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da Silva ANR, Pereira GRC, Bonet LFS, Outeiro TF, De Mesquita JF. In silico analysis of alpha-synuclein protein variants and posttranslational modifications related to Parkinson's disease. J Cell Biochem 2024; 125:e30523. [PMID: 38239037 DOI: 10.1002/jcb.30523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 03/12/2024]
Abstract
Parkinson's disease (PD) is among the most prevalent neurodegenerative disorders, affecting over 10 million people worldwide. The protein encoded by the SNCA gene, alpha-synuclein (ASYN), is the major component of Lewy body (LB) aggregates, a histopathological hallmark of PD. Mutations and posttranslational modifications (PTMs) in ASYN are known to influence protein aggregation and LB formation, possibly playing a crucial role in PD pathogenesis. In this work, we applied computational methods to characterize the effects of missense mutations and PTMs on the structure and function of ASYN. Missense mutations in ASYN were compiled from the literature/databases and underwent a comprehensive predictive analysis. Phosphorylation and SUMOylation sites of ASYN were retrieved from databases and predicted by algorithms. ConSurf was used to estimate the evolutionary conservation of ASYN amino acids. Molecular dynamics (MD) simulations of ASYN wild-type and variants A30G, A30P, A53T, and G51D were performed using the GROMACS package. Seventy-seven missense mutations in ASYN were compiled. Although most mutations were not predicted to affect ASYN stability, aggregation propensity, amyloid formation, and chaperone binding, the analyzed mutations received relatively high rates of deleterious predictions and predominantly occurred at evolutionarily conserved sites within the protein. Moreover, our predictive analyses suggested that the following mutations may be possibly harmful to ASYN and, consequently, potential targets for future investigation: K6N, T22I, K34E, G36R, G36S, V37F, L38P, G41D, and K102E. The MD analyses pointed to remarkable flexibility and essential dynamics alterations at nearly all domains of the studied variants, which could lead to impaired contact between NAC and the C-terminal domain triggering protein aggregation. These alterations may have functional implications for ASYN and provide important insight into the molecular mechanism of PD, supporting the design of future biomedical research and improvements in existing therapies for the disease.
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Affiliation(s)
- Aloma N R da Silva
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel R C Pereira
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiz Felippe Sarmento Bonet
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Joelma F De Mesquita
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
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2
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Sunda AP, Sharma AK. Molecular Insights into Cu/Zn Metal Response to the Amyloid β-Peptide (1-42). ACS PHYSICAL CHEMISTRY AU 2024; 4:57-66. [PMID: 38283784 PMCID: PMC10811771 DOI: 10.1021/acsphyschemau.3c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 01/30/2024]
Abstract
Aβ1-40 peptide and Aβ1-42 peptide are the building units of beta-amyloid plaques present in Alzheimer's disease (AD)-affected brain. The binding affinity of various divalent metal ions such as Cu and Zn present in AD-affected brain with different amino acids available in Aβ-peptide became the focus to explore their role in soluble neurotoxic oligomer formation. Cu2+ metal ions are known to enhance the neurotoxicity of the Aβ1-42 peptide by catalyzing the formation of soluble neurotoxic oligomers. The competitive preference of both Cu2+ and Zn2+ simultaneously to interact with the Aβ-peptide is unknown. The divalent Cu and Zn ions were inserted in explicit aqueous Aβ1-42 peptide configurations to get insights into the binding competence of these metal ions with peptides using classical molecular dynamics (MD) simulations. The metal-ion interactions reveal that competitive binding preferences of various peptide sites become metal-ion-specific and differ significantly. For Cu2+, interactions are found to be more significant with respect to those of Asp-7, His-6, Glu-11, and His-14. Asp-1, Glu-3, Asp-7, His-6, Glu-11, and His-13 amino acid residues show higher affinity toward Zn2+ ions. MD simulations show notable variation in the solvent-accessible surface area in the hydrophobic region of the peptide. Infinitesimal mobility was obtained for Zn2+ compared to Cu2+ in an aqueous solution and Cu2+ diffusivity deviated significantly at different time scales, proving its labile features in aqueous Aβ1-42 peptides.
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Affiliation(s)
- Anurag Prakash Sunda
- Department
of Chemistry, J. C. Bose University of Science
and Technology, YMCA, Faridabad 121006, India
| | - Anuj Kumar Sharma
- Department
of Chemistry, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer 305817, India
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3
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Whitfield JF, Rennie K, Chakravarthy B. Alzheimer's Disease and Its Possible Evolutionary Origin: Hypothesis. Cells 2023; 12:1618. [PMID: 37371088 PMCID: PMC10297544 DOI: 10.3390/cells12121618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/29/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The enormous, 2-3-million-year evolutionary expansion of hominin neocortices to the current enormity enabled humans to take over the planet. However, there appears to have been a glitch, and it occurred without a compensatory expansion of the entorhinal cortical (EC) gateway to the hippocampal memory-encoding system needed to manage the processing of the increasing volume of neocortical data converging on it. The resulting age-dependent connectopathic glitch was unnoticed by the early short-lived populations. It has now surfaced as Alzheimer's disease (AD) in today's long-lived populations. With advancing age, processing of the converging neocortical data by the neurons of the relatively small lateral entorhinal cortex (LEC) inflicts persistent strain and high energy costs on these cells. This may result in their hyper-release of harmless Aβ1-42 monomers into the interstitial fluid, where they seed the formation of toxic amyloid-β oligomers (AβOs) that initiate AD. At the core of connectopathic AD are the postsynaptic cellular prion protein (PrPC). Electrostatic binding of the negatively charged AβOs to the positively charged N-terminus of PrPC induces hyperphosphorylation of tau that destroys synapses. The spread of these accumulating AβOs from ground zero is supported by Aβ's own production mediated by target cells' Ca2+-sensing receptors (CaSRs). These data suggest that an early administration of a strongly positively charged, AβOs-interacting peptide or protein, plus an inhibitor of CaSR, might be an effective AD-arresting therapeutic combination.
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Affiliation(s)
- James F. Whitfield
- Human Health Therapeutics, National Research Council, Ottawa, ON K1A 0R6, Canada
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4
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Yuce-Erarslan E, Domb AAJ, Kasem H, Uversky VN, Coskuner-Weber O. Intrinsically Disordered Synthetic Polymers in Biomedical Applications. Polymers (Basel) 2023; 15:polym15102406. [PMID: 37242981 DOI: 10.3390/polym15102406] [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: 03/16/2023] [Revised: 04/29/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
In biology and medicine, intrinsically disordered synthetic polymers bio-mimicking intrinsically disordered proteins, which lack stable three-dimensional structures, possess high structural/conformational flexibility. They are prone to self-organization and can be extremely useful in various biomedical applications. Among such applications, intrinsically disordered synthetic polymers can have potential usage in drug delivery, organ transplantation, artificial organ design, and immune compatibility. The designing of new syntheses and characterization mechanisms is currently required to provide the lacking intrinsically disordered synthetic polymers for biomedical applications bio-mimicked using intrinsically disordered proteins. Here, we present our strategies for designing intrinsically disordered synthetic polymers for biomedical applications based on bio-mimicking intrinsically disordered proteins.
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Affiliation(s)
- Elif Yuce-Erarslan
- Chemical Engineering, Istanbul University-Cerrahpasa, Avcilar, Istanbul 34320, Turkey
| | - Abraham Avi J Domb
- School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Haytam Kasem
- Azrieli College of Engineering, 26 Ya'akov Schreiboim Street, Jerusalem 9103501, Israel
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey
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5
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Castillo-Rangel C, Marin G, Hernández-Contreras KA, Vichi-Ramírez MM, Zarate-Calderon C, Torres-Pineda O, Diaz-Chiguer DL, De la Mora González D, Gómez Apo E, Teco-Cortes JA, Santos-Paez FDM, Coello-Torres MDLÁ, Baldoncini M, Reyes Soto G, Aranda-Abreu GE, García LI. Neuroinflammation in Parkinson's Disease: From Gene to Clinic: A Systematic Review. Int J Mol Sci 2023; 24:5792. [PMID: 36982866 PMCID: PMC10051221 DOI: 10.3390/ijms24065792] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/22/2023] Open
Abstract
Parkinson's disease is a neurodegenerative disease whose progression and clinical characteristics have a close bidirectional and multilevel relationship with the process of neuroinflammation. In this context, it is necessary to understand the mechanisms involved in this neuroinflammation-PD link. This systematic search was, hereby, conducted with a focus on the four levels where alterations associated with neuroinflammation in PD have been described (genetic, cellular, histopathological and clinical-behavioral) by consulting the PubMed, Google Scholar, Scielo and Redalyc search engines, including clinical studies, review articles, book chapters and case studies. Initially, 585,772 articles were included, and, after applying the inclusion and exclusion criteria, 84 articles were obtained that contained information about the multilevel association of neuroinflammation with alterations in gene, molecular, cellular, tissue and neuroanatomical expression as well as clinical-behavioral manifestations in PD.
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Affiliation(s)
- Carlos Castillo-Rangel
- Neurosurgery Department, “Hospital Regional 1° de Octubre”, Institute of Social Security and Services for State Workers (ISSSTE), México City 07300, Mexico; (C.C.-R.); (D.L.D.-C.)
| | - Gerardo Marin
- Neural Dynamics and Modulation Lab, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Karla Aketzalli Hernández-Contreras
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
| | - Micheel Merari Vichi-Ramírez
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
| | - Cristofer Zarate-Calderon
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
| | - Osvaldo Torres-Pineda
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
| | - Dylan L. Diaz-Chiguer
- Neurosurgery Department, “Hospital Regional 1° de Octubre”, Institute of Social Security and Services for State Workers (ISSSTE), México City 07300, Mexico; (C.C.-R.); (D.L.D.-C.)
| | - David De la Mora González
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
| | - Erick Gómez Apo
- Pathology Department, “Hospital General de México”, Dr. Eduardo Liceaga, México City 06720, Mexico; (E.G.A.); (J.A.T.-C.)
| | - Javier Alejandro Teco-Cortes
- Pathology Department, “Hospital General de México”, Dr. Eduardo Liceaga, México City 06720, Mexico; (E.G.A.); (J.A.T.-C.)
| | - Flor de María Santos-Paez
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
| | | | - Matías Baldoncini
- Laboratory of Microsurgical Neuroanatomy, Second Chair of Gross Anatomy, University of Buenos Aires, Buenos Aires C1052AAA, Argentina;
| | | | - Gonzalo Emiliano Aranda-Abreu
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
| | - Luis I. García
- Brain Research Institute, Universidad Veracruzana, Xalapa 91192, Mexico; (K.A.H.-C.); or (M.M.V.-R.); (C.Z.-C.); (O.T.-P.); (D.D.l.M.G.); (F.d.M.S.-P.); (G.E.A.-A.); (L.I.G.)
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6
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Basu S, Chakravarty D, Hou Q, Uversky VN. Editorial: From the hydrophobic core to the globular-disorder interface: New challenges and insights into protein design. Front Mol Biosci 2023; 10:1151676. [PMID: 36814642 PMCID: PMC9939879 DOI: 10.3389/fmolb.2023.1151676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Affiliation(s)
- Sankar Basu
- Department of Microbiology, Asutosh College, University of Calcutta, Kolkata, India,*Correspondence: Sankar Basu, ; Vladimir N. Uversky,
| | - Devlina Chakravarty
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, United States
| | - Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States,*Correspondence: Sankar Basu, ; Vladimir N. Uversky,
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7
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Coskuner-Weber O, Yuce-Erarslan E, Uversky VN. Paving the Way for Synthetic Intrinsically Disordered Polymers for Soft Robotics. Polymers (Basel) 2023; 15:polym15030763. [PMID: 36772065 PMCID: PMC9919048 DOI: 10.3390/polym15030763] [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: 12/07/2022] [Revised: 01/15/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Nature is full of examples of processes that, through evolution, have been perfected over the ages to effectively use matter and sustain life. Here, we present our strategies for designing intrinsically disordered smart polymers for soft robotics applications that are bio-inspired by intrinsically disordered proteins. Bio-inspired intrinsically disordered smart and soft polymers designed using our deep understanding of intrinsically disordered proteins have the potential to open new avenues in soft robotics. Together with other desirable traits, such as robustness, dynamic self-organization, and self-healing abilities, these systems possess ideal characteristics that human-made formations strive for but often fail to achieve. Our main aim is to develop materials for soft robotics applications bio-inspired by intrinsically disordered proteins to address what we see as the largest current barriers in the practical deployment of future soft robotics in various areas, including defense. Much of the current literature has focused on the de novo synthesis of tailor-made polymers to perform specific functions. With bio-inspired polymers, the complexity of protein folding mechanisms has limited the ability of researchers to reliably engineer specific structures. Unlike existing studies, our work is focused on utilizing the high flexibility of intrinsically disordered proteins and their self-organization characteristics using synthetic quasi-foldamers.
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Affiliation(s)
- Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey
- Correspondence:
| | - Elif Yuce-Erarslan
- Chemical Engineering, Istanbul University-Cerrahpasa, Avcılar, Istanbul 34320, Turkey
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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Piccoli T, Blandino V, Maniscalco L, Matranga D, Graziano F, Guajana F, Agnello L, Lo Sasso B, Gambino CM, Giglio RV, La Bella V, Ciaccio M, Colletti T. Biomarkers Related to Synaptic Dysfunction to Discriminate Alzheimer's Disease from Other Neurological Disorders. Int J Mol Sci 2022; 23:10831. [PMID: 36142742 PMCID: PMC9501545 DOI: 10.3390/ijms231810831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Recently, the synaptic proteins neurogranin (Ng) and α-synuclein (α-Syn) have attracted scientific interest as potential biomarkers for synaptic dysfunction in neurodegenerative diseases. In this study, we measured the CSF Ng and α-Syn concentrations in patients affected by AD (n = 69), non-AD neurodegenerative disorders (n-AD = 50) and non-degenerative disorders (n-ND, n = 98). The concentrations of CSF Ng and α-Syn were significantly higher in AD than in n-AD and n-ND. Moreover, the Aβ42/Ng and Aβ42/α-Syn ratios showed statistically significant differences between groups and discriminated AD patients from n-AD patients, better than Ng or α-Syn alone. Regression analyses showed an association of higher Ng concentrations with MMSE < 24, pathological Aβ 42/40 ratios, pTau, tTau and the ApoEε4 genotype. Aβ 42/Ng was associated with MMSE < 24, an AD-related FDG-PET pattern, the ApoEε4 genotype, pathological Aβ 42 levels and Aβ 42/40 ratios, pTau, and tTau. Moreover, APO-Eε4 carriers showed higher Ng concentrations than non-carriers. Our results support the idea that the Aβ 42/Ng ratio is a reliable index of synaptic dysfunction/degeneration able to discriminate AD from other neurological conditions.
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Affiliation(s)
- Tommaso Piccoli
- Unit of Neurology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90129 Palermo, Italy
| | - Valeria Blandino
- Unit of Neurology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90129 Palermo, Italy
| | - Laura Maniscalco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy
| | - Domenica Matranga
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy
| | - Fabiola Graziano
- Unit of Neurology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90129 Palermo, Italy
| | - Fabrizio Guajana
- Unit of Neurology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90129 Palermo, Italy
| | - Luisa Agnello
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine and Clinical Laboratory Medicine, University of Palermo, 90127 Palermo, Italy
| | - Bruna Lo Sasso
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine and Clinical Laboratory Medicine, University of Palermo, 90127 Palermo, Italy
- Department of Laboratory Medicine, University Hospital “P. Giaccone”, 90127 Palermo, Italy
| | - Caterina Maria Gambino
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine and Clinical Laboratory Medicine, University of Palermo, 90127 Palermo, Italy
- Department of Laboratory Medicine, University Hospital “P. Giaccone”, 90127 Palermo, Italy
| | - Rosaria Vincenza Giglio
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine and Clinical Laboratory Medicine, University of Palermo, 90127 Palermo, Italy
- Department of Laboratory Medicine, University Hospital “P. Giaccone”, 90127 Palermo, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Center and Laboratory of Neurochemistry, Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90129 Palermo, Italy
| | - Marcello Ciaccio
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine and Clinical Laboratory Medicine, University of Palermo, 90127 Palermo, Italy
| | - Tiziana Colletti
- ALS Clinical Research Center and Laboratory of Neurochemistry, Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90129 Palermo, Italy
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Kekenes-Huskey PM, Burgess DE, Sun B, Bartos DC, Rozmus ER, Anderson CL, January CT, Eckhardt LL, Delisle BP. Mutation-Specific Differences in Kv7.1 ( KCNQ1) and Kv11.1 ( KCNH2) Channel Dysfunction and Long QT Syndrome Phenotypes. Int J Mol Sci 2022; 23:7389. [PMID: 35806392 PMCID: PMC9266926 DOI: 10.3390/ijms23137389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
The electrocardiogram (ECG) empowered clinician scientists to measure the electrical activity of the heart noninvasively to identify arrhythmias and heart disease. Shortly after the standardization of the 12-lead ECG for the diagnosis of heart disease, several families with autosomal recessive (Jervell and Lange-Nielsen Syndrome) and dominant (Romano-Ward Syndrome) forms of long QT syndrome (LQTS) were identified. An abnormally long heart rate-corrected QT-interval was established as a biomarker for the risk of sudden cardiac death. Since then, the International LQTS Registry was established; a phenotypic scoring system to identify LQTS patients was developed; the major genes that associate with typical forms of LQTS were identified; and guidelines for the successful management of patients advanced. In this review, we discuss the molecular and cellular mechanisms for LQTS associated with missense variants in KCNQ1 (LQT1) and KCNH2 (LQT2). We move beyond the "benign" to a "pathogenic" binary classification scheme for different KCNQ1 and KCNH2 missense variants and discuss gene- and mutation-specific differences in K+ channel dysfunction, which can predispose people to distinct clinical phenotypes (e.g., concealed, pleiotropic, severe, etc.). We conclude by discussing the emerging computational structural modeling strategies that will distinguish between dysfunctional subtypes of KCNQ1 and KCNH2 variants, with the goal of realizing a layered precision medicine approach focused on individuals.
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Affiliation(s)
- Peter M. Kekenes-Huskey
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Don E. Burgess
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.E.B.); (E.R.R.)
| | - Bin Sun
- Department of Pharmacology, Harbin Medical University, Harbin 150081, China;
| | | | - Ezekiel R. Rozmus
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.E.B.); (E.R.R.)
| | - Corey L. Anderson
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (C.L.A.); (C.T.J.); (L.L.E.)
| | - Craig T. January
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (C.L.A.); (C.T.J.); (L.L.E.)
| | - Lee L. Eckhardt
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (C.L.A.); (C.T.J.); (L.L.E.)
| | - Brian P. Delisle
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (D.E.B.); (E.R.R.)
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10
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Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases. Biophys Rev 2022; 14:679-707. [DOI: 10.1007/s12551-022-00968-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/28/2022] [Indexed: 12/14/2022] Open
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11
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Savva L, Platts JA. Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein. J Biomol Struct Dyn 2022:1-16. [PMID: 35670576 DOI: 10.1080/07391102.2022.2082534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loizos Savva
- School of Chemistry, Cardiff University, Cardiff, UK
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12
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Rajendran R, Ragavan RP, Al-Sehemi AG, Uddin MS, Aleya L, Mathew B. Current understandings and perspectives of petroleum hydrocarbons in Alzheimer's disease and Parkinson's disease: a global concern. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:10928-10949. [PMID: 35000177 DOI: 10.1007/s11356-021-17931-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Over the last few decades, the global prevalence of neurodevelopmental and neurodegenerative illnesses has risen rapidly. Although the aetiology remains unclear, evidence is mounting that exposure to persistent hydrocarbon pollutants is a substantial risk factor, predisposing a person to neurological diseases later in life. Epidemiological studies correlate environmental hydrocarbon exposure to brain disorders including neuropathies, cognitive, motor and sensory impairments; neurodevelopmental disorders like autism spectrum disorder (ASD); and neurodegenerative disorders like Alzheimer's disease (AD) and Parkinson's disease (PD). Particulate matter, benzene, toluene, ethylbenzene, xylenes, polycyclic aromatic hydrocarbons and endocrine-disrupting chemicals have all been linked to neurodevelopmental problems in all class of people. There is mounting evidence that supports the prevalence of petroleum hydrocarbon becoming neurotoxic and being involved in the pathogenesis of AD and PD. More study is needed to fully comprehend the scope of these problems in the context of unconventional oil and natural gas. This review summarises in vitro, animal and epidemiological research on the genesis of neurodegenerative disorders, highlighting evidence that supports inexorable role of hazardous hydrocarbon exposure in the pathophysiology of AD and PD. In this review, we offer a summary of the existing evidence gathered through a Medline literature search of systematic reviews and meta-analyses of the most important epidemiological studies published so far.
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Affiliation(s)
- Rajalakshmi Rajendran
- Department of Pharmacy Practice, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, 682041, Kerala, India
| | - Roshni Pushpa Ragavan
- Research Center for Advanced Materials Science, King Khalid University, Abha, 61413, Saudi Arabia.
| | - Abdullah G Al-Sehemi
- Research Center for Advanced Materials Science, King Khalid University, Abha, 61413, Saudi Arabia
- Department of Chemistry, King Khalid University, Abha, 61413, Saudi Arabia
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Lotfi Aleya
- Laboratoire Chrono-Environment, CNRS6249, Universite de Bourgogne Franche-Comte, Besancon, France
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
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13
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Uversky VN. Protein folding, misfolding, and un/non-folding: overview of the SP16 Session at the 20 th IUPAB congress, 45 th Annual Meeting of SBBf, and 50 th Annual Meeting of SBBq. Biophys Rev 2022; 13:879-882. [PMID: 35059012 DOI: 10.1007/s12551-021-00885-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
The classical and idealistic consideration of the protein universe as a set of well-ordered proteinaceous machines with unique spatial organizations conducting unique biological functions is changed because of the recognition that proteins can fold, misfold, or be disordered to different degree. Functional repertoires of intrinsically disordered proteins complement functions of ordered proteins, whereas protein misfolding and concomitant oligomerization, aggregation, and fibrillation are related to the pathogenesis of numerous human diseases. Flexible proteins can undergo liquid-liquid phase separation, which is at the heart of the biogenesis of numerous membrane-less organelles. Many of these aspects were highlighted in four talks delivered at the SP16 Session at the 20th IUPAB congress, 45th Annual Meeting of SBBf, and 50th Annual Meeting of SBBq.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL MDC07 USA
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14
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Roterman I, Stapor K, Gądek K, Gubała T, Nowakowski P, Fabian P, Konieczny L. On the Dependence of Prion and Amyloid Structure on the Folding Environment. Int J Mol Sci 2021; 22:ijms222413494. [PMID: 34948291 PMCID: PMC8707753 DOI: 10.3390/ijms222413494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 01/22/2023] Open
Abstract
Currently available analyses of amyloid proteins reveal the necessity of the existence of radical structural changes in amyloid transformation processes. The analysis carried out in this paper based on the model called fuzzy oil drop (FOD) and its modified form (FOD-M) allows quantifying the role of the environment, particularly including the aquatic environment. The starting point and basis for the present presentation is the statement about the presence of two fundamentally different methods of organizing polypeptides into ordered conformations—globular proteins and amyloids. The present study shows the source of the differences between these two paths resulting from the specificity of the external force field coming from the environment, including the aquatic and hydrophobic one. The water environment expressed in the fuzzy oil drop model using the 3D Gauss function directs the folding process towards the construction of a micelle-like system with a hydrophobic core in the central part and the exposure of polarity on the surface. The hydrophobicity distribution of membrane proteins has the opposite characteristic: Exposure of hydrophobicity at the surface of the membrane protein with an often polar center (as in the case of ion channels) is expected. The structure of most proteins is influenced by a more or less modified force field generated by water through the appropriate presence of a non-polar (membrane-like) environment. The determination of the proportion of a factor different from polar water enables the assessment of the protein status by indicating factors favoring the structure it represents.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, 31-034 Kopernika 7, 30-688 Krakow, Poland
- Correspondence:
| | - Katarzyna Stapor
- Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Krzysztof Gądek
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Tomasz Gubała
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Piotr Nowakowski
- Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland; (K.G.); (T.G.); (P.N.)
| | - Piotr Fabian
- Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland;
| | - Leszek Konieczny
- Department of Medical Biochemistry, Jagiellonian University Medical College, 31-034 Kopernika 7, 31-034 Krakow, Poland;
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15
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Rezaei Kamelabad M, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A, Ajamgard M. Influence of curcumin and rosmarinic acid on disrupting the general properties of Alpha-Synuclein oligomer: Molecular dynamics simulation. J Mol Graph Model 2021; 107:107963. [PMID: 34147836 DOI: 10.1016/j.jmgm.2021.107963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/25/2023]
Abstract
Alpha-Synuclein (αS) is a protein involved in Parkinson's disease (PD) and is probably the main cause of the pathology of the disease. During pathogenesis, αS monomers aggregate, leading to the formation of a variety of oligomeric species. Recent research studies suggest that the oligomeric toxic species may be one of the main processes for pathology and disease. Here, we studied influence of two natural polyphenolic compounds, Curcumin (CUR) and Rosmarinic acid (RA), on disrupting the general properties of αS oligomer by molecular dynamics (MD) simulation method. The hydrophobic central domain of αS (NAC), is the most essential district responsible for protein self-aggregation; so, in this study, our systems have been developed to form a quintuplet NAC region of αS called 5mer; they have 10 and 20 CUR and RA molecules and a 5mer with no ligand. The several important and efficient analyzes were performed to investigate the effect of ligands on the structural properties of αS oligomers. The results indicated that both ligands can be successful in disrupting the original structure of αS oligomers; therefore, they can be considered suitable candidates for designing Parkinson's drugs.
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Affiliation(s)
- Mahrokh Rezaei Kamelabad
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran.
| | - Alireza Rastkar Ebrahimzadeh
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Physics, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
| | - Marzieh Ajamgard
- Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran; Molecular Sciences and Engineering Research Group (MSERG), Iran
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16
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Studying the effect of alpha-synuclein and Parkinson's disease linked mutants on inter pathway connectivities. Sci Rep 2021; 11:16365. [PMID: 34381149 PMCID: PMC8358055 DOI: 10.1038/s41598-021-95889-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease is a common neurodegenerative disease. The differential expression of alpha-synuclein within Lewy Bodies leads to this disease. Some missense mutations of alpha-synuclein may resultant in functional aberrations. In this study, our objective is to verify the functional adaptation due to early and late-onset mutation which can trigger or control the rate of alpha-synuclein aggregation. In this regard, we have proposed a computational model to study the difference and similarities among the Wild type alpha-synuclein and mutants i.e., A30P, A53T, G51D, E46K, and H50Q. Evolutionary sequence space analysis is also performed in this experiment. Subsequently, a comparative study has been performed between structural information and sequence space outcomes. The study shows the structural variability among the selected subtypes. This information assists inter pathway modeling due to mutational aberrations. Based on the structural variability, we have identified the protein-protein interaction partners for each protein that helps to increase the robustness of the inter-pathway connectivity. Finally, few pathways have been identified from 12 semantic networks based on their association with mitochondrial dysfunction and dopaminergic pathways.
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17
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Chakraborty R, Dey S, Sil P, Paul SS, Bhattacharyya D, Bhunia A, Sengupta J, Chattopadhyay K. Conformational distortion in a fibril-forming oligomer arrests alpha-Synuclein fibrillation and minimizes its toxic effects. Commun Biol 2021; 4:518. [PMID: 33941845 PMCID: PMC8093279 DOI: 10.1038/s42003-021-02026-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
The fibrillation pathway of alpha-Synuclein, the causative protein of Parkinson's disease, encompasses transient, heterogeneous oligomeric forms whose structural understanding and link to toxicity are not yet understood. We report that the addition of the physiologically-available small molecule heme at a sub-stoichiometric ratio to either monomeric or aggregated α-Syn, targets a His50 residue critical for fibril-formation and stabilizes the structurally-heterogeneous populations of aggregates into a minimally-toxic oligomeric state. Cryo-EM 3D reconstruction revealed a 'mace'-shaped structure of this monodisperse population of oligomers, which is comparable to a solid-state NMR Greek key-like motif (where the core residues are arranged in parallel in-register sheets with a Greek key topology at the C terminus) that forms the fundamental unit/kernel of protofilaments. Further structural analyses suggest that heme binding induces a distortion in the Greek key-like architecture of the mace oligomers, which impairs their further appending into protofilaments and fibrils. Additionally, our study reports a novel mechanism of prevention as well as reclamation of amyloid fibril formation by blocking an inter-protofilament His50 residue using a small molecule.
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Affiliation(s)
- Ritobrita Chakraborty
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sandip Dey
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Pallabi Sil
- Department of Physics, University of Alberta, Edmonton, AB, Canada
| | - Simanta Sarani Paul
- Department of Medicine, Centre for Prion and Protein folding disease, University of Alberta, Edmonton, AB, Canada
| | - Dipita Bhattacharyya
- Department of Biophysics, Bose Institute- Centenary Campus, P-1/12C.I.T. Scheme VII-M, Kolkata, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute- Centenary Campus, P-1/12C.I.T. Scheme VII-M, Kolkata, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
| | - Krishnananda Chattopadhyay
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
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18
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Ermakova EA, Makshakova ON, Zuev YF, Sedov IA. Fibril fragments from the amyloid core of lysozyme: An accelerated molecular dynamics study. J Mol Graph Model 2021; 106:107917. [PMID: 33887522 DOI: 10.1016/j.jmgm.2021.107917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Protein aggregation and formation of amyloid fibrils are associated with many diseases and present a ubiquitous problem in protein science. Hen egg white lysozyme (HEWL) can form fibrils both from the full length protein and from its fragments. In the present study, we simulated unfolding of the amyloidogenic fragment of HEWL encompassing residues 49-101 to study the conformational aspects of amyloidogenesis. The accelerated molecular dynamics approach was used to speed up the sampling of the fragment conformers under enhanced temperature. Analysis of conformational transformation and intermediate structures was performed. During the unfolding, the novel short-living and long-living β-structures are formed along with the unstructured random coils. Such β-structure enriched monomers can interact with each other and propagate into fibril-like forms. The stability of oligomers assembled from these monomers was evaluated in the course of MD simulations with explicit water. The residues playing a key role in fibril stabilization were determined. The work provides new insights into the processes occurring at the early stages of amyloid fibril assembly.
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Affiliation(s)
- Elena A Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia.
| | - Olga N Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
| | - Yuriy F Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111, Kazan, Russia
| | - Igor A Sedov
- Kazan Federal University, Kremlevskaya Str.,18, 420111, Kazan, Russia; Sirius University of Science and Technology, Olympic Ave, 1, 354340, Sochi, Russia
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19
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Caliskan M, Mandaci SY, Uversky VN, Coskuner-Weber O. Secondary structure dependence of amyloid-β(1-40) on simulation techniques and force field parameters. Chem Biol Drug Des 2021; 97:1100-1108. [PMID: 33580600 DOI: 10.1111/cbdd.13830] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/21/2021] [Accepted: 02/07/2021] [Indexed: 12/21/2022]
Abstract
Our recent studies revealed that none of the selected widely used force field parameters and molecular dynamics simulation techniques yield structural properties for the intrinsically disordered α-synuclein that are in agreement with various experiments via testing different force field parameters. Here, we extend our studies on the secondary structure properties of the disordered amyloid-β(1-40) peptide in aqueous solution. For these purposes, we conducted extensive replica exchange molecular dynamics simulations and obtained extensive molecular dynamics simulation trajectories from David E. Shaw group. Specifically, these molecular dynamics simulations were conducted using various force field parameters and obtained results are compared to our replica exchange molecular dynamics simulations and experiments. In this study, we calculated the secondary structure abundances and radius of gyration values for amyloid-β(1-40) that were simulated using varying force field parameter sets and different simulation techniques. In addition, the intrinsic disorder propensity, as well as sequence-based secondary structure predisposition of amyloid-β(1-40) and compared the findings with the results obtained from molecular simulations using various force field parameters and different simulation techniques. Our studies clearly show that the epitope region identification of amyloid-β(1-40) depends on the chosen simulation technique and chosen force field parameters. Based on comparison with experiments, we find that best computational results in agreement with experiments are obtained using the a99sb*-ildn, charmm36m, and a99sb-disp parameters for the amyloid-β(1-40) peptide in molecular dynamics simulations without parallel tempering or via replica exchange molecular dynamics simulations.
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Affiliation(s)
- Murat Caliskan
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Sunay Y Mandaci
- Molecular Biotechnology, Turkish-German University, Istanbul, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia
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20
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Cingolani M, Mummolo L, Lugli F, Zaffagnini M, Genovese D. Protein aggregation detection with fluorescent macromolecular and nanostructured probes: challenges and opportunities. NEW J CHEM 2021. [DOI: 10.1039/d1nj01606g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoprobes based on various nanomaterials, polymers or AIEgens are overcoming previous limitations for diagnosis and therapy of early-stage protein aggregation.
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Affiliation(s)
- Matteo Cingolani
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Liviana Mummolo
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Francesca Lugli
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Mirko Zaffagnini
- Dipartimento di Farmacia e Biotecnologia
- Università di Bologna
- 40126 Bologna
- Italy
| | - Damiano Genovese
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
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21
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Kour A, Sharma S, Dube T, Bisht A, Sharma M, Mishra J, Ali ME, Panda JJ. l-3,4-Dihydroxyphenylalanine templated anisotropic gold nano/micro-roses as potential disrupters/inhibitors of α-crystallin protein and its gleaned model peptide aggregates. Int J Biol Macromol 2020; 163:2374-2391. [PMID: 32961180 DOI: 10.1016/j.ijbiomac.2020.09.112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/25/2020] [Accepted: 09/16/2020] [Indexed: 11/26/2022]
Abstract
Cataract, the major cause of blindness worldwide occurs due to the misfolding and aggregation of the protein crystallin, which constitute a major portion of the lens protein. Other than the whole protein crystallin, the peptide sequences generated from crystallin as a result of covalent protein damage have also been shown to possess and foster protein aggregation, which can be established as crystallin aggregation models. Thus, the disaggregation or inhibition of these protein aggregates could be a viable approach to combat cataract and preserve lens proteostasis. Herein, we tried to explore the disruption as well as inhibition of the intact α-crystallin protein and α-crystallin derived model peptide aggregates by l-3,4-dihydroxyphenylalanine (levodopa) coated gold (Au) nano/micro-roses as modulators. Thioflavin T fluorescence enhancement assay, and electron microscopic analysis were being employed to probe the anti-aggregation behavior of the Au nano/micro-roses towards the aggregating α-crystallin peptides/protein. Further, computational studies were performed to reveal the nature of molecular interactions between the levodopa molecule and the α-crystallin derived model peptides. Interestingly, both levodopa coated Au nano/micro-roses were found to be capable of inhibiting as well as preventing the aggregation of the intact α-crystallin protein and other model peptides derived from it.
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Affiliation(s)
- Avneet Kour
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
| | - Shikha Sharma
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
| | - Taru Dube
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
| | - Anjali Bisht
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
| | - Manju Sharma
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
| | - Jibanananda Mishra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India
| | - Jiban Jyoti Panda
- Institute of Nano Science and Technology, Mohali, Punjab 160062, India.
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22
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Akbayrak IY, Caglayan SI, Ozcan Z, Uversky VN, Coskuner-Weber O. Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations. Curr Alzheimer Res 2020; 17:805-818. [PMID: 33167839 DOI: 10.2174/1567205017666201109094908] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 11/22/2022]
Abstract
Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations - including our own - revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.
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Affiliation(s)
- Ibrahim Y Akbayrak
- Materials Science and Technologies, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
| | - Sule I Caglayan
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
| | - Zilan Ozcan
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States
| | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
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23
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Saini R, Shuaib S, Goyal D, Goyal B. Impact of Mutations on the Conformational Transition from α-Helix to β-Sheet Structures in Arctic-Type Aβ 40: Insights from Molecular Dynamics Simulations. ACS OMEGA 2020; 5:23219-23228. [PMID: 32954172 PMCID: PMC7495726 DOI: 10.1021/acsomega.0c02983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/13/2020] [Indexed: 05/13/2023]
Abstract
The amyloid-β (Aβ) protein aggregation into toxic oligomers and fibrils has been recognized as a key player in the pathogenesis of Alzheimer's disease. Recent experiments reported that a double alanine mutation (L17A/F19A) in the central hydrophobic core (CHC) region of [G22]Aβ40 (familial Arctic mutation) diminished the self-assembly propensity of [G22]Aβ40. However, the molecular mechanism behind the decreased aggregation tendency of [A17/A19/G22]Aβ40 is not well understood. Herein, we carried out molecular dynamics simulations to elucidate the structure and dynamics of [G22]Aβ40 and [A17/A19/G22]Aβ40. The results for the secondary structure analysis reveal a significantly increased amount of the helical content in the CHC and C-terminal region of [A17/A19/G22]Aβ40 as compared to [G22]Aβ40. The bending free-energy analysis of D23-K28 salt bridge suggests that the double alanine mutation in the CHC region of [G22]Aβ40 has the potential to reduce the fibril formation rate by 0.57 times of [G22]Aβ40. Unlike [G22]Aβ40, [A17/A19/G22]Aβ40 largely sampled helical conformation, as determined by the minimum energy conformations extracted from the free-energy landscape. The present study provided atomic level details into the experimentally observed diminished aggregation tendency of [A17/A19/G22]Aβ40 as compared to [G22]Aβ40.
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Affiliation(s)
- Rajneet
Kaur Saini
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Suniba Shuaib
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Bhupesh Goyal
- School
of Chemistry & Biochemistry, Thapar
Institute of Engineering & Technology, Patiala 147004, Punjab, India
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24
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Radko SP, Khmeleva SA, Kaluzhny DN, Kechko OI, Kiseleva YY, Kozin SA, Mitkevich VA, Makarov AA. The English (H6R) Mutation of the Alzheimer's Disease Amyloid-β Peptide Modulates Its Zinc-Induced Aggregation. Biomolecules 2020; 10:E961. [PMID: 32630528 PMCID: PMC7355780 DOI: 10.3390/biom10060961] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/15/2022] Open
Abstract
The coordination of zinc ions by histidine residues of amyloid-beta peptide (Aβ) plays a critical role in the zinc-induced Aβ aggregation implicated in Alzheimer's disease (AD) pathogenesis. The histidine to arginine substitution at position 6 of the Aβ sequence (H6R, English mutation) leads to an early onset of AD. Herein, we studied the effects of zinc ions on the aggregation of the Aβ42 peptide and its isoform carrying the H6R mutation (H6R-Aβ42) by circular dichroism spectroscopy, dynamic light scattering, turbidimetric and sedimentation methods, and bis-ANS and thioflavin T fluorescence assays. Zinc ions triggered the occurrence of amorphous aggregates for both Aβ42 and H6R-Aβ42 peptides but with distinct optical properties. The structural difference of the formed Aβ42 and H6R-Aβ42 zinc-induced amorphous aggregates was also supported by the results of the bis-ANS assay. Moreover, while the Aβ42 peptide demonstrated an increase in the random coil and β-sheet content upon complexing with zinc ions, the H6R-Aβ42 peptide showed no appreciable structural changes under the same conditions. These observations were ascribed to the impact of H6R mutation on a mode of zinc/peptide binding. The presented findings further advance the understanding of the pathological role of the H6R mutation and the role of H6 residue in the zinc-induced Aβ aggregation.
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Affiliation(s)
- Sergey P. Radko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.N.K.); (O.I.K.); (S.A.K.); (V.A.M.); (A.A.M.)
- Institute of Biomedical Chemistry, 119121 Moscow, Russia;
| | | | - Dmitry N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.N.K.); (O.I.K.); (S.A.K.); (V.A.M.); (A.A.M.)
| | - Olga I. Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.N.K.); (O.I.K.); (S.A.K.); (V.A.M.); (A.A.M.)
| | - Yana Y. Kiseleva
- Russian Scientific Center of Roentgenoradiology, 117485 Moscow, Russia;
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.N.K.); (O.I.K.); (S.A.K.); (V.A.M.); (A.A.M.)
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.N.K.); (O.I.K.); (S.A.K.); (V.A.M.); (A.A.M.)
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (D.N.K.); (O.I.K.); (S.A.K.); (V.A.M.); (A.A.M.)
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25
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Saranya V, Mary PV, Vijayakumar S, Shankar R. The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective. Biophys Chem 2020; 263:106394. [PMID: 32480019 DOI: 10.1016/j.bpc.2020.106394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ42 peptide due to its interaction of toxic gas (CO, CO2, SO2 and NO2). During the 400 ns simulation, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes have smaller Root Mean Square Deviation values when compared to the Aβ42 peptide, which shows that the interaction of toxic gases (CO, CO2, SO2, and NO2) would increase the Aβ42 peptide structural stability. The radius of gyration analysis also supports that Aβ42 interacted CO2 and SO2 complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ42 interacted CO2 and SO2 complexes have a greater compact structure in comparison to Aβ42 interacted CO and NO2 complexes. Furthermore, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India
| | - Pitchumani Violet Mary
- Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641 062, India
| | | | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India.
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26
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Rezaei Kamelabad M, Jahanbin Sardroodi J, Rastkar Ebrahimzadeh A. The Interaction of Curcumin and Rosmarinic Acid with Non‐Amyloid‐Component Domain of Alpha‐Synuclein: A Molecular Dynamics Study. ChemistrySelect 2020. [DOI: 10.1002/slct.201904799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mahrokh Rezaei Kamelabad
- Molecular Simulation Lab, Department of ChemistryAzarbaijan Shahid Madani University Tabriz Iran
| | - Jaber Jahanbin Sardroodi
- Molecular Simulation Lab, Department of ChemistryAzarbaijan Shahid Madani University Tabriz Iran
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27
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Saini RK, Thakur H, Goyal B. Effect of Piedmont mutation (L34V) on the structure, dynamics, and aggregation of Alzheimer's Aβ 40 peptide. J Mol Graph Model 2020; 97:107571. [PMID: 32143150 DOI: 10.1016/j.jmgm.2020.107571] [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] [Received: 08/29/2019] [Revised: 01/26/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022]
Abstract
The amyloid-β (Aβ) aggregation in the brain has been associated with the development of Alzheimer's disease (AD). The previous studies have reported that Piedmont mutation (L34V) increases the rate of Aβ40 aggregation. However, the underlying molecular mechanism of the effect of L34V mutation on Aβ40 structure, dynamics, and aggregation remains largely unclear. In the present study, molecular dynamics (MD) simulations were performed to elucidate the effect of L34V mutation on the structural changes and conformational dynamics of Aβ40. The secondary structure analysis highlight that L34V mutation enhances Aβ40 self-assembly due to the formation of aggregation-prone β-sheet structure at the C-terminus of Aβ40 monomeric structure. The higher probability of Asp23-Lys28 salt bridge interaction in Aβ40(L34V) leads to aggregation prone β-sheet conformations, which has the potential to increase the fibril formation rate. The free energy landscape (FEL) analysis depict a sampling of coil conformation in the free energy minima of Aβ40, whereas the aggregation-prone β-sheet conformation was observed at the C-terminal region of Aβ40(L34V) in the minimum energy conformations extracted from FEL of Aβ40(L34V). MD simulations, in agreement with experiment, highlight that L34V mutation increases Aβ40 aggregation as the sampling of the aggregation-prone β-sheet conformation substantially increased. Overall, MD simulations provided atomic level details into the increased fibril formation tendency upon L34V mutation and physical insights into the L34V-mediated conformational as well as structural changes in Aβ40.
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Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Hema Thakur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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28
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Abstract
PURPOSE OF REVIEW Dementia is rapidly growing as sources of morbidity and mortality as the US population ages, but its pathophysiology remains poorly understood. As a result, no disease-modifying treatments currently exist. We review the evidence that nonesterified fatty acids may play a key role in this condition. RECENT FINDINGS Nonesterified fatty acids appear to influence several pathways leading to dementia. In addition to their vascular effects, these moieties cross the blood-brain barrier, where they are toxic to several cell types. They may also influence insulin metabolism in the brain directly and indirectly, and some drugs that lower circulating levels appear to slow cognitive decline and brain atrophy in diabetes. SUMMARY Nonesterified fatty acids may contribute to dementia, much as they do to diabetes and cardiovascular disease. Several therapeutic agents lower circulating levels of nonesterified fatty acids and should be tested for their potential preventive effects on cognitive decline in healthy populations before irreversible neuronal attrition occurs.
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Affiliation(s)
- Kenneth J Mukamal
- Beth Israel Deaconess Medical Center, General Medicine, Brookline, Massachusetts, USA
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29
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Agrawal L, Korkutata M, Vimal SK, Yadav MK, Bhattacharyya S, Shiga T. Therapeutic potential of serotonin 4 receptor for chronic depression and its associated comorbidity in the gut. Neuropharmacology 2020; 166:107969. [PMID: 31982703 DOI: 10.1016/j.neuropharm.2020.107969] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
The latest estimates from world health organization suggest that more than 450 million people are suffering from depression and other psychiatric conditions. Of these, 50-60% have been reported to have progression of gut diseases. In the last two decades, researchers introduced incipient physiological roles for serotonin (5-HT) receptors (5-HTRs), suggesting their importance as a potential pharmacological target in various psychiatric and gut diseases. A growing body of evidence suggests that 5-HT systems affect the brain-gut axis in depressive patients, which leads to gut comorbidity. Recently, preclinical trials of 5-HT4R agonists and antagonists were promising as antipsychotic and prokinetic agents. In the current review, we address the possible pharmacological role and contribution of 5-HT4R in the pathophysiology of chronic depression and associated gut abnormalities. Physiologically, during depression episodes, centers of the sympathetic and parasympathetic nervous system couple together with neuroendocrine systems to alter the function of hypothalamic-pituitary-adrenal (HPA) axis and enteric nervous system (ENS), which in turn leads to onset of gastrointestinal tract (GIT) disorders. Consecutively, the ENS governs a broad spectrum of physiological activities of gut, such as visceral pain and motility. During the stages of emotional stress, hyperactivity of the HPA axis alters the ENS response to physiological and noxious stimuli. Consecutively, stress-induced flare, swelling, hyperalgesia and altered reflexes in gut eventually lead to GIT disorders. In summary, the current review provides prospective information about the role and mechanism of 5-HT4R-based therapeutics for the treatment of depressive disorder and possible consequences for the gut via brain-gut axis interactions. This article is part of the special issue entitled 'Serotonin Research: Crossing Scales and Boundaries'.
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Affiliation(s)
- Lokesh Agrawal
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1, 305-8577, Tennodai, Tsukuba, Ibaraki, Japan.
| | - Mustafa Korkutata
- Department of Neurology, Division of Sleep Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Sunil Kumar Vimal
- Department of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
| | - Manoj Kumar Yadav
- School of Integrative and Global Majors, University of Tsukuba, 1-1-1, 305-8577, Tennodai, Tsukuba, Ibaraki, Japan; Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Sanjib Bhattacharyya
- Department of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, PR China
| | - Takashi Shiga
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1, 305-8577, Tennodai, Tsukuba, Ibaraki, Japan; Department of Neurobiology, Faculty of Medicine, University of Tsukuba,1-1-1, Tennodai, Tsukuba, 305-8577, Ibaraki, Japan.
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30
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Mandaci SY, Caliskan M, Sariaslan MF, Uversky VN, Coskuner‐Weber O. Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of α‐synuclein on simulation techniques and force field parameters. Chem Biol Drug Des 2020; 96:659-667. [DOI: 10.1111/cbdd.13662] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/14/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Sunay Y. Mandaci
- Molecular Biotechnology Turkish‐German University Istanbul Turkey
| | - Murat Caliskan
- Molecular Biotechnology Turkish‐German University Istanbul Turkey
| | | | - Vladimir N. Uversky
- Department of Molecular Medicine USF Health Byrd Alzheimer's Research Institute Morsani College of Medicine University of South Florida Tampa FL USA
- Laboratory of New Methods in Biology Institute for Biological Instrumentation of the Russian Academy of Sciences Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” Pushchino Russia
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31
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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32
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Mehra R, Kepp KP. Cell size effects in the molecular dynamics of the intrinsically disordered Aβ peptide. J Chem Phys 2019; 151:085101. [DOI: 10.1063/1.5115085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Rukmankesh Mehra
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
| | - Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, Denmark
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33
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Coskuner O, Uversky VN. Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer's and Parkinson's diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:145-223. [PMID: 31521231 DOI: 10.1016/bs.pmbts.2019.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Amyloid-β (Aβ) and α-synuclein (αS) are two intrinsically disordered proteins (IDPs) at the centers of the pathogenesis of Alzheimer's and Parkinson's diseases, respectively. Different hypotheses have been proposed for explanation of the molecular mechanisms of the pathogenesis of these two diseases, with these two IDPs being involved in many of these hypotheses. Currently, we do not know, which of these hypothesis is more accurate. Experiments face challenges due to the rapid conformational changes, fast aggregation processes, solvent and paramagnetic effects in studying these two IDPs in detail. Furthermore, pathological modifications impact their structures and energetics. Theoretical studies using computational chemistry and computational biology have been utilized to understand the structures and energetics of Aβ and αS. In this chapter, we introduce Aβ and αS in light of various hypotheses, and discuss different experimental and theoretical techniques that are used to study these two proteins along with their weaknesses and strengths. We suggest that a promising solution for studying Aβ and αS at the center of varying hypotheses could be provided by developing new techniques that link quantum mechanics, statistical mechanics, thermodynamics, bioinformatics to machine learning. Such new developments could also lead to development in experimental techniques.
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Affiliation(s)
- Orkid Coskuner
- Turkish-German University, Molecular Biotechnology, Istanbul, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Moscow, Russia.
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34
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Tung N, Derreumaux P, Vu VV, Nam PC, Ngo ST. C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ 11-42 Tetramer in Solution: Intensive MD Study. ACS OMEGA 2019; 4:11066-11073. [PMID: 31460204 PMCID: PMC6648102 DOI: 10.1021/acsomega.9b00992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer's disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms → oligomers → photofibrils → mature fibrils → plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ11-42 tetramer (S4Aβ11-42) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ11-42 oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ42 aggregation. The sequences 27-35 and 39-40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is ∼42 ± 3%. Furthermore, the dissociation free energy of the S4Aβ11-42 peptide was predicted using a biased sampling method. The obtained free energy is ΔG US = -58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ17-42 peptide. We anticipate that the obtained S4Aβ11-42 structures could be used as targets for AD inhibitor screening over the in silico study.
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Affiliation(s)
- Nguyen
Thanh Tung
- Institute
of Materials Science, Vietnam Academy of
Science and Technology, Hanoi 10307, Vietnam
| | - Philippe Derreumaux
- Laboratory of Theoretical and Chemistry, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty
of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Van V. Vu
- NTT
Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Pham Cam Nam
- Department
of Chemical Engineering, The University
of Da Nang—University of Science and Technology, Da Nang City 550000, Vietnam
| | - Son Tung Ngo
- Laboratory
of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang
University, Ho Chi
Minh City 758307, Vietnam
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35
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Martinelli AHS, Lopes FC, John EBO, Carlini CR, Ligabue-Braun R. Modulation of Disordered Proteins with a Focus on Neurodegenerative Diseases and Other Pathologies. Int J Mol Sci 2019; 20:ijms20061322. [PMID: 30875980 PMCID: PMC6471803 DOI: 10.3390/ijms20061322] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) do not have rigid 3D structures, showing changes in their folding depending on the environment or ligands. Intrinsically disordered proteins are widely spread in eukaryotic genomes, and these proteins participate in many cell regulatory metabolism processes. Some IDPs, when aberrantly folded, can be the cause of some diseases such as Alzheimer′s, Parkinson′s, and prionic, among others. In these diseases, there are modifications in parts of the protein or in its entirety. A common conformational variation of these IDPs is misfolding and aggregation, forming, for instance, neurotoxic amyloid plaques. In this review, we discuss some IDPs that are involved in neurodegenerative diseases (such as beta amyloid, alpha synuclein, tau, and the “IDP-like” PrP), cancer (p53, c-Myc), and diabetes (amylin), focusing on the structural changes of these IDPs that are linked to such pathologies. We also present the IDP modulation mechanisms that can be explored in new strategies for drug design. Lastly, we show some candidate drugs that can be used in the future for the treatment of diseases caused by misfolded IDPs, considering that cancer therapy has more advanced research in comparison to other diseases, while also discussing recent and future developments in this area of research. Therefore, we aim to provide support to the study of IDPs and their modulation mechanisms as promising approaches to combat such severe diseases.
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Affiliation(s)
- Anne H S Martinelli
- Department of Molecular Biology and Biotechnology & Department of Biophysics, Biosciences Institute-IB, (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Fernanda C Lopes
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Elisa B O John
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Célia R Carlini
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 91410-000, RS, Brazil.
- Brain Institute-InsCer, Laboratory of Neurotoxins, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Department of Pharmaceutical Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre CEP 90050-170, RS, Brazil.
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36
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Semenyuk P, Muronetz V. Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications. Int J Mol Sci 2019; 20:E1252. [PMID: 30871103 PMCID: PMC6429204 DOI: 10.3390/ijms20051252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.
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Affiliation(s)
- Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia.
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37
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Coskuner-Weber O, Uversky VN. Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β42. J Chem Inf Model 2019; 59:871-884. [DOI: 10.1021/acs.jcim.8b00926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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38
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Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci 2019; 20:ijms20030548. [PMID: 30696058 PMCID: PMC6386852 DOI: 10.3390/ijms20030548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 12/25/2022] Open
Abstract
Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations-whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context in which it occurs. Such information may positively aid drug-design. Furthermore, due to the intrinsic plasticity of proteins, even mutations involving radical change of the structural and physico⁻chemical properties of the amino acids (native vs. mutant) can still have minimal effects on protein thermodynamics. However, if a mutation causes significant perturbation by either folding or binding free energies, it is quite likely to be deleterious. Mitigating such effects is a promising alternative to the traditional approaches of designing inhibitors. This can be done by structure-based in silico screening of small molecules for which binding to the dysfunctional protein restores its wild type thermodynamics. In this review we emphasize the effects of mutations on two important biophysical properties, stability and binding affinity, and how structures can be used for structure-based drug design to mitigate the effects of disease-causing variants on the above biophysical properties.
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Affiliation(s)
- Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Sankar Basu
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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Trumbore CN. Shear-induced amyloid formation of IDPs in the brain. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:225-309. [DOI: 10.1016/bs.pmbts.2019.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Suplatov D, Kopylov K, Sharapova Y, Švedas V. Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod. J Biomol Struct Dyn 2018; 37:2049-2060. [PMID: 29749295 DOI: 10.1080/07391102.2018.1475260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the 'out' state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod's binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry Suplatov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Kirill Kopylov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Yana Sharapova
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Vytas Švedas
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
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Ilie IM, Caflisch A. Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study. J Phys Chem B 2018; 122:11072-11082. [PMID: 29965774 DOI: 10.1021/acs.jpcb.8b05236] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present a simulation study of the early events of peptide dissociation from a fibril of the Alzheimer's Aβ42 peptide. The fibril consists of layers of two adjacent Aβ42 peptides each folded in an S-shaped structure which has been determined by solid state NMR spectroscopy of a monomorphic disease-relevant species. Multiple molecular dynamics runs (16 at 310 K and 15 at 370 K) were carried out starting from an 18-peptide protofibril for a cumulative sampling of about 15 μs. The simulations show structural stability of the fibrillar core and an overall increase in the twist to about 3 degrees. The N-terminal segment 1-14 is disordered in all peptides. At both ends of the fibril, the central segment 21-29, which includes part of the β2 strand, dissociates in some of the simulations. The β1 and β3 strands, residues 15-20 and 35-41, respectively, are structurally stable. The transient binding of the N-terminal stretch to the β3 strand of the adjacent peptide at the tip is likely to contribute to the arrest phase of the stop-and-go mechanism.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry , University of Zürich , 8057 Zürich , Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry , University of Zürich , 8057 Zürich , Switzerland
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42
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Galante D, Cavallo E, Perico A, D'Arrigo C. Effect of ferric citrate on amyloid-beta peptides behavior. Biopolymers 2018; 109:e23224. [PMID: 29897618 DOI: 10.1002/bip.23224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/06/2018] [Accepted: 04/19/2018] [Indexed: 12/26/2022]
Abstract
Amyloid beta (Aβ) aggregation and oxidative stress are two of the central events in Alzheimer's Disease (AD). Both these phenomena can be caused by the interaction of Aβ with metal ions. In the last years the interaction between ZnII , CuII , and Aβ was much studied, but between iron and Aβ it is still little known. In this work we determine how three Aβ peptides, present in AD, interact with FeIII -citrate. The three Aβ peptides are: full length Aβ1-42, an isoform truncated at Glutamic acid in position three, Aβ3-42, and its pyroglutamated form AβpE3-42. Conformation and morphology of the three peptides, aggregated with and without FeIII -citrate were studied. Besides, we have determined the strength of the interactions Aβ/FeIII -citrate studying the effect of ethylenediaminetetraacetic acid as chelator. Results reported here demonstrate that FeIII -citrate promotes the aggregation in all the three peptides. Moreover, Aspartic acid 1, Glutamic acid 3, and Tyrosine 10 have an important role in the coordination with iron, generating a more stable complex for Aβ1-42 compared to that for the truncated peptides.
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Affiliation(s)
- D Galante
- Institute for Macromolecular Studies, National Research Council, Genova, 16149, Italy
| | - E Cavallo
- Institute for Macromolecular Studies, National Research Council, Genova, 16149, Italy.,Department of Chemistry and Industrial Chemistry, University of Genova, Via Dodecaneso 31, Genova, 16146, Italy
| | - A Perico
- Institute for Macromolecular Studies, National Research Council, Genova, 16149, Italy
| | - C D'Arrigo
- Institute for Macromolecular Studies, National Research Council, Genova, 16149, Italy
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Ngo ST, Hung HM, Hong ND, Tung NT. The influences of E22Q mutant on solvated 3Aβ 11-40 peptide: A REMD study. J Mol Graph Model 2018; 83:122-128. [PMID: 29902674 DOI: 10.1016/j.jmgm.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/03/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
The residue E22 plays a critical role in the aggregation process of Amyloid beta (Aβ) peptides. The effect of E22Q mutant on the shapes of the solvated Aβ11-40 trimer is clarified using a replica exchange molecular dynamics (REMD) simulation employing ∼20.6 μs of MD simulations with 48 disparate replicas. The increase of intramolecular polar contacts and salt bridge between the residue D23 to residues (24-29) was observed. The residual secondary structure of the mutated trimer is shifted in a similar way to the picture observed in previous investigations of F19W mutant. The free energy surface (FES) of the mutated E22Q system has a fewer number of minima in comparison with the wild-type trimer. The optimized shapes of the mutated E22Q form a significant increase in beta structure (47%) and serious decrease in coil content (46%) compared with the wild-type (of 36 and 56%, respectively). The binding affinity of constituting chains to the rest is of -43.7 ± 6.5 kcal/mol, implying that the representative structure of E22Q is more stable than the wild-type one. Furthermore, the E22Q mutant increases the size of stable structures due to larger collision cross section (CCS) and solvent accessible area (SASA). The observed results may enhance the Aβ inhibition throughout the contribution to the knowledge of the Aβ oligomerization/aggregation.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Nam Dao Hong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science and Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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Basu S, Biswas P. Salt-bridge dynamics in intrinsically disordered proteins: A trade-off between electrostatic interactions and structural flexibility. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:624-641. [DOI: 10.1016/j.bbapap.2018.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/13/2018] [Accepted: 03/07/2018] [Indexed: 12/29/2022]
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