NDLI: Thermodynamic environments in proteins: fundamental determinants of fold specificity.

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Thermodynamic environments in proteins: fundamental determinants of fold specificity.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Hilser, Vincent J. Larson, Scott A. Wrabl, James O.
Description	Country affiliation: United States Author Affiliation: Wrabl JO ( Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston 77555-1055, USA.)
Abstract	To investigate the relationship between an amino acid sequence and its corresponding protein fold, a database of thermodynamic stability information was assembled as a function of residue type from 81 nonhomologous proteins. This information was obtained using the COREX algorithm, which computes an ensemble-based description of the native state of proteins. Dissection of the COREX stability constant into its fundamental energetic components resulted in 12 thermodynamic environments describing the tertiary architecture of protein folds. Because of the observation that residue types partitioned unequally between these environments, it was hypothesized that thermodynamic environments contained energetic information that connected sequence to fold. To test the significance of this hypothesis, the thermodynamic stability information was incorporated into a three-dimensional-to-one-dimensional scoring matrix, and simple fold recognition experiments were performed in a manner such that information about the fold target was never included in the scoring. For 60 out of 81 fold targets, the correct sequence for the target scored in the top 5% of 3858 decoy sequences, with Z-scores ranging from 1.76 to 12.23. Furthermore, a scoring matrix assembled from the residues of 40 nonhomologous all-alpha proteins was used to thread sequences against 12 nonhomologous all-beta protein targets. In 10 of 12 cases, sequences known to adopt the native all-beta structure scored in the top 5% of 3858 decoy sequences, with Z-scores ranging from 1.99 to 7.94. These results indicate that energetic information encoded by thermodynamic environments represents a fundamental property of proteins that underlies classifications based on secondary structure.
ISSN	09618368
e-ISSN	1469896X
Journal	Protein Science
Issue Number	8
Volume Number	11
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2002-08-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Algorithms Proteins Chemistry Amino Acid Sequence Amino Acids Animals Databases, Protein Models, Molecular Models, Statistical Molecular Sequence Data Protein Folding Protein Structure, Secondary Protein Structure, Tertiary Classification Thermodynamics Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s. Research Support, U.s. Gov't, P.h.s. Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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