How Photoisomerization Drives Peptide Folding and Unfolding: Insights from QM/MM and MM Dynamics Simulations

Abstract

Photoswitchable azobenzene cross-linkers can control the folding and unfolding of peptides by photoisomerization and can thus regulate peptide affinities and enzyme activities.U sing quantum mechanics/molecular mechanics (QM/MM) methods and classical MM force fields,w er eport the first molecular dynamics simulations of the photoinduced folding and unfolding processes in the azobenzene crosslinked FK-11 peptide.Wefind that the interactions between the peptide and the azobenzene cross-linker are crucial for controlling the evolution of the secondary structure of the peptide and responsible for accelerating the folding and unfolding events.T hey also modify the photoisomerization mechanism of the azobenzene cross-linker compared with the situation in vacuo or in solution.Anefficient light-sensitive peptide can be constructed by cross-linking aphotoswitchable small cross-linker molecule to the peptide backbone;photoinduced structural changes of the cross-linker can trigger reversible changes in peptide conformations.T his kind of photoresponse can provide an avenue for probing and manipulating complex living systems.[1] Thep hotoinduced conformational dynamics of peptides with built-in azobenzenes has been exploited to probe functional changes of proteins,t omanipulate enzyme activities,a nd to control cell signaling.[2] However,adetailed mechanistic understanding of these processes at the atomistic level is still lacking.Experimentally,t ime-resolved infrared spectroscopy was employed to monitor the conformational dynamics of crosslinked peptides;itwas found that both folding and unfolding processes show complex spectral kinetics and strongly depend on the photoexcitation wavelength and on temperature. [3] Computationally,a zobenzene-linked peptides were explored by classical molecular dynamics (MD) simulations.[4] However,i nt hese studies,t he initial nonadiabatic photoisomerization was not considered or was only simulated using as imple model potential, and the effects of the photoisomerization on the subsequent conformational dynamics of peptides were not investigated;m oreover,o nly the photoinduced folding dynamics was simulated in those studies. [4] Theu nfolding dynamics of cross-linked peptides has rarely been explored experimentally because peptide unfolding processes are generally endothermic and difficult to study. [4f] Asalient dynamical feature of these cross-linked peptides is that their folding and unfolding processes are significantly accelerated compared with peptides without cross-linkers. [3a] This speedup must originate from the interaction between the cross-linker and the peptide.Athorough understanding of this interplay is crucial to rationalize the folding and unfolding dynamics of cross-linked peptides,t os elect appropriate cross-linkers,t ooptimize cross-linking positions,a nd eventually to control these photoinduced conformational changes. It is difficult to obtain detailed information on these interactions solely from experiment, and it is thus desirable to perform th...

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