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Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

[ Vol. 17 , Issue. 9 ]

Author(s):

Ibrahim Y. Akbayrak, Sule I. Caglayan, Zilan Ozcan, Vladimir N. Uversky and Orkid Coskuner-Weber*   Pages 805 - 818 ( 14 )

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.

Keywords:

Alzheimer's disease, amyloid-β, α-synuclein, neurodegenerative diseases, intrinsically disordered proteins, computer simulations.

Affiliation:

Materials Science and Technologies, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820



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