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arXiv · 2304.06884

Structural transition induced by a local chemical/mechanical perturbation in biomolecules

Fumio Hirata
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Abstract

Structural transition induced by a local conformational change in biomolecules is formulated based on the generalized Langevin theory for the structural fluctuation of a molecule in solution, and the linear response theory, derived by Kim and Hirata in 2012. A chemical/mechanical change introduced at a moiety of biomolecules, such as an amino acid substitution or a structural change of a chromophore by the photo-excitation, is considered as a perturbation, and the rest of the protein as the reference system. The linear-response equation consists of two parts: a mechanical/chemical perturbation introduced at the moiety, and the variance-covariance matrix of the reference system that works as a response function. The physical meaning of the equation is transparent: the force exerted by atoms in the moiety induces the displacement in an atom of protein, which propagates through the variance-covariance matrix to cause a global conformational change in the molecule. A few examples of possible application of the theory, including those in industry, are suggested.

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Fumio Hirata. 2023-04-14. Structural transition induced by a local chemical/mechanical perturbation in biomolecules. https://doi.org/10.5488/cmp.26.43803

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