Model organisms like Homo sapiens, Drosophila, and E. coli, while useful to various fields of study, present a problem to the scientific community: many other organisms’ proteins, metabolic processes, and biochemical mechanisms are not as well understood by comparison. Pocillopora damicornis (Pdam), like many other coral organisms, faces environmental stresses and threats to its survival in ocean ecosystems with limited understanding of its biochemical mechanisms, making it difficult to help preserve. However, upon analyzing the symbiotic relationship of Pdam and photosynthetic algae, it was reasoned that the coral organism is capable of detecting light. Following up with results of prior bioinformatics analysis courtesy of Kumar, L., Klein-Seetharaman, J., Et. Al, it was proposed that light sensitive proteins in corals are the following four candidates: 2270, 12246, 629, 19775. If chromophores form and their opsin shifts can be visualized in the case in any of the coral candidate opsin genes, it supports the hypothesis that the proteins are indeed a light sensitive opsin protein. If a light sensitive opsin protein is identified, it provides a direction by which efforts can be directed towards to understand corals at the biochemical level for their preservation in the face of unprecedented threats to sustainability.

Oceanic life is facing the deleterious aftermath of coral bleaching. To reverse the damages introduced by anthropological means, it is imperative to study fundamental properties of corals. One way to do so is to understand the metabolic pathways and protein functions of corals that contribute to the resilience of coral reefs. Although genomic sequencing and structural modeling has yielded significant insights for well-studied organisms, more investigation must be conducted for corals. Better yet, quantifiable experiments are far more crucial to the understanding of corals. The objective is to clone, purify, and assess coral proteins from the cauliflower coral species known as Pocillopora damicornis. Presented here is the pipeline for how 3-D structural modeling can help support the experimental data from studying soluble proteins in corals. Using a multi-step selection approach, 25 coral genes were selected and retrieved from the genomic database. Using Escherischia coli and Homo sapiens homologues for sequence alignment, functional properties of each protein were predicted to aid in the production of structural models. Using D-SCRIPT, potential pairwise protein-protein interactions (PPI) were predicted amongst these 25 proteins, and further studied for identifying putative interfaces using the ClusPro server. 10 binding pockets were inferred for each pair of proteins. Standard cloning strategies were applied to express 4 coral proteins for purification and functional assays. 2 of the 4 proteins had visible bands on the Coomassie stained gel and were able to advance to the purification step. Both proteins exhibited a faint band at the expected migration distance for at least one of the elutions. Finally, PPI was carried out by mixing protein samples and running in a native gel, resulting in one potential pair of PPI.