Date of Completion


Embargo Period



Alfredo Angeles-Boza, Amy Howell

Field of Study



Master of Science

Open Access

Open Access


This study utilized a QM/MM methodology to model and explore the protein structure and active site of invertebrate squid rhodopsin, and employed time dependent density functional theory (td-dft) calculations to further investigate the excited states of this protein. The high-resolution (2.5 Å) X-ray crystal structure of squid rhodopsin (species Todarodes pacificus) was the first Gq-coupled Guanine Protein Coupled Receptor (GPCR) structure to be determined. The availability of this novel x-ray structure data, in conjunction with computational tools, provided the opportunity to study the relationship between certain structural attributes of squid rhodopsin in the vicinity of the photoreactive center, and the absorption properties of this light sensitive molecule.

This study found that computational results varied depending upon the choice of computational parameters used. Results varied significantly when the definition of the quantum region was modified between experiments. Therefore, absolute comparison of the change in energy (∆ E) between optimized Todarodes pacificus rhodopsin models was found to be inappropriate and conclusions were difficult to draw.

Because of these issues this study was expanded to include other species of squid, and a more meaningful study subsequently emerged through the relative comparison of computational results between species. The study was broadened to include the squid species Loligo forbesii and Alloteuthis subulata, in addition to Todarodes pacificus. By replacing key active center residues in the Todarodes pacificus model with key residues from these other species, and by keeping computational parameters constant between experiments, experimental absorption shifts between species were replicated.

Major Advisor

Jose A. Gascon