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Admane N, Srivastava A, Jamal S, Kundu B, Grover A. Protective Effects of a Neurohypophyseal Hormone Analogue on Prion Aggregation, Cellular Internalization, and Toxicity. ACS Chem Neurosci 2020; 11:2422-2430. [PMID: 31407881 DOI: 10.1021/acschemneuro.9b00299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Herein, we report novel neuroprotective activity of the neurohypophyseal hormone analogue desmopressin (DDAVP) against toxic conformations of human prion protein. Systematic analysis using biophysical techniques in conjunction with surface plasmon resonance, high-end microscopy, conformational antibodies, and cell-based assays demonstrated DDAVP's specific binding and potent antiaggregating effects on prion protein (rPrPres). In addition to subjugating conformational conversion of rPrPres into oligomeric forms, DDAVP also exhibits potent fibril modulatory effects. It eventually ameliorated neuronal toxicity of rPrPres oligomers by significantly reducing their cellular internalization. Molecular dynamics simulations showed that DDAVP prevents β-sheet transitions in the N-terminal amyloidogenic region of prion and induces antagonistic mobilities in its α2-α3 and β2-α2 loop regions. Collectively, our data proposes DDAVP as a new structural motif for rational drug discovery against prion diseases.
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Affiliation(s)
- Nikita Admane
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Ankit Srivastava
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Salma Jamal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
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Chamachi NG, Chakrabarty S. Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization. J Phys Chem B 2016; 120:7332-45. [DOI: 10.1021/acs.jpcb.6b03690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Neharika G. Chamachi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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Zhang T, Faraggi E, Li Z, Zhou Y. Intrinsically semi-disordered state and its role in induced folding and protein aggregation. Cell Biochem Biophys 2014; 67:1193-205. [PMID: 23723000 PMCID: PMC3838602 DOI: 10.1007/s12013-013-9638-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) refer to those proteins without fixed three-dimensional structures under physiological conditions. Although experiments suggest that the conformations of IDPs can vary from random coils, semi-compact globules, to compact globules with different contents of secondary structures, computational efforts to separate IDPs into different states are not yet successful. Recently, we developed a neural-network-based disorder prediction technique SPINE-D that was ranked as one of the top performing techniques for disorder prediction in the biannual meeting of critical assessment of structure prediction techniques (CASP 9, 2010). Here, we further analyze the results from SPINE-D prediction by defining a semi-disordered state that has about 50% predicted probability to be disordered or ordered. This semi-disordered state is partially collapsed with intermediate levels of predicted solvent accessibility and secondary structure content. The relative difference in compositions between semi-disordered and fully disordered regions is highly correlated with amyloid aggregation propensity (a correlation coefficient of 0.86 if excluding four charged residues and proline, 0.73 if not). In addition, we observed that some semi-disordered regions participate in induced folding, and others play key roles in protein aggregation. More specifically, a semi-disordered region is amyloidogenic in fully unstructured proteins (such as alpha-synuclein and Sup35) but prone to local unfolding that exposes the hydrophobic core to aggregation in structured globular proteins (such as SOD1 and lysozyme). A transition from full disorder to semi-disorder at about 30-40 Qs is observed in the poly-Q (poly-glutamine) tract of huntingtin. The accuracy of using semi-disorder to predict binding-induced folding and aggregation is compared with several methods trained for the purpose. These results indicate the usefulness of three-state classification (order, semi-disorder, and full-disorder) in distinguishing nonfolding from induced-folding and aggregation-resistant from aggregation-prone IDPs and in locating weakly stable, locally unfolding, and potentially aggregation regions in structured proteins. A comparison with five representative disorder-prediction methods showed that SPINE-D is the only method with a clear separation of semi-disorder from ordered and fully disordered states.
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Affiliation(s)
- Tuo Zhang
- School of Informatics, Indiana University Purdue University, Indianapolis, IN, 46202, USA
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Shimizu Y, Shimizu T, Nara M, Kikumoto M, Kojima H, Morii H. Effects of the KIF2C neck peptide on microtubules: lateral disintegration of microtubules and β-structure formation. FEBS J 2013; 280:1681-92. [PMID: 23398918 DOI: 10.1111/febs.12182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/23/2013] [Accepted: 02/07/2013] [Indexed: 11/29/2022]
Abstract
Members of the kinesin-13 sub-family, including KIF2C, depolymerize microtubules. The positive charge-rich 'neck' region extending from the N-terminus of the catalytic head is considered to be important in the depolymerization activity. Chemically synthesized peptides, covering the basic region (A182-E200), induced a sigmoidal increase in the turbidity of a microtubule suspension. The increase was suppressed by salt addition or by reduction of basicity by amino acid substitutions. Electron microscopic observations revealed ring structures surrounding the microtubules at high peptide concentrations. Using the peptide A182-D218, we also detected free thin straight filaments, probably protofilaments disintegrated from microtubules. Therefore, the neck region, even without the catalytic head domain, may induce lateral disintegration of microtubules. With microtubules lacking anion-rich C-termini as a result of subtilisin treatment, addition of the peptide induced only a moderate increase in turbidity, and rings and protofilaments were rarely detected, while aggregations, also thought to be caused by lateral disintegration, were often observed in electron micrographs. Thus, the C-termini are not crucial for the action of the peptides in lateral disintegration but contribute to structural stabilization of the protofilaments. Previous structural studies indicated that the neck region of KIF2C is flexible, but our IR analysis suggests that the cation-rich region (K190-A204) forms β-structure in the presence of microtubules, which may be of significance with regard to the action of the neck region. Therefore, the neck region of KIF2C is sufficient to cause disintegration of microtubules into protofilaments, and this may contribute to the ability of KIF2C to cause depolymerization of microtubules.
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Affiliation(s)
- Youské Shimizu
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Hyogo, Japan
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Pimenta J, Domingos A, Santos P, Marques CC, Cantante C, Santos A, Barbas JP, Baptista MC, Horta AEM, Viegas A, Mesquita P, Gonçalves J, Fontes CA, Prates JAM, Pereira RMLN. Is prnt a pseudogene? Identification of ram Prt in testis and ejaculated spermatozoa. PLoS One 2012; 7:e42957. [PMID: 22937002 PMCID: PMC3427297 DOI: 10.1371/journal.pone.0042957] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
A hallmark of prion diseases or transmissible spongiform encephalopaties is the conversion of the cellular prion protein (PrP(C)), expressed by the prion gene (prnp), into an abnormally folded isoform (PrP(Sc)) with amyloid-like features that causes scrapie in sheep among other diseases. prnp together with prnd (which encodes a prion-like protein designated as Doppel), and prnt (that encodes the prion protein testis specific--Prt) with sprn (shadow of prion protein gene, that encodes Shadoo or Sho) genes, constitute the "prion gene complex". Whereas a role for prnd in the proper functioning of male reproductive system has been confirmed, the function of prnt, a recently discovered prion family gene, comprises a conundrum leading to the assumption that ruminant prnt is a pseudogene with no protein expression. The main objective of the present study was to identify Prt localization in the ram reproductive system and simultaneously to elucidate if ovine prnt gene is transcribed into protein-coding RNA. Moreover, as Prt is a prnp-related protein, the amyloid propensity was also tested for ovine and caprine Prt. Recombinant Prt was used to immunize BALB/c mice, and the anti-Prt polyclonal antibody (APPA) immune response was evaluated by ELISA and Western Blot. When tested by indirect immunofluorescence, APPA showed high avidity to the ram sperm head apical ridge subdomain, before and after induced capacitation, but did not show the same behavior against goat spermatozoa, suggesting high antibody specificity against ovine-Prt. Prt was also found in the testis when assayed by immunohistochemistry during ram spermatogenesis, where spermatogonia, spermatocytes, spermatids and spermatozoa, stained positive. These observations strongly suggest ovine prnt to be a translated protein-coding gene, pointing to a role for Prt protein in the ram reproductive physiology. Besides, caprine Prt appears to exhibit a higher amyloid propensity than ovine Prt, mostly associated with its phenylalanine residue.
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Affiliation(s)
- Jorge Pimenta
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
- CIISA, Faculdade de Medicina Veterinária (FMV), Universidade Técnica de Lisboa, Lisboa, Portugal
| | - Ana Domingos
- IHMT-CMDT – Instituto de Higiene e Medicina Tropical, Centro de Malária e Doenças Tropicais, Lisboa, Portugal
| | - Pedro Santos
- Hospital Universitário de Coimbra, Coimbra, Portugal
| | - Carla C. Marques
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - Cátia Cantante
- Unidade de Retrovírus e Infecções Associadas (URIA), ADEIM-Centro de Patogénese Molecular/Instituto de Medicina Molecular (IMM), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Santos
- Unidade de Retrovírus e Infecções Associadas (URIA), ADEIM-Centro de Patogénese Molecular/Instituto de Medicina Molecular (IMM), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - João P. Barbas
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - Maria C. Baptista
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - António E. M. Horta
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - Aldino Viegas
- REQUIMTE/CQFB Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Patrícia Mesquita
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
| | - João Gonçalves
- Unidade de Retrovírus e Infecções Associadas (URIA), ADEIM-Centro de Patogénese Molecular/Instituto de Medicina Molecular (IMM), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos A. Fontes
- CIISA, Faculdade de Medicina Veterinária (FMV), Universidade Técnica de Lisboa, Lisboa, Portugal
| | - José A. M. Prates
- CIISA, Faculdade de Medicina Veterinária (FMV), Universidade Técnica de Lisboa, Lisboa, Portugal
| | - Rosa M. L. N. Pereira
- Unidade de Recursos Genéticos, Reprodução e Melhoramento Animal, Instituto Nacional dos Recursos Biológicos (INRB) L-INIA Santarém, Quinta da Fonte Boa, Vale de Santarém, Portugal
- Escola Universitária Vasco da Gama, Coimbra, Portugal
- * E-mail:
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