The Detection of transmembrane domains of Nucleocytoplasmic Large DNA Viruses

Abstract

It is estimated that transmembrane proteins (TMPs) represent 20-30% of all proteins encoded by a given genome, and they constitute 60% of current drug targets. These proteins participate in cell signaling, forming the integrity of the cellular membrane, and transporting substances across the cell membrane. In addition, TMPs have exhibited high conservation levels within distantly related members of the tree of life, making them valuable for tracing ancestral history. Not alone the most abundant entities, viruses also rely on TMPs in many pivotal functions, including viral fusion and entry, replication, along with maintaining their envelopes (if present). Nucleocytoplasmic Double stranded DNA Viruses (NCLDVs) have large virion sizes and extensive genome lengths compared to other viruses, which prompted scientists to reevaluate the concept of viruses and delve deeper into their evolutionary history. TMPs are one of the most critical fields in virology, which was invaluable in the recent pandemic of corona virus. Although the identification of TMPs through experimental approaches is highly accurate and precise, it is extremely time-consuming and costly. The development of computational power and tools facilitated studying proteomics, specifically TMP detection and evolution. In this study, we adapted a comprehensive workflow to catalog TMPs in NCLDVs, trace their evolution history, and annotate poorly annotated TM proteins with structural predictions.