Influence of NaCl and sorbitol on the stability of conformations of cytochrome c

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.

Structural transformations of cytochrome c upon interaction with cardiolipin

Interactions of cytochrome c (cyt c) with cardiolipin (CL) play a critical role in early stages of apoptosis. Upon binding to CL, cyt c undergoes changes in secondary and tertiary structure that lead to a dramatic increase in its peroxidase activity. Insertion of the protein into membranes, insertion of CL acyl chains into the protein interior, and extensive unfolding of cyt c after adsorption to the membrane have been proposed as possible modes for interaction of cyt c with CL. Dissociation of Met80 is accompanied by opening of the heme crevice and binding of another heme ligand. Fluorescence studies have revealed conformational heterogeneity of the lipid-bound protein ensemble with distinct polypeptide conformations that vary in the degree of protein unfolding. We correlate these recent findings to other biophysical observations and rationalize the role of experimental conditions in defining conformational properties and peroxidase activity of the cyt c ensemble. Latest time-resolved studies propose the trigger and the sequence of cardiolipin-induced structural transitions of cyt c.

Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein

A compendium of different types of abiotic chemical syntheses identifies a consensus set of 10 "prebiotic" α-amino acids. Before the emergence of biosynthetic pathways, this set is the most plausible resource for protein formation (i.e., proteogenesis) within the overall process of abiogenesis. An essential unsolved question regarding this prebiotic set is whether it defines a "foldable set"--that is, does it contain sufficient chemical information to permit cooperatively folding polypeptides? If so, what (if any) characteristic properties might such polypeptides exhibit? To investigate these questions, two "primitive" versions of an extant protein fold (the β-trefoil) were produced by top-down symmetric deconstruction, resulting in a reduced alphabet size of 12 or 13 amino acids and a percentage of prebiotic amino acids approaching 80%. These proteins show a substantial acidification of pI and require high salt concentrations for cooperative folding. The results suggest that the prebiotic amino acids do comprise a foldable set within the halophile environment.

Mechanisms for the direct electron transfer of cytochrome c induced by multi-walled carbon nanotubes

Multi-walled carbon nanotube (MWCNT)-modified electrodes can promote the direct electron transfer (DET) of cytochrome c (Cyt c). There are several possible mechanisms that explain the DET of Cyt c. In this study, several experimental methods, including Fourier transform infrared spectroscopy, circular dichroism, ultraviolet-visible absorption spectroscopy, and electron paramagnetic resonance spectroscopy were utilized to investigate the conformational changes of Cyt c induced by MWCNTs. The DET mechanism was demonstrated at various nano-levels: secondary structure, spatial orientation, and spin state. In the presence of MWCNTs, the secondary structure of Cyt c changes, which exposes the active site, then, the orientation of the heme is optimized, revolving the exposed active center to the optimum spatial orientation for DET; and finally, a transition of spin states is induced, providing relatively high energy and a more open microenvironment for electron transfer. These changes at different nano-levels are closely connected and form a complex process that promotes the electron transfer of Cyt c.