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Korneev A, Begun A, Liubimov S, Kachlishvili K, Molochkov A, Niemi AJ, Maisuradze GG. Exploring Structural Flexibility and Stability of α-Synuclein by the Landau-Ginzburg-Wilson Approach. J Phys Chem B 2022; 126:6878-6890. [PMID: 36053833 PMCID: PMC9482328 DOI: 10.1021/acs.jpcb.2c04651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
α-Synuclein (αS) is the principal protein component of the Lewy body and Lewy neurite deposits that are found in the brains of the victims of one of the most prevalent neurodegenerative disorders, Parkinson's disease. αS can be qualified as a chameleon protein because of the large number of different conformations that it is able to adopt: it is disordered under physiological conditions in solution, in equilibrium with a minor α-helical tetrameric form in the cytoplasm, and is α-helical when bound to a cell membrane. Also, in vitro, αS forms polymorphic amyloid fibrils with unique arrangements of cross-β-sheet motifs. Therefore, it is of interest to elucidate the origins of the structural flexibility of αS and what makes αS stable in different conformations. We address these questions here by analyzing the experimental structures of the micelle-bound, tetrameric, and fibrillar αS in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is illustrated that without molecular dynamics simulations the kinks are capable of identifying the key residues causing structural flexibility of αS. Also, the stability of the experimental structures of αS is investigated by simulating heating/cooling trajectories using the Glauber algorithm. The findings are consistent with experiments.
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Affiliation(s)
- Anatolii Korneev
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Alexander Begun
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Sergei Liubimov
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Khatuna Kachlishvili
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, U. S. A
| | - Alexander Molochkov
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
| | - Antti J. Niemi
- Pacific Quantum Center, Far Eastern Federal University, 690922, Vladivostok, Russia
- Nordita, Stockholm University and Uppsala University, SE-106 91 Stockholm, Sweden
- Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, F37200, Tours, France
- School of Physics, Beijing Institute of Technology, Beijing 100081, P.R. China
| | - Gia G. Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, U. S. A
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Sieradzan AK, Korneev A, Begun A, Kachlishvili K, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics. J Chem Theory Comput 2021; 17:3203-3220. [PMID: 33909430 DOI: 10.1021/acs.jctc.1c00155] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP218-62) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time dependence of formation of contacts between Cαs of selected pairs of residues. The key residues involved in the folding of the pT37pT46 4E-BP218-62 are elucidated by this analysis. The correlations between local and global motions are identified. Moreover, for a better understanding of the physics of the formation of the folded state, the experimental structure of the pT37pT46 4E-BP218-62 is analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is shown that without molecular dynamics simulations the kinks are able to identify not only the phosphorylated sites of protein, the key players in folding, but also the reasons for the weak stability of the pT37pT46 4E-BP218-62.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Anatolii Korneev
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Alexander Begun
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Khatuna Kachlishvili
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Alexander Molochkov
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia
| | - Patrick Senet
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States.,Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Antti J Niemi
- Pacific Quantum Center, Far Eastern Federal University, 10 Ajax Bay, 690922 Russky Island, Vladivostok, Russia.,Laboratoire de Mathematiques et Physique Theorique, CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours, France.,Nordita, Stockholm University and Uppsala University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden.,School of Physics, Beijing Institute of Technology, Beijing 100081, P.R. China
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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Kachlishvili K, Korneev A, Maisuradze L, Liu J, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain. J Phys Chem B 2020; 124:3855-3872. [PMID: 32271570 DOI: 10.1021/acs.jpcb.0c00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases. Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to overcome. Recently, we studied the origins and prevention of formation of intermediate states with the example of the Formin binding protein 28 (FBP28) WW domain. We demonstrated that the replacement of Leu26 by Asp26 or Trp26 (in ∼15% of the folding trajectories) can alter the folding scenario from three-state folding, a major folding scenario for the FBP28 WW domain (WT) and its mutants, toward two-state or downhill folding at temperatures below the melting point. Here, for a better understanding of the physics of the formation/elimination of intermediates, (i) the dynamics and energetics of formation of β-strands in folding, misfolding, and nonfolding trajectories of these mutants (L26D and L26W) is investigated; (ii) the experimental structures of WT, L26D, and L26W are analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. We show that the formation of each β-strand in folding trajectories is accompanied by the emergence of kinks in internal coordinate space as well as a decrease in local free energy. In particular, the decrease in downhill folding trajectory is ∼7 kcal/mol, while it varies between 31 and 48 kcal/mol for the three-state folding trajectory. The kink analyses of the experimental structures give new insights into formation of intermediates, which may become a useful tool for preventing aggregation.
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Affiliation(s)
- Khatuna Kachlishvili
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States
| | - Anatolii Korneev
- Laboratory of Physics of Living Matter, Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia
| | - Luka Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States.,Biochemistry, Quantitative Biology, Biophysics, and Structural Biology (BQBS) Track, Yale University, New Haven 06520-8084, ConnecticutUnited States
| | - Jiaojiao Liu
- School of Physics, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States
| | - Alexander Molochkov
- Laboratory of Physics of Living Matter, Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia
| | - Patrick Senet
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States.,Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. de Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, Dijon Cedex F-21078, France
| | - Antti J Niemi
- Laboratory of Physics of Living Matter, Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia.,School of Physics, Beijing Institute of Technology, Beijing 100081, P. R. China.,Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, Tours F37200, France.,Nordita, Stockholm University, Roslagstullsbacken 23, Stockholm SE-106 91, Sweden
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States
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