Early events in protein folding explored by rapid mixing methods

Article Abstract:

Rapid mixing methods remain the method of choice for studies of protein folding reactions far from equilibrium transition region where intermediate states are most likely to accumulate. Rapid mixing experiments involve large changes in denaturant concentration, which is the case of protein folding or unfolding, pose additional challenges related to the increase in solvent viscosity, which slows down the mixing process, convective flow due to density gradients across the mixer and the heat of mixing which can give rise to thermal artifacts.

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Conformation of the backbone in unfolded proteins

Article Abstract:

Even though the random coil model has a long history of interpreting experimental results on unfolded proteins, it is inconsistent with older observations from Krimm's group as well as wealth of spectroscopic techniques that demonstrate the presence of well-defined backbone structure within the unfolded states of proteins and peptides. It is known for a long time that each residue residue/peptide backbone has a slightly different pK(sub a) value as well as distinctive inductive and blocking effects.

Peptides, Conformational analysis

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Protein-Folding simulation

Article Abstract:

A focus is made on molecular dynamics (MD) simulations of proteins in solution to investigate the detailed processes of protein folding and unfolding. Proteins can be expected to fairly reliably depict protein folding/unfolding transition states, intermediate states and denatured states, provided explicit solvent and good simulation techniques are employed.

Science & research, Research, Molecular dynamics

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