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
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
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
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
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
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
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
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
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
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
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
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