Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling Steven R. Ahrendt 1 , 2 , 3 , Edgar Mauricio Medina 4 , 5 , Chia-en A. Chang 2 , 6 and Jason E. Stajich 1 , 2 Department of Plant Pathology & Microbiology, University of California, Riverside, CA, USA Institute for Integrative Genome Biology, University of California, Riverside, CA, USA Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA, USA Department of Biology, Duke University, Durham, NC, USA Center for Genomic and Computational Biology, Duke University, Durham, NC, USA Department of Chemistry, University of California, Riverside, CA, USA ABSTRACT Submitted 1 September 2016 Accepted 20 March 2017 Published 27 April 2017 Corresponding authors Steven R. Ahrendt, sahrendt0@gmail.com, sahrendt0@berkeley.edu Jason E. Stajich, jason.stajich@ucr.edu Academic editor Pedro Silva Additional Information and Declarations can be found on page 15 DOI 10.7717/peerj.3206 Copyright 2017 Ahrendt et al. Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if the sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9- cis-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi. Distributed under Creative Commons CC-BY 4.0 OPEN ACCESS How to cite this article Ahrendt et al. (2017), Exploring the binding properties and structural stability of an opsin in the chytrid Spizel- lomyces punctatus using comparative and molecular modeling. PeerJ 5:e3206; DOI 10.7717/peerj.3206