Computational protocol: Directed DNA Shuffling of Retrovirus and Retrotransposon Integrase Protein Domains

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Protocol publication

[…] HIV-1 and PFV IN structural and in vitro studies have defined IN NTD, CCD, and CTD domains , , , . Because comparable information is not available for Ty3 IN, candidate domain boundary assignments were predicted using comparative in silico approaches. We focused on the definition of the Ty3 CCD, using sequence alignment, evolutionary mapping, fold recognition, domain prediction, threading, and refinement. The CCD domain is the most similar to retroviral domains, and also delimits the flanking NTD and CTD domains. Initial candidate domain boundaries were obtained from multiple sequence alignments constructed using Cobalt , ClustalW , and T-Coffee for HIV-1 IN (GB:AEA11266.1), PFV IN (PDB: 3L2Q:A), Ty3 IN (GB:AAA98435.1) ( and ), and Moloney murine leukemia virus IN (GB: NP_955592.1). A PSI-BLAST search with these sequences plus ASV IN (PDB: 1CXQ:A) identified a gypsy retrotransposon IN-like sequence in the human genome, NP-060146.2, intermediate between PFV and Ty3 IN. The PFV IN CCD and other candidate domain boundaries were mapped onto NP-060146.2 and then onto the Ty3 IN primary sequence. These candidate boundaries were further analyzed using other bioinformatics tools, including Phyre , SAM-T08 , SMART , Jpred , PSIPRED , and Meta-TASSER . The final domain boundary assignments represented a consensus based on these different approaches. […]

Pipeline specifications

Software tools Clustal W, T-Coffee, BLASTP, Phyre, SAM-T08, JPred, PSIPRED
Application Protein structure analysis
Organisms Saccharomyces cerevisiae, Homo sapiens
Diseases Immunologic Deficiency Syndromes, HIV Infections