Retinal location and structure in squid rhodopsin

In order to understand retinal we calculated the dihedral angles around carbon axis IOC-12C, since two different carbon sequences 9C-10C-11C-12C and 10C-11C-12C-13C exist. We also calculated the distances between two specified carbon pairs. Those results are tabulated. Photon absorption changes the conformation of retinal conformation. This fact is confirmed from dihedral angle changes and distance changes of targeted of retinal carbon atoms. These matters are discussed in the present paper.Copyright Information: Copyright the autho

Atomic configuration around retinal in squid rhodopsin

Distances among retinal carbons and amino acid residues around a retinal molecule are calculated. We draw an image for chain-A and chain-B contact with squid retinal. Thus the area of each retinal's chain-A and chain-B is decided in an average sense that is not exact. We discuss about distances and determined areas of retinals

A quantum chemical study of the retinal of squid rhodopsin

The squid retinal structure obtained from the Protein Data Bank (PDB ids 2Z73 and 2ZIY) is studied in a quantum chemistry method using MOPAC2009 based on a semi-empirical method with PM6 parametrization. The interaction between retinal and light (an electromagnetic field) is effectively described by the interaction between dipoles and electromagnetic fields. Thus we investigated the dipole moment and effective charge distribution of retinal. We also looked at molecular orbitals, especially the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital). MO shifting between a double bonded site and single bonded site is seen by comparing HOMO and LUMO results. Retinal changes its conformation from cis to trans at carbon 11. This carbon's effective charge is very small so that it is free from electric interactions. Then it can change conformation with a small change in energy