Cargando…

Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions

Equilibrium dynamics of different folding intermediates and denatured states is strongly connected to the exploration of the conformational space on the nanosecond time scale and might have implications in understanding protein folding. For the first time, the same protein system apomyoglobin has be...

Descripción completa

Detalles Bibliográficos
Autores principales: Balacescu, Livia, Schrader, Tobias E., Radulescu, Aurel, Zolnierczuk, Piotr, Holderer, Olaf, Pasini, Stefano, Fitter, Jörg, Stadler, Andreas M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6994677/
https://www.ncbi.nlm.nih.gov/pubmed/32005832
http://dx.doi.org/10.1038/s41598-020-57775-4
_version_ 1783493244049424384
author Balacescu, Livia
Schrader, Tobias E.
Radulescu, Aurel
Zolnierczuk, Piotr
Holderer, Olaf
Pasini, Stefano
Fitter, Jörg
Stadler, Andreas M.
author_facet Balacescu, Livia
Schrader, Tobias E.
Radulescu, Aurel
Zolnierczuk, Piotr
Holderer, Olaf
Pasini, Stefano
Fitter, Jörg
Stadler, Andreas M.
author_sort Balacescu, Livia
collection PubMed
description Equilibrium dynamics of different folding intermediates and denatured states is strongly connected to the exploration of the conformational space on the nanosecond time scale and might have implications in understanding protein folding. For the first time, the same protein system apomyoglobin has been investigated using neutron spin-echo spectroscopy in different states: native-like, partially folded (molten globule) and completely unfolded, following two different unfolding paths: using acid or guanidinium chloride (GdmCl). While the internal dynamics of the native-like state can be understood using normal mode analysis based on high resolution structural information of myoglobin, for the unfolded and even for the molten globule states, models from polymer science are employed. The Zimm model accurately describes the slowly-relaxing, expanded GdmCl-denaturated state, ignoring the individuality of the different aminoacid side chain. The dynamics of the acid unfolded and molten globule state are similar in the framework of the Zimm model with internal friction, where the chains still interact and hinder each other: the first Zimm relaxation time is as large as the internal friction time. Transient formation of secondary structure elements in the acid unfolded and presence of α-helices in the molten globule state lead to internal friction to a similar extent.
format Online
Article
Text
id pubmed-6994677
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-69946772020-02-06 Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions Balacescu, Livia Schrader, Tobias E. Radulescu, Aurel Zolnierczuk, Piotr Holderer, Olaf Pasini, Stefano Fitter, Jörg Stadler, Andreas M. Sci Rep Article Equilibrium dynamics of different folding intermediates and denatured states is strongly connected to the exploration of the conformational space on the nanosecond time scale and might have implications in understanding protein folding. For the first time, the same protein system apomyoglobin has been investigated using neutron spin-echo spectroscopy in different states: native-like, partially folded (molten globule) and completely unfolded, following two different unfolding paths: using acid or guanidinium chloride (GdmCl). While the internal dynamics of the native-like state can be understood using normal mode analysis based on high resolution structural information of myoglobin, for the unfolded and even for the molten globule states, models from polymer science are employed. The Zimm model accurately describes the slowly-relaxing, expanded GdmCl-denaturated state, ignoring the individuality of the different aminoacid side chain. The dynamics of the acid unfolded and molten globule state are similar in the framework of the Zimm model with internal friction, where the chains still interact and hinder each other: the first Zimm relaxation time is as large as the internal friction time. Transient formation of secondary structure elements in the acid unfolded and presence of α-helices in the molten globule state lead to internal friction to a similar extent. Nature Publishing Group UK 2020-01-31 /pmc/articles/PMC6994677/ /pubmed/32005832 http://dx.doi.org/10.1038/s41598-020-57775-4 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Balacescu, Livia
Schrader, Tobias E.
Radulescu, Aurel
Zolnierczuk, Piotr
Holderer, Olaf
Pasini, Stefano
Fitter, Jörg
Stadler, Andreas M.
Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
title Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
title_full Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
title_fullStr Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
title_full_unstemmed Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
title_short Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions
title_sort transition between protein-like and polymer-like dynamic behavior: internal friction in unfolded apomyoglobin depends on denaturing conditions
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6994677/
https://www.ncbi.nlm.nih.gov/pubmed/32005832
http://dx.doi.org/10.1038/s41598-020-57775-4
work_keys_str_mv AT balacesculivia transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions
AT schradertobiase transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions
AT radulescuaurel transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions
AT zolnierczukpiotr transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions
AT holdererolaf transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions
AT pasinistefano transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions
AT fitterjorg transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions
AT stadlerandreasm transitionbetweenproteinlikeandpolymerlikedynamicbehaviorinternalfrictioninunfoldedapomyoglobindependsondenaturingconditions