant for the pathogenesis of TSEs associated with GPI-anchored PrPSc, which involves major cellular membrane distortions in neurons. In this review, we update the current knowledge on the molecular mechanisms underlying three fundamental aspects of the basic biology of prions such as the putative mechanism of prion protein conversion to the pathogenic form PrPSc and its propagation, the molecular basis of prion strains, and the mechanism of induced neurotoxicity by PrPSc aggregates.
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Lee JH, Bae SE, Jung S, Ahn I, Son HS. Discriminant analysis of prion sequences for prediction of susceptibility. Exp Mol Med 2013; 45:e48. [PMID: 24113272 PMCID: PMC3809358 DOI: 10.1038/emm.2013.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 11/09/2022] Open
Abstract
Prion diseases, including ovine scrapie, bovine spongiform encephalopathy (BSE), human kuru and Creutzfeldt-Jakob disease (CJD), originate from a conformational change of the normal cellular prion protein (PrP(C)) into abnormal protease-resistant prion protein (PrP(Sc)). There is concern regarding these prion diseases because of the possibility of their zoonotic infections across species. Mutations and polymorphisms of prion sequences may influence prion-disease susceptibility through the modified expression and conformation of proteins. Rapid determination of susceptibility based on prion-sequence polymorphism information without complex structural and molecular biological analyses may be possible. Information regarding the effects of mutations and polymorphisms on prion-disease susceptibility was collected based on previous studies to classify the susceptibilities of sequences, whereas the BLOSUM62 scoring matrix and the position-specific scoring matrix were utilised to determine the distance of target sequences. The k-nearest neighbour analysis was validated with cross-validation methods. The results indicated that the number of polymorphisms did not influence prion-disease susceptibility, and three and four k-objects showed the best accuracy in identifying the susceptible group. Although sequences with negative polymorphisms showed relatively high accuracy for determination, polymorphisms may still not be an appropriate factor for estimating variation in susceptibility. Discriminant analysis of prion sequences with scoring matrices was attempted as a possible means of determining susceptibility to prion diseases. Further research is required to improve the utility of this method.
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Affiliation(s)
- Ji-Hae Lee
- 1] Laboratory of Computational Biology and Bioinformatics, Graduate School of Public Health, Seoul National University, Gwanak-gu, Korea [2] Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, Gwanak-gu, Korea
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Venko K, Župerl Š, Novič M. Prediction of antiprion activity of therapeutic agents with structure–activity models. Mol Divers 2013; 18:133-48. [DOI: 10.1007/s11030-013-9477-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/31/2013] [Indexed: 10/26/2022]
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Giachin G, Biljan I, Ilc G, Plavec J, Legname G. Probing early misfolding events in prion protein mutants by NMR spectroscopy. Molecules 2013; 18:9451-76. [PMID: 23966072 PMCID: PMC6270549 DOI: 10.3390/molecules18089451] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/01/2013] [Accepted: 08/05/2013] [Indexed: 01/17/2023] Open
Abstract
The post-translational conversion of the ubiquitously expressed cellular form of the prion protein, PrPC, into its misfolded and pathogenic isoform, known as prion or PrPSc, plays a key role in prion diseases. These maladies are denoted transmissible spongiform encephalopathies (TSEs) and affect both humans and animals. A prerequisite for understanding TSEs is unraveling the molecular mechanism leading to the conversion process whereby most α-helical motifs are replaced by β-sheet secondary structures. Importantly, most point mutations linked to inherited prion diseases are clustered in the C-terminal domain region of PrPC and cause spontaneous conversion to PrPSc. Structural studies with PrP variants promise new clues regarding the proposed conversion mechanism and may help identify "hot spots" in PrPC involved in the pathogenic conversion. These investigations may also shed light on the early structural rearrangements occurring in some PrPC epitopes thought to be involved in modulating prion susceptibility. Here we present a detailed overview of our solution-state NMR studies on human prion protein carrying different pathological point mutations and the implications that such findings may have for the future of prion research.
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Affiliation(s)
- Gabriele Giachin
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265,Trieste I-34136, Italy; E-Mail:
| | - Ivana Biljan
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, Zagreb HR-10000, Croatia; E-Mail:
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia; E-Mails: (G.I.); (J.P.)
- EN-FIST Center of Excellence, Ljubljana SI-1000, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia; E-Mails: (G.I.); (J.P.)
- EN-FIST Center of Excellence, Ljubljana SI-1000, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265,Trieste I-34136, Italy; E-Mail:
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Zhou Z, Xiao G. Conformational conversion of prion protein in prion diseases. Acta Biochim Biophys Sin (Shanghai) 2013; 45:465-76. [PMID: 23580591 DOI: 10.1093/abbs/gmt027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Prion diseases are a group of infectious fatal neurodegenerative diseases. The conformational conversion of a cellular prion protein (PrP(C)) into an abnormal misfolded isoform (PrP(Sc)) is the key event in prion diseases pathology. Under normal conditions, the high-energy barrier separates PrP(C) from PrP(Sc) isoform. However, pathogenic mutations, modifications as well as some cofactors, such as glycosaminoglycans, nucleic acids, and lipids, could modulate the conformational conversion process. Understanding the mechanism of conformational conversion of prion protein is essential for the biomedical research and the treatment of prion diseases. Particularly, the characterization of cofactors interacting with prion protein might provide new diagnostic and therapeutic strategies.
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Affiliation(s)
- Zheng Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Basu U, Guan LL, Moore SS. Functional genomics approach for identification of molecular processes underlying neurodegenerative disorders in prion diseases. Curr Genomics 2013; 13:369-78. [PMID: 23372423 PMCID: PMC3401894 DOI: 10.2174/138920212801619223] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 12/11/2022] Open
Abstract
Prion diseases or transmissible spongiform encephalopathies (TSEs) are infectious neurodegenerative disorders leading to death. These include Cresutzfeldt-Jakob disease (CJD), familial, sporadic and variant CJD and kuru in humans; and animal TSEs include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) of mule deer and elk, and transmissible mink encephalopathy. All these TSEs share common pathological features such as accumulation of mis-folded prion proteins in the central nervous system leading to cellular dysfunction and cell death. It is important to characterize the molecular pathways and events leading to prion induced neurodegeneration. Here we discuss the impact of the functional genomics approaches including microarrays, subtractive hybridization and microRNA profiling in elucidating transcriptional cascades at different stages of disease. Many of these transcriptional changes have been observed in multiple neurodegenerative diseases which may aid in identification of biomarkers for disease. A comprehensive characterization of expression profiles implicated in neurodegenerative disorders will undoubtedly advance our understanding on neuropathology and dysfunction during prion disease and other neurodegenerative disorders. We also present an outlook on the future work which may focus on analysis of structural genetic variation, genome and transcriptome sequencing using next generation sequencing with an integrated approach on animal and human TSE related studies.
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Affiliation(s)
- Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
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Spevacek AR, Evans EGB, Miller JL, Meyer HC, Pelton JG, Millhauser GL. Zinc drives a tertiary fold in the prion protein with familial disease mutation sites at the interface. Structure 2013; 21:236-46. [PMID: 23290724 DOI: 10.1016/j.str.2012.12.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/04/2012] [Accepted: 12/11/2012] [Indexed: 12/21/2022]
Abstract
The cellular prion protein PrP(C) consists of two domains--a flexible N-terminal domain, which participates in copper and zinc regulation, and a largely helical C-terminal domain that converts to β sheet in the course of prion disease. These two domains are thought to be fully independent and noninteracting. Compelling cellular and biophysical studies, however, suggest a higher order structure that is relevant to both PrP(C) function and misfolding in disease. Here, we identify a Zn²⁺-driven N-terminal to C-terminal tertiary interaction in PrP(C). The C-terminal surface participating in this interaction carries the majority of the point mutations that confer familial prion disease. Investigation of mutant PrPs finds a systematic relationship between the type of mutation and the apparent strength of this domain structure. The structural features identified here suggest mechanisms by which physiologic metal ions trigger PrP(C) trafficking and control prion disease.
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Affiliation(s)
- Ann R Spevacek
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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38
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Chen J, Thirumalai D. Helices 2 and 3 are the initiation sites in the PrP(C) → PrP(SC) transition. Biochemistry 2012; 52:310-9. [PMID: 23256626 DOI: 10.1021/bi3005472] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
It is established that prion protein is the sole causative agent in a number of diseases in humans and animals. However, the nature of conformational changes that the normal cellular form, PrP(C), undergoes in its conversion to a self-replicating state is still not fully understood. The ordered C-terminus of PrP(C) proteins has three helices (H1-H3). Here, we use statistical coupling analysis (SCA) to infer covariations at various locations using a family of evolutionarily related sequences and the response of mouse and human PrP(C)s to mechanical force to decipher the initiation sites for the transition from PrP(C) to an aggregation-prone PrP* state. Sequence-based SCA predicts that the clustered residues in nonmammals are localized in the stable core (near H1) of PrP(C), whereas in mammalian PrP(C), they are localized in frustrated helices H2 and H3 where most of the pathogenic mutations are found. Force-extension curves and free energy profiles as a function of extension of mouse and human PrP(C) in the absence of a disulfide (SS) bond between residues Cys179 and Cys214, generated by applying mechanical force to the ends of the molecule, show a sequence of unfolding events starting first with rupture of H2 and H3. This is followed by disruption of structure in two strands. Helix H1, stabilized by three salt bridges, resists substantial force before unfolding. Force extension profiles and the dynamics of rupture of tertiary contacts also show that even in the presence of an SS bond the instabilities in most of H3 and parts of H2 still determine the propensity to form the PrP* state. In mouse PrP(C) with an SS bond, there are ∼10 residues that retain their order even at high forces. Both SCA and single-molecule force simulations show that in the conversion from PrP(C) to PrP(SC) major conformational changes occur (at least initially) in H2 and H3, which because of their sequence compositions are frustrated in the helical state. Implications of our findings for the structural model for the scrapie form of PrP(C) are discussed.
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Affiliation(s)
- Jie Chen
- Biophysics Program, Institute for Physical Science and Technology, and ‡Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, USA
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Poggiolini I, Legname G. Mapping the prion protein distribution in marsupials: insights from comparing opossum with mouse CNS. PLoS One 2012; 7:e50370. [PMID: 23209725 PMCID: PMC3510215 DOI: 10.1371/journal.pone.0050370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 10/18/2012] [Indexed: 02/04/2023] Open
Abstract
The cellular form of the prion protein (PrPC) is a sialoglycoprotein widely expressed in the central nervous system (CNS) of mammalian species during neurodevelopment and in adulthood. The location of the protein in the CNS may play a role in the susceptibility of a species to fatal prion diseases, which are also known as the transmissible spongiform encephalopathies (TSEs). To date, little is known about PrPC distribution in marsupial mammals, for which no naturally occurring prion diseases have been reported. To extend our understanding of varying PrPC expression profiles in different mammals we carried out a detailed expression analysis of PrPC distribution along the neurodevelopment of the metatherian South American short-tailed opossum (Monodelphis domestica). We detected lower levels of PrPC in white matter fiber bundles of opossum CNS compared to mouse CNS. This result is consistent with a possible role for PrPC in the distinct neurodevelopment and neurocircuitry found in marsupials compared to other mammalian species.
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Affiliation(s)
- Ilaria Poggiolini
- Department of Neuroscience, Laboratory of Prion Biology, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Giuseppe Legname
- Department of Neuroscience, Laboratory of Prion Biology, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- ELETTRA Laboratory, Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
- * E-mail:
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40
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Serpa JJ, Patterson AP, Pan J, Han J, Wishart DS, Petrotchenko EV, Borchers CH. Using multiple structural proteomics approaches for the characterization of prion proteins. J Proteomics 2012; 81:31-42. [PMID: 23085224 DOI: 10.1016/j.jprot.2012.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 10/07/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
Structural proteomics approaches are valuable tools, particularly in cases where the exact mechanisms of protein conformational changes or the structures of proteins and protein complexes cannot be elucidated by traditional structural biology techniques like X-ray crystallography or NMR methods. Each structural proteomics method can provide a different set of data, all of which can be used as structural constraints for modeling the protein. We have applied a combination of limited proteolysis, surface modification, chemical crosslinking, and hydrogen/deuterium exchange for the characterization of structural differences in prion proteins in native monomeric and in the aggregated β-oligomeric states. Data from these multiple proteomics approaches are in remarkable agreement in pointing to the rearrangement of the beta sheet 1-helix1-beta sheet 2-helix 2 (β1-H1-β2-H2) region as a major conformational change between the native and oligomeric prion protein forms. This data is also consistent with the β1-H1-β2 loop moving away from the H2-H3 core during the prion protein conversion. This is an example of how complementary data from multiple structural proteomics approaches can provide novel insights into the three-dimensional structures of proteins and protein complexes. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Jason J Serpa
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, British Columbia, Canada V8Z 7X8
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41
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Biljan I, Ilc G, Giachin G, Plavec J, Legname G. Structural Rearrangements at Physiological pH: Nuclear Magnetic Resonance Insights from the V210I Human Prion Protein Mutant. Biochemistry 2012; 51:7465-74. [DOI: 10.1021/bi3009856] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivana Biljan
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000
Ljubljana, Slovenia
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000
Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1001 Ljubljana,
Slovenia
| | - Gabriele Giachin
- Laboratory of Prion
Biology, Department
of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste, Italy
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000
Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1001 Ljubljana,
Slovenia
- Faculty of Chemistry and Chemical
Technology, University of Ljubljana, Aškerčeva
cesta 5, SI-1000 Ljubljana, Slovenia
| | - Giuseppe Legname
- Laboratory of Prion
Biology, Department
of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste, Italy
- ELETTRA Laboratory, Sincrotrone Trieste S.C.p.A., I-34149 Basovizza, Trieste,
Italy
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42
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Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism. Biochem J 2012; 446:243-51. [DOI: 10.1042/bj20111940] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The most common form of prion disease in humans is sCJD (sporadic Creutzfeldt–Jakob disease). The naturally occurring E219K polymorphism in the HuPrP (human prion protein) is considered to protect against sCJD. To gain insight into the structural basis of its protective influence we have determined the NMR structure of recombinant HuPrP (residues 90–231) carrying the E219K polymorphism. The structure of the HuPrP(E219K) protein consists of a disordered N-terminal tail (residues 90–124) and a well-structured C-terminal segment (residues 125–231) containing three α-helices and two short antiparallel β-strands. Comparison of NMR structures of the wild-type and HuPrPs with pathological mutations under identical experimental conditions revealed that, although the global architecture of the protein remains intact, replacement of Glu219 with a lysine residue introduces significant local structural changes. The structural findings of the present study suggest that the protective influence of the E219K polymorphism is due to the alteration of surface charge distribution, in addition to subtle structural rearrangements localized within the epitopes critical for prion conversion.
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Abstract
The conversion to a disease-associated conformer (PrP(Sc)) of the cellular prion protein (PrP(C)) is the central event in prion diseases. Wild-type PrPC converts to PrP(Sc) in the sporadic forms of the disorders through an unknown mechanism. These forms account for up to 85% of all human (Hu) occurrences; the infectious types contribute for less than 1%, while genetic incidence of the disease is about 15%. Familial Hu prion diseases are associated with about forty point mutations of the gene coding for the PrP denominated PRNP. Most of the variants associated with these mutations are located in the globular domain of the protein. In a recent work in collaboration with the German Research School for Simulation Science, in Jülich, Germany, we performed molecular dynamics simulations for each of these mutants to investigate their structure in aqueous solution. Structural analysis of the various point mutations present in the globular domain unveiled common folding traits that may allow to a better understanding of the early conformational changes leading to the formation of monomeric PrP(Sc). Recent experimental data support these findings, thus opening novel approaches to determine initial structural determinants of prion formation.
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Affiliation(s)
- Giuseppe Legname
- Laboratory of Prion Biology, Neurobiology Sector, Scuola Internazionale Superiore di Studi Avanzati-SISSA, Trieste, Italy.
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44
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D'Angelo P, Della Longa S, Arcovito A, Mancini G, Zitolo A, Chillemi G, Giachin G, Legname G, Benetti F. Effects of the pathological Q212P mutation on human prion protein non-octarepeat copper-binding site. Biochemistry 2012; 51:6068-79. [PMID: 22788868 DOI: 10.1021/bi300233n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Prion diseases are a class of fatal neurodegenerative disorders characterized by brain spongiosis, synaptic degeneration, microglia and astrocytes activation, neuronal loss and altered redox control. These maladies can be sporadic, iatrogenic and genetic. The etiological agent is the prion, a misfolded form of the cellular prion protein, PrP(C). PrP(C) interacts with metal ions, in particular copper and zinc, through the octarepeat and non-octarepeat binding sites. The physiological implication of this interaction is still unclear, as is the role of metals in the conversion. Since prion diseases present metal dyshomeostasis and increased oxidative stress, we described the copper-binding site located in the human C-terminal domain of PrP-HuPrP(90-231), both in the wild-type protein and in the protein carrying the pathological mutation Q212P. We used the synchrotron-based X-ray absorption fine structure technique to study the Cu(II) and Cu(I) coordination geometries in the mutant, and we compared them with those obtained using the wild-type protein. By analyzing the extended X-ray absorption fine structure and the X-ray absorption near-edge structure, we highlighted changes in copper coordination induced by the point mutation Q212P in both oxidation states. While in the wild-type protein the copper-binding site has the same structure for both Cu(II) and Cu(I), in the mutant the coordination site changes drastically from the oxidized to the reduced form of the copper ion. Copper-binding sites in the mutant resemble those obtained using peptides, confirming the loss of short- and long-range interactions. These changes probably cause alterations in copper homeostasis and, consequently, in redox control.
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Affiliation(s)
- Paola D'Angelo
- Department of Chemistry, University of Rome La Sapienza, P.le Aldo Moro 5, I-00185 Rome, Italy.
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Behmard E, Abdolmaleki P, Asadabadi EB. Mutation in a valine residue induces drastic changes in 3D structure of human prion protein. FRONTIERS IN LIFE SCIENCE 2012. [DOI: 10.1080/21553769.2013.775078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Scouras AD, Daggett V. Disruption of the X-loop turn of the prion protein linked to scrapie resistance. Protein Eng Des Sel 2012; 25:243-9. [PMID: 22447804 DOI: 10.1093/protein/gzs009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The prion diseases are a class of neurodegenerative diseases caused by the misfolding and aggregation of the prion protein (PrP(C)) into toxic and infectious oligomers (PrP(Sc)). These oligomers are critical to understanding and combating these diseases. Differences in the sequence of PrP affect disease susceptibility, likely by shifting the tolerance of the protein for adaptation to PrP(Sc) conformations and/or the recognition event between PrP(Sc) and PrP(C) prior to conversion of the PrP(C). We selected two sets of PrP(Sc)-resistant mutant sequences for solvated atomistic molecular dynamics simulation to investigate the structural basis of resistance. The first group involved mutation in the X-loop (residues 164-171) resulting from selective breeding of sheep. The second group included eight mutants in mice identified by random mutagenesis targeting helix C followed by screening in cell cultures. Multiple simulations were performed of 14 different mutant and control constructs under different pH conditions for a total of 3.6 μs of simulation time. The X-loop formed a stable turn at neutral pH in wild-type PrP from both species. PrP(Sc)-resistant mutations disrupted this turn even though only one of the mutants is in the X-loop. The X-loop is compact and buried in our previously described spiral models of PrP(Sc)-like oligomers. On the basis of the findings presented here and in the context of the spiral oligomer model, we propose that expansion of the X-loop disrupts protofibril packing, providing a structural basis for resistance.
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Affiliation(s)
- Alexander D Scouras
- Department of Biochemistry, University of Washington, Seattle, WA 98195-5013, USA
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Petrotchenko EV, Serpa JJ, Hardie DB, Berjanskii M, Suriyamongkol BP, Wishart DS, Borchers CH. Use of proteinase K nonspecific digestion for selective and comprehensive identification of interpeptide cross-links: application to prion proteins. Mol Cell Proteomics 2012; 11:M111.013524. [PMID: 22438564 DOI: 10.1074/mcp.m111.013524] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chemical cross-linking combined with mass spectrometry is a rapidly developing technique for structural proteomics. Cross-linked proteins are usually digested with trypsin to generate cross-linked peptides, which are then analyzed by mass spectrometry. The most informative cross-links, the interpeptide cross-links, are often large in size, because they consist of two peptides that are connected by a cross-linker. In addition, trypsin targets the same residues as amino-reactive cross-linkers, and cleavage will not occur at these cross-linker-modified residues. This produces high molecular weight cross-linked peptides, which complicates their mass spectrometric analysis and identification. In this paper, we examine a nonspecific protease, proteinase K, as an alternative to trypsin for cross-linking studies. Initial tests on a model peptide that was digested by proteinase K resulted in a "family" of related cross-linked peptides, all of which contained the same cross-linking sites, thus providing additional verification of the cross-linking results, as was previously noted for other post-translational modification studies. The procedure was next applied to the native (PrP(C)) and oligomeric form of prion protein (PrPβ). Using proteinase K, the affinity-purifiable CID-cleavable and isotopically coded cross-linker cyanurbiotindipropionylsuccinimide and MALDI-MS cross-links were found for all of the possible cross-linking sites. After digestion with proteinase K, we obtained a mass distribution of the cross-linked peptides that is very suitable for MALDI-MS analysis. Using this new method, we were able to detect over 60 interpeptide cross-links in the native PrP(C) and PrPβ prion protein. The set of cross-links for the native form was used as distance constraints in developing a model of the native prion protein structure, which includes the 90-124-amino acid N-terminal portion of the protein. Several cross-links were unique to each form of the prion protein, including a Lys(185)-Lys(220) cross-link, which is unique to the PrPβ and thus may be indicative of the conformational change involved in the formation of prion protein oligomers.
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Affiliation(s)
- Evgeniy V Petrotchenko
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
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