Most proteins that are to be imported into the mitochondrial matrix are synthesized as precursors, each composed of an N-terminal targeting sequence followed by a mature domain. Precursors are recognized through their targeting sequences by receptors at the mitochondrial surface and are then threaded through import channels into the matrix. Both the targeting sequence and the mature domain cont...

Questioning practice constitutes one of the typical and fundamental interactional tools in L2 teaching. Much L2 research on teacher questions has been quantitative studies focusing on identifying question types and their roles in language acquisition and meaning negotiation. However, by drawing on conversation analysis within a sociocultural perspective, this study examines qualitatively how EF...

The relative importance of amino acid sequence and native topology in the unfolding process of two SH3 domains and two circular permutants was investigated by 120 molecular dynamics runs at 375 K for a total simulation time of 0.72 micros. The alpha-spectrin (aSH3) and src SH3 (sSH3) domains, which have the same topology and a sequence identity of only 34%, show similar unfolding pathways. The ...

The usefulness of targeted molecular dynamics (TMD) for the simulation of large conformational transitions is assessed in this work on the unfolding process of chymotrypsin inhibitor 2 (CI2). In TMD the force field is supplemented with a harmonic restraint which promotes either the increase of the conformational distance from the native state or the decrease of the distance from a target unfold...

Reduced lattice models of proteins and Monte Carlo dynamics were used to simulate the initial stages of the unfolding of several proteins of various structural types, and the results were compared to experiment. The models semiquantitatively reproduce the approximate order of events of unfolding as well as subtle mutation effects and effects resulting from differences in sequences of similar fo...

We investigate the thermodynamics and kinetics of RNA unfolding and refolding under mechanical tension. The hierarchical nature of RNA structure and the existence of thermodynamic parameters for base pair formation based on nearest-neighbour interactions allows modelling of sequence-dependent folding dynamics for any secondary structure. We calculate experimental observables such as the transit...

We have performed 128 folding and 45 unfolding molecular dynamics runs of chymotrypsin inhibitor 2 (CI2) with an implicit solvation model for a total simulation time of 0.4 microseconds. Folding requires that the three-dimensional structure of the native state is known. It was simulated at 300 K by supplementing the force field with a harmonic restraint which acts on the root-mean-square deviat...

The effect of temperature on mechanical unfolding of proteins is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. The behavior of the I27 domain of titin and its serial repeats is contrasted to that of simple secondary structures. In all cases, thermal fluctuations accelerate the unraveling process, decreasing the unfolding force nearly linearly...

Native-state hydrogen exchange experiments under EX1 conditions can distinguish partially unfolded intermediates by their formation rates and identify the amide hydrogens exposed and protected in each. Results obtained define a cytochrome c intermediate seen only poorly before and place it early on the major unfolding pathway. Four distinct unfolding steps are found to be kinetically ordered in...

G-quadruplex unfolding within a sequence of two quadruplex units was characterized by gel electrophoresis, calorimetry and spectroscopy. The obtained results suggest that the kinetics and thermodynamics of the individual quadruplex unfolding are affected by its interaction with other DNA secondary structural elements.