Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations
Date
2018
Authors
Mei, Longcan
Zhou, Yanping
Zhu, Lizhe
Liu, Changlin
Wu, Zhuo
Wang, Fangkui
Hao, Gefei
Yu, Di
Yuan, Hong
Cui, Yan Fang
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MDPI Publishing
Abstract
A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.
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Keywords
ensemble allosteric model, dynamic network, cross-correlation, dynamic network pathways
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Source
International Journal of Molecular Sciences
Type
Journal article
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Open Access
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Creative Commons Attribution (CC BY) license
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