Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations

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Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations Publisher

Rahmati S¹ ; Bagherzadeh K^{2, 3} ; Arab SS⁴ ; Torkashvand F¹ ; Amanlou M⁵ ; Vaziri B¹

Source: Journal of Biomolecular Structure and Dynamics Published:2023

Abstract

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. Communicated by Ramaswamy H. Sarma. © 2023 Informa UK Limited, trading as Taylor & Francis Group.

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Style	Citing Format
MLA	Rahmati S, et al.. "Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations." Journal of Biomolecular Structure and Dynamics, vol. , no. , 2023, pp. -.
APA	Rahmati S, Bagherzadeh K, Arab SS, Torkashvand F, Amanlou M, Vaziri B (2023). Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations. Journal of Biomolecular Structure and Dynamics, (), -.
Chicago	Rahmati S, Bagherzadeh K, Arab SS, Torkashvand F, Amanlou M, Vaziri B. "Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations." Journal of Biomolecular Structure and Dynamics , no. (2023): -.
Harvard	Rahmati S et al. (2023) 'Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations', Journal of Biomolecular Structure and Dynamics, (), pp. -.
Vancouver	Rahmati S, Bagherzadeh K, Arab SS, Torkashvand F, Amanlou M, Vaziri B. Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations. Journal of Biomolecular Structure and Dynamics. 2023;():-.
BibTex	@article{ author = {Rahmati S and Bagherzadeh K and Arab SS and Torkashvand F and Amanlou M and Vaziri B}, title = {Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations}, journal = {Journal of Biomolecular Structure and Dynamics}, volume = {}, number = {}, pages = {-}, year = {2023} }
RIS	TY - JOUR AU - Rahmati S AU - Bagherzadeh K AU - Arab SS AU - Torkashvand F AU - Amanlou M AU - Vaziri B TI - Computational Designing of the Ligands of Protein L Affinity Chromatography Based on Molecular Docking and Molecular Dynamics Simulations JO - Journal of Biomolecular Structure and Dynamics VL - IS - SP - EP - PY - 2023 ER -

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