Relaxation time prediction for a light switchable peptide by molecular dynamics.

Area of Science:

• Computational Chemistry
• Biophysics
• Spectroscopy

Background:

• Azobenzene-containing peptides offer light-switchable conformational control.
• Understanding photoisomerization-induced dynamics is crucial for designing responsive biomaterials.

Purpose of the Study:

• To investigate the conformational dynamics of a monocyclic peptide (cAPB) with an integrated azobenzene dye.
• To elucidate the peptide backbone relaxation following ultrafast cis/trans photoisomerization.
• To compare the accuracy of CHARMM22 and CHARMM22 with CMAP force fields for NMR restraints.

Main Methods:

• Molecular dynamics (MD) simulations using CHARMM22 and CHARMM22 with CMAP force fields.
• Replica exchange technique for enhanced sampling of conformational ensembles.
• Picosecond time-resolved IR spectroscopy in the amide I range.
• Non-equilibrium MD simulations to interpret experimental kinetics.

Main Results:

• The CHARMM22 with CMAP force field better describes NMR distance restraints compared to CHARMM22 alone.
• Ultrafast photoisomerization of the azobenzene dye triggers peptide backbone relaxation dynamics.
• Experimental decay kinetics align with non-equilibrium MD simulations, predicting a 23 ns relaxation time scale to the trans ensemble.

Conclusions:

• Azobenzene photoisomerization effectively controls peptide conformation and dynamics.
• MD simulations combined with spectroscopy provide a powerful approach to study non-equilibrium processes in peptides.
• Full relaxation to the equilibrium trans ensemble occurs on a timescale of tens of nanoseconds.