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  Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds

Bergues Pupo, A. E., Lipowsky, R., & Vila Verde, A. (2020). Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds. Soft Matter, 16(43), 9917-9928. doi:10.1039/D0SM01166E.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-17E4-E Version Permalink: http://hdl.handle.net/21.11116/0000-0007-70E6-7
Genre: Journal Article

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 Creators:
Bergues Pupo, Ana Elisa1, Author              
Lipowsky, Reinhard2, Author              
Vila Verde, Ana1, Author              
Affiliations:
1Ana Vila Verde, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_2205638              
2Reinhard Lipowsky, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_1863327              

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 Abstract: Single alpha helices (SAHs) stable in isolated form are often found in motor proteins where they bridge functional domains. Understanding the mechanical response of SAHs is thus critical to understand their function. The quasi-static force-extension relation of a small number of SAHs is known from single-molecule experiments. Unknown, or still controversial, are the molecular scale details behind those observations. We show that the deformation mechanism of SAHs pulled from the termini at pull speeds approaching the quasi-static limit differs from that of typical helices found in proteins, which are stable only when interacting with other protein domains. Using molecular dynamics simulations with atomistic resolution at low pull speeds previously inaccessible to simulation, we show that SAHs start unfolding from the termini at all pull speeds we investigated. Unfolding proceeds residue-by-residue and hydrogen bond breaking is not the main event determining the barrier to unfolding. We use the molecular simulation data to test the cooperative Sticky Chain model. This model yields excellent fits of the force-extension curves and quantifies the distance, xE = 0.13 nm, to the transition state, the natural frequency of bond vibration, ν0 = 0.82 ns−1, and the height, V0=2.9 kcal/mol, of the free energy barrier associated with the deformation of single residues. Our results demonstrate that the Sticky Chain model could advantageously be used to analyze experimental force-extension curves of SAHs and other biopolymers.

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Language(s): eng - English
 Dates: 2020-09-302020
 Publication Status: Published in print
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 Identifiers: DOI: 10.1039/D0SM01166E
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Title: Soft Matter
  Abbreviation : Soft Matter
Source Genre: Journal
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Publ. Info: Cambridge, UK : Royal Society of Chemistry
Pages: - Volume / Issue: 16 (43) Sequence Number: - Start / End Page: 9917 - 9928 Identifier: ISSN: 1744-683X