Toward Intelligent Molecular Machines:  Directed Motions of Biological and Artificial Molecules and Assemblies

Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well defined internal mechanical motions to various initial deformations and that these motions are robust against external perturbations. We show that this behavior is not characteristic for random elastic networks. However, special network architectures with such properties can be designed by evolutionary optimization methods. Using them, an example of an artificial elastic network, operating as a cyclic machine powered by ligand binding, is constructed.complex systems ͉ protein machines ͉ molecular motors ͉ evolutionary optimization U nderstanding design principles of single-molecule machines is a major challenge. Experimental and theoretical studies of proteins, acting as motors (1-5), ion pumps (6-8), or channels (6, 9), and enzymes (10-14), show that their operation involves functional conformational motions (see ref. 15). Such motions are slow and cannot therefore be reproduced by full molecular dynamics simulations. Within the last decade, approximate descriptions based on elastic network models of proteins have been developed (16)(17)(18)(19)(20)(21). In this approach, structural elements of a protein are viewed as identical point particles, with two particles connected by an elastic string if the respective elements lie close enough in the native state of the considered protein. Thus, a network of elastic connections corresponding to a protein is constructed. So far, the attention has been focused on linear dynamics of elastic networks, characterized in terms of their normal vibrational modes. It has been found that ligand-induced conformational changes in many proteins agree with the patterns of atomic displacements in their slowest vibrational modes (refs. 22-25 and see also refs. 26 and 27), even though nonlinear elastic effects must become important for large deviations from the equilibrium (28, 29). The focus of this article is on nonlinear relaxation phenomena in elastic networks seen as complex dynamical systems.Generally, a machine is a mechanical device that performs ordered internal motions that are robust against external perturbations. In machines representing single molecules, energy is typically supplied in discrete portions, through individual reaction events. Therefore, their cycles consist of the processes of conformational relaxation that follow after energetic excitations. For a robust machine operation, special nonlinear relaxation dynamics is required. We expect that, starting from a broad range of initial deformations, such dynamical systems would return to the same final equilibrium state. Moreover, the relaxation would proceed along a well defined trajectory (or a low-dimensional manifold), rapidly approached starting from different initial states and robust against external perturbations. These attractive relaxation trajectories would define internal mechanical motions of the machine inside its operation cycle.This special confor...

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“…Similar methods can further be used for engineering of nonprotein machine-like nanodevices (see ref. 34). …”

Section: Discussionmentioning

confidence: 99%

Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines

Togashi

Mikhailov

2007

Proc. Natl. Acad. Sci. U.S.A.

113

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“…[5,6] These bioinspired, smart materials are attracting more and more interest because of their unique properties, which have paved the way to many real-world applications, e.g., biomimetic fins, [7] actively moving polymers, [8] neural memory devices, [9] smart micro-/nanocontainers for drug delivery, [10] various biosensors, [11][12][13] dual/multi-responsive materials. [14,15] Also, many of these smart materials have surfaces that dynamically alter their physicochemical properties in response to changes in their environmental conditions and a triggered control of interfacial properties at the solid/water interface can be found in ion channels, [13] directional surface motions, [16] and bioinspired, smart surfaces with controllable wettability and adhesion.…”

Section: Introductionmentioning

confidence: 99%

Bio‐Inspired, Smart, Multiscale Interfacial Materials

2008

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In this review a strategy for the design of bioinspired, smart, multiscale interfacial (BSMI) materials is presented and put into context with recent progress in the field of BSMI materials spanning natural to artificial to reversibly stimuli‐sensitive interfaces. BSMI materials that respond to single/dual/multiple external stimuli, e.g., light, pH, electrical fields, and so on, can switch reversibly between two entirely opposite properties. This article utilizes hydrophobicity and hydrophilicity as an example to demonstrate the feasibility of the design strategy, which may also be extended to other properties, for example, conductor/insulator, p‐type/n‐type semiconductor, or ferromagnetism/anti‐ferromagnetism, for the design of other BSMI materials in the future.

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“…1 Of these systems, perhaps the most well-known is ATP synthase, 2 which converts the energy stored in chemical bonds into directed rotary motion. Owing to their potential applications in nanotechnology, [3][4][5] the design of synthetic molecular motors capable of mimicking Nature's precision and delicacy is a major research field [6][7][8][9][10][11][12][13] that was pioneered by Kelly 14 and Feringa 15,16 and their coworkers in the late nineties.…”

Section: Introductionmentioning

confidence: 99%

Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects

Oruganti

Fang

Durbeej

2015

Phys. Chem. Chem. Phys.

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We report a systematic computational investigation of the possibility to accelerate the rate-limiting thermal isomerizations of the rotary cycles of synthetic light-driven overcrowded alkene-based molecular motors through modulation of steric interactions.Choosing as reference system a second-generation motor known to accomplish rotary motion in the MHz regime and using density functional theory methods, we propose a three-step mechanism for the thermal isomerizations of this motor and show that variation of the steric bulkiness of the substituent at the stereocenter can reduce the (already small) free-energy barrier of the rate-determining step by a further 15−17 kJ mol -1 . This finding holds promise for future motors of this kind to reach beyond the MHz regime. Furthermore, we demonstrate and explain why one particular step is kinetically favored by decreasing and another step is kinetically favored by increasing the steric bulkiness of this substituent, and identify a possible back reaction capable of impeding the rotary rate.3

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Toward Intelligent Molecular Machines: Directed Motions of Biological and Artificial Molecules and Assemblies

Cited by 826 publications

References 210 publications

Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines

Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines

Bio‐Inspired, Smart, Multiscale Interfacial Materials

Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects

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