Computational protocol: SECRET domain of variola virus CrmB protein can be a member of poxviral type II chemokine-binding proteins family

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Protocol publication

[…] Prediction of secondary structure of VARV-CrmB SECRET domain was done using PSIPRED server []. Spatial structure of SECRET domain was modeled using I-TASSER web-server []. The server selected the structure of cowpox virus (CPXV) vCCI (viral CC-chemokine inhibitor) protein [PDB:1CQ3] as the best template for modelling SECRET domain. Electrostatic potential of molecular surfaces of all compared proteins was calculated using DelPhi software []. Superpositions of the structures were made using CEalign []. All molecular graphic images were produced using PyMOL []. VARV-CrmB amino acid sequence used in this work was taken from [Swiss-Prot:P34015]. Amino acid sequences of CPXV vCCI [PDB:1CQ3], vaccinia virus (VACV) A41 chemokine-binding protein [PDB:2VGA] and VARV-CrmB SECRET domain were structurally aligned using TM-align server []. Alignment was manually edited taking in mind the secondary structures (shown above corresponding sequences) of the proteins using Aline software []. […]

Pipeline specifications

Software tools PSIPRED, I-TASSER, PyMOL, TM-align
Databases UniProt
Application Protein structure analysis
Organisms Variola virus, Cowpox virus, Vaccinia virus
Diseases Neoplasms