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Abstract
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.
Highlights
Most dynamical processes in biological cells involve proteins which operate as molecular machines and motors
Starting with an explanation of the concept of evolutionary optimization, we present what we believe marks the origin of the idea to design complex mechanical networks with protein-inspired responses, namely, the design of an elastic network structure which mimics the cycles of ATP-powered conformational motions in protein machines [9]
After obtaining the two functional networks, we focused on understanding the mechanisms by which each of them is able to establish the allosteric communication which is encoded in their structure as a result of evolution
Summary
Most dynamical processes in biological cells involve proteins which operate as molecular machines and motors. Each bead typically corresponds to a single amino acid residue, and elastic connections mediate effective interactions between beads Despite obvious simplifications, such models can reproduce conformational fluctuations in proteins, and, remarkably, normal modes of elastic networks have been shown to be able to describe even the large-amplitude motions related to ATP binding and hydrolysis in various molecular machines and motors (e.g., [6,7,8]). Several groups have successfully designed networks which, inspired by allosteric effects in proteins, reveal pronounced communication between spatially remote regions, and their functional properties have been analyzed [18,19,20,21] In this topical review, we summarize our contributions to this exciting and emerging field with emphasis placed on the perspective of the study of protein dynamics employing physics-based coarse-grained elastic networks. We provide a discussion on the prospects of designed functional networks as structurally resolved model systems to better understand the design and functional principles of complex protein machines
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