It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common Gō interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-l...

Recent works have shown success in mimicking the flapping flight of bats on the robotic platform Bat Bot (B2). This robot has only five actuators but retains the ability to flap and fold-unfold its wings in flight. However, this bat-like robot has been unable to perform folding-unfolding of its wings within the period of a wingbeat cycle, about 100 ms. The DC motors operating the spindle mechan...

Recent experimental studies suggest that the mature GFP has an unconventional landscape composed of an early folding event with a typical funneled landscape, followed by a very slow search and rearrangement step into the locked, active chromophore-containing structure. As we have shown previously, the substantial difference in time scales is what generates the observed hysteresis in thermodynam...

The amino acid sequence of a protein determines both its final folded structure and the folding mechanism by which this structure is attained. The differences in folding behaviour between homologous proteins provide direct insights into the factors that influence both thermodynamic and kinetic properties. Here, we present a comprehensive thermodynamic and kinetic analysis of three homologous ho...

The PK1 pseudoknot is a well-characterized super secondary structure from Aquifex aeolicus transfer-messenger RNA that participates in the ribosomal trans-translation rescue mechanism. Extensive all-atom molecular dynamics simulations were conducted across worldwide distributed computing network to study folding, unfolding, misfolding, and conformational plasticity of twenty-two nucleotide pseu...

Protein folding is subject to the effects of solvation environment. A variety of organic solvents are used as additives for in vitro refolding of denatured proteins. Examination of the solvent effects on protein folding could be of fundamental importance to understand the molecular interactions in determining protein structure. This article investigated the folding of α-helix and β-hairpin stru...

in this work, different types of chaotic 1-manifolds which lie on the chaotic spheres or on a torus are introduced. some types of retractions of the chaotic spheres affect on the 1-chaotic systems, and other types of retractions occur to the geometric manifold but make the 1-chaotic manifold invariant. the existed retractions are discussed through new proved theorems. also we construct diffe...

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...

The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a ...