Thermodynamic prediction of structural determinants of the molten globule state of barnase.
Recently, it has been demonstrated that the enthalpy and heat capacity changes for protein folding/unfolding can be predicted rather accurately from the crystallographic or NMR solution structure of a protein. (K.P. Murphy, V. Bhakuni, D. Xie and E. Freire, Mol. Biol. 227 (1992) 293-306.) Under some conditions proteins do not unfold completely, giving rise to states in which the molecule remains in a compact configuration after denaturation. These compact denatured or molten globule states retain a hydrophobic core, exhibit residual structure and a compactness close to that of the native state. This phenomenon is reflected in the thermodynamics of the process. By using the structural parametrization of the energetics, it is possible to develop an algorithm aimed at selecting partly folded states that conform to the experimental thermodynamic constraints of the molten globule. We have applied our molten globule search algorithm to the globular protein barnase. This approach has allowed a structure based selection of a unique family of structural states that satisfy the experimental criteria of the molten globule. The prediction of the molten globule search algorithm indicates that the first helix together with most of the beta-sheet structure (beta 2, beta 3-5) and loop 5 constitute the main determinants of the molten globule intermediate, in agreement with the NMR data. These results open the prospect for an automated search of the structural determinants of the molten globule state of proteins and suggest that solvation parameters can be effectively used to probe structural states of proteins.
Freire
E
E
Department of Biology, Johns Hopkins University, Baltimore, MD 21218.
Xie
D
D
D000465:Algorithms; D001426:Bacterial Proteins; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D012260:Ribonucleases / Q000737:chemistry*; D013816:Thermodynamics
D001426:Bacterial Proteins; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease