In the last couple of years, there has been increasing debate as to the presence and role of intermediate states on the folding pathways of several small proteins, including the 76-residue protein ubiquitin. Here, we present detailed kinetic studies to establish whether an intermediate state is ever populated during the folding of this protein. We show that the differences observed in previous ...

Molecular chaperones assist de novo protein folding and facilitate the refolding of stress-denatured proteins. The molecular chaperone concept was coined nearly 35 years ago, and since then, tremendous strides have been made in understanding how these factors support protein folding. Here, we focus on how various chaperone proteins were first identified to play roles in protein folding. Example...

Every year, cut-off low (COL) pressure systems produce severe weather conditions and heavy rainfall, often leading to flooding, devastation disruption of socio-economic activities in South Africa. COLs are defined as cold-cored synoptic-scale mid-tropospheric low-pressure which occur the mid-latitudes cause persistent rainfall. As they throughout these important rainfall producing that also ass...

Understanding how proteins fold is essential to our quest in discovering how life works at the molecular level. Current computation power enables researchers to produce a huge amount of folding simulation data. Hence there is a pressing need to be able to interpret and identify novel folding features from them. In this paper, we model each folding trajectory as a multi-dimensional curve. We the...

Proteins consisting of repeating amino acid motifs are abundant in all kingdoms of life, especially in higher eukaryotes. Repeat-containing proteins self-organize into elongated non-globular structures. Do the same general underlying principles that dictate the folding of globular domains apply also to these extended topologies? Using a simplified structure-based model capturing a perfectly fun...

The concomitant folding of a protein with its synthesis on the ribosome is influenced by a number of different timescales including the translation rate. Here we present a kinetic formalism to describe cotranslational folding and predict the effects of variable translation rates on this process. Our approach, which utilizes equilibrium data from arrested ribosome nascent chain complexes, provid...

[1] We show that the flux of mass crossing in one direction (the ‘‘gross’’ flux) through any specified surface S that divides anadvective-diffusive flow in a closed domain is infinite. That is, the flux, F (t), through S of the fluid mass that spent at least time t on one side of S diverges like t 1/2 as t ! 0, in the continuum limit. The gross flux is completely dominated by fluid elements res...

Characterizing the equilibrium ensemble of folding pathways, including their relative probability, is one of the major challenges in protein folding theory today. Although this information is in principle accessible via all-atom molecular dynamics simulations, it is difficult to compute in practice because protein folding is a rare event and the affordable simulation length is typically not suf...