Thermodynamics of small-amplitude conformational fluctuations in native globular proteins.

Conformational preferences of amino acids in globular proteins.

In a previous paper [Levitt, M., and Greer, J. (1977), J. Mol. Biol. 114, 181--239], an objective compilation of the secondary-structure regions in more than 50 different globular proteins was produced automatically. In the present paper, these assignments of secondary structure are analyzed to give the frequency of occurrence of the 20 naturally occurring amino acids in alpha helix, beta sheet...

Universal behavior of localization of residue fluctuations in globular proteins.

Localization properties of residue fluctuations in globular proteins are studied theoretically by using a Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and archite...

Protein thermodynamics: Are native proteins metastable?

A Model for the Thermodynamics of Globular Proteins

We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water interactions. The model contains both hot and cold folding transitions. In addition it predicts a critical point at a given temperature and chemical potential of the surrounding water. The universality class of this...

Structural features that predict real-value fluctuations of globular proteins.

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective c...