Modeling of Protein–Protein Interaction within Landau–Ginzburg–Wilson Approach Using α-Synuclein As an Example

Wang W., Nema S., Teagarden D. 2010. Protein aggregation – Pathways and influencing factors. Int. J. Pharm. 390 (2), 89–99. https://doi.org/10.1016/j.ijpharm.2010.02.025

Article  CAS  PubMed  Google Scholar 

Keskin O., Nussinov R. 2007. Similar binding sites and different partners: Implications to shared proteins in cellular pathways. Structure. 15 (3), 341–354. https://doi.org/10.1016/j.str.2007.01.007

Article  CAS  PubMed  Google Scholar 

Zilkha-Falb R., Ziv I., Nardi N., Offen D., Melamed E., Barzilai, A. 1997. Monoamine-induced apoptotic neuronal cell death. Cell. Mol. Neurobiol. 17 (1), 101–118. https://doi.org/10.1023/a:1026333222008

Article  CAS  PubMed  PubMed Central  Google Scholar 

Custodio F.L., Barbosa H.J.C., Dardenne L.E. 2010. Full-atom ab initio protein structure prediction with a Genetic Algorithm using a similarity-based surrogate model. IEEE CEC. 1–8. https://doi.org/10.1109/CEC.2010.5585959

Sheinerman F.B., Honig B. 2002. On the role of electrostatic interactions in the design of protein–protein interface. J. Mol. Biol. 318 (1), 161–177. https://doi.org/10.1016/s0022-2836(02)00030-x

Article  CAS  PubMed  Google Scholar 

Niemi A.J. 2014. Gauge field, strings, solitons, anomalies and the speed of life. Theor. Math. Phys. 181 (1), 1235–1262. https://doi.org/10.1007/s11232-014-0210-x

Article  Google Scholar 

Ulmer T.S., Bax A., Cole N.B., Nussbaum R.L. 2004. Structure and dynamics of micelle‑bound human alpha-synuclein. J. Biol. Chem. 280 (10), 9595–9603. https://doi.org/10.1074/jbc.m411805200

Article  PubMed  Google Scholar 

Korneev A., Begun A., Liubimov S., Kachlishvili K., Molochkov A., Niemi A.J., Maisuradze G.G. 2022. Exploring structural flexibility and stability of α‑synuclein by the Landau–Ginzburg–Wilson approach. J. Phys. Chem. B. 126 (36), 6878–6890. https://doi.org/10.1021/acs.jpcb.2c04651

Article  CAS  PubMed  Google Scholar 

Bungeroth M., Appenzeller S., Regulin A., Völker W., Lorenzen I., Grötzinger J., Pendziwiat M., Kuhlenbäumer G. 2014. Differential aggregation properties of alpha‑synuclein isoforms. Neurobiol. Aging. 35 (8), 1913–1919. https://doi.org/10.1016/j.neurobiolaging.2014.02.009

Article  CAS  PubMed  Google Scholar 

Wilson K.G., Kogut J. 1974. The renormalization group and the epsilon expansion. Phys. Rept. 12 (2), 75–199. https://doi.org/10.1016/0370-1573(74)90023-4

Article  Google Scholar 

Goldenfeld N. 1992. Lectures on phase transitions and the renormalization group. Massachusetts: Reading.

Begun A, Molochkov A., Niemi A.J. 2019. Protein tertiary structure and the myoglobin phase diagram. Sci. Rep. 9 (1), 10819. https://doi.org/10.1038/s41598-019-47317-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu S., Krokhotin A., Niemi A.J., Peng X. 2011. Towards quantitative classification of folded proteins in terms of elementary functions. Phys. Rev. E. 83 (4), 041907. https://doi.org/10.1103/physreve.83.041907

Article  Google Scholar 

Krokhotin A., Liwo A., Maisuradze G.G., Niemi A.J., Scheraga H.A. 2014. Kinks, loops, and protein folding with protein A as an example. J. Chem. Phys. 140 (2), 025101. https://doi.org/10.1063/1.4855735

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chernodub M., Hu S., Niemi A.J. 2010. Topological solitons and folded proteins. Phys. Rev. E. 82 (1), 011916. https://doi.org/10.1103/physreve.82.011916

Article  Google Scholar 

Molkenthin N., Hu S., Niemi A.J. 2011. Discrete nonlinear Schrödinger equation and polygonal solitons with applications to collapsed proteins. Phys. Rev. Lett. 106 (7), 078102. https://doi.org/10.1103/physrevlett.106.078102

Article  PubMed  Google Scholar 

Hu S., Lundgren M., Niemi A.J. 2011. Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins. Phys. Rev. E. 83 (6), 061908. https://doi.org/10.1103/PhysRevE.83.061908

Article  CAS  Google Scholar 

Krokhotin A., Niemi A.J., Peng X. 2012. Soliton concepts and protein structure. Phys. Rev. E. 85 (3), 031906. https://doi.org/10.1103/physreve.85.031906

Article  Google Scholar 

Krokhotin A., Liwo A., Niemi A.J., Scheraga H.A. 2012. Coexistence of phases in a protein heterodimer. J. Chem. Phys. 137 (3), 035101. https://doi.org/10.1063/1.4734019

Article  CAS  PubMed  PubMed Central  Google Scholar 

Krokhotin A., Lundgren M., Niemi A.J. 2012. Solitons and collapse in the λ-repressor protein. Phys. Rev. E. 86 (2), 021923. https://doi.org/10.1103/physreve.86.021923

Article  Google Scholar 

Molochkov A., Begun A., Niemi A.J. 2017. Gauge symmetries and structure of proteins. EPJ Web Conf. 137, 04004. https://doi.org/10.1051/epjconf/201713704004

Levitt M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104 (1), 59–107. https://doi.org/10.1016/0022-2836(76)90004-8

Article  CAS  PubMed  Google Scholar 

Okazaki K.-i., Sato T., Takano M. 2012. Temperature enhanced association of proteins due to electrostatic interaction: A coarse-grained simulation of actin–myosin binding. J. Am. Chem. Soc. 134 (21), 8918−8925.https://doi.org/10.1021/ja301447j

Article  CAS  PubMed  Google Scholar 

Luengo D., Martino L., Bugallo M., Elvira V., S. Särkkä S. 2020. A survey of Monte Carlo methods for parameter estimation. EURASIP J. Adv. Signal Process. 25, 8–11. https://doi.org/10.48550/arXiv.2107.11820

Article  Google Scholar 

Randall D., Tetali P. 2000. Analyzing Glauber dynamics by comparison of Markov chains. J. Math. Phys. 41 (3), 1598–1615. https://doi.org/10.1063/1.533199

Article  Google Scholar 

Comments (0)

No login
gif