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Duran-Romaña R, Houben B, De Vleeschouwer M, Louros N, Wilson MP, Matthijs G, Schymkowitz J, Rousseau F. N-glycosylation as a eukaryotic protective mechanism against protein aggregation. SCIENCE ADVANCES 2024; 10:eadk8173. [PMID: 38295165 PMCID: PMC10830103 DOI: 10.1126/sciadv.adk8173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
The tendency for proteins to form aggregates is an inherent part of every proteome and arises from the self-assembly of short protein segments called aggregation-prone regions (APRs). While posttranslational modifications (PTMs) have been implicated in modulating protein aggregation, their direct role in APRs remains poorly understood. In this study, we used a combination of proteome-wide computational analyses and biophysical techniques to investigate the potential involvement of PTMs in aggregation regulation. Our findings reveal that while most PTM types are disfavored near APRs, N-glycosylation is enriched and evolutionarily selected, especially in proteins prone to misfolding. Experimentally, we show that N-glycosylation inhibits the aggregation of peptides in vitro through steric hindrance. Moreover, mining existing proteomics data, we find that the loss of N-glycans at the flanks of APRs leads to specific protein aggregation in Neuro2a cells. Our findings indicate that, among its many molecular functions, N-glycosylation directly prevents protein aggregation in higher eukaryotes.
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Affiliation(s)
- Ramon Duran-Romaña
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Matthias De Vleeschouwer
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Matthew P. Wilson
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Gert Matthijs
- Laboratory for Molecular Diagnosis, Center for Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
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Li J, Guo M, Chen L, Chen Z, Fu Y, Chen Y. Amyloid aggregates induced by the p53-R280T mutation lead to loss of p53 function in nasopharyngeal carcinoma. Cell Death Dis 2024; 15:35. [PMID: 38212344 PMCID: PMC10784298 DOI: 10.1038/s41419-024-06429-8] [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: 06/17/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant tumor that is highly prevalent in Southeast Asia, especially in South China. The pathogenesis of NPC is complex, and genetic alterations of tumor suppressors and proto-oncogenes play important roles in NPC carcinogenesis. p53 is unexpectedly highly expressed in NPC and possesses an uncommon mutation of R280T, which is different from a high frequency of hotspot mutations or low expression in other tumors. However, the mechanism of p53 loss of function and its correlation with R280T in NPC are still unclear. In this study, p53 amyloid aggregates were found to be widespread in NPC and can be mainly induced by the R280T mutation. Aggregated p53-R280T impeded its entry into the nucleus and was unable to initiate the transcription of downstream target genes, resulting in decreased NPC cell cycle arrest and apoptosis. In addition, NPC cells with p53-R280T amyloid aggregates also contributed aggressively to tumor growth in vivo. Transcriptome analysis suggested that p53 amyloid aggregation dysregulated major signaling pathways associated with the cell cycle, proliferation, apoptosis, and unfolded protein response (UPR). Further studies revealed that Hsp90, as a key molecular chaperone in p53 folding, was upregulated in NPC cells with p53-R280T aggregation, and the upregulated Hsp90 facilitated p53 aggregation in turn, forming positive feedback. Therefore, Hsp90 inhibitors could dissociate p53-R280T aggregation and restore the suppressor function of p53 in vitro and in vivo. In conclusion, our study demonstrated that p53-R280T may misfold to form aggregates with the help of Hsp90, resulting in the inability of sequestered p53 to initiate the transcription of downstream target genes. These results revealed a new mechanism for the loss of p53 function in NPC and provided novel mechanistic insight into NPC pathogenesis.
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Affiliation(s)
- Jingzhi Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Obstetrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Lin Chen
- Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, CAL, 90089, USA
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ying Fu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratory for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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3
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Aubrey LD, Ninkina N, Ulamec SM, Abramycheva NY, Vasili E, Devine OM, Wilkinson M, Mackinnon E, Limorenko G, Walko M, Muwanga S, Amadio L, Peters OM, Illarioshkin SN, Outeiro TF, Ranson NA, Brockwell DJ, Buchman VL, Radford SE. Substitution of Met-38 to Ile in γ-synuclein found in two patients with amyotrophic lateral sclerosis induces aggregation into amyloid. Proc Natl Acad Sci U S A 2024; 121:e2309700120. [PMID: 38170745 PMCID: PMC10786281 DOI: 10.1073/pnas.2309700120] [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: 06/08/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
α-, β-, and γ-Synuclein are intrinsically disordered proteins implicated in physiological processes in the nervous system of vertebrates. α-synuclein (αSyn) is the amyloidogenic protein associated with Parkinson's disease and certain other neurodegenerative disorders. Intensive research has focused on the mechanisms that cause αSyn to form amyloid structures, identifying its NAC region as being necessary and sufficient for amyloid assembly. Recent work has shown that a 7-residue sequence (P1) is necessary for αSyn amyloid formation. Although γ-synuclein (γSyn) is 55% identical in sequence to αSyn and its pathological deposits are also observed in association with neurodegenerative conditions, γSyn is resilient to amyloid formation in vitro. Here, we report a rare single nucleotide polymorphism (SNP) in the SNCG gene encoding γSyn, found in two patients with amyotrophic lateral sclerosis (ALS). The SNP results in the substitution of Met38 with Ile in the P1 region of the protein. These individuals also had a second, common and nonpathological, SNP in SNCG resulting in the substitution of Glu110 with Val. In vitro studies demonstrate that the Ile38 variant accelerates amyloid fibril assembly. Contrastingly, Val110 retards fibril assembly and mitigates the effect of Ile38. Substitution of residue 38 with Leu had little effect, while Val retards, and Ala increases the rate of amyloid formation. Ile38 γSyn also results in the formation of γSyn-containing inclusions in cells. The results show how a single point substitution can enhance amyloid formation of γSyn and highlight the P1 region in driving amyloid formation in another synuclein family member.
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Affiliation(s)
- Liam D. Aubrey
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Ninkina
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sabine M. Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Y. Abramycheva
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Eftychia Vasili
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Oliver M. Devine
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Eilish Mackinnon
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Galina Limorenko
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Sarah Muwanga
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Leonardo Amadio
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Owen M. Peters
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Sergey N. Illarioshkin
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Tiago F. Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen37075, Germany
- Max Planck Institute for Multidisciplinary Sciences, Goettingen37075, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon TyneNE2 4HH, United Kingdom
- Scientific employee with a honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen, Göttingen37075, Germany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Vladimir L. Buchman
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
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Bhoite SS, Kolli D, Gomulinski MA, Chapman MR. Electrostatic interactions mediate the nucleation and growth of a bacterial functional amyloid. Front Mol Biosci 2023; 10:1070521. [PMID: 36756360 PMCID: PMC9900396 DOI: 10.3389/fmolb.2023.1070521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Bacterial biofilm formation can have severe impacts on human and environmental health. Enteric bacteria produce functional amyloid fibers called curli that aid in biofilm formation and host colonization. CsgA is the major proteinaceous component of curli amyloid fibers and is conserved in many gram-negative enteric bacteria. The CsgA amyloid core consists of five imperfect repeats (R1-R5). R2, R3, and R4 have aspartic acid (D) and glycine (G) residues that serve as "gatekeeper" residues by modulating the intrinsic aggregation propensity of CsgA. Here, using mutagenesis, salt-mediated charge screening, and by varying pH conditions, we show that the ability of CsgA variants to nucleate and form amyloid fibers is dictated by the charge state of the gatekeeper residues. We report that in Citrobacter youngae CsgA, certain arginine (R) and lysine (K) residues also act as gatekeeper residues. A mechanism of gatekeeping is proposed wherein R and K residues electrostatically interact with negatively charged D residues, tempering CsgA fiber formation.
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The First Homozygote Mutation c.499G>T (Asp167Tyr) in the RPE65 Gene Encoding Retinoid Isomerohydrolase Causing Retinal Dystrophy. Curr Issues Mol Biol 2022; 44:6397-6403. [PMID: 36547097 PMCID: PMC9777422 DOI: 10.3390/cimb44120436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
RPE65, an abundant membrane-associated protein present in the retinal pigment epithelium (RPE), is a vital retinoid isomerase necessary for regenerating 11-cis-retinaldehyde from all-trans retinol in the visual cycle. In patients with inherited retinal dystrophy (IRD), precise genetic diagnosis is an indispensable approach as it is required to establish eligibility for the genetic treatment of RPE65-associated IRDs. This case report aims to report the specific phenotype−genotype correlation of the first patient with a homozygous missense variant RPE65 c.499G>T, p. (Asp167Tyr). We report a case of a 66-year-old male who demonstrated a unique phenotype manifesting less severe functional vision deterioration in childhood and adolescence, and extensive nummular pigment clusters. The underlying causes of the differences in the typical bone spicule and atypical nummular pigment clumping are unknown, but suggest that the variant itself influenced the rate of photoreceptor death. Functional studies are needed to define whether the substitution of aspartate impairs the folding of the tertiary RPE65 structure only and does not lead to the complete abolishment of chromophore production, thus explaining the less severe phenotype in adolescence.
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6
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Pal S, Udgaonkar JB. Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form. J Mol Biol 2022; 434:167854. [PMID: 36228749 DOI: 10.1016/j.jmb.2022.167854] [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: 07/25/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The misfolding of the prion protein has been linked to several neurodegenerative diseases. Despite extensive studies, the mechanism of the misfolding process remains poorly understood. The present study structurally delineates the role of the conserved proline residues present in the structured C-terminal domain of the mouse prion protein (moPrP) in the misfolding process. It is shown that mutation of these Pro residues to Ala leads to destabilization of the native (N) state, and also to rapid misfolding. Using hydrogen-deuterium exchange (HDX) studies coupled with mass spectrometry (MS), it has been shown that the N state of moPrP is in rapid equilibrium with a partially unfolded form (PUF2*) at pH 4. It has been shown that the Pro to Ala mutations make PUF2* energetically more accessible from the N state by stabilizing it relative to the unfolded (U) state. The apparent rate constant of misfolding is found to be linearly proportional to the extent to which PUF2* is populated in equilibrium with the N state, strongly indicating that misfolding commences from PUF2*. It has also been shown that the Pro residues restrict the boundary of the structural core of the misfolded oligomers. Overall, this study highlights how the conserved proline residues control misfolding of the prion protein by modulating the stability of the partially unfolded form from which misfolding commences.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research, Pune, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research, Pune, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
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7
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Randhawa S, Abidi SMS, Dar AI, Acharya A. The curious cases of nanoparticle induced amyloidosis during protein corona formation and anti-amyloidogenic nanomaterials: Paradox or prejudice? Int J Biol Macromol 2021; 193:1009-1020. [PMID: 34728302 DOI: 10.1016/j.ijbiomac.2021.10.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022]
Abstract
Protein corona (PC) formation remains a major hurdle in the successful delivery of nanomedicines to the target sites. Interacting proteins have been reported to undergo structural changes on the nanoparticle (NP) surface which invariably impacts their biological activities. Such structural changes are the result of opening of more binding sites of proteins to adsorb on the NP surface. The process of conversion of α-helix proteins to their β-sheet enriched counterpart is termed as amyloidosis and in case of PC formation, NPs apparently play the crucial role of being the nucleation centres where this process takes place. Conversely, increasing numbers of artificial nano-chaperones are being used to treat the protein misfolding disorders. Anti-amyloidogenic nanomaterials (NM) have been gaining utmost importance in inhibiting Aβ42 (hallmark peptide for Alzheimer's disease) and Hen egg white lysozyme (HEWL, model protein for systemic amyloidosis) aggregation. Interestingly, in this process, NPs inhibit protein β-sheet enrichment. These two seemingly opposite roles of NPs, propelling confirmatory change onto the smorgasbord of adsorbed native proteins and the ability of NPs in inhibiting amyloidosis creates a paradox, which has not been discussed earlier. Here, we highlight the key points from both the facets of the NP behaviour with respect to their physicochemical properties and the nature of proteins they adsorb onto them to unravel the mystery. BRIEF: Protein corona formation remains a major hurdle in achieving the desired efficacy of nanomedicine. Proteins when interact with nanoparticle (NP) surface, undergo both structural and biological changes. Again, NPs are known to exhibit anti-amyloidogenic behaviour where these play the crucial role of preventing any change in their native structure. Such seemingly different roles of NPs need sincere inquisition.
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Affiliation(s)
- Shiwani Randhawa
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Syed M S Abidi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aqib Iqbal Dar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amitabha Acharya
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (H.P.) 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nat Commun 2021; 12:6414. [PMID: 34741024 PMCID: PMC8571348 DOI: 10.1038/s41467-021-26720-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 10/15/2021] [Indexed: 11/09/2022] Open
Abstract
While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium. .,Department of Biochemistry and Biophysics, UCSF, San Francisco, CA, USA.
| | - Pathmanaban Ramasamy
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium ,grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Jasper Zuallaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium ,grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Robbin Bouwmeester
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Berre Van Moer
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Davy Maddelein
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Demet Turan
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Niels Hulstaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hannah Eeckhaut
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Elien Vandermarliere
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lennart Martens
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sven Degroeve
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Wesley De Neve
- grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Wim Vranken
- grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
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9
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Lei J, Cai M, Shen Y, Lin D, Deng X. Molecular dynamics study on the inhibition mechanisms of ReACp53 peptide for p53-R175H mutant aggregation. Phys Chem Chem Phys 2021; 23:23032-23041. [PMID: 34612239 DOI: 10.1039/d1cp03094a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
p53 mutant aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, involving in tumor growth. Finding inhibition methods of p53 mutant aggregation is a key step for developing new therapeutics against aggregation-associated cancers. Recent studies have shown that a cell-permeable peptide, ReACp53, can inhibit aggregation of the p53 mutant and restore p53 nuclear function as a transcriptional factor, showing extraordinary therapeutic potential. However, the molecular mechanism underlying the inhibition of p53 mutant aggregation by the ReAp53 peptide is unclear. In this work, we used all-atom molecular dynamics (MD) simulations to investigate the effect of ReACp53 peptide on the structural and dynamic properties of the p53 core domain (p53C) of the aggregation-prone R175H mutant. Our simulations revealed that the ReACp53 peptide can stabilize the ordered secondary structure and decrease the flexibility of disordered loops of the R175H mutant through increasing the intra-interactions of p53C. Moreover, we found that ReACp53 peptide specifically binds to the fragment (residues 180-233) of the R175H mutant through strong hydrophobic interactions with residues L188 and L201 and a salt bridge or hydrogen bond formation with residues D186, E198, D204, E221 and E224. The specific binding pattern protects the aggregation-prone fragment (residues 182-213) from exposure to water. Hence, we suggested that the ReACp53 peptide inhibits aggregation of the R175H mutant by restoring the wild-type conformation from an aggregation-prone state and reducing the exposure of the aggregation-prone segment. These results provide molecular mechanistic insight into inhibition of the ReACp53 peptide on amyloid aggregation of the R175H mutant.
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Affiliation(s)
- Jiangtao Lei
- Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
| | - Mengqiang Cai
- Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
| | - Yun Shen
- Department of Physics, School of Sciences, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China
| | - Dongdong Lin
- Department of Physics and Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang City 315211, China
| | - Xiaohua Deng
- Institute of Space Science and Technology, Nanchang University, Xuefu Avenue 999, Nanchang City 330031, China.
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10
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Pigazzini ML, Lawrenz M, Margineanu A, Kaminski Schierle GS, Kirstein J. An Expanded Polyproline Domain Maintains Mutant Huntingtin Soluble in vivo and During Aging. Front Mol Neurosci 2021; 14:721749. [PMID: 34720872 PMCID: PMC8554126 DOI: 10.3389/fnmol.2021.721749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/30/2021] [Indexed: 02/02/2023] Open
Abstract
Huntington's disease is a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG repeat, encoding for the amino acid glutamine (Q), present in the first exon of the protein huntingtin. Over the threshold of Q39 HTT exon 1 (HTTEx1) tends to misfold and aggregate into large intracellular structures, but whether these end-stage aggregates or their on-pathway intermediates are responsible for cytotoxicity is still debated. HTTEx1 can be separated into three domains: an N-terminal 17 amino acid region, the polyglutamine (polyQ) expansion and a C-terminal proline rich domain (PRD). Alongside the expanded polyQ, these flanking domains influence the aggregation propensity of HTTEx1: with the N17 initiating and promoting aggregation, and the PRD modulating it. In this study we focus on the first 11 amino acids of the PRD, a stretch of pure prolines, which are an evolutionary recent addition to the expanding polyQ region. We hypothesize that this proline region is expanding alongside the polyQ to counteract its ability to misfold and cause toxicity, and that expanding this proline region would be overall beneficial. We generated HTTEx1 mutants lacking both flanking domains singularly, missing the first 11 prolines of the PRD, or with this stretch of prolines expanded. We then followed their aggregation landscape in vitro with a battery of biochemical assays, and in vivo in novel models of C. elegans expressing the HTTEx1 mutants pan-neuronally. Employing fluorescence lifetime imaging we could observe the aggregation propensity of all HTTEx1 mutants during aging and correlate this with toxicity via various phenotypic assays. We found that the presence of an expanded proline stretch is beneficial in maintaining HTTEx1 soluble over time, regardless of polyQ length. However, the expanded prolines were only advantageous in promoting the survival and fitness of an organism carrying a pathogenic stretch of Q48 but were extremely deleterious to the nematode expressing a physiological stretch of Q23. Our results reveal the unique importance of the prolines which have and still are evolving alongside expanding glutamines to promote the function of HTTEx1 and avoid pathology.
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Affiliation(s)
- Maria Lucia Pigazzini
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Mandy Lawrenz
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
| | - Anca Margineanu
- Advanced Light Microscopy, Max-Delbrück Centrum for Molecular Medicine (MDC), Berlin, Germany
| | - Gabriele S. Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Janine Kirstein
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- Department of Cell Biology, University of Bremen, Bremen, Germany
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11
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Prabakaran R, Rawat P, Yasuo N, Sekijima M, Kumar S, Gromiha MM. Effect of charged mutation on aggregation of a pentapeptide: Insights from molecular dynamics simulations. Proteins 2021; 90:405-417. [PMID: 34460128 DOI: 10.1002/prot.26230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/30/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022]
Abstract
Aggregation of therapeutic monoclonal antibodies (mAbs) can negatively affect their chemistry, manufacturing, and control attributes and lead to undesirable immune responses in patients. Therefore, optimization of lead mAb drug candidates during discovery stages to mitigate aggregation is increasingly becoming an integral part of their developability assessments. The disruption of short sequence motifs called aggregation prone regions (APRs) found in amino acid sequences of mAb candidates can potentially mitigate their aggregation. In this work, we have performed molecular dynamics simulations to study the aggregation of an APR (VLVIY) found in λ light chains of human antibodies and its single point mutant KLVIY. Eighteen different multicopy peptide simulation systems of "VLVIY" and "KLVIY" were constructed by varying their concentrations, temperatures, termini capping, and flanking gate-keeper regions. Within 20 ns of the simulation, peptide "VLVIY" formed an aggregate of 100 peptides at ~0.1 M concentration with a 60% reduction in solvent accessible surface area (SASA). Furthermore, analysis of the SASA change, peptide cluster distribution, and water residence time demonstrated how Val ➔ Lys mutation resists aggregation and improves solubility. Presence of Lys slows down aggregation kinetics via charge-charge repulsions and by raising the kinetic barrier to formation of large oligomers. However, the effect of the Val ➔ Lys mutation is dependent on sequence and structural contexts around the APR. This mutation also alters the solvation shell around the peptide by favoring solute-solvent interactions, thereby increasing its solubility. This work has provided a detailed mechanistic explanation of how APR disruption can mitigate aggregation in biotherapeutics and improve their developability.
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Affiliation(s)
- R Prabakaran
- Protein Bioinformatics Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Puneet Rawat
- Protein Bioinformatics Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Nobuaki Yasuo
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Masakazu Sekijima
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, Connecticut, USA
| | - M Michael Gromiha
- Protein Bioinformatics Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India.,Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
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12
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Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M, Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T, Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function. Nat Commun 2021; 12:3962. [PMID: 34172723 PMCID: PMC8233319 DOI: 10.1038/s41467-021-23985-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/26/2021] [Indexed: 02/05/2023] Open
Abstract
Missense mutations in p53 are severely deleterious and occur in over 50% of all human cancers. The majority of these mutations are located in the inherently unstable DNA-binding domain (DBD), many of which destabilize the domain further and expose its aggregation-prone hydrophobic core, prompting self-assembly of mutant p53 into inactive cytosolic amyloid-like aggregates. Screening an oligopyridylamide library, previously shown to inhibit amyloid formation associated with Alzheimer's disease and type II diabetes, identified a tripyridylamide, ADH-6, that abrogates self-assembly of the aggregation-nucleating subdomain of mutant p53 DBD. Moreover, ADH-6 targets and dissociates mutant p53 aggregates in human cancer cells, which restores p53's transcriptional activity, leading to cell cycle arrest and apoptosis. Notably, ADH-6 treatment effectively shrinks xenografts harboring mutant p53, while exhibiting no toxicity to healthy tissue, thereby substantially prolonging survival. This study demonstrates the successful application of a bona fide small-molecule amyloid inhibitor as a potent anticancer agent.
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Affiliation(s)
- L Palanikumar
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Laura Karpauskaite
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mohamed Al-Sayegh
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Ibrahim Chehade
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Maheen Alam
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sarah Hassan
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Debabrata Maity
- Department of Chemistry, New York University, New York, NY, USA
| | - Liaqat Ali
- Core Technology Platforms, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Mona Kalmouni
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Yamanappa Hunashal
- Chemistry Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.,DAME, Università di Udine, Udine, Italy
| | - Jemil Ahmed
- Department of Chemistry and Biochemistry and Knoebel Institute for Healthy Aging, The University of Denver, Denver, CO, USA
| | - Tatiana Houhou
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Shake Karapetyan
- Physics Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Zackary Falls
- Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), Buffalo, NY, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, School of Medicine and Biomedical Sciences, State University of New York (SUNY), Buffalo, NY, USA
| | - Renu Pasricha
- Core Technology Platforms, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Gennaro Esposito
- Chemistry Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.,INBB, Rome, Italy
| | - Ahmed J Afzal
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | | | - Sunil Kumar
- Department of Chemistry and Biochemistry and Knoebel Institute for Healthy Aging, The University of Denver, Denver, CO, USA.
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates.
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13
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AbsoluRATE: An in-silico method to predict the aggregation kinetics of native proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140682. [PMID: 34102324 DOI: 10.1016/j.bbapap.2021.140682] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/12/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Protein aggregation has two aspects, namely, mechanistic and kinetics. Understanding protein aggregation kinetics is critical for prediction of progression of diseases caused by amyloidosis, accumulation of aggregates in biotherapeutics during storage and engineering commercial nano-biomaterials. In this work, we have collected experimentally determined absolute protein aggregation rates and developed an SVM based regression model to predict absolute rates of protein and peptide aggregation near-physiological conditions. The regression model achieved a correlation coefficient of 0.72 with MAE of 0.91 (natural log of kapp, where kapp is in hour-1) using leave-one-out cross-validation on a dataset of 82 non-redundant proteins/peptides. The model accounts for the experimental conditions (such as temperature, pH, ionic and protein concentration) and sequence-based properties. The amino acid sequence features revealed by this model as being important for aggregation kinetics, are also associated with the aggregation mechanism. In particular, inherent aggregation propensity of the protein/peptide sequence and number of aggregation prone regions (APRs) unpunctuated by the gatekeeping residues, were found to play important roles in the prediction of the absolute aggregation rates. This analysis shows that mechanism and kinetics of protein aggregation are coupled via common sequence attributes. The aggregation kinetic prediction method developed in this work is available at https://web.iitm.ac.in/bioinfo2/absolurate-pred/index.html.
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14
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Khodaparast L, Wu G, Khodaparast L, Schmidt BZ, Rousseau F, Schymkowitz J. Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention. Front Mol Biosci 2021; 8:681855. [PMID: 34150852 PMCID: PMC8206779 DOI: 10.3389/fmolb.2021.681855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cells have evolved a complex molecular network, collectively called the protein homeostasis (proteostasis) network, to produce and maintain proteins in the appropriate conformation, concentration and subcellular localization. Loss of proteostasis leads to a reduction in cell viability, which occurs to some degree during healthy ageing, but is also the root cause of a group of diverse human pathologies. The accumulation of proteins in aberrant conformations and their aggregation into specific beta-rich assemblies are particularly detrimental to cell viability and challenging to the protein homeostasis network. This is especially true for bacteria; it can be argued that the need to adapt to their changing environments and their high protein turnover rates render bacteria particularly vulnerable to the disruption of protein homeostasis in general, as well as protein misfolding and aggregation. Targeting bacterial proteostasis could therefore be an attractive strategy for the development of novel antibacterial therapeutics. This review highlights advances with an antibacterial strategy that is based on deliberately inducing aggregation of target proteins in bacterial cells aiming to induce a lethal collapse of protein homeostasis. The approach exploits the intrinsic aggregation propensity of regions residing in the hydrophobic core regions of the polypeptide sequence of proteins, which are genetically conserved because of their essential role in protein folding and stability. Moreover, the molecules were designed to target multiple proteins, to slow down the build-up of resistance. Although more research is required, results thus far allow the hope that this strategy may one day contribute to the arsenal to combat multidrug-resistant bacterial infections.
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Affiliation(s)
- Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
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15
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Ulamec SM, Brockwell DJ, Radford SE. Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins. Front Neurosci 2020; 14:611285. [PMID: 33335475 PMCID: PMC7736610 DOI: 10.3389/fnins.2020.611285] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid proteins are involved in many neurodegenerative disorders such as Alzheimer’s disease [Tau, Amyloid β (Aβ)], Parkinson’s disease [alpha-synuclein (αSyn)], and amyotrophic lateral sclerosis (TDP-43). Driven by the early observation of the presence of ordered structure within amyloid fibrils and the potential to develop inhibitors of their formation, a major goal of the amyloid field has been to elucidate the structure of the amyloid fold at atomic resolution. This has now been achieved for a wide variety of sequences using solid-state NMR, microcrystallography, X-ray fiber diffraction and cryo-electron microscopy. These studies, together with in silico methods able to predict aggregation-prone regions (APRs) in protein sequences, have provided a wealth of information about the ordered fibril cores that comprise the amyloid fold. Structural and kinetic analyses have also shown that amyloidogenic proteins often contain less well-ordered sequences outside of the amyloid core (termed here as flanking regions) that modulate function, toxicity and/or aggregation rates. These flanking regions, which often form a dynamically disordered “fuzzy coat” around the fibril core, have been shown to play key parts in the physiological roles of functional amyloids, including the binding of RNA and in phase separation. They are also the mediators of chaperone binding and membrane binding/disruption in toxic amyloid assemblies. Here, we review the role of flanking regions in different proteins spanning both functional amyloid and amyloid in disease, in the context of their role in aggregation, toxicity and cellular (dys)function. Understanding the properties of these regions could provide new opportunities to target disease-related aggregation without disturbing critical biological functions.
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Affiliation(s)
- Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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16
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Prabakaran R, Rawat P, Kumar S, Michael Gromiha M. ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins. J Mol Biol 2020; 433:166707. [PMID: 33972019 DOI: 10.1016/j.jmb.2020.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022]
Abstract
Short aggregation prone sequence motifs can trigger aggregation in peptide and protein sequences. Most algorithms developed so far to identify potential aggregation prone regions (APRs) use amino acid residue composition and/or sequence pattern features. In this work, we have investigated the importance of atomic-level characteristics rather than residue level to understand the initiation of aggregation in proteins and peptides. Using atomic-level features an ensemble-classifier, ANuPP has been developed to predict the aggregation-nucleating regions in peptides and proteins. In a dataset of 1279 hexapeptides, ANuPP achieved an area under the curve (AUC) of 0.831 with 77% accuracy on 10-fold cross-validation and an AUC of 0.883 with 83% accuracy in a blind test dataset of 142 hexapeptides. Further, it showed an average SOV of 48.7% on identifying APR regions in 37 proteins. The performance of ANuPP is better than other methods reported in the literature on both amyloidogenic hexapeptide prediction and APR identification. We have developed a web server for ANuPP and it is available at https://web.iitm.ac.in/bioinfo2/ANuPP/. Insights gained from this work demonstrate the importance of atomic and functional group characteristics towards diversity of atomic level origins as well as mechanisms of protein aggregation.
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Affiliation(s)
- R Prabakaran
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Puneet Rawat
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT, USA.
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India; School of Computing, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan.
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17
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Houben B, Michiels E, Ramakers M, Konstantoulea K, Louros N, Verniers J, van der Kant R, De Vleeschouwer M, Chicória N, Vanpoucke T, Gallardo R, Schymkowitz J, Rousseau F. Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues. EMBO J 2020; 39:e102864. [PMID: 32237079 PMCID: PMC7265246 DOI: 10.15252/embj.2019102864] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
Many chaperones favour binding to hydrophobic sequences that are flanked by basic residues while disfavouring acidic residues. However, the origin of this bias in protein quality control remains poorly understood. Here, we show that while acidic residues are the most efficient aggregation inhibitors, they are also less compatible with globular protein structure than basic amino acids. As a result, while acidic residues allow for chaperone-independent control of aggregation, their use is structurally limited. Conversely, we find that, while being more compatible with globular structure, basic residues are not sufficient to autonomously suppress protein aggregation. Using Hsp70, we show that chaperones with a bias towards basic residues are structurally adapted to prioritize aggregating sequences whose structural context forced the use of the less effective basic residues. The hypothesis that emerges from our analysis is that the bias of many chaperones for basic residues results from fundamental thermodynamic and kinetic constraints of globular structure. This also suggests the co-evolution of basic residues and chaperones allowed for an expansion of structural variety in the protein universe.
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Affiliation(s)
- Bert Houben
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Meine Ramakers
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Katerina Konstantoulea
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Joffré Verniers
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Rob van der Kant
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Matthias De Vleeschouwer
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Nuno Chicória
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Thomas Vanpoucke
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Rodrigo Gallardo
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KULeuven, Leuven, Belgium
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18
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Langenberg T, Gallardo R, van der Kant R, Louros N, Michiels E, Duran-Romaña R, Houben B, Cassio R, Wilkinson H, Garcia T, Ulens C, Van Durme J, Rousseau F, Schymkowitz J. Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins. Cell Rep 2020; 31:107512. [PMID: 32294448 PMCID: PMC7175379 DOI: 10.1016/j.celrep.2020.03.076] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/12/2020] [Accepted: 03/23/2020] [Indexed: 11/19/2022] Open
Abstract
The amyloid-like aggregation propensity present in most globular proteins is generally considered to be a secondary side effect resulting from the requirements of protein stability. Here, we demonstrate, however, that mutations in the globular and amyloid state are thermodynamically correlated rather than simply associated. In addition, we show that the standard genetic code couples this structural correlation into a tight evolutionary relationship. We illustrate the extent of this evolutionary entanglement of amyloid propensity and globular protein stability. Suppressing a 600-Ma-conserved amyloidogenic segment in the p53 core domain fold is structurally feasible but requires 7-bp substitutions to concomitantly introduce two aggregation-suppressing and three stabilizing amino acid mutations. We speculate that, rather than being a corollary of protein evolution, it is equally plausible that positive selection for amyloid structure could have been a driver for the emergence of globular protein structure.
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Affiliation(s)
- Tobias Langenberg
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Rodrigo Gallardo
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Rob van der Kant
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Ramon Duran-Romaña
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Rafaela Cassio
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Hannah Wilkinson
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Teresa Garcia
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Chris Ulens
- Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Joost Van Durme
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
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19
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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20
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Computational Assessment of Bacterial Protein Structures Indicates a Selection Against Aggregation. Cells 2019; 8:cells8080856. [PMID: 31398930 PMCID: PMC6721704 DOI: 10.3390/cells8080856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
The aggregation of proteins compromises cell fitness, either because it titrates functional proteins into non-productive inclusions or because it results in the formation of toxic assemblies. Accordingly, computational proteome-wide analyses suggest that prevention of aggregation upon misfolding plays a key role in sequence evolution. Most proteins spend their lifetimes in a folded state; therefore, it is conceivable that, in addition to sequences, protein structures would have also evolved to minimize the risk of aggregation in their natural environments. By exploiting the AGGRESCAN3D structure-based approach to predict the aggregation propensity of >600 Escherichia coli proteins, we show that the structural aggregation propensity of globular proteins is connected with their abundance, length, essentiality, subcellular location and quaternary structure. These data suggest that the avoidance of protein aggregation has contributed to shape the structural properties of proteins in bacterial cells.
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21
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Chen D, Drombosky KW, Hou Z, Sari L, Kashmer OM, Ryder BD, Perez VA, Woodard DR, Lin MM, Diamond MI, Joachimiak LA. Tau local structure shields an amyloid-forming motif and controls aggregation propensity. Nat Commun 2019; 10:2493. [PMID: 31175300 PMCID: PMC6555816 DOI: 10.1038/s41467-019-10355-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Tauopathies are neurodegenerative diseases characterized by intracellular amyloid deposits of tau protein. Missense mutations in the tau gene (MAPT) correlate with aggregation propensity and cause dominantly inherited tauopathies, but their biophysical mechanism driving amyloid formation is poorly understood. Many disease-associated mutations localize within tau's repeat domain at inter-repeat interfaces proximal to amyloidogenic sequences, such as 306VQIVYK311. We use cross-linking mass spectrometry, recombinant protein and synthetic peptide systems, in silico modeling, and cell models to conclude that the aggregation-prone 306VQIVYK311 motif forms metastable compact structures with its upstream sequence that modulates aggregation propensity. We report that disease-associated mutations, isomerization of a critical proline, or alternative splicing are all sufficient to destabilize this local structure and trigger spontaneous aggregation. These findings provide a biophysical framework to explain the basis of early conformational changes that may underlie genetic and sporadic tau pathogenesis.
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Affiliation(s)
- Dailu Chen
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kenneth W Drombosky
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zhiqiang Hou
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Levent Sari
- Green Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Omar M Kashmer
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bryan D Ryder
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Valerie A Perez
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - DaNae R Woodard
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Milo M Lin
- Green Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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22
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Foy SG, Wilson BA, Bertram J, Cordes MHJ, Masel J. A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution. Genetics 2019; 211:1345-1355. [PMID: 30692195 PMCID: PMC6456324 DOI: 10.1534/genetics.118.301719] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/25/2019] [Indexed: 01/06/2023] Open
Abstract
To detect a direction to evolution, without the pitfalls of reconstructing ancestral states, we need to compare "more evolved" to "less evolved" entities. But because all extant species have the same common ancestor, none are chronologically more evolved than any other. However, different gene families were born at different times, allowing us to compare young protein-coding genes to those that are older and hence have been evolving for longer. To be retained during evolution, a protein must not only have a function, but must also avoid toxic dysfunction such as protein aggregation. There is conflict between the two requirements: hydrophobic amino acids form the cores of protein folds, but also promote aggregation. Young genes avoid strongly hydrophobic amino acids, which is presumably the simplest solution to the aggregation problem. Here we show that young genes' few hydrophobic residues are clustered near one another along the primary sequence, presumably to assist folding. The higher aggregation risk created by the higher hydrophobicity of older genes is counteracted by more subtle effects in the ordering of the amino acids, including a reduction in the clustering of hydrophobic residues until they eventually become more interspersed than if distributed randomly. This interspersion has previously been reported to be a general property of proteins, but here we find that it is restricted to old genes. Quantitatively, the index of dispersion delineates a gradual trend, i.e., a decrease in the clustering of hydrophobic amino acids over billions of years.
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Affiliation(s)
- Scott G Foy
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Benjamin A Wilson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Jason Bertram
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Matthew H J Cordes
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
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23
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Choi EH, Suh S, Sander CL, Hernandez CJO, Bulman ER, Khadka N, Dong Z, Shi W, Palczewski K, Kiser PD. Insights into the pathogenesis of dominant retinitis pigmentosa associated with a D477G mutation in RPE65. Hum Mol Genet 2019; 27:2225-2243. [PMID: 29659842 DOI: 10.1093/hmg/ddy128] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/06/2018] [Indexed: 12/31/2022] Open
Abstract
RPE65 is the essential trans-cis isomerase of the classical retinoid (visual) cycle. Mutations in RPE65 give rise to severe retinal dystrophies, most of which are associated with loss of protein function and recessive inheritance. The only known exception is a c.1430G>A (D477G) mutation that gives rise to dominant retinitis pigmentosa with delayed onset and choroidal and macular involvement. Position 477 is distant from functionally critical regions of RPE65. Hence, the mechanism of D477G pathogenicity remains unclear, although protein misfolding and aggregation mechanisms have been suggested. We characterized a D477G knock-in mouse model which exhibited mild age-dependent changes in retinal structure and function. Immunoblot analysis of protein extracts from the eyes of these knock-in mice demonstrated the presence of ubiquitinated RPE65 and reduced RPE65 expression. We observed an accumulation of retinyl esters in the knock-in mice as well as a delay in rhodopsin regeneration kinetics and diminished electroretinography responses, indicative of RPE65 functional impairment induced by the D477G mutation in vivo. However, a cell line expressing D477G RPE65 revealed protein expression levels, cellular localization and retinoid isomerase activity comparable to cells expressing wild-type protein. Structural analysis of an RPE65 chimera suggested that the D477G mutation does not perturb protein folding or tertiary structure. Instead, the mutation generates an aggregation-prone surface that could induce cellular toxicity through abnormal complex formation as suggested by crystal packing analysis. These results indicate that a toxic gain-of-function induced by the D477G RPE65 substitution may play a role in the pathogenesis of this form of dominant retinitis pigmentosa.
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Affiliation(s)
- Elliot H Choi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Susie Suh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Christopher L Sander
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Christian J Ortiz Hernandez
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,University of Puerto Rico at Humacao, Humacao, PR, USA
| | - Elizabeth R Bulman
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA
| | - Nimesh Khadka
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Zhiqian Dong
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Polgenix Inc., Cleveland, OH 44106, USA
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Philip D Kiser
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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24
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Jha NN, Ranganathan S, Kumar R, Mehra S, Panigrahi R, Navalkar A, Ghosh D, Kumar A, Padinhateeri R, Maji SK. Complexation of NAC-Derived Peptide Ligands with the C-Terminus of α-Synuclein Accelerates Its Aggregation. Biochemistry 2018; 57:791-804. [DOI: 10.1021/acs.biochem.7b01090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Narendra Nath Jha
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | | | - Rakesh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Rajlaxmi Panigrahi
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
| | | | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India
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25
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Shigemitsu Y, Hiroaki H. Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis. J Biochem 2018; 163:11-18. [PMID: 28992347 DOI: 10.1093/jb/mvx056] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/17/2017] [Indexed: 01/23/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are either completely unstructured or contain large disordered regions in their native state; they have drawn much attention in the field of molecular pathology. Some of them substantially tend to form protein self-assemblies, such as toxic or non-toxic aggregates and fibrils, and have been postulated to relate to diseases. These disease-related IDPs include Aβ(1-42) [Alzheimer's disease (AD)], Tau (AD and tauopathy), α-synuclein (Parkinson's disease) and p53 (cancer). Several studies suggest that these aggregation and/or fibril formation processes are often initiated by transient conformational changes of the IDPs prior to protein self-assembly. Interestingly, the pathological molecular processes of these IDPs share multiple common features with those of protein misfolding diseases, such as transmissible spongiform encephalopathy (PrPsc) and AL-amyloidosis (VL-domain of γ-immunoglobulin). This review provides an overview of solution NMR techniques that can help analyse the early and transient events of conformational equilibrium of IDPs and folded proteins.
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Affiliation(s)
- Yoshiki Shigemitsu
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
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26
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André EA, Braatz EM, Liu JP, Zeitlin SO. Generation and Characterization of Knock-in Mouse Models Expressing Versions of Huntingtin with Either an N17 or a Combined PolyQ and Proline-Rich Region Deletion. J Huntingtons Dis 2017; 6:47-62. [PMID: 28211815 PMCID: PMC5389044 DOI: 10.3233/jhd-160231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background: The polyglutamine (polyQ) stretch of the Huntingtin protein (HTT) in mammals is flanked by a highly conserved 17 amino acid N-terminal domain (N17), and a proline-rich region (PRR). The PRR is a binding site for many HTT-interacting proteins, and the N17 domain regulates several normal HTT functions, including HTT’s ability to associate with membranes and organelles. Objective: This study investigates the consequence of deleting mouse Huntingtin’s (Htt’s) N17 domain or a combination of its polyQ stretch and PRR (QP) on normal Htt function in mice. Methods: Knock-in mice expressing versions of Htt lacking either the N17 domain (HttΔN17) or both the polyQ and PRR domains (HttΔQP) were generated, and their behavior, autophagy function, and neuropathology were evaluated. Results: Homozygous and hemizygous HttΔQP/ΔQP, HttΔN17/ΔN17, HttΔQP/–, and HttΔN17/– mice were generated at the expected Mendelian frequency. HttΔQP/ΔQP mutants exhibit improvements in motor coordination compared to controls (Htt+/+). In contrast, HttΔN17/ΔN17 mutants do not exhibit any changes in motor coordination, but they do display variable changes in spatial learning that are dependent on their age at testing. Neither mutant exhibited any changes in basal autophagy in comparison to controls, but thalamostriatal synapses in the dorsal striatum of 24-month-old HttΔN17/ΔN17 mice were decreased compared to controls. Conclusions: These findings support the hypothesis that Htt’s N17 and QP domains are dispensable for its critical functions during early embryonic development, but are likely more important for Htt functions in CNS development or maintenance.
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Affiliation(s)
| | | | | | - Scott O. Zeitlin
- Correspondence to: Scott O. Zeitlin, Ph.D., Department of Neuroscience, University of Virginia School of Medicine, 409 Lane Rd., Box 801392, MR4-5022, Charlottesville, VA 22908 USA. Tel.: +1 434 924 5011; Fax: +1 434 982 4380; E-mail:
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27
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Zapadka KL, Becher FJ, Gomes Dos Santos AL, Jackson SE. Factors affecting the physical stability (aggregation) of peptide therapeutics. Interface Focus 2017; 7:20170030. [PMID: 29147559 DOI: 10.1098/rsfs.2017.0030] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use. Here, we review the numerous factors that influence the physical stability of peptides including both intrinsic and external factors, wherever possible illustrating these with examples that are of therapeutic interest. The effects of sequence, concentration, pH, net charge, excipients, chemical degradation and modification, surfaces and interfaces, and impurities are all discussed. In addition, the effects of physical parameters such as pressure, temperature, agitation and lyophilization are described. We provide an overview of the structures of aggregates formed, as well as our current knowledge of the mechanisms for their formation.
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Affiliation(s)
| | - Frederik J Becher
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Sophie E Jackson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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28
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Prabakaran R, Goel D, Kumar S, Gromiha MM. Aggregation prone regions in human proteome: Insights from large-scale data analyses. Proteins 2017; 85:1099-1118. [DOI: 10.1002/prot.25276] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/10/2017] [Accepted: 02/24/2017] [Indexed: 12/25/2022]
Affiliation(s)
- R. Prabakaran
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
| | - Dhruv Goel
- Department of Computer Science and Engineering; Motilal Nehru National Institute of Technology; Allahabad 211004 India
| | - Sandeep Kumar
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc; 700 Chesterfield Parkway West Chesterfield Missouri 63017, USA
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences; Indian Institute of Technology Madras; Chennai 600036 India
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29
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Influence of Amino Acid Properties for Characterizing Amyloid Peptides in Human Proteome. INTELLIGENT COMPUTING THEORIES AND APPLICATION 2017. [DOI: 10.1007/978-3-319-63312-1_47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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30
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Neveklovska M, Clabough EBD, Steffan JS, Zeitlin SO. Deletion of the huntingtin proline-rich region does not significantly affect normal huntingtin function in mice. J Huntingtons Dis 2016; 1:71-87. [PMID: 22956985 DOI: 10.3233/jhd-2012-120016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The N-terminus of Huntingtin, the protein encoded by the Huntington's disease gene, contains a stretch of polyglutamine residues that is expanded in Huntington's disease. The polyglutamine stretch is flanked by two conserved protein domains in vertebrates: an N1-17 domain, and a proline-rich region (PRR). The PRR can modulate the structure of the adjacent polyglutamine stretch, and is a binding site for several interacting proteins. To determine the role of the PRR in Huntingtin function, we have generated a knock-in allele of the mouse Huntington's disease gene homolog that expresses full-length normal huntingtin lacking the PRR. Mice that are homozygous for the huntingtin PRR deletion are born at the normal Mendelian frequency, suggesting that the PRR is not required for essential huntingtin functions during embryonic development. Moreover, adult homozygous mutants did not exhibit any significant differences from wild-type controls in general motor function and motor learning. However, 18 month-old male, but not female, homozygous PRR deletion mutants exhibited deficits in the Morris water task, suggesting that age-dependent spatial learning and memory may be affected in a sex-specific fashion by the huntingtin PRR deletion.
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Affiliation(s)
- Michelle Neveklovska
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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31
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Lei J, Qi R, Wei G, Nussinov R, Ma B. Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant. Phys Chem Chem Phys 2016; 18:8098-107. [PMID: 26923710 PMCID: PMC6456058 DOI: 10.1039/c5cp06538k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Recent studies suggested that p53 aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, with adverse cancer consequences. The p53 aggregation-nucleating (251)ILTIITL(257) fragment is a key segment in wild-type p53 aggregation; however, an I254R mutation can prevent it. It was suggested that self-assembly of wild-type p53 and its cross-interaction with mutants differ from the classical amyloid nucleation-growth mechanism. Here, using replica exchange molecular dynamics (REMD) simulations, we studied the cross-interactions of this p53 core fragment and its aggregation rescue I254R mutant. We found that the core fragment displays strong aggregation propensity, whereas the gatekeeper I254R mutant tends to be disordered, consistent with experiments. Our cross-interaction results reveal that the wild-type p53 fragment promotes β-sheet formation of the I254R mutant by shifting the disordered mutant peptides into aggregating states. As a result, the system has similar oligomeric structures, inter-peptide interactions and free energy landscape as the wild type fragment does, revealing a prion-like process. We also found that in the cross-interaction system, the wild-type species has higher tendency to interact with the mutant than with itself. This phenomenon illustrates synergistic effects between the p53 (251)ILTIITL(257) fragment and the mutant resembling prion cross-species propagation, cautioning against exploiting it in drug discovery.
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Affiliation(s)
- Jiangtao Lei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China.
| | - Ruxi Qi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China.
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA. and Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA.
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32
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Kumar S, Thangakani AM, Nagarajan R, Singh SK, Velmurugan D, Gromiha MM. Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions. Sci Rep 2016; 6:22258. [PMID: 26924748 PMCID: PMC4770294 DOI: 10.1038/srep22258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
Why do patients suffering from neurodegenerative diseases generate autoantibodies that selectively bind soluble aggregates of amyloidogenic proteins? Presently, molecular basis of interactions between the soluble aggregates and human immune system is unknown. By analyzing sequences of experimentally validated T-cell autoimmune epitopes, aggregating peptides, amyloidogenic proteins and randomly generated peptides, here we report overlapping regions that likely drive aggregation as well as generate autoantibodies against the aggregates. Sequence features, that make short peptides susceptible to aggregation, increase their incidence in human T-cell autoimmune epitopes by 4–6 times. Many epitopes are predicted to be significantly aggregation prone (aggregation propensities ≥10%) and the ones containing experimentally validated aggregating regions are enriched in hydrophobicity by 10–20%. Aggregate morphologies also influence Human Leukocyte Antigen (HLA) - types recognized by the aggregating regions containing epitopes. Most (88%) epitopes that contain amyloid fibril forming regions bind HLA-DR, while majority (63%) of those containing amorphous β-aggregating regions bind HLA-DQ. More than two-thirds (70%) of human amyloidogenic proteins contain overlapping regions that are simultaneously aggregation prone and auto-immunogenic. Such regions help clear soluble aggregates by generating selective autoantibodies against them. This can be harnessed for early diagnosis of proteinopathies and for drug/vaccine design against them.
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Affiliation(s)
- Sandeep Kumar
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield MO 63017, USA
| | - A Mary Thangakani
- Center for Advanced Studies in Crystallography and Biophysics and Bioinformatics Infrastructure Facility, University of Madras, Chennai 600025, India
| | - R Nagarajan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Satish K Singh
- Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., 700 Chesterfield Parkway West, Chesterfield MO 63017, USA
| | - D Velmurugan
- Center for Advanced Studies in Crystallography and Biophysics and Bioinformatics Infrastructure Facility, University of Madras, Chennai 600025, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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33
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Sant'Anna R, Navarro S, Ventura S, Paraoan L, Foguel D. Amyloid properties of the leader peptide of variant B cystatin C: implications for Alzheimer and macular degeneration. FEBS Lett 2016; 590:644-54. [PMID: 26865059 DOI: 10.1002/1873-3468.12093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 12/12/2022]
Abstract
Variant B (VB) of cystatin C has a mutation in its signal peptide (A25T), which interferes with its processing leading to reduced secretion and partial retention in the vicinity of the mitochondria. There are genetic evidences of the association of VB with Alzheimer's disease (AD) and age-related macular degeneration (AMD). Here, we investigated aggregation and amyloid propensities of unprocessed VB combining computational and in vitro studies. Aggregation predictors revealed the presence of four aggregation-prone regions, with a strong one at the level of the signal peptide, which indeed formed toxic aggregates and mature amyloid fibrils in solution. In light of these results, we propose for the first time the role of the signal peptide in pathogenesis of AD and AMD.
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Affiliation(s)
- Ricardo Sant'Anna
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Luminita Paraoan
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, UK
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural, Universidade Federal do Rio de Janeiro, Brazil
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Aguilera P, Marcoleta A, Lobos-Ruiz P, Arranz R, Valpuesta JM, Monasterio O, Lagos R. Identification of Key Amino Acid Residues Modulating Intracellular and In vitro Microcin E492 Amyloid Formation. Front Microbiol 2016; 7:35. [PMID: 26858708 PMCID: PMC4729943 DOI: 10.3389/fmicb.2016.00035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/11/2016] [Indexed: 12/30/2022] Open
Abstract
Microcin E492 (MccE492) is a pore-forming bacteriocin produced and exported by Klebsiella pneumoniae RYC492. Besides its antibacterial activity, excreted MccE492 can form amyloid fibrils in vivo as well as in vitro. It has been proposed that bacterial amyloids can be functional playing a biological role, and in the particular case of MccE492 it would control the antibacterial activity. MccE492 amyloid fibril's morphology and formation kinetics in vitro have been well-characterized, however, it is not known which amino acid residues determine its amyloidogenic propensity, nor if it forms intracellular amyloid inclusions as has been reported for other bacterial amyloids. In this work we found the conditions in which MccE492 forms intracellular amyloids in Escherichia coli cells, that were visualized as round-shaped inclusion bodies recognized by two amyloidophilic probes, 2-4'-methylaminophenyl benzothiazole and thioflavin-S. We used this property to perform a flow cytometry-based assay to evaluate the aggregation propensity of MccE492 mutants, that were designed using an in silico prediction of putative aggregation hotspots. We established that the predicted amino acid residues 54-63, effectively act as a pro-amyloidogenic stretch. As in the case of other amyloidogenic proteins, this region presented two gatekeeper residues (P57 and P59), which disfavor both intracellular and in vitro MccE492 amyloid formation, preventing an uncontrolled aggregation. Mutants in each of these gatekeeper residues showed faster in vitro aggregation and bactericidal inactivation kinetics, and the two mutants were accumulated as dense amyloid inclusions in more than 80% of E. coli cells expressing these variants. In contrast, the MccE492 mutant lacking residues 54-63 showed a significantly lower intracellular aggregation propensity and slower in vitro polymerization kinetics. Electron microscopy analysis of the amyloids formed in vitro by these mutants revealed that, although with different efficiency, all formed fibrils morphologically similar to wild-type MccE492. The physiological implication of MccE492 intracellular amyloid formation is probably similar to the inactivation process observed for extracellular amyloids, and could be used as a mean of sequestering potentially toxic species inside the cell when this bacteriocin is produced in large amounts.
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Affiliation(s)
- Paulina Aguilera
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Andrés Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Pablo Lobos-Ruiz
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Rocío Arranz
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - José M Valpuesta
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
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35
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Ventura S. Curing bacterial infections with protein aggregates. Mol Microbiol 2016; 99:827-30. [PMID: 26714186 DOI: 10.1111/mmi.13293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2015] [Indexed: 12/14/2022]
Abstract
A growing number of human diseases seem to be associated with protein misfolding and deposition into aggregates. Bednarska and colleagues exploit the cytotoxic nature of protein aggregates to target bacterial infections. Protein aggregation is at the same time generic and sequence dependent; this allowed the authors to develop novel aggregation-prone antimicrobial peptides that penetrate bacteria and induce a peptide specific proteostatic collapse that leads to fast bacterial death, without any observable effects on host cells. The applicability of this intriguing strategy was demonstrated by curing animal models from bacterial sepsis. Although the precise mechanisms underlying the bactericidal activity of the peptide aggregates are still not clear, there is no doubt that this approach offers an exciting therapeutic alternative to conventional antibiotics.
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Affiliation(s)
- Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193-, Bellaterra, (Barcelona), Spain
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36
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Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR. Int J Mol Sci 2015; 16:15743-60. [PMID: 26184172 PMCID: PMC4519922 DOI: 10.3390/ijms160715743] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/17/2015] [Accepted: 07/01/2015] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an "indirect/reflected" detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR). This approach employs a "chimeric membrane protein"-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding)-fold domain (named NfeDC domain), connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.
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Affiliation(s)
- Natsuko Goda
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Kana Shimizu
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo 135-0046, Japan.
| | - Yohta Kuwahara
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
| | - Takeshi Tenno
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan.
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Hidekazu Hiroaki
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
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37
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Serebrinsky G, Calvo M, Fernandez S, Saito S, Ohno K, Wallace E, Warnock D, Sakuraba H, Politei J. Late onset variants in Fabry disease: Results in high risk population screenings in Argentina. Mol Genet Metab Rep 2015; 4:19-24. [PMID: 26937405 PMCID: PMC4750630 DOI: 10.1016/j.ymgmr.2015.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/29/2015] [Accepted: 05/29/2015] [Indexed: 01/03/2023] Open
Abstract
Background Screening for Fabry disease (FD) in high risk populations yields a significant number of individuals with novel, ultra rare genetic variants in the GLA gene, largely without classic manifestations of FD. These variants often have significant residual α-galactosidase A activity. The establishment of the pathogenic character of previously unknown or rare variants is challenging but necessary to guide therapeutic decisions. Objectives To present 2 cases of non-classical presentations of FD with renal involvement as well as to discuss the importance of high risk population screenings for FD. Results Our patients with non-classical variants were diagnosed through FD screenings in dialysis units. However, organ damage was not limited to kidneys, since LVH, vertebrobasilar dolichoectasia and cornea verticillata were also present. Lyso-Gb3 concentrations in plasma were in the pathologic range, compatible with late onset FD. Structural studies and in silico analysis of p.(Cys174Gly) and p.(Arg363His), employing different tools, suggest that enzyme destabilization and possibly aggregation could play a role in organ damage. Conclusions Screening programs for FD in high risk populations are important as FD is a treatable multisystemic disease which is frequently overlooked in patients who present without classical manifestations.
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Affiliation(s)
| | - M Calvo
- Nephrology Department, Hospital Zonal General de Agudos Evita, Buenos Aires, Argentina
| | - S Fernandez
- Nephrology Department, Centro Médico CIPERCA, Catamarca, Argentina
| | - S Saito
- Department of Medical Management and Informatics, Hokkaido Information University, Ebetsu, Hokkaido, Japan
| | - K Ohno
- Department of Research, Not-for-Profit Organization for the Promotion of Research on Intellectual Property Tokyo, Chiyoda, Tokyo, Japan
| | - E Wallace
- Department of Medicine, University of Alabama, Birmingham, AL, United States
| | - D Warnock
- Department of Medicine, University of Alabama, Birmingham, AL, United States
| | - H Sakuraba
- Department of Clinical Genetics, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
| | - J Politei
- Fundación para el Estudio de las Enfermedades Neurometabólicas (FESEN), Buenos Aires, Argentina
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Ganesan A, Debulpaep M, Wilkinson H, Van Durme J, De Baets G, Jonckheere W, Ramakers M, Ivarsson Y, Zimmermann P, Van Eldere J, Schymkowitz J, Rousseau F. Selectivity of Aggregation-Determining Interactions. J Mol Biol 2015; 427:236-47. [DOI: 10.1016/j.jmb.2014.09.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/26/2014] [Accepted: 09/02/2014] [Indexed: 01/11/2023]
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39
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Investigating the intrinsic aggregation potential of evolutionarily conserved segments in p53. Biochemistry 2014; 53:5995-6010. [PMID: 25181279 DOI: 10.1021/bi500825d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein aggregation and amyloid formation are known to play a role both in diseases and in biological functions. Transcription factor p53 plays a major role in tumor suppression by maintaining genomic stability. Recent studies have suggested that amyloid formation of p53 could lead to its loss of physiological function as a tumor suppressor. Here, we investigated the intrinsic amyloidogenic nature of wild-type p53 using sequence analysis. We used bioinformatics and aggregation prediction algorithms to establish the evolutionarily conserved nature of aggregation-prone sequences in wild-type p53. Further, we analyzed the amyloid forming capacity of conserved and aggregation-prone p53-derived peptides PILTIITL and YFTLQI in vitro using various biophysical techniques, including all atom molecular dynamics simulation. Finally, we probed the seeding ability of the PILTIITL peptide on p53 aggregation in vitro and in cells. Our data demonstrate the intrinsic amyloid forming ability of a sequence stretch of the p53 DNA binding domain (DBD) and its aggregation templating behavior on full-length and p53 core domain. Therefore, p53 aggregation, instigated through an amyloidogenic segment in its DBD, could be a putative driving force for p53 aggregation in vivo.
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40
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Sant'Anna R, Braga C, Varejão N, Pimenta KM, Graña-Montes R, Alves A, Cortines J, Cordeiro Y, Ventura S, Foguel D. The importance of a gatekeeper residue on the aggregation of transthyretin: implications for transthyretin-related amyloidoses. J Biol Chem 2014; 289:28324-37. [PMID: 25086037 PMCID: PMC4192486 DOI: 10.1074/jbc.m114.563981] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Protein aggregation into β-sheet-enriched amyloid fibrils is associated with an increasing number of human disorders. The adoption of such amyloid conformations seems to constitute a generic property of polypeptide chains. Therefore, during evolution, proteins have adopted negative design strategies to diminish their intrinsic propensity to aggregate, including enrichment of gatekeeper charged residues at the flanks of hydrophobic aggregation-prone segments. Wild type transthyretin (TTR) is responsible for senile systemic amyloidosis, and more than 100 mutations in the TTR gene are involved in familial amyloid polyneuropathy. The TTR 26–57 segment bears many of these aggressive amyloidogenic mutations as well as the binding site for heparin. We demonstrate here that Lys-35 acts as a gatekeeper residue in TTR, strongly decreasing its amyloidogenic potential. This protective effect is sequence-specific because Lys-48 does not affect TTR aggregation. Lys-35 is part of the TTR basic heparin-binding motif. This glycosaminoglycan blocks the protective effect of Lys-35, probably by neutralization of its side chain positive charge. A K35L mutation emulates this effect and results in the rapid self-assembly of the TTR 26–57 region into amyloid fibrils. This mutation does not affect the tetrameric protein stability, but it strongly increases its aggregation propensity. Overall, we illustrate how TTR is yet another amyloidogenic protein exploiting negative design to prevent its massive aggregation, and we show how blockage of conserved protective features by endogenous factors or mutations might result in increased disease susceptibility.
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Affiliation(s)
- Ricardo Sant'Anna
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Carolina Braga
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Nathalia Varejão
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Karinne M Pimenta
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Ricardo Graña-Montes
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aline Alves
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Juliana Cortines
- the Instituto de Microbiologia Professor Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP 21941-590, Brazil and
| | | | - Salvador Ventura
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Debora Foguel
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural,
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41
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Are proposed early genetic codes capable of encoding viable proteins? J Mol Evol 2014; 78:263-74. [PMID: 24826911 DOI: 10.1007/s00239-014-9622-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/28/2014] [Indexed: 01/10/2023]
Abstract
Proteins are elaborate biopolymers balancing between contradicting intrinsic propensities to fold, aggregate, or remain disordered. Assessing their primary structural preferences observable without evolutionary optimization has been reinforced by the recent identification of de novo proteins that have emerged from previously non-coding sequences. In this paper we investigate structural preferences of hypothetical proteins translated from random DNA segments using the standard genetic code and three of its proposed evolutionarily predecessor models encoding 10, 6, and 4 amino acids, respectively. Our only main assumption is that the disorder, aggregation, and transmembrane helix predictions used are able to reflect the differences in the trends of the protein sets investigated. We found that the 10-residue code encodes proteins that resemble modern proteins in their predicted structural properties. All of the investigated early genetic codes give rise to proteins with enhanced disorder and diminished aggregation propensities. Our results suggest that an ancestral genetic code similar to the proposed 10-residue one is capable of encoding functionally diverse proteins but these might have existed under conditions different from today's common physiological ones. The existence of a protein functional repertoire for the investigated earlier stages which is quite distinct as it is today can be deduced from the presented results.
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42
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Stein KC, True HL. Extensive diversity of prion strains is defined by differential chaperone interactions and distinct amyloidogenic regions. PLoS Genet 2014; 10:e1004337. [PMID: 24811344 PMCID: PMC4014422 DOI: 10.1371/journal.pgen.1004337] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/13/2014] [Indexed: 11/27/2022] Open
Abstract
Amyloidogenic proteins associated with a variety of unrelated diseases are typically capable of forming several distinct self-templating conformers. In prion diseases, these different structures, called prion strains (or variants), confer dramatic variation in disease pathology and transmission. Aggregate stability has been found to be a key determinant of the diverse pathological consequences of different prion strains. Yet, it remains largely unclear what other factors might account for the widespread phenotypic variation seen with aggregation-prone proteins. Here, we examined a set of yeast prion variants of the [RNQ+] prion that differ in their ability to induce the formation of another yeast prion called [PSI+]. Remarkably, we found that the [RNQ+] variants require different, non-contiguous regions of the Rnq1 protein for both prion propagation and [PSI+] induction. This included regions outside of the canonical prion-forming domain of Rnq1. Remarkably, such differences did not result in variation in aggregate stability. Our analysis also revealed a striking difference in the ability of these [RNQ+] variants to interact with the chaperone Sis1. Thus, our work shows that the differential influence of various amyloidogenic regions and interactions with host cofactors are critical determinants of the phenotypic consequences of distinct aggregate structures. This helps reveal the complex interdependent factors that influence how a particular amyloid structure may dictate disease pathology and progression.
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Affiliation(s)
- Kevin C. Stein
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Heather L. True
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
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43
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Hauser CAE, Maurer-Stroh S, Martins IC. Amyloid-based nanosensors and nanodevices. Chem Soc Rev 2014; 43:5326-45. [DOI: 10.1039/c4cs00082j] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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44
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De Baets G, Van Durme J, Rousseau F, Schymkowitz J. A genome-wide sequence-structure analysis suggests aggregation gatekeepers constitute an evolutionary constrained functional class. J Mol Biol 2014; 426:2405-12. [PMID: 24735868 DOI: 10.1016/j.jmb.2014.04.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/27/2014] [Accepted: 04/06/2014] [Indexed: 11/15/2022]
Abstract
Protein aggregation is geared by aggregation-prone regions that self-associate by β-strand interactions. Charged residues and prolines are enriched at the flanks of aggregation-prone regions resulting in decreased aggregation. It is still unclear what drives the overrepresentation of these "aggregation gatekeepers", that is, whether their presence results from structural constraints determining protein stability or whether they constitute a bona fide functional class selectively maintained to control protein aggregation. As functional residues are typically conserved regardless of their cost to protein stability, we compared sequence conservation and thermodynamic cost of these residues in 2659 protein families in Escherichia coli. Across protein families, we find gatekeepers to be under strong selective conservation while at the same time representing a significant thermodynamic cost to protein structure. This finding supports the notion that aggregation gatekeepers are not structurally determined but evolutionary selected to control protein aggregation.
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Affiliation(s)
- Greet De Baets
- Switch Laboratory, Flanders Institute for Biotechnology (Vlaams Instituut voor Biotechnologie), 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Joost Van Durme
- Switch Laboratory, Flanders Institute for Biotechnology (Vlaams Instituut voor Biotechnologie), 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Frederic Rousseau
- Switch Laboratory, Flanders Institute for Biotechnology (Vlaams Instituut voor Biotechnologie), 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Joost Schymkowitz
- Switch Laboratory, Flanders Institute for Biotechnology (Vlaams Instituut voor Biotechnologie), 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Herestraat 49, 3000 Leuven, Belgium.
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45
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Graña-Montes R, Marinelli P, Reverter D, Ventura S. N-terminal protein tails act as aggregation protective entropic bristles: the SUMO case. Biomacromolecules 2014; 15:1194-203. [PMID: 24564702 DOI: 10.1021/bm401776z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The formation of β-sheet enriched amyloid fibrils constitutes the hallmark of many diseases but is also an intrinsic property of polypeptide chains in general, because the formation of compact globular proteins comes at the expense of an inherent sequential aggregation propensity. In this context, identification of strategies that enable proteins to remain functional and soluble in the cell has become a central issue in chemical biology. We show here, using human SUMO proteins as a model system, that the recurrent presence of disordered tails flanking globular domains might constitute yet another of these protective strategies. These short, disordered, and highly soluble protein segments would act as intramolecular entropic bristles, reducing the overall protein intrinsic aggregation propensity and favoring thus the attainment and maintenance of functional conformations.
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Affiliation(s)
- Ricardo Graña-Montes
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona , 08193 Bellaterra, Barcelona, Spain
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46
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Gu J, Ghayur T. Rationale and development of multispecific antibody drugs. Expert Rev Clin Pharmacol 2014; 3:491-508. [DOI: 10.1586/ecp.10.28] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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47
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Buck PM, Kumar S, Singh SK. On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses. PLoS Comput Biol 2013; 9:e1003291. [PMID: 24146608 PMCID: PMC3798281 DOI: 10.1371/journal.pcbi.1003291] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/30/2013] [Indexed: 11/18/2022] Open
Abstract
The various roles that aggregation prone regions (APRs) are capable of playing in proteins are investigated here via comprehensive analyses of multiple non-redundant datasets containing randomly generated amino acid sequences, monomeric proteins, intrinsically disordered proteins (IDPs) and catalytic residues. Results from this study indicate that the aggregation propensities of monomeric protein sequences have been minimized compared to random sequences with uniform and natural amino acid compositions, as observed by a lower average aggregation propensity and fewer APRs that are shorter in length and more often punctuated by gate-keeper residues. However, evidence for evolutionary selective pressure to disrupt these sequence regions among homologous proteins is inconsistent. APRs are less conserved than average sequence identity among closely related homologues (≥80% sequence identity with a parent) but APRs are more conserved than average sequence identity among homologues that have at least 50% sequence identity with a parent. Structural analyses of APRs indicate that APRs are three times more likely to contain ordered versus disordered residues and that APRs frequently contribute more towards stabilizing proteins than equal length segments from the same protein. Catalytic residues and APRs were also found to be in structural contact significantly more often than expected by random chance. Our findings suggest that proteins have evolved by optimizing their risk of aggregation for cellular environments by both minimizing aggregation prone regions and by conserving those that are important for folding and function. In many cases, these sequence optimizations are insufficient to develop recombinant proteins into commercial products. Rational design strategies aimed at improving protein solubility for biotechnological purposes should carefully evaluate the contributions made by candidate APRs, targeted for disruption, towards protein structure and activity. Biotechnology requires the large-scale expression, yield, and storage of recombinant proteins. Each step in protein production has the potential to cause aggregation as proteins, not evolved to exist outside the cell, endure the various steps involved in commercial manufacturing processes. Mechanistic studies into protein aggregation have revealed that certain sequence regions contribute more to the aggregation propensity of a protein than other sequence regions do. Efforts to disrupt these regions have thus far indicated that rational sequence engineering is a useful technique to reduce the aggregation of biotechnologically relevant proteins. To improve our ability to rationally engineer proteins with enhanced expression, solubility, and shelf-life we conducted extensive analyses of aggregation prone regions (APRs) within protein sequences to characterize the various roles these regions play in proteins. Findings from this work indicate that protein sequences have evolved by minimizing their aggregation propensities. However, we also found that many APRs are conserved in protein families and are essential to maintain protein stability and function. Therefore, the contributions that APRs, targeted for disruption, make towards protein stability and function should be carefully evaluated when improving protein solubility via rational design.
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Affiliation(s)
- Patrick M Buck
- Pharmaceutical Research and Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, Missouri, United States of America
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48
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Marchante R, Rowe M, Zenthon J, Howard MJ, Tuite MF. Structural definition is important for the propagation of the yeast [PSI+] prion. Mol Cell 2013; 50:675-85. [PMID: 23746351 PMCID: PMC3679450 DOI: 10.1016/j.molcel.2013.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Revised: 04/12/2013] [Accepted: 05/02/2013] [Indexed: 11/30/2022]
Abstract
Prions are propagated in Saccharomyces cerevisiae with remarkable efficiency, yet we know little about the structural basis of sequence variations in the prion protein that support or prohibit propagation of the prion conformation. We show that certain single-amino-acid substitutions in the prion protein Sup35 impact negatively on the maintenance of the associated prion-based [PSI(+)] trait by combining in vivo phenotypic analysis with solution NMR structural studies. A clear correlation is observed between mutationally induced conformational differences in one of the oligopeptide repeats (R2) in the N terminus of Sup35 and the relative ability to propagate [PSI(+)]. Strikingly, substitution of one of a Gly-Gly pair with highly charged residues that significantly increase structural definition of R2 lead to a severe [PSI(+)] propagation defect. These findings offer a molecular explanation for the dominant-negative effects of such psi-no-more (PNM) mutations and demonstrate directly the importance of localized structural definition in prion propagation.
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Affiliation(s)
- Ricardo Marchante
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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Bednarska NG, Schymkowitz J, Rousseau F, Van Eldere J. Protein aggregation in bacteria: the thin boundary between functionality and toxicity. MICROBIOLOGY-SGM 2013; 159:1795-1806. [PMID: 23894132 DOI: 10.1099/mic.0.069575-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Misfolding and aggregation of proteins have a negative impact on all living organisms. In recent years, aggregation has been studied in detail due to its involvement in neurodegenerative diseases, including Alzheimer's, Parkinson's and Huntington's diseases, and type II diabetes--all associated with accumulation of amyloid fibrils. This research highlighted the central importance of protein homeostasis, or proteostasis for short, defined as the cellular state in which the proteome is both stable and functional. It implicates an equilibrium between synthesis, folding, trafficking, aggregation, disaggregation and degradation. In accordance with the eukaryotic systems, it has been documented that protein aggregation also reduces fitness of bacterial cells, but although our understanding of the cellular protein quality control systems is perhaps most detailed in bacteria, the use of bacterial proteostasis as a drug target remains little explored. Here we describe protein aggregation as a normal physiological process and its role in bacterial virulence and we shed light on how bacteria defend themselves against the toxic threat of aggregates. We review the impact of aggregates on bacterial viability and look at the ways that bacteria use to maintain a balance between aggregation and functionality. The proteostasis in bacteria can be interrupted via overexpression of proteins, certain antibiotics such as aminoglycosides, as well as antimicrobial peptides--all leading to loss of cell viability. Therefore intracellular protein aggregation and disruption of proteostatic balance in bacteria open up another strategy that should be explored towards the discovery of new antimicrobials.
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Affiliation(s)
- Natalia G Bednarska
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology & Immunology, KU Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
- Switch Laboratory, VIB, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Belgium
- Switch Laboratory, VIB, Leuven, Belgium
| | - Johan Van Eldere
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology & Immunology, KU Leuven, Belgium
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Shirota M, Kinoshita K. Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins. Protein Sci 2013; 22:725-33. [PMID: 23526551 DOI: 10.1002/pro.2255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/26/2013] [Accepted: 03/14/2013] [Indexed: 11/10/2022]
Abstract
The amino acid sequences of soluble, ordered proteins with stable structures have evolved due to biological and physical requirements, thus distinguishing them from random sequences. Previous analyses have focused on extracting the features that frequently appear in protein substructures, such as α-helix and β-sheet, but the universal features of protein sequences have not been addressed. To clarify the differences between native protein sequences and random sequences, we analyzed 7368 soluble, ordered protein sequences, by inspecting the observed and expected occurrences of 400 amino acid pairs in local proximity, up to 10 residues along the sequence in comparison with their expected occurrence in random sequence. We found the trend that the hydrophobic residue pairs and the polar residue pairs are significantly decreased, whereas the pairs between a hydrophobic residue and a polar residue are increased. This trend was universally observed regardless of the secondary structure content but was not observed in protein sequences that include intrinsically disordered regions, indicating that it can be a general rule of protein foldability. The possible benefits of this rule are discussed from the viewpoints of protein aggregation and disorder, which are both caused by low-complexity regions of hydrophobic or polar residues.
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Affiliation(s)
- Matsuyuki Shirota
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.
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