Positional Dependence, Cliques, and Predictive Motifs in the bHLH Protein Domain

@article{Atchley1999PositionalDC,
  title={Positional Dependence, Cliques, and Predictive Motifs in the bHLH Protein Domain},
  author={W. Atchley and W. Terhalle and A. Dress},
  journal={Journal of Molecular Evolution},
  year={1999},
  volume={48},
  pages={501-516}
}
Abstract. Quantitative analyses were carried out on a large number of proteins that contain the highly conserved basic helix–loop–helix domain. Measures derived from information theory were used to examine the extent of conservation at amino acid sites within the bHLH domain as well as the extent of mutual information among sites within the domain. Using the Boltzmann entropy measure, we described the extent of amino acid conservation throughout the bHLH domain. We used position association (pa… Expand
Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis.
TLDR
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. Expand
A statistical approach to analyse positional dependencies in protein domains
Motivation: Protein domains are usually identified by conserved regions in the primary amino acid structure. Protein functions are dependent on the 3-dimensional structure and the biochemicalExpand
Networks of coevolving sites in structural and functional domains of serpin proteins.
TLDR
This research provides a better understanding on how protein structure evolves and elucidates the selective forces creating coevolution among protein sites. Expand
Molecular architecture of the DNA-binding region and its relationship to classification of basic helix-loop-helix proteins.
TLDR
Using multivariate statistical analyses, discriminant analyses describe the multidimensional aspects of physiochemical variation and clarify the structural basis of the prevailing evolutionary classification of basic helix-loop-helix proteins. Expand
Spectral Analysis of Sequence Variability in Basic-Helix-loop-helix (bHLH) Protein Domains
TLDR
Spectral analyses provide strong evidence that the patterns of amino acid variation in large numbers of sequences conform to the classical α-helix three-dimensional structure periodicity of 3.6 amino acids per turn. Expand
Prediction of Functional Sites in Proteins by Evolutionary Methods
Functional sites are well-defined regions that are relevant for protein function, and that include characteristic groups of amino acids. These regions may be involved in the interaction betweenExpand
Modeling the Molecular Evolution of Protein Domains and Networks.
MCFERRIN, LISA GAIL. Modeling the Molecular Evolution of Protein Domains and Networks. (Under the direction of William R. Atchley and Eric Stone.) Protein sequences are subject to a mosaic ofExpand
Evolution of the Max and Mlx Networks in Animals
TLDR
These analyses on Max and Mlx network members provide a model for characterizing the evolution of TFs involved in essential networks, and identify clear relationships among protein families with distinct points of radiation and divergence. Expand
Amino acid residue burial & co-evolution in proteins
Analysis of the amino-acid co-substitution patterns has long promised the prediction of protein structure but has failed to deliver. One possible reason is that most methods presume thatExpand
Evolution of bHLH transcription factors: modular evolution by domain shuffling?
Multidomain proteins usually contain several conserved and apparently independently evolved domains. As a result, classifications based on only a single small domain may obscure the true evolutionaryExpand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 25 REFERENCES
A natural classification of the basic helix-loop-helix class of transcription factors.
  • W. Atchley, W. Fitch
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1997
TLDR
A natural classification is provided for 242 basic helix-loop-helix (bHLH) motif-containing proteins and it is suggested that bHLH proteins containing a leucine zipper are not a natural, monophyletic group. Expand
Covariation of residues in the homeodomain sequence family
  • N. Clarke
  • Biology, Medicine
  • Protein science : a publication of the Protein Society
  • 1995
TLDR
Covariation of amino acid residues in the homeodomain family has been investigated to see whether strongly covariant residue pairs can be understood in terms of the structure and function of these domains. Expand
The loop region of the helix-loop-helix protein Id1 is critical for its dominant negative activity.
TLDR
It is found that the HLH domain of Id1 is necessary and nearly sufficient for its activity, and it is shown that two amino acid residues at the amino terminus of the Id1 loop are critical for itsActivity, perhaps by specifying the correct dimerization partners. Expand
Crystal structure of MyoD bHLH domain-DNA complex: Perspectives on DNA recognition and implications for transcriptional activation
TLDR
It is shown that Ala-114 and Thr-115, which are required for positive control in the myogenic proteins, are buried at the protein-DNA interface and suggest that the conformation of this arginine, which is different in the two structures, may play an important role in myogenic transcription. Expand
Discrimination between related DNA sites by a single amino acid residue of Myc-related basic-helix-loop-helix proteins.
TLDR
The results suggest that this conserved arginine residue in the basic regions of Myc-related bHLH proteins discriminates between CAC(A/G)TG and related sites. Expand
Structure and function of the b/HLH/Z domain of USF
TLDR
Hydrodynamic measurements show that the b/HLH/Z DNA binding domain of USF exists as a bivalent homotetramer, and this tetramer forms at the USF physiological intranuclear concentration, and depends on the integrity of the leucine zipper motif. Expand
Single amino acid substitutions alter helix‐loop‐helix protein specificity for bases flanking the core CANNTG motif.
TLDR
It is shown that bases outside this core 6 bp are involved in determining the specificity of binding of the yeast bHLH protein PHO4, but not CPF‐1, which is inhibited by the presence of a T residue immediately 5′ to their common CACGTG recognition sequence. Expand
Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer.
TLDR
The crystal structure of the transcription factor E47 bHLH domain bound to DNA is reported, indicating that sequence discrimination at the center of the E box may result from interaction with both the DNA bases and the phosphodiester backbone. Expand
Determination of eukaryotic protein coding regions using neural networks and information theory.
TLDR
High accuracies stemming from calculations of mutual information (a correlation measure) of spatially separated codons in exons, and in introns are reported, suggesting that dicodon frequencies of adjacent codons are important for intron/exon discrimination. Expand
The PAS domain confers target gene specificity of Drosophila bHLH/PAS proteins.
TLDR
It is postulate that the capacity of bHLH/PAS heterodimers to associate, through the PAS domain, with additional distinct proteins that bind target-gene DNA, is essential to confer specificity. Expand
...
1
2
3
...