Annotation and Homology Modeling of the Multidrug Transport Protein P-Glycoprotein (ABCB1) of Equus Caballus
DOI:
https://doi.org/10.47611/jsr.v11i1.1535Keywords:
BLAST, annotation, homology modeling, P-glycoprotein, QMEAN, SWISS-MODEL, energy minimizationAbstract
The function of ABC transporter proteins, such as ABCB1, is to transport substrates across cell membranes in many organs. ABCB1 can be found in multiple species, however, the sequence we annotated is derived from Equus caballus (horse). The objective of this research was to annotate and derive a structural homology model of the horse-derived P-glycoprotein. We classified the protein as a transmembrane ATP-binding cassette (ABC) protein ABCB1. Annotation of the sequence (which is not yet manually curated in NCBI) was carried out using various tools including BLAST, TMHMM, PFAM, HMM Logo, etc, and supports its designation as ABCB1 or P-glycoprotein of horse. The homology model was constructed using SWISS-MODEL based on the structure of human P-glycoprotein (PDB code: 6c0v). Three structures that share high sequence identity were chosen for analysis. Two homology models were prepared using the cryo-EM structures of human ABCB1 (PDB code: 6qex, % sequence identity) and human P-glycoprotein. The model using the structure of human P-glycoprotein as a template had the highest QMEAN score, Ramachandran favorability, and the most favorable Molprobity score. That model was evaluated using ProCheck and energy minimized using Chiron to give rise to the final model. Energy minimization resolved an unmodeled loop from Q625 to V691 and corrected other minor distortions. The clash ratio of the energy minimized model indicated that there are few clashes in the structure. Based on analysis of the structure validation parameters, the best homology model of equine P-glycoprotein was derived using the human P-glycoprotein as a template.
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Copyright (c) 2022 Barachel Butler; Karobi Moitra, CFD, MS, PhD
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