Functional and structural analysis of hypothetical outer membrane proteins of Salmonella typhimurium (SL1344)

Salmonella typhimurium strain SL1344 (S.typhi) majorly infects the human gastrointestinal tract, a harmful pathogen; non- typhoidal organism may cause infinite infections some times which may lead to the human death. Salmonella typhimurium strain SL1344 (S.typhi) is a gram negative pathogenic bacteria mostly found in gastrointestinal tract of humans and mammals. It produce toxins due to the presence of lipopolysaccharides (LPS) in its outer membrane to protect itself from the environment. When bacteria         infiltrate intestinal epithelial cells, they cause ruffling in the host, which destroys the cell's microvilli on the surface. This may cause an influx of white blood cells into the mucosa, disrupting the balance between secretion and absorption and resulting in diarrhoea. It causes symptoms resembling typhoid fever in humans.   A comparative study of hypothetical outer membrane proteins of Salmonella typhimurium strain SL1344 (S.typhi) is done by using bioinformatics tools, In this study we reported the cellular function, pathway of enzyme interaction, antibiotic resistance property. The structural and functional prediction of these proteins will lead into understanding and also the mechanism of drug transportation. Thirteen uncharacterized and hypothetical protein present in outer membrane of the bacteria S.typhi is selected from UniProt (Table 1) and studied its structure and function. . Bioinformatics is a source to analyse whole genomic sequence of a vast number of uncharacterized genes. Online databases like UniProt, Expasy’s Protparam server, Pfam, SOUSI engine, Conserved Domain Database, String, Psortb and PS square-v2 were used. In this study we reported the cellular function, pathway of enzyme interaction, antibiotic resistance property. The structural and functional prediction of these proteins will lead into understanding and also the mechanism of drug transportation. There is a need for protein annotation study for unknown proteins, for which structure is known for these proteins but not functions are known as hypothetical or conserved protein, uncharacterized proteins [1].Structural studies provide a plenty of structures to the hypothetical protein in an increased level without functional annotation. The structural analysis could aid research into molecular systems. Many hypothetical proteins' structures are solved in pipelines at structural genomics institutes, which typically lack the capacity to perform in-depth functional characterization of each solved structure [2].Detection of new hypothetical proteins represents the new structure and also the function [3].     Table 1. Hypothetical protein used in this study SNo UniProt ID Protein names Gene names Organism length 1 A0A0H3N859 Outer membrane usher protein stfc (Hypothetical fimbrial outer membrane usher) stfC Salmonella typhimurium (strain SL1344) 885 2 A0A0H3ND79 Hypothetical outer membrane usher protein stcC Salmonella typhimurium (strain SL1344) 829 3 A0A0H3NHB2 Hypothetical outer membrane protein yiaD Salmonella typhimurium (strain SL1344) 209 4 A0A0H3NCC6 Hypothetical outer membrane protein mipA Salmonella typhimurium (strain SL1344) 248 5 A0A0H3NAS4 Hypothetical outer membrane virulence protein (PagD) pagD Salmonella typhimurium (strain SL1344) 87 6 A0A0H3NB04 Hypothetical outer membrane protein SL1344_1263 Salmonella typhimurium (strain SL1344) 319 7 A0A0H3NG10 Hypothetical outer membrane protein ydiY Salmonella typhimurium (strain SL1344) 252 8 A0A0H3NHA5 Hypothetical outer membrane protein OmpW Salmonella typhimurium (strain SL1344) 212 9 A0A0H3NJG9 Hypothetical outer membrane protein SL1344_4502 Salmonella typhimurium (strain SL1344) 229 10 A0A0H3ND56 Hypothetical outer membrane assembly protein asmA Salmonella typhimurium (strain SL1344) 618 11 A0A0H3NIM2 Hypothetical exported outer membrane protein SL1344_0531 Salmonella typhimurium (strain SL1344) 274 12 A0A0H3NCX0 Hypothetical exported protein erfK Salmonella typhimurium (strain SL1344) 309 13 A0A0H3N9J0 Hypothetical outer membrane protein YbfM Salmonella typhimurium (strain SL1344) 468