Cytochrome-c (cyt-c) is an electron transport protein, and it is present throughout the evolution. More than 280 sequences have been reported in the protein sequence database (www.uniprot.org). Though sequentially diverse, cyt-c has essentially retained its tertiary structure or fold. Thus a vast data set of varied sequences with retention of similar structure and fun...

cytochrome-c (cyt-c) is an electron transport protein, and it is present throughout the evolution. more than 280 sequences have been reported in the protein sequence database (www.uniprot.org). though sequentially diverse, cyt-c has essentially retained its tertiary structure or fold. thus a vast data set of varied sequences with retention of similar structure and function makes it a primary ca...

A diffusion-collision-like model is proposed for helical proteins with three-state folding dynamics. The model generalizes a previous scheme based on the dynamics of putatively essential parts of the protein (foldons) that was successfully tested on proteins with two-state folding. We show that the extended model, unlike the original one, allows satisfactory calculation of the folding rate and ...

The folding of larger proteins generally differs from the folding of similarly large nucleic acids in the number and stability of the intermediates involved. To date, however, no similar comparison has been made between the folding of smaller proteins, which typically fold without well-populated intermediates, and the folding of small, simple nucleic acids. In response, in this study, we compar...

I study the conceptual framework of protein folding considering an exactly solvable model — the Rubik’s magic snake model. I discuss the mathematical representation of the model, the model Levinthal paradox, the non-unique compact folded structure, the function of the chain, the ground state energy, the commensurability between the folded structure and the potential sequence, the relationship b...

background: rna plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. rna secondary structure represents various significant portions of rna tertiary structure. since the biological function of rna is concluded indirectly from its primary structure, it would be important to analyze the relations between the rna sequences and t...

The relative folding rates of simple, single-domain proteins, proteins whose folding energy landscapes are smooth, are highly dispersed and strongly correlated with native-state topology. In contrast, the relative folding rates of small, Gō-potential lattice polymers, which also exhibit smooth energy landscapes, are poorly dispersed and insignificantly correlated with native-state topology. Her...

A number of puzzling characteristics appear repeatedly in protein folding studies. Some proteins fold in a fast two-state manner with no apparent intermediates while others fold much more slowly in a multistate way. Many proteins fold heterogeneously; within the same controlled experiment some fraction of the population reaches the native state rapidly and others more slowly. These contradictor...

Understanding how kinetics in the unfolded state affects protein folding is a fundamentally important yet less well-understood issue. Here we employ three different models to analyze the unfolded landscape and folding kinetics of the miniprotein Trp-cage. The first is a 208 μs explicit solvent molecular dynamics (MD) simulation from D. E. Shaw Research containing tens of folding events. The sec...