Thermodynamic propensities of amino acids in the native state ensemble: implications for fold recognition.

ABSTRACT: An amino acid sequence, in the context of the solvent environment, contains all of the thermodynamic information necessary to encode a three-dimensional protein structure. To investigate the relationship between an amino acid sequence and its corresponding protein fold, a database of thermodynamic stability information was assembled that spanned 2951 residues from 44 nonhomologous proteins. This information was obtained using the COREX algorithm, which computes an ensemble-based description of the native state of a protein. It was observed that amino acid types partitioned unequally into high, medium, and low thermodynamic stability environments. Furthermore, these distributions were reproducible and were significantly different than those expected from random partitioning. To assess the s

SUBMITTER: Wrabl JO 

PROVIDER: S-EPMC2374190 | biostudies-literature | 2001 May

REPOSITORIES: biostudies-literature