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

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Year: 2001 Volume: 10 Issue: 4

Year: 2001 Volume: 10 Issue: 3

Year: 2001 Volume: 10 Issue: 2

Year: 2001 Volume: 10 Issue: 1

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

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Larson, S. A. Wrabl, J. O. Hilser, V. J.
Description	Country affiliation: United States Author Affiliation: Wrabl JO ( Department of Human Biological Chemistry & Genetics and Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas 77555-1055, USA.)
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 structural importance of the distributions, simple fold-recognition experiments were performed based on a 3D-1D scoring matrix containing only COREX residue stability information. This procedure was able to recover amino acid sequences corresponding to correct target structures more effectively than scoring matrices derived from randomized data. High-scoring sequences were often aligned correctly with their corresponding target profiles, suggesting that calculated thermodynamic stability profiles have the potential to encode sequence information. As a control, identical fold-recognition experiments were performed on the same database of proteins using DSSP secondary structure information in the scoring matrix, instead of COREX residue stability information. The comparable performance of both approaches suggested that COREX residue stability information and secondary structure information could be of equivalent utility in more sophisticated fold-recognition techniques. The results of this work are a consequence of the idea that amino acid sequences fold not into single, rigidly stable structures but rather into thermodynamic ensembles best represented by a time-averaged structure.
ISSN	09618368
e-ISSN	1469896X
Journal	Protein Science
Issue Number	5
Volume Number	10
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2001-05-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Amino Acids Metabolism Computational Biology Protein Folding Proteins Chemistry Algorithms Computer Simulation Databases As Topic Hydrogen Models, Molecular Protein Structure, Secondary Protein Structure, Tertiary Reproducibility Of Results Sequence Alignment Thermodynamics Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s. Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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

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

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

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