Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition

Translational diffusion is the most fundamental form of transport in chemical and biological systems. The diffusion coefficient is highly sensitive to changes in the size of the diffusing species; hence, it provides important information on the variety of macromolecular processes, such as self-assembly or folding–unfolding. Here, we investigate the behavior of the diffusion coefficient of a macromolecule in the vicinity of heat-induced transition from folded to unfolded state. We derive the equation that describes the diffusion coefficient of the macromolecule in the vicinity of the transition and use it to fit the experimental data from pulsed-field-gradient nuclear magnetic resonance (PFG NMR) experiments acquired for two globular proteins, lysozyme and RNase A, undergoing temperature-induced unfolding. A very good qualitative agreement between the theoretically derived diffusion coefficient and experimental data is observed

2D [¹H,¹⁵N]-HSQC spectra of the PAI subdomain.

<p>The spectra were collected in 25 mM aqueous sodium phosphate buffer at pH 5.0 (top panel) and 7.0 (bottom panel) in the range of temperatures from 5 to 45°C with a 5°C increment.</p

DNA-binding of folded and unfolded conformations of the PAI subdomain.

<p>(A) 2D [¹H,¹⁵N]-HSQC spectrum of the PAI subdomain collected at the temperature of 5°C in 25 mM aqueous sodium phosphate buffer at pH 5.0 in the presence of 250 mM NaCl. The folded and unfolded conformations exist in slow exchange on the NMR time scale. Thus, two resonances are observed for each residue. Non-overlapping resonances originating from the same residue in both the folded and unfolded conformations are labeled. (B) Cartoon representation of the PAI subdomain (PDB code 2m8e <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112114#pone.0112114-Carpentier1" target="_blank">[7]</a>). The DNA-binding site is colored blue. Side chains of the residues that were used for the analysis of the DNA-binding are labeled and shown as red sticks. (C) Relative intensities of resonances corresponding to the folded and unfolded conformations are plotted as a function of PAI:DNA molar ratio. Relative intensities were calculated by dividing the resonance intensity at a given PAI:DNA molar ratio by the intensity of this resonance in the absence of DNA.</p

Intrinsic tyrosine fluorescence.

<p>(Left panel) The location of Y46 on the cartoon representation of the PAI subdomain (PDB code 2m8e <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112114#pone.0112114-Carpentier1" target="_blank">[7]</a>) is shown. (Right panel) The integral fluorescence of Y46 at pH 5.0 (squares) and pH 7.0 (circles) is plotted vs. temperature. Shown data is the average of three independent experiments. Error bars in many cases do not exceed the size of the symbol. Solid lines represent best fits of experimental data.</p

Self-diffusion coefficients.

<p>The PAI self-diffusion coefficient at pH 5.0 (squares) and 7.0 (circles) are plotted vs. temperature over the range from 5 to 35°C. Protein samples were prepared in 25 mM sodium phosphate buffer using 100% D₂O. The temperature dependence of the self-diffusion coefficient of BPTI (stars) is shown for comparison. Solid lines represent fits of Arrhenius dependence of the self-diffusion coefficient to experimental data.</p