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

On-the-fly simulation of time-resolved fluorescence spectra and anisotropy

We combine on-the-fly trajectory surface hopping simulations and the doorway-window representation of nonlinear optical response functions to create an efficient protocol for the evaluation of time- and frequency-resolved fluorescence (TFRF) spectra and anisotropies of the realistic polyatomic systems. This approach gives the effective description of the proper (e.g., experimental) pulse envelopes, laser field polarizations, and the proper orientational averaging of TFRF signals directly from the well-established on-the-fly nonadiabatic dynamic simulations without extra computational cost. To discuss the implementation details of the developed protocol, we chose cis-azobenzene as a prototype to simulate the time evolution of the TFRF spectra governed by its nonadiabatic dynamics. The results show that the TFRF is determined by the interplay of several key factors, i.e., decays of excited-state populations, evolution of the transition dipole moments along with the dynamic propagation, and scaling factor of the TFRF signals associated with the cube of emission frequency. This work not only provides an efficient and effective approach to simulate the TFRF and anisotropies of realistic polyatomic systems but also discusses the important relationship between the TFRF signals and the underlining nonadiabatic dynamics.

Unravelling Structural Dynamics within a Photoswitchable Single Peptide: A Step Towards Multimodal Bioinspired Nanodevices

The majority of the protein structures have been elucidated under equilibrium conditions. The aim herein is to provide a better understanding of the dynamic behavior inherent to proteins by fabricating a label-free nanodevice comprising a single-peptide junction to measure real-time conductance, from which their structural dynamic behavior can be inferred. This device contains an azobenzene photoswitch for interconversion between a well-defined cis, and disordered trans isomer. Real-time conductance measurements revealed three distinct states for each isomer, with molecular dynamics simulations showing each state corresponds to a specific range of hydrogen bond lengths within the cis isomer, and specific dihedral angles in the trans isomer. These insights into the structural dynamic behavior of peptides may rationally extend to proteins. Also demonstrated is the capacity to modulate conductance which advances the design and development of bioinspired electronic nanodevices.

Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex

Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.

Unfolding Dynamics of a Photoswitchable Helical Peptide

We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structures, ranging from a partially unfolded peptide to a fully unfolded structure. The averaged computed far-ultraviolet circular dichroism (CD) spectrum of the set of structures, which was simulated using the newly developed force field, agrees well with experiment. The rate of the simulated unfolding process was estimated to have a time constant of 5.80 ± 0.03 ns from the time evolution of the CD spectrum of the peptide, computed from the backbone conformations sampled over 40 simulated trajectories. Our estimated time constant is faster than, but not inconsistent with, previous experimental estimates from time-resolved infrared and optical rotatory dispersion spectroscopy.

Interactions of the cis and trans states of an azobenzene photoswitch with lysozyme induced by red and blue light

Exploring the interaction between an azobenzene-based photoswitch and natural protein can help elucidate how the photo-control of an optical molecule participates in the transmission and delivery of proteins, as well as the effects of azo-switch trans and cis states on protein configurations. In this study, fluorescence analysis, circular dichroism spectroscopy, molecular docking, and molecular dynamics simulations were used to study the interaction among different configurations of tetra-ortho-methoxy substituted azobenzene di-maleimide (toM-ABDM), a red light-induced optical azo-switch, and lysozyme (LYZ). Results showed that toM-ABDM caused the static quenching of LYZ. The cis toM-ABDM had stronger binding affinity than trans toM-ABDM. The noncovalent interaction, hydrogen bonds and van der Waals forces, could not regulate the conformation of LYZ in photo-control. A binding model of toM-ABDM and LYZ in different forms induced by red and blue light was further established by computer simulation.

Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells

Artificial rotary molecular motors convert energy into controlled motion and drive a system out of equilibrium with molecular precision. The molecular motion is harnessed to mediate the adsorbed protein layer and then ultimately to direct the fate of human bone marrow-derived mesenchymal stem cells (hBM-MSCs). When influenced by the rotary motion of light-driven molecular motors grafted on surfaces, the adsorbed protein layer primes hBM-MSCs to differentiate into osteoblasts, while without rotation, multipotency is better maintained. We have shown that the signaling effects of the molecular motion are mediated by the adsorbed cell-instructing protein layer, influencing the focal adhesion-cytoskeleton actin transduction pathway and regulating the protein and gene expression of hBM-MSCs. This unique molecular-based platform paves the way for implementation of dynamic interfaces for stem cell control and provides an opportunity for novel dynamic biomaterial engineering for clinical applications.

Thermodynamics of Helix formation in small peptides of varying lengthin vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields

Helix formation is of great significance in protein folding. The helix-forming tendencies of amino acids are accumulated along the sequence to determine the helix-forming tendency of peptides. Computer simulation can be used to model this process in atomic details and give structural insights. In the current work, we employ equilibrate-state free energy simulation to systematically study the folding/unfolding thermodynamics of a series of mutated peptides. Two AMBER force fields including AMBER99SB and AMBER14SB are compared. The new 14SB force field uses refitted torsion parameters compared with 99SB and they share the same atomic charge scheme. We find that in vacuo the helix formation is mutation dependent, which reflects the different helix propensities of different amino acids. In general, there are helix formers, helix indifferent groups and helix breakers. The helical structure becomes more favored when the length of the sequence becomes longer, which arises from the formation of additional backbone hydrogen bonds in the lengthened sequence. Therefore, the helix indifferent groups and helix breakers will become helix formers in long sequences. Also, protonation-dependent helix formation is observed for ionizable groups. In 14SB, the helical structures are more stable than in 99SB and differences can be observed in their grouping schemes, especially in the helix indifferent group. In solvents, all mutations are helix indifferent due to protein–solvent interactions. The decrease in the number of backbone hydrogen bonds is the same with the increase in the number of protein–water hydrogen bonds. The 14SB in explicit solvent is able to capture the free energy minima in the helical state while 14SB in implicit solvent, 99SB in explicit solvent and 99SB in implicit solvent cannot. The helix propensities calculated under 14SB agree with the corresponding experimental values, while the 99SB results obviously deviate from the references. Hence, implicit solvent models are unable to correctly describe the thermodynamics even for the simple helix formation in isolated peptides. Well-developed force fields and explicit solvents are needed to correctly describe the protein dynamics. Aside from the free energy, differences in conformational ensemble under different force fields in different solvent models are observed. The numbers of hydrogen bonds formed under different force fields agree and they are mostly determined by the solvent model.

QM/MM Studies on Photoisomerization Dynamics of Azobenzene Chromophore Tethered to a DNA Duplex: Local Unpaired Nucleobase Plays a Crucial Role

The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S₁ state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment. This acceleration is primarily caused by complex steric interactions between azobenzene and the nearby unpaired thymine nucleobase, which also change the photoisomerization mechanism of azobenzene in the DNA duplex.

QM/MM methods for free energies and photochemistry

Hybrid computational methods describing a small region of a biomolecular system with quantum mechanics and the bulk with molecular mechanics, referred to as QM/MM methods, are now a central part of computational biochemistry. This review considers developments in the QM/MM approach that make it easier to calculate free energies using accurate QM-based potential energy expressions. We also describe techniques to treat electronic coupling between the core region and the MM environment. Polarizability of the protein matrix is important but so is electronic coupling. Applications of these new methods, especially to photochemistry, are discussed.

Photosensitive Cationic Azobenzene Surfactants: Thermodynamics of Hydration and the Complex Formation with Poly(methacrylic acid)

In this computational work, we investigate the photosensitive cationic surfactants with the trimethylammonium or polyamine hydrophilic head and the azobenzene-containing hydrophobic tail. The azobenzene-based molecules are known to undergo a reversible trans-cis-trans isomerization reaction when subjected to UV-visible light irradiation. Combining the density functional theory and the all-atom molecular dynamics simulations, the structural and the hydration properties of the trans- and the cis-isomers and their interaction with the oppositely charged poly(methacrylic acid) in aqueous solution are investigated. We establish and quantify the correlations of the molecular structure and the isomerization state of the surfactants and their hydrophilicity/hydrophobicity and the self-assembling altered by light. For this reason, we compare the hydration free energies of the trans- and the cis-isomers. Moreover, the investigations of the interaction strength between the azobenzene molecules and the polyanion provide additional elucidations of the recent experimental and theoretical studies on the light triggered reversible deformation behavior of the microgels and the polymer brushes loaded with azobenzene surfactants.

Photochromic Mechanism of a Bridged Diarylethene: Combined Electronic Structure Calculations and Nonadiabatic Dynamics Simulations

Intramolecularly bridged diarylethenes exhibit improved photocyclization quantum yields because the anti-syn isomerization that originally suppresses photocyclization in classical diarylethenes is blocked. Experimentally, three possible channels have been proposed to interpret experimental observation, but many details of photochromic mechanism remain ambiguous. In this work we have employed a series of electronic structure methods (OM2/MRCI, DFT, TDDFT, RI-CC2, DFT/MRCI, and CASPT2) to comprehensively study excited state properties, photocyclization, and photoreversion dynamics of 1,2-dicyano[2,2]metacyclophan-1-ene. On the basis of optimized stationary points and minimum-energy conical intersections, we have refined experimentally proposed photochromic mechanism. Only an S₁/S₀ minimum-energy conical intersection is located; thus, we can exclude the third channel experimentally proposed. In addition, we find that both photocyclization and photoreversion processes use the same S₁/S₀ conical intersection to decay the S₁ system to the S₀ state, so we can unify the remaining two channels into one. These new insights are verified by our OM2/MRCI nonadiabatic dynamics simulations. The S₁ excited-state lifetimes of photocyclization and photoreversion are estimated to be 349 and 453 fs, respectively, which are close to experimentally measured values: 240 ± 60 and 250 fs in acetonitrile solution. The present study not only interprets experimental observations and refines previously proposed mechanism but also provides new physical insights that are valuable for future experiments.

Photoisomerization of Arylazopyrazole Photoswitches: Stereospecific Excited-State Relaxation

Electronic structure calculations and nonadiabatic dynamics simulations (more than 2000 trajectories) are used to explore the Z-E photoisomerization mechanism and excited-state decay dynamics of two arylazopyrazole photoswitches. Two chiral S1 /S0 conical intersections with associated enantiomeric S1 relaxation paths that are barrierless and efficient (timescale of ca. 50 fs) were found. For the parent arylazopyrazole (Z8) both paths contribute evenly to the S1 excited-state decay, whereas for the dimethyl derivative (Z11) each of the two chiral cis minima decays almost exclusively through one specific enantiomeric S1 relaxation path. To our knowledge, the Z11 arylazopyrazole is thus the first example for nearly stereospecific unidirectional excited-state relaxation.