Long-Range Conformational Transition of a Photoswitchable Allosteric Protein: Molecular Dynamics Simulation Study

Abstract

A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligandbound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and the trans state of the photoswitch, in explicit water. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes, that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein. October 9, 2014 * To whom correspondence should be addressed 1 Abstract A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligandbound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and the trans state of the photoswitch, in explicit water. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes, that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein.

Engineered control of enzyme structural dynamics and function

“…150 MD simulations also supported the notion that the photoswitch mimicked the transitions between ligand free and bound forms of the protein. 151 In another example, multiple azobenzenecrosslinked derivatives of the restriction enzyme PvuII were generated, 152 guided by the sGAL program that helps to find suitable surface-exposed sites for Cys-mediated crosslinks 153 [Fig. 4(B)].…”

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

“…32. To force the photoswitch to be either in the cis or the trans-configuration, the double minimum potential for the central C-N=N-C dihedral angle was replaced by a single minimum potential, [33][34][35] and the force constant increased by a factor 3 such that the potential around the minimum agrees reasonably well with that of the original double minimum potential.…”

A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine

“…This would be a new approach to investigate the allosteric coupling of cooperative protein-based molecular switches and machines, and might complement existing approaches such as normal mode analysis (Bahar and Rader, 2005;Levitt et al, 1985) and molecular dynamics simulations (Dror et al, 2012;Karplus and McCammon, 2002;Levitt and Warshel, 1975) that have been applied successfully to similar systems (Bahar and Rader, 2005;Buchenberg et al, 2014;Nam et al, 2014;Uyar et al, 2014). One advantage of our approach is that it combines relatively inexpensive simulations with direct experimental tests that measure the response to light-induced distance changes of engineered azobenzene crosslinks that were predicted computationally.…”