When can a protein be regarded as a polymer? Form and dynamics characterization of different folding states of horse-heart Apomyoglobin
- Wann kann ein Protein als Polymer betrachtet werden? Charakterisierung der Form und Dynamik unterschiedlicher Faltungszustände von Apomyoglobin aus Pferdeherzen
Balacescu, Livia; Fitter, Jörg (Thesis advisor); Stadler, Andreas (Thesis advisor)
Aachen : RWTH Aachen University (2021)
Dissertation / PhD Thesis
Dissertation, RWTH Aachen University, 2021
Equilibrium dynamics of folding intermediates is related 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, the haeme free form of myoglobin, 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: first, using acid and second, using 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. However, the Zimm with internal friction model is not perfectly characterizing these states. Other models from the polymer science have been employed, none leading to better results.Moreover, this work contains details about the development of in situ dynamic light scattering (DLS) setups at the small angle neutron scattering instrument KWS-2 and at the neutron spin-echo instrument J-NSE at MLZ in Garching. By performing in situ DLS measurements during the neutron beamtime, it was ensured that the investigated protein solutions did not have any aggregates which could hinder the analysis of the structure and dynamics of the protein molecules.