Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume -, Issue -, Pages -Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/07391102.2023.2268219
Keywords
Protein L; antibody fragments; affinity chromatography; molecular docking; molecular dynamics simulations
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In this study, molecular dynamics simulations and computational biology methods were used to design high-affinity mutants of Protein L single B domains, which were then polymerized into a ligand with six B domains. The results showed that these mutants exhibited higher binding affinity to Fab compared to the wild type.
Protein L is a multidomain protein from Peptostreptococcus magnus with binding affinity to kappa light chain of human immunoglobulin (Ig) which is used for the purification of antibody fragments by affinity chromatography. The advances in protein engineering and computational biology approaches lead to the development of engineered affinity ligands with improved properties including binding affinity. In this study, molecular dynamics simulations (MDs) and Osprey software were used to design single B domains of the Protein L with higher affinity to antibody fragments. The modified B domains were then polymerized to ligand with six B domains by homology modeling methods. The results showed that single B domain mutants of MB1 (Thr865Trp) and MB2 (Thr847Met-Thr865Trp) had higher binding affinity to Fab compared to the wild single B domain. Also, MDs and molecular docking results showed that the polymerized Proteins L including the wild and mutated six B domains (6B0, 6B1, and 6B2) were stable during MDs and the two mutants of 6B1 and 6B2 showed higher binding affinity to Fab relative to the wild type.
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