We have investigated the fibrillation propensity of different conformational isomers of an archetypal, all α-helical protein, namely, bovine serum albumin (BSA), under different pH conditions and ionic strengths using fluorescence and circular dichroism (CD) spectroscopy. At low pH and higher protein concentration, the partially folded conformers associate to form oligomers that are converted into ordered amyloid-like fibrils when incubated at elevated temperature. We have elucidated the mechanism of fibril formation, especially the early steps, by monitoring the kinetics of structural changes during the aggregation process. Various structural probes in tandem were utilized to decipher the temporal evolution of both conformational and size changes by measuring the time dependence of fluorescence intensity and anisotropy of intrinsic tryptophans and several extrinsic fluorophores during the aggregation. Additionally, CD spectroscopy was utilized to monitor the changes in protein secondary structural content during fibrillation. Our findings suggest that the conformational conversion occurs in the oligomers that serve as precursors to amyloid fibrils and precedes the overall fibrillar growth.

The fundamental backbone dynamics of unfolded proteins arising due to intrinsic ϕ-ψ dihedral angle fluctuations dictate the course of protein folding, binding, assembly, and function. These internal fluctuations are also critical for protein misfolding associated with a range of human diseases. However, direct observation and unambiguous assignment of this inherent dynamics in chemically denatured proteins is extremely challenging due to various experimental limitations. To directly map the backbone torsional mobility in the ϕ-ψ dihedral angle space, we used a model intrinsically disordered protein, namely, α-synuclein, that adopts an expanded state under native conditions. We took advantage of nonoccurrence of tryptophan in α-synuclein and created a number of single-tryptophan variants encompassing the entire polypeptide chain. We then utilized highly sensitive picosecond time-resolved fluorescence depolarization measurements that allowed us to discern the site-specific torsional relaxation at a low protein concentration under physiological conditions. For all the locations, the depolarization kinetics exhibited two well-separated rotational-correlation-time components. The shorter, subnanosecond component arises due to the local mobility of the indole side chain, whereas the longer rotational-correlation-time component (1.37 ± 0.15 ns), independent of global tumbling, represents a characteristic timescale for short-range conformational exchange in the ϕ-ψ dihedral space. This correlation time represents an intrinsic timescale for torsional relaxation and is independent of position, which is expected for an extended polypeptide chain having little or no propensity to form persistent structures. We were also able to capture this intrinsic timescale at the N-terminal unstructured domain of the prion protein. Our estimated timescale of the segmental mobility is similar to that of unfolded proteins studied by nuclear magnetic resonance in conjunction with molecular dynamics simulations. Our results have broader implications for a diverse range of functionally and pathologically important intrinsically disordered proteins and disordered regions.

Natively unfolded or intrinsically disordered proteins (IDPs) are under intense scrutiny due to their involvement in both normal biological functions and abnormal protein misfolding disorders. Polypeptide chain collapse of amyloidogenic IDPs is believed to play a key role in protein misfolding, oligomerization, and aggregation leading to amyloid fibril formation, which is implicated in a number of human diseases. In this work, we used bovine κ-casein, which serves as an archetypal model protein for amyloidogenic IDPs. Using a variety of biophysical tools involving both prediction and spectroscopic techniques, we first established that monomeric κ-casein adopts a collapsed premolten-globule-like conformational ensemble under physiological conditions. Our time-resolved fluorescence and light-scattering data indicate a change in the mean hydrodynamic radius from ∼4.6 nm to ∼1.9 nm upon chain collapse. We then took the advantage of two cysteines separated by 77 amino-acid residues and covalently labeled them using thiol-reactive pyrene maleimide. This dual-labeled protein demonstrated a strong excimer formation upon renaturation from urea- and acid-denatured states under both equilibrium and kinetic conditions, providing compelling evidence of polypeptide chain collapse under physiological conditions. The implication of the IDP chain collapse in protein aggregation and amyloid formation is also discussed.

Protein aggregation leading to various nanoscale assemblies is under scrutiny due to its implications in a broad range of human diseases. In the present study, we have used ovalbumin, a model non-inhibitory serpin, to elucidate the molecular events involved in amyloid assembly using a diverse array of spectroscopic and imaging tools such as fluorescence, laser Raman, circular dichroism spectroscopy, and atomic force microscopy (AFM). The AFM images revealed a progressive morphological transition from spherical oligomers to nanoscopic annular pores that further served as templates for higher-order supramolecular assembly into larger amyloid pores. Raman spectroscopic investigations illuminated in-depth molecular details into the secondary structural changes of the protein during amyloid assembly and pore formation. Additionally, Raman measurements indicated the presence of antiparallel β-sheets in the amyloid core. Overall, our studies revealed that the protein conformational switch in the context of the oligomers triggers the hierarchical assembly into nanoscopic amyloid pores. Our results will have broad implications in the structural characterization of amyloid pores derived from a variety of disease-related proteins.

Serum albumins are multi-domain all α-helical proteins that are present in the circulatory system and aid in the transport of a variety of metabolites, endogenous ligands, drugs etc. Earlier observations have indicated that serum albumins adopt a range of reversible conformational isomers depending on the pH of the solution. Herein, we report the concurrent changes in the protein conformation and size that are inherent to the pH-induced conformational isomers of bovine serum albumin (BSA). We have investigated the fluorescence properties of both intrinsic (tryptophan) and extrinsic (ANS, pyrene) fluorophores to shed light into the structural features of the pH-dependent conformers. We have been able to identify a number of conformational isomers using multiple fluorescence observables as a function of pH titration. Our results indicate that at pH 3, a partially-folded, 'molten-globule-like' state is populated. Moreover, equilibrium unfolding studies indicated that the 'molten-globule-like' state unfolds in a non-cooperative fashion and is thermodynamically less stable than the native state. The fluorescence-based approach described in the present work has implications in the study of pH-induced conformational plasticity of other physiologically relevant proteins.