Unfolding Pathway of Proteins Predicted by Elastic Network Model
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ORIGINAL RESEARCH
Unfolding Pathway of Proteins Predicted by Elastic Network Model Kilho Eom1 Received: 16 October 2020 / Revised: 24 October 2020 / Accepted: 26 October 2020 © Korean Multi-Scale Mechanics (KMSM) 2020
Abstract Proteins exhibit an excellent mechanical function and properties, which are attributed to their folding structure that can sustain a force. The mechanical function and properties are determined by the unfolding of protein structure. Though atomistic simulations are able to provide the unfolding mechanism of proteins at atomic scale, they are computationally restrictive for understanding the unfolding of large protein structures. Here, we consider an elastic network model (ENM), which is a coarse-grained model for protein structure, to study the unfolding pathway of proteins. It is shown that ENM is able to predict the anisotropic unfolding behavior of protein and its unfolding pathway. In addition, we show that the unfolding pathway of a protein due to thermal denaturation is comparable to the unfolding pathway driven by a mechanical force. Our study sheds light on the ENM for quantitative understanding of the unfolding mechanisms of proteins with computational efficiency. Keywords Elastic network model · Protein unfolding · Unfolding pathway · Mechanical unfolding
Introduction Proteins have received significant attention due to their excellent mechanical functions and properties, which are attributed to the force-driven unfolding mechanism [1–3]. Specifically, the folding structure of a protein can sustain a mechanical force until the force exerted by a protein reaches a critical value, at which the folding structure is denatured. This suggests that for understanding the mechanical functions and properties of proteins, the unfolding mechanisms of proteins have to be analyzed. For such an analysis, for recent decades, atomistic simulations [1, 2] have allowed for detailed insight into the force-driven unfolding mechanisms of proteins. Nonetheless, the atomistic simulations are restrictive in analyzing the unfolding mechanics of large proteins due to the computational limitation of atomistic simulations.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s42493-020-00054-1) contains supplementary material, which is available to authorized users. * Kilho Eom [email protected] 1
Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
For last two decades, there are efforts that have been made to develop a coarse-grained model [4, 5] that enables a computationally efficient analysis of protein dynamics and mechanics. One of renowned coarse-grained models is an elastic network model (ENM) [6–9], which describes a protein structure as a network of elastic springs connected between neighboring alpha carbon atoms. ENM has been able to successfully analyze the thermal fluctuation behavior of proteins [7, 10, 11], their conformational changes upon ligand-binding [12, 13], and protein–prot
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