Single-Molecule Analysis of Cytochrome c Folding by Monitoring the Lifetime of an Attached Fluorescent Probe

Assessing the impact of choline chloride and benzyltrimethylammonium chloride-based deep eutectic solvents on the structure and conformational dynamics of bovine serum albumin: a combined steady-state, time-resolved fluorescence and fluorescence correlation spectroscopic study

Although deep eutectic solvents (DESs) are regarded as useful substitutes for both ionic liquids and common organic solvents for storage and applications of biomolecules, it is still unclear whether all DESs or only specific types of DESs will be suitable for the said purpose. In view of this, the current study aims to report on the structure and conformational dynamics of BSA in the presence of two DESs, namely ethaline (choline chloride:ethylene glycol) and BMEG (benzyltrimethyl ammonium chloride:ethylene glycol), having the same hydrogen bond donor but with a distinct hydrogen bond acceptor, so that how small changes in one constituent of a DES alter the protein-DES interaction at the molecular level can be understood. The protein-DES interaction is investigated by exploiting both ensemble-averaged measurements like steady-state and time-resolved fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and single-molecule sensitive techniques based on fluorescence correlation spectroscopy (FCS). Interestingly, the results obtained from these studies have demonstrated that while a very small quantity of BMEG completely unfolds the native structure of the protein, it remains in a partially unfolded state even at very high ethaline content. More interestingly, it has been found that at very high concentrations of BMEG, the unfolded protein undergoes enhanced protein-protein interaction resulting in the aggregation of BSA. All of the results obtained from these investigations have essentially suggested that both protein-DES interaction and interspecies interaction among the constituent of DESs play a crucial role in governing the overall stability and conformational dynamics of the protein in DESs.

On the Stability and Conformational Dynamics of Cytochrome c in Ammonium Ionic Liquids

Owing to their potential applications in the extraction, purification, and preservation of biomolecules and biocatalysis, ionic liquids (ILs) have gained great attention in biotechnology. Although it is known that the structure and dynamics of proteins in ILs depend on the nature of both proteins and ILs, the biophysical mechanism governing the protein-IL interaction, which determines the stability of proteins or the activity of an enzyme in these nonconventional media, is yet to be understood clearly. Herein, we study the effect of two ammonium ILs, triethylammonium dihydrogen phosphate (TEAP) and tributylammonium dihydrogen phosphate (TBAP), on the stability and conformational dynamics of cytochrome c (Cyt c) in its native and unfolded states, employing primarily the single molecule-based fluorescence correlation spectroscopy (FCS) technique. The results show that the native structure of Cyt c is not significantly altered by TEAP, but the tertiary structure is perturbed to a great extent by TBAP, which comprises a longer alkyl chain. Fluctuations of the fluorescence intensity of Alexa488 dye-labeled Cyt c in FCS measurements reveal conformational dynamics (67 ± 10 μs) in the native state of Cyt c that is accelerated in the presence of both ILs but not affected when Cyt c is in its unfolded state. The present findings demonstrate how the stability of this protein can be modulated by using ammonium ILs of different alkyl chain lengths.

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

K(+) preference at the NaK channel entrance revealed by fluorescence lifetime and anisotropy analysis of site-specifically incorporated (7-hydroxycoumarin-4-yl)ethylglycine

The fluorescent unnatural amino acid, (7-hydroxycoumarin-4-yl)ethylglycine (HC), was site-specifically incorporated at the Phe69 site, close to the entrance of the selectivity filter of the NaK channel. Decreased fluorescence lifetime and elevated time-resolved anisotropy of NaK-F69HC in buffers with high K(+)/Na(+) molar ratios indicated the K(+) preference at the entrance of the NaK channel, consistent with previous crystal structure results of the NaK channel.

Direct conversion of cytochrome c spectral shifts to fluorescence using photochromic FRET

Photochromic fluorescence resonance energy transfer (pcFRET) was used to monitor the redox activity of non-fluorescent heme protein. Venus fluorescent protein was used as a donor where its emission intensity was reversibly modulated by the absorption change of Cytochrome c.