ABSTRACT
Objective: The docking and superantigen activity sites of staphylococcal enterotoxin-like W (SElW) and T cell receptor (TCR) were predicted, and its SElW was cloned, expressed and purified. Methods: AlphaFold was used to predict the 3D structure of SElW protein monomers, and the protein models were evaluated with the help of the SAVES online server from ERRAT, Ramachandran plot, and Verify_3D. The ZDOCK server simulates the docking conformation of SElW and TCR, and the amino acid sequences of SElW and other serotype enterotoxins were aligned. The primers were designed to amplify selw, and the fragment was recombined into the pMD18-T vector and sequenced. Then recombinant plasmid pMD18-T was digested with BamHⅠand Hind Ⅲ. The target fragment was recombined into the expression plasmid pET-28a(+). After identification of the recombinant plasmid, the protein expression was induced by isopropyl-beta-D- thiogalactopyranoside. The SElW expressed in the supernatant was purified by affinity chromatography and quantified by the BCA method. Results: The predicted three-dimensional structure showed that the SElW protein was composed of two domains, the amino-terminal and the carboxy-terminal. The amino-terminal domain was composed of 3 α-helices and 6 β-sheets, and the carboxy-terminal domain included 2 α-helices and 7 antiparallel β-sheets composition. The overall quality factor score of the SElW protein model was 98.08, with 93.24% of the amino acids having a Verify_3D score ≥0.2 and no amino acids located in disallowed regions. The docking conformation with the highest score (1 521.328) was selected as the analysis object, and the 19 hydrogen bonds between the corresponding amino acid residues of SElW and TCR were analyzed by PyMOL. Combined with sequence alignment and the published data, this study predicted and found five important superantigen active sites, namely Y18, N19, W55, C88, and C98. The highly purified soluble recombinant protein SElW was obtained with cloning, expression, and protein purification. Conclusions: The study found five superantigen active sites in SElW protein that need special attention and successfully constructed and expressed the SElW protein, which laid the foundation for further exploration of the immune recognition mechanism of SElW.
Subject(s)
Humans , Enterotoxins/genetics , Superantigens/genetics , Catalytic Domain , Selenoprotein W/metabolism , Receptors, Antigen, T-CellABSTRACT
Objective To investigate the feasibility of differential expression proteins identification in peripheral blood mononuclear cells (PBMCs) of sepsis patients using Data Independent Acquisition liquid chromatography-mass spectrometry (DIA LC-MS). Methods Prospective studies were employed and targeted at 10 sepsis patients admitted to the Intensive Care Unit (ICU) of Shanghai Fifth People's Hospital Affiliated to Fudan University from April 2016 to July 2016. And 10 patients admitted to the ICU with similar age and sex that were not complicated with sepsis were served as the control group.The proteins from peripheral blood mononuclear cells in 10 sepsis patients and 10 control persons were analyzed using the latest DIA LC-MS technology and the skyline data extraction software; the model of data obtained from the above analysis was further discriminatorily analyzed with principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA); then the differential proteins of peripheral blood mononuclear cells were analyzed by Pathway analysis and GO analysis. The possible markers were identified by preliminary screening according to variable importance in the projection (VIP). The top 3 proteins (VIP > 1, P< 0.05) were verified by ELISA and their ROC curves were analyzed. Results Totally 1062 fragment ions were identified and 119 proteins were obtained. Among them, 31 proteins were up-regulated and 88 proteins down-regulated. Pathway analysis showed that carbon metabolism, platelet activation, bacterial invasion of epithelium, and complement coagulation cascade activation were participated in the development of sepsis. ELISA showed that significant difference of HMGB-1, MMP-8, and LCN2 in the expression of peripheral blood mononuclear cells in the sepsis and control people (P<0.01). The area under the ROC curve is greater than 0.85, which has good sensitivity and specificity. Conclusions DIA-MS is a compelling way for detecting differential expression proteins. PCA, PLSDA and OPLSDA are suitable for pattern recognition. The high expression of HMGB-1, NGAL and MMP-8 in immune cells may be the potential biomarker of the disease, which lays the foundation for research of early diagnosis and treatment of sepsis.