Molecular Architecture of the DNA-Binding Region and Its Relationship to Classification of Basic Helix-Loop-Helix Proteins

Atchley, William R.; Zhao, Jieping

doi:10.1093/molbev/msl143

Cited by 22 publications

(30 citation statements)

References 24 publications

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“…These residues all directly contact the core NN sequence of the E-box; residues six and nine also have a direct physical interaction with the CA sequence (Figure 2b). Our analysis supports previous experimental observations for mutant Max homodimers (46) and predictions provided by computational studies (33,34). …”

Section: Resultssupporting

confidence: 91%

“…structures for Pro6-containing bHLH dimers were not available) for our analysis. Some bHLH proteins that have Pro6 are members of the Hairy class of bHLH proteins (34) and these proteins can bind to the N-Box, which is an E-box-like sequence (CACNAG) (42,43). Other Pro6-containing bHLH proteins are from the HAND1 group of bHLH TFs, have Thr13 and bind NRTCTG (44).…”

Section: Resultsmentioning

confidence: 99%

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Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

Masi

Grove

Vedenko

et al. 2011

Nucleic Acids Research

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Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically recognize similar DNA sequences. Knowledge of the molecular determinants of protein–DNA recognition by paralogous TFs is of central importance for understanding how small differences in DNA specificities can dictate target gene selection. Previously, we determined the in vitro DNA binding specificities of 19 Caenorhabditis elegans basic helix-loop-helix (bHLH) dimers using protein binding microarrays. These TFs bind E-box (CANNTG) and E-box-like sequences. Here, we combine these data with logics, bHLH–DNA co-crystal structures and computational modeling to infer which bHLH monomer can interact with which CAN E-box half-site and we identify a critical residue in the protein that dictates this specificity. Validation experiments using mutant bHLH proteins provide support for our inferences. Our study provides insights into the mechanisms of DNA recognition by bHLH dimers as well as a blueprint for system-level studies of the DNA binding determinants of other TF families in different model organisms and humans.

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Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

Masi

Grove

Vedenko

et al. 2011

Nucleic Acids Research

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“…S1, Supplementary Material online). Other positions of the basic region allow a better discrimination of the target DNA sequences and are easily distinguishable in the major animal bHLH groups (Atchley and Fitch 1997; Ledent and Vervoort 2001; Jones 2004; Atchley and Zhao 2007). Animal group A proteins bind the CAGCTG (or CACCTG) E-box configuration and have a diagnostic arginine (R) at position 8.…”

Section: Resultsmentioning

confidence: 99%

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

Pires

Dolan

2009

Molecular Biology and Evolution

506

564

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Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use whole-genome sequences from nine species of land plants and algae to define the relationships between these proteins in plants. We show that few (less than 5) bHLH proteins are encoded in the genomes of chlorophytes and red algae. In contrast, many bHLH proteins (100–170) are encoded in the genomes of land plants (embryophytes). Phylogenetic analyses suggest that plant bHLH proteins are monophyletic and constitute 26 subfamilies. Twenty of these subfamilies existed in the common ancestors of extant mosses and vascular plants, whereas six further subfamilies evolved among the vascular plants. In addition to the conserved bHLH domains, most subfamilies are characterized by the presence of highly conserved short amino acid motifs. We conclude that much of the diversity of plant bHLH proteins was established in early land plants, over 440 million years ago.

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“…These properties were described with the following five factors by Atchley et al [75, 76]: (i) polarity (AAF-1), (ii) secondary structure (AAF-2), (iii) molecular volume (AAF-3), (iv) codon diversity (AAF-4), and (v) electrostatic charge (AAF-5). They were used to predict posttranslational modification sites [22, 77, 78].…”

Section: Methodsmentioning

confidence: 99%

iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach

Qiu

Xiao

Wei

et al. 2014

BioMed Research International

141

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Before becoming the native proteins during the biosynthesis, their polypeptide chains created by ribosome's translating mRNA will undergo a series of “product-forming” steps, such as cutting, folding, and posttranslational modification (PTM). Knowledge of PTMs in proteins is crucial for dynamic proteome analysis of various human diseases and epigenetic inheritance. One of the most important PTMs is the Arg- or Lys-methylation that occurs on arginine or lysine, respectively. Given a protein, which site of its Arg (or Lys) can be methylated, and which site cannot? This is the first important problem for understanding the methylation mechanism and drug development in depth. With the avalanche of protein sequences generated in the postgenomic age, its urgency has become self-evident. To address this problem, we proposed a new predictor, called iMethyl-PseAAC. In the prediction system, a peptide sample was formulated by a 346-dimensional vector, formed by incorporating its physicochemical, sequence evolution, biochemical, and structural disorder information into the general form of pseudo amino acid composition. It was observed by the rigorous jackknife test and independent dataset test that iMethyl-PseAAC was superior to any of the existing predictors in this area.

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Molecular Architecture of the DNA-Binding Region and Its Relationship to Classification of Basic Helix-Loop-Helix Proteins

Cited by 22 publications

References 24 publications

Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach

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