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Int. J. Mol. Sci. 2018, 19(10), 3152;

Designed Elastic Networks: Models of Complex Protein Machinery

Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
Author to whom correspondence should be addressed.
Received: 20 July 2018 / Revised: 4 October 2018 / Accepted: 11 October 2018 / Published: 13 October 2018
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Recently, the design of mechanical networks with protein-inspired responses has become increasingly popular. Here, we review contributions which were motivated by studies of protein dynamics employing coarse-grained elastic network models. First, the concept of evolutionary optimization that we developed to design network structures which execute prescribed tasks is explained. We then review what presumably marks the origin of the idea to design complex functional networks which encode protein-inspired behavior, namely the design of an elastic network structure which emulates the cycles of ATP-powered conformational motion in protein machines. Two recent applications are reviewed. First, the construction of a model molecular motor, whose operation incorporates both the tight coupling power stroke as well as the loose coupling Brownian ratchet mechanism, is discussed. Second, the evolutionary design of network structures which encode optimal long-range communication between remote sites and represent mechanical models of allosteric proteins is presented. We discuss the prospects of designed protein-mimicking elastic networks as model systems to elucidate the design principles and functional signatures underlying the operation of complex protein machinery. View Full-Text
Keywords: mechanical networks; evolution; design; protein machines; molecular motors; Brownian ratchet; power stroke; allostery; conformational motions; synthetic protein mechanical networks; evolution; design; protein machines; molecular motors; Brownian ratchet; power stroke; allostery; conformational motions; synthetic protein

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Flechsig, H.; Togashi, Y. Designed Elastic Networks: Models of Complex Protein Machinery. Int. J. Mol. Sci. 2018, 19, 3152.

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