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当代阿耳茨海默病研究

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ISSN (Print): 1567-2050
ISSN (Online): 1875-5828

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Review Article

通过计算机模拟研究神经退行性疾病中固有紊乱蛋白的当前挑战和局限性

卷 17, 期 9, 2020

页: [805 - 818] 页: 14

弟呕挨: 10.2174/1567205017666201109094908

价格: $65

摘要

由于快速的构象变化和增强的聚集倾向，实验在分析溶液中内在无序的蛋白质时面临挑战。 计算研究是对实验的补充，被广泛用于分析内在失调的蛋白质，尤其是位于神经退行性疾病中心的蛋白质。 但是，最近的调查（包括我们自己的调查）表明，计算机仿真本身面临着巨大的挑战和局限。 在这篇综述中，我们介绍并讨论了对内在无序蛋白进行的计算研究的一些科学挑战和局限性。 我们还概述了计算化学和计算物理领域中未来发展的重要性，这些领域将需要从计算机模拟中为固有无序蛋白生成更准确的数据。 本文还讨论了可以开发的其他理论策略。

关键词: 阿尔茨海默氏病，β-淀粉样蛋白，α-突触核蛋白，神经退行性疾病，内在失调的蛋白质，计算机模拟。

« Previous Next »
[1]
Walsh DM, Selkoe DJ. Amyloid β-protein and beyond: The path forward in Alzheimer’s disease. Curr Opin Neurobiol 2020; 61: 116-24.
[http://dx.doi.org/10.1016/j.conb.2020.02.003] [PMID: 32197217]
[2]
Coskuner O, Uversky VN. Tyrosine regulates β-sheet structure formation in amyloid-β42: A new clustering algorithm for disordered proteins. J Chem Inf Model 2017; 57(6): 1342-58.
[http://dx.doi.org/10.1021/acs.jcim.6b00761] [PMID: 28474890]
[3]
Coskuner O, Wise-Scira O. Arginine and disordered amyloid-β peptide structures: molecular level insights into the toxicity in Alzheimer’s disease. ACS Chem Neurosci 2013; 4(12): 1549-58.
[http://dx.doi.org/10.1021/cn4001389] [PMID: 24041422]
[4]
Mroczko B, Groblewska M, Litman-Zawadzka A, Kornhuber J, Lewczuk P. Amyloid β oligomers (AβOs) in Alzheimer’s disease. J Neural Transm (Vienna) 2018; 125(2): 177-91.
[http://dx.doi.org/10.1007/s00702-017-1820-x] [PMID: 29196815]
[5]
Reiss AB, Arain HA, Stecker MM, Siegart NM, Kasselman LJ. Amyloid toxicity in Alzheimer’s disease. Rev Neurosci 2018; 29(6): 613-27.
[http://dx.doi.org/10.1515/revneuro-2017-0063] [PMID: 29447116]
[6]
Wise-Scira O, Xu L, Kitahara T, Perry G, Coskuner O. Amyloid-β peptide structure in aqueous solution varies with fragment size. J Chem Phys 2011; 135(20)205101
[http://dx.doi.org/10.1063/1.3662490] [PMID: 22128957]
[7]
Teil M, Arotcarena M-L, Faggiani E, Laferriere F, Bezard E, Dehay B. Targeting α-synuclein for PD therapeutics: A pursuit on all fronts. Biomolecules 2020; 10(3): 391.
[http://dx.doi.org/10.3390/biom10030391] [PMID: 32138193]
[8]
Coskuner O, Wise-Scira O. Structures and free energy landscapes of the A53T mutant-type α-synuclein protein and impact of A53T mutation on the structures of the wild-type α-synuclein protein with dynamics. ACS Chem Neurosci 2013; 4(7): 1101-13.
[http://dx.doi.org/10.1021/cn400041j] [PMID: 23607785]
[9]
Wise-Scira O, Aloglu AK, Dunn A, Sakallioglu IT, Coskuner O. Structures and free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins with dynamics. ACS Chem Neurosci 2013; 4(3): 486-97.
[http://dx.doi.org/10.1021/cn300198q] [PMID: 23374072]
[10]
Wise-Scira O, Dunn A, Aloglu AK, Sakallioglu IT, Coskuner O. Structures of the E46K mutant-type α-synuclein protein and impact of E46K mutation on the structures of the wild-type α-synuclein protein. ACS Chem Neurosci 2013; 4(3): 498-508.
[http://dx.doi.org/10.1021/cn3002027] [PMID: 23374074]
[11]
Coskuner-Weber O, Uversky VN. Insights into the molecular mechanisms of Alzheimer’s and Parkinson’s diseases with molecular simulations: Understanding the roles of artificial and pathological missense mutations in intrinsically disordered proteins related to pathology. Int J Mol Sci 2018; 19(2): 336.
[http://dx.doi.org/10.3390/ijms19020336] [PMID: 29364151]
[12]
Tiwari V, Solanki V, Tiwari M. In-Vivo and in-Vitro techniques used to investigate Alzheimer’s disease. Front Life Sci 2015; 8(4): 332-47.
[http://dx.doi.org/10.1080/21553769.2015.1044129]
[13]
METALLIC SYSTEMS A Quantum Chemist’s Perspective 2017.
[14]
Wise O, Coskuner O. New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue. J Comput Chem 2014; 35(17): 1278-89.
[http://dx.doi.org/10.1002/jcc.23622] [PMID: 24777820]
[15]
Coskuner O, Deiters UK. Hydrophobic interactions of xenon by monte carlo simulations. Z Phys Chem 2007; 221(6): 785-99.
[http://dx.doi.org/10.1524/zpch.2007.221.6.785]
[16]
Coskuner O, Bergeron DE, Rincon L, Hudgens JW, Gonzalez CA. Identification of active sites of biomolecules. 1. Methyl-α-mannopyranoside and Fe(III)). J Phys Chem A 2008; 112(13): 2940-7.
[http://dx.doi.org/10.1021/jp711759q] [PMID: 18302355]
[17]
Coskuner O, Bergeron DE, Rincon L, Hudgens JW, Gonzalez CA. Identification of active sites of biomolecules II: Saccharide and transition metal ion in aqueous solution. J Phys Chem A 2009; 113(11): 2491-9.
[http://dx.doi.org/10.1021/jp805747f] [PMID: 19236000]
[18]
Weber OC, Uversky VN. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β42 in water. Intrinsically Disord Proteins 2017; 5(1)e1377813
[http://dx.doi.org/10.1080/21690707.2017.1377813] [PMID: 30250773]
[19]
Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-grained protein models and their applications. Chem Rev 2016; 116(14): 7898-936.
[http://dx.doi.org/10.1021/acs.chemrev.6b00163] [PMID: 27333362]
[20]
Strodel B, Coskuner-Weber O. Transition metal ion interactions with disordered amyloid-β peptides in the pathogenesis of Alzheimer’s Disease: Insights from computational chemistry studies. J Chem Inf Model 2019; 59(5): 1782-805.
[http://dx.doi.org/10.1021/acs.jcim.8b00983] [PMID: 30933519]
[21]
Car R, Parrinello M. Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 1985; 55(22): 2471-4.
[http://dx.doi.org/10.1103/PhysRevLett.55.2471] [PMID: 10032153]
[22]
Warshel A, Levitt M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 1976; 103(2): 227-49.
[http://dx.doi.org/10.1016/0022-2836(76)90311-9] [PMID: 985660]
[23]
Kroese DP, Brereton T, Taimre T, Botev ZI. Why the monte carlo method is so important today: Why the MCM is so important today. Wiley Interdiscip Rev Comput Stat 2014; 6(6): 386-92.
[http://dx.doi.org/10.1002/wics.1314]
[24]
Nguyen PH, Li MS, Derreumaux P. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ(16-22) dimer and trimer. Phys Chem Chem Phys 2011; 13(20): 9778-88.
[http://dx.doi.org/10.1039/c1cp20323a] [PMID: 21487594]
[25]
Somavarapu AK, Kepp KP. The dependence of Amyloid-β dynamics on protein force fields and water models. ChemPhysChem 2015; 16(15): 3278-89.
[http://dx.doi.org/10.1002/cphc.201500415] [PMID: 26256268]
[26]
Carballo-Pacheco M, Strodel B. Comparison of force fields for Alzheimer’s A β42: A case study for intrinsically disordered proteins. Protein Sci 2017; 26(2): 174-85.
[http://dx.doi.org/10.1002/pro.3064] [PMID: 27727496]
[27]
Shabane PS, Izadi S, Onufriev AV. General purpose water model can improve atomistic simulations of intrinsically disordered proteins. J Chem Theory Comput 2019; 15(4): 2620-34.
[http://dx.doi.org/10.1021/acs.jctc.8b01123] [PMID: 30865832]
[28]
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(1): 659-67.
[29]
Mehra R, Kepp KP. Cell size effects in the molecular dynamics of the intrinsically disordered Aβ peptide. J Chem Phys 2019; 151(8)085101
[http://dx.doi.org/10.1063/1.5115085] [PMID: 31470695]
[30]
Pickhardt M, Neumann T, Schwizer D, et al. Identification of small molecule inhibitors of tau aggregation by targeting monomeric tau as a potential therapeutic approach for tauopathies. Curr Alzheimer Res 2015; 12(9): 814-28.
[http://dx.doi.org/10.2174/156720501209151019104951] [PMID: 26510979]
[31]
Kovacech B, Novak M. Tau truncation is a productive posttranslational modification of neurofibrillary degeneration in Alzheimer’s disease. Curr Alz Dis 2010; 7(8): 708-16.
[http://dx.doi.org/10.2174/156720510793611556]

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