Computational protocol: Perforin-like protein PPLP2 permeabilizes the red blood cell membrane during egress of Plasmodium falciparum gametocytes

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Protocol publication

[…] The structural representations were generated based on templates discovered by HH-Suite and a pre-prepared PDB library (Soeding, ; Remmert et al., ). PDB entries 2RD7 (Slade et al., ), 3NSJ (Law et al., ), 3OJY (Lovelace et al., ) and 3T5O (Aleshin et al., ) were selected as homology modelling templates. PSIPRED (Jones, ) was used to predict the PPLP2 secondary structure from a PSI-BLAST (Altschul et al., ) alignment of evolutionary related proteins. Final homology models were designed by the MODELLER (Eswar et al., ) software package using multi-template modelling and additional restraints taken from the predicted secondary structure. pGenTHREADER and pDomTHREADER server (Lobley et al., ) were used to identify proteins structurally related to the PPLP2 sequence. Missing regions of the full model including N- and C-terminal sites were generated by QUARK online prediction server (Xu and Zhang, ) in multiple overlapping structural templates. All parts together with the generated template-based model and secondary structure restraints were structurally concatenated by MODELLER. For the final models generated main-chain and full-atomic energy minimizations were performed by ModRefiner (Xu and Zhang, ) in an 8 h run. For structure quality assessment PDBsum server (Laskowski, ) was used to inspect Psi/Phi Ramachandran plots. Structural images were generated using PyMOL (The PyMOL Molecular Graphics System, Version 1.6.0.0 Schrödinger, LLC). Protein domain analysis and prediction were performed by SMART (Schultz et al., ), CDD (Marchler-Bauer et al., ) and PROSITE (Sigrist et al., ) online servers. […]

Pipeline specifications

Software tools HHalign, PSIPRED, BLASTP, MODELLER, QUARK, ModRefiner, PyMOL
Databases PROSITE
Applications Protein structure analysis, Amino acid sequence alignment
Organisms Plasmodium falciparum
Diseases Malaria
Chemicals Calcium