Structure and dynamics of the chemically denatured bovine serum albumin protein investigated with neutron scattering

Ameseder, Felix; Richtering, Walter (Thesis advisor); Richter, Dieter (Thesis advisor)

Aachen (2019)
Dissertation / PhD Thesis

Dissertation, RWTH Aachen University, 2019

Abstract

The subject of the present work is the structure and the dynamics of the native and chemically denatured bovine serum albumin (BSA) protein. The dependence of the protein’s conformation on the denaturant concentration and dynamic protein properties are investigated. Neutrons as a probe are especially suited for the structural analysis on the mesoscopic length scale and the analysis of collective protein dynamics. The aim of the thesis is the combination of results of the neutron scattering experiments with models based on analytical functions. This enables to discuss the importance of structural elements and domain motions for the proteins formation and function. Circular dichroism (CD) spectroscopy was used to detect properties of the secondary structure as response to solvent condition. Dynamics light scattering (DLS) was employed to determine hydrodynamic properties with nanometer resolution and on the microsecond timescale. Small angle scattering (SAS) measurements were conducted to determine the shape and internal structure on the Angstrom to nanometer length scale. Finally, neutron spin-echo spectroscopy (NSE) and quasielastic incoherent neutron scattering spectroscopy (QENS) were used to gain information about the dynamics from the picosecond to one hundred nanosecond time scale and on the mesoscopic scale in the nanometer range. The protein is dissolved in aqueous buffers and is denaturated by guanidinium hydrochloride (GndCl).Alternatively, the protein’s disulphide bonds are reduced by the addition of the reducing agent β-mercaptoethanol. CD data show that the protein is fully denatured above a denaturant concentration of4M guanidinium hydrochloride. SANS data of respective structures are properly modelled by a linear polymer chain. The structural difference between the swollen protein with active disulphide bonds and the collapsed protein without disulphide bonds is considered. The QENS and NSE measurements of the denatured structures reveal an immense increase of mobility compared to the native protein. While QENS results comprise the collective motions of the amino acids residues, the NSE data pictures dynamics of the peptide backbone. The values of the effective diffusion D$_{eff}$ gained from NSE measurements extrapolate towards wider length scales and coincide with the values gained from DLS data. This behaviour follows the prediction of the Zimm theory for diffusive motions of linear polymer chains in aqueous solution. In the field of structural biology, the quantification of amplitudes and time scales for amino acid’s motions is considered fundamental for the understanding of protein folding. Hence, the focus of the present work is the modelling of the dynamics of the unfolded amino acid chain using polymer theory. The model is designed with respect to hydrodynamic interactions and structural protein properties. It is remarkable that this basic model resembles the experimental results while imposing a reduction of the amplitudes of motion and a cut-off for fast motions. The stiffness of the amino acid chain enforced by the disulphide bonds and the steric hindrance between neighbouring amino acids are assumed to cause these restrictions. In a separate section the perspective is turned to the dynamics of the native monomer and dimer. Monomer and dimer crystal structures were employed to model the amplitudes of motion observed in the NSE measurements. The monomers inside the dimer are connected by a disulphide bond acting as molecular hinge. The observed dynamics were discussed as the motions of the rigid monomers around the hinge’s axis.

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