Effect of a variable nonbonded attractive pair interaction on the relaxation dynamics of in Vacuo unfolded lysozyme

Article Abstract:

The configurational transitions and molecular shape changes that accompany the relaxation of the protein are studied with the help of a partly unfolded conformer of in vacuo lysozyme. The findings indicate that quantitatively, folding behavior may not be strongly dependent on the details of the model force field, but rather a feature associated with a range of potential energy functions.

Molecular dynamics

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Transitions in chain entanglement and compactness associated with in vacuo unfolding of lysozyme ions

Article Abstract:

The experiments were done by using chain entanglement and compactness properties to study the large-scale shape features and in vacuo unfolding of charged lysozyme ions. The results are in agreement with gas-phase experiments on lysozyme and suggest that unfolding results from the combined effect of heating and the Coulomb repulsion between charged particles.

Analysis, Chemical properties, Transition state (Chemistry), Chain reactions

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A limiting-case study of protein structure prediction: energy-based searches of reduced conformational space

Article Abstract:

The accurate prediction of the 3-dimensional structure of a protein from its sequence is examined with the help of an atom-based energy function and a systematic search procedure. The Fins\dings reveal that the energy surfaces are found to become steeper as the absolute energy minimum is approached.

Amino acids, Structure

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