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

Protein Science : a Publication of the Protein Society
James O WrablVincent J Hilser

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, sugges...Continue Reading

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Citations

Jan 16, 2002·Protein Science : a Publication of the Protein Society·Buyong MaRuth Nussinov
Apr 3, 2010·PLoS Computational Biology·James O Wrabl, Vincent J Hilser
Nov 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Loren StaggPernilla Wittung-Stafshede
Jul 27, 2002·Protein Science : a Publication of the Protein Society·James O WrablVincent J Hilser
Jun 21, 2011·Biophysical Chemistry·James O WrablVincent J Hilser
Jun 25, 2004·Protein Science : a Publication of the Protein Society·Scott A Larson, Vincent J Hilser
Mar 5, 2004·Proteins·Wiktor JurkowskiIrena Roterman
Dec 13, 2006·Biophysical Journal·Amarda ShehuCecilia Clementi
Sep 10, 2020·Proceedings of the National Academy of Sciences of the United States of America·Min-Hyung ChoVincent J Hilser
Jun 19, 2003·The Journal of Biological Chemistry·Barbara CampaniniStefano Bettati
Sep 3, 2009·Biochemistry·David M LeMasterGriselda Hernández
May 15, 2020·Journal of the American Chemical Society·Karine MazmanianCarmay Lim

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