2021
DOI: 10.3390/ijms221910501
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Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes

Abstract: Protein dynamics has been investigated since almost half a century, as it is believed to constitute the fundamental connection between structure and function. Elastic network models (ENMs) have been widely used to predict protein dynamics, flexibility and the biological mechanism, from which remarkable results have been found regarding the prediction of protein conformational changes. Starting from the knowledge of the reference structure only, these conformational changes have been usually predicted either by… Show more

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Cited by 7 publications
(5 citation statements)
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References 70 publications
(172 reference statements)
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“…Along the same lines, Scaramozzino et al 16,17 extended the Langevin equation solution to the ANM, and analyzed protein fluctuations in response to random external forces, validating our previous results 18 for the GNM. ANM was used for a quantitative analysis of dynamic allostery by Huang et al 19 In summary, our study contributes to the understanding of allosteric information transfer in proteins and highlights the importance of considering spatial heterogeneity and viscosity in modeling protein dynamics.…”
Section: Introductionsupporting
confidence: 76%
See 1 more Smart Citation
“…Along the same lines, Scaramozzino et al 16,17 extended the Langevin equation solution to the ANM, and analyzed protein fluctuations in response to random external forces, validating our previous results 18 for the GNM. ANM was used for a quantitative analysis of dynamic allostery by Huang et al 19 In summary, our study contributes to the understanding of allosteric information transfer in proteins and highlights the importance of considering spatial heterogeneity and viscosity in modeling protein dynamics.…”
Section: Introductionsupporting
confidence: 76%
“…The Anisotropic Network Model (ANM) of proteins is adopted in these studies which, unlike the simple isotropic GNM, accounts for directional effects of ligand binding. Along the same lines, Scaramozzino et al 16,17 extended the Langevin equation solution to the ANM, and analyzed protein fluctuations in response to random external forces, validating our previous results 18 for the GNM. ANM was used for a quantitative analysis of dynamic allostery by Huang et al 19 …”
Section: Introductionsupporting
confidence: 71%
“…Causality, defined by the difference in influence between residue i on j and j on i over time, is a critical aspect of protein dynamics as it forms the foundation for information transfer and allostery. Recently, Scaramozzino et al 6, 7 extended the Langevin equation solution to another elastic network model, the Anisotropic Network Model (ANM), and analyzed protein fluctuations in response to random external forces, validating our previous results for the GNM.…”
Section: Introductionsupporting
confidence: 54%
“…It is worth mentioning that many protein functions are associated with or governed by the natural vibration motions in proteins at sub-THz frequencies in solution as investigated in the literatures. 24 , 25 , 26 , 27 Then, under the terahertz stimulation, the interaction of the electromagnetic stimulation at sub-THz frequencies and the natural vibration motions in protein molecules would have impact on the protein functions and thus lead to a potential amplification/deamplification of the protein activity. This, in the case of the ion channel protein in the cell membrane, is probably the amplification/deamplification of ion flow via the ion channel protein.…”
Section: Discussionmentioning
confidence: 99%