Computational protocol: Laminin Receptor in Shrimp Is a Cellular Attachment Receptor for White Spot Syndrome Virus

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Protocol publication

[…] The membrane topology of VP31 predictions were predicted with TMHMM (http://www.cbs.dtu.dk/services/TMHMM-2.0/; []) and HMMTOP (http://www.enzim.hu/hmmtop/) [, ] based on the deduced aa sequence of VP31. Both methods were used in single-sequence mode, with all user-adjustable parameters set at default values. To further investigate the membrane topology of VP31 in the WSSV virion, experiments were done as described []. For a duration of 2 h at 37°C, aliquots (5 μg of total protein) of purified virions were treated with 5 μg/ml trypsin (Promega) in 100 μl of buffer (50 mM Tris-HCl [pH 7.5], 1 mM CaCl2, 100 mM NaCl). Triton X-100 (final concentration, 1%) was added in some samples prior to trypsin digestion, and this was done in order to dissolve the viral envelope and expose internal structures to trypsin. For the purpose of analyzing samples, Western blotting using antibodies against VP31 [] was implemented, and with the aim of facilitating comparisons it was also implemented against tegument protein VP26 and the envelope protein VP28. The present study involves a WSSV virion; healthy crayfish (Procambarus clarkii) were challenged with WSSV-T1 strain and virus purified for the purpose of preparing the WSSV virion. Please see the description in Xie and Yang []. […]

Pipeline specifications

Software tools TMHMM, HMMTOP
Application Membrane protein analysis
Organisms Shrimp white spot syndrome virus, Penaeus monodon, Homo sapiens
Diseases Dental Caries, HIV Infections