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Photoisomerization of a rotaxane hydrogen bonding template: light-induced acceleration of a large amplitude rotational motion.

ABSTRACT: Establishing methods for controlling aspects of large amplitude submolecular movements is a prerequisite for the development of artificial devices that function through rotary motion at the molecular level. Here we demonstrate that the rate of rotation of the interlocked components of fumaramide-derived [2]rotaxanes can be accelerated, by >6 orders of magnitude, by isomerizing them to the corresponding maleamide [2]rotaxanes by using light.

SUBMITTER: Gatti FG

PROVIDER: S-EPMC140866 | biostudies-literature | 2003 Jan

REPOSITORIES: biostudies-literature

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Photoisomerization of a rotaxane hydrogen bonding template: light-induced acceleration of a large amplitude rotational motion.

Gatti Francesco G FG León Salvador S Wong Jenny K Y JK Bottari Giovanni G Altieri Andrea A Morales M Angeles Farran MA Teat Simon J SJ Frochot Céline C Leigh David A DA Brouwer Albert M AM Zerbetto Francesco F

Proceedings of the National Academy of Sciences of the United States of America 20021227 1

Establishing methods for controlling aspects of large amplitude submolecular movements is a prerequisite for the development of artificial devices that function through rotary motion at the molecular level. Here we demonstrate that the rate of rotation of the interlocked components of fumaramide-derived [2]rotaxanes can be accelerated, by >6 orders of magnitude, by isomerizing them to the corresponding maleamide [2]rotaxanes by using light. ...[more]

PMID: 12506193

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Project description:Elastic network models (ENMs) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have contributed significantly to insights into protein molecular mechanisms and function. However, despite a shared purpose of these approaches, the topological nature of rigidity analysis, and thereby the absence of motion modes, has impeded a direct comparison. Here, we present an alternative, kinematic approach to rigidity analysis, which circumvents these drawbacks. We introduce a novel protein hydrogen bond network spectral decomposition, which provides an orthonormal basis for collective motions modulated by noncovalent interactions, analogous to the eigenspectrum of normal modes. The zero modes decompose proteins into rigid clusters identical to those from topological rigidity, while nonzero modes rank protein motions by their hydrogen bond collective energy penalty. Our kinematic flexibility analysis bridges topological rigidity theory and ENM, enabling a detailed analysis of motion modes obtained from both approaches. Analysis of a large, structurally diverse data set revealed that collectivity of protein motions, reported by the Shannon entropy, is significantly reduced for rigidity theory compared to normal mode approaches. Strikingly, kinematic flexibility analysis suggests that the hydrogen bonding network encodes a protein-fold specific, spatial hierarchy of motions, which goes nearly undetected in ENM. This hierarchy reveals distinct motion regimes that rationalize experimental and simulated protein stiffness variations. Kinematic motion modes highly correlate with reported crystallographic B factors and molecular dynamics simulations of adenylate kinase. A formal expression for changes in free energy derived from the spectral decomposition indicates that motions across nearly 40% of modes obey enthalpy-entropy compensation. Taken together, our results suggest that hydrogen bond networks have evolved to modulate protein structure and dynamics, which can be efficiently probed by kinematic flexibility analysis.

Dataset Information

Photoisomerization of a rotaxane hydrogen bonding template: light-induced acceleration of a large amplitude rotational motion.

Publications

Photoisomerization of a rotaxane hydrogen bonding template: light-induced acceleration of a large amplitude rotational motion.

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