Unfolding Dynamics of a Photoswitchable Helical Peptide

An Improved Diabatization Scheme for Computing the Electronic Circular Dichroism of Proteins

We advance the quality of first-principles calculations of protein electronic circular dichroism (CD) through an amelioration of a key deficiency of a previous procedure that involved diabatization of electronic states on the amide chromophore (to obtain interamide couplings) in a β-strand conformation of a diamide. This yields substantially improved calculated far-ultraviolet (far-UV) electronic circular dichroism (CD) spectra for β-sheet conformations. The interamide couplings from the diabatization procedure for 13 secondary structural elements (13 diamide structures) are applied to compute the CD spectra for seven example proteins: myoglobin (α helix), jacalin (β strand), concanavalin A (β type I), elastase (β type II), papain (α + β), 310-helix bundle (310-helix) and snow flea antifreeze protein (polyproline). In all cases, except concanavalin A and papain, the CD spectra computed using the interamide couplings from the diabatization procedure yield improved agreement with experiment with respect to previous first-principles calculations.

Understanding the Fast-Triggering Unfolding Dynamics of FK-11 upon Photoexcitation of Azobenzene

Photoswitchable molecules can control the activity and functions of biomolecules by triggering conformational changes. However, it is still challenging to fully understand such fast-triggering conformational evolution from nonequilibrium to equilibrium distribution at the molecular level. Herein, we successfully simulated the unfolding of the FK-11 peptide upon the photoinduced trans-to-cis isomerization of azobenzene based on the Markov state model. We found that the ensemble of FK-11 contains five conformational states, constituting two unfolding pathways. More intriguingly, we observed the microsecond-scale conformational propagation of the FK-11 peptide from the fully folded state to the equilibrium populations of the five states. The computed CD spectra match well with the experimental data, validating our simulation method. Overall, our study not only offers a protocol to study the photoisomerization-induced conformational changes of enzymes but also could orientate the rational design of a photoswitchable molecule to manipulate biological functions.

Advances in Application of Azobenzene as a Trigger in Biomedicine: Molecular Design and Spontaneous Assembly

Azobenzene is a well-known derivative of stimulus-responsive molecular switches and has shown superior performance as a functional material in biomedical applications. The results of multiple studies have led to the development of light/hypoxia-responsive azobenzene for biomedical use. In recent years, long-wavelength-responsive azobenzene has been developed. Matching the longer wavelength absorption and hypoxia-response characteristics of the azobenzene switch unit to the bio-optical window results in a large and effective stimulus response. In addition, azobenzene has been used as a hypoxia-sensitive connector via biological cleavage under appropriate stimulus conditions. This has resulted in on/off state switching of properties such as pharmacology and fluorescence activity. Herein, recent advances in the design and fabrication of azobenzene as a trigger in biomedicine are summarized.