Statistical mechanics of protein structural transitions: Insights from the island model

Abstract

The so-called island model of protein structural transition holds that hydrophobic interactions are the key to both the folding and function of proteins. Herein, the genesis and statistical mechanical basis of the island model of transitions are reviewed, by presenting the results of simulations of such transitions. Elucidating the physicochemical mechanism of protein structural formation is the foundation for understanding the hierarchical structure of life at the microscopic level. Based on the results obtained to date using the island model, remaining problems and future work in the field of protein structures are discussed, referencing Professor Saitô’s views on the hierarchic structure of science.

Salt-bridge dynamics in intrinsically disordered proteins: A trade-off between electrostatic interactions and structural flexibility

“…The deviation in the corresponding persistence values were found to be negligible, as reflected in the calculated pairwise root mean square deviations (0.0035: 20 ps vs. 50ps; 0.0051: 100 ps vs. 50 ps) (Supplementary Table S2) of the persistent salt-bridges. The choice of the 50 ps time interval was motivated by the range of reported time scales for secondary structural transitions in proteins [31].…”

“…A protein, being a hetero-polymer, can not grow linearly for an indefinite period in space; it has to take a turn at some point [31,54]. This was the key idea behind the proposition of the cotranslational folding model in proteins [55,56], later proven experimentally [56] and supported by plausible genetic mechanisms (viz., pause codons) [57].…”

Obituary: Nobuhiko Saitô, a man who understood protein folding in his own way

“…After graduating from Tokyo Imperial University, he devoted his time to the physics of macromolecules. The scientific details of his achievements are well narrated in the accompanying paper by Yukio Kobayashi in this special issue [1]. To complement Dr. Kobayashi’s review and complete the picture of Nobuhiko Saito’s role in biophysics, I will describe other aspects of his life and work.…”

Memorial Issue for Professor Nobuhiko Saitô

“…She was one of the first students of him in 1960s when Nobuhiko Saitô moved from Kobayasi Institute of Physical Research to Waseda University. Yukio Kobayashi, one of the students in 1980s, contributed an extensive review of Nobuhiko Saitô’s achievement on biopolymers [3]. After the three manuscripts focusing on the achievement of Nobuhiko Saitô, the contribution from Hiroshi Wako turned our perspective to the future and extension of the work done by him.…”