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

Scientific Reports, vol. 10, pp. 1570

Abstract

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.

Authors 8

1. Livia Balacescu Aachen I. Physikalisches Institut

   Forschungszentrum Jülich · Heinz Maier-Leibnitz Zentrum · RWTH Aachen University

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany

   I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Germany

2. Tobias E. Schrader corresponding

   Forschungszentrum Jülich · Heinz Maier-Leibnitz Zentrum

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany. t.schrader@fz-juelich.de

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany

3. Aurel Rădulescu

   Forschungszentrum Jülich · Heinz Maier-Leibnitz Zentrum

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany

4. Piotr A. Zolnierczuk

   Forschungszentrum Jülich · Spallation Neutron Source

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) Outstation at Spallation Neutron Source (SNS), Oak Ridge, TN, 37831, USA

5. Olaf Holderer

   Forschungszentrum Jülich · Heinz Maier-Leibnitz Zentrum

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany

6. Stefano Pasini

   Forschungszentrum Jülich · Heinz Maier-Leibnitz Zentrum

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany

7. Jörg Fitter Aachen I. Physikalisches Institut

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Institute for Complex Systems (ICS-5), 52425, Jülich, Germany

   I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Germany

8. Andreas Maximilian Stadler Aachen Institute of Physical Chemistry

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), 52425, Jülich, Germany

   Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056, Aachen, Germany