Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis

Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress A (2000)
Molecular Biology and Evolution 17(1): 164-178.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Atchley, William R.; Wollenberg, Kurt R.; Fitch, Walter M.; Terhalle, Werner; Dress, AndreasUniBi
Abstract / Bemerkung
An information theoretic approach is used to examine the magnitude and origin of associations among amino acid sites in the basic helix-loop-helix (bHLH) family of transcription factors. Entropy and mutual information values are used to summarize the variability and covariability of amino acids comprising the bHLH domain for 242 sequences. When these quantitative measures are integrated with crystal structure data and summarized using helical wheels, they provide important insights into the evolution of three-dimensional structure in these proteins. We show that amino acid sites in the bHLH domain known to pack against each other have very low entropy values, indicating little residue diversity at these contact sites. Noncontact sites, on the other hand, exhibit significantly larger entropy values, as well as statistically significant levels of mutual information or association among sites. High levels of mutual information indicate significant amounts of intercorrelation among amino acid residues at these various sites. Using computer simulations based on a parametric bootstrap procedure, we are able to partition the observed covariation among various amino acid sites into that arising from phylogenetic (common ancestry) and stochastic causes and those resulting from structural and functional constraints. These results show that a significant amount of the observed covariation among amino acid sites is due to structural/functional constraints, over and above the covariation arising from phylogenetic constraints. These quantitative analyses provide a highly integrated evolutionary picture of the multidimensional dynamics of sequence diversity and protein structure.
Stichworte
helix-loop-helix; protein evolution; entropy; parametric bootstrap; mutual information
Erscheinungsjahr
2000
Zeitschriftentitel
Molecular Biology and Evolution
Band
17
Ausgabe
1
Seite(n)
164-178
ISSN
0737-4038
Page URI
https://pub.uni-bielefeld.de/record/1620816

Zitieren

Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress A. Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis. Molecular Biology and Evolution. 2000;17(1):164-178.
Atchley, W. R., Wollenberg, K. R., Fitch, W. M., Terhalle, W., & Dress, A. (2000). Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis. Molecular Biology and Evolution, 17(1), 164-178. https://doi.org/10.1093/oxfordjournals.molbev.a026229
Atchley, W. R., Wollenberg, K. R., Fitch, W. M., Terhalle, W., and Dress, A. (2000). Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis. Molecular Biology and Evolution 17, 164-178.
Atchley, W.R., et al., 2000. Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis. Molecular Biology and Evolution, 17(1), p 164-178.
W.R. Atchley, et al., “Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis”, Molecular Biology and Evolution, vol. 17, 2000, pp. 164-178.
Atchley, W.R., Wollenberg, K.R., Fitch, W.M., Terhalle, W., Dress, A.: Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis. Molecular Biology and Evolution. 17, 164-178 (2000).
Atchley, William R., Wollenberg, Kurt R., Fitch, Walter M., Terhalle, Werner, and Dress, Andreas. “Correlations Among Amino Acid Sites in bHLH Protein Domains: An Information Theoretic Analysis”. Molecular Biology and Evolution 17.1 (2000): 164-178.

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 10666716
PubMed | Europe PMC

Suchen in

Google Scholar