The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.1c11911
Abstract: The accurate reading of genetic information during transcription is essential for the expression of genes. Sequence binding specificity very often is attributed to short-range, usually specific interactions between amino acid residues and individual nucleotide bases… read more here.
Keywords: dna; binding specificity; sequence; mechanism ... See more keywords
The origins of binding specificity of a lanthanide ion binding peptide
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-76527-y
Abstract: Lanthanide ions (Ln3+) show similar physicochemical properties in aqueous solutions, wherein they exist as + 3 cations and exhibit ionic radii differences of less than 0.26 Å. A flexible linear peptide lanthanide binding tag (LBT), which recognizes… read more here.
Keywords: peptide; ln3; affinity; binding specificity ... See more keywords
UV irradiation remodels the specificity landscape of transcription factors
Sign Up to like & getrecommendations! Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2217422120
Abstract: Somatic mutations are highly enriched at transcription factor (TF) binding sites, with the strongest trend being observed for ultraviolet light (UV)-induced mutations in melanomas. One of the main mechanisms proposed for this hyper-mutation pattern is… read more here.
Keywords: dna; transcription; binding specificity; dna binding ... See more keywords
SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad191
Abstract: Accurately predicting the antigen-binding specificity of adaptive immune receptors (AIRs), such as T-cell receptors (TCRs) and B-cell receptors (BCRs), is essential for discovering new immune therapies. However, the diversity of AIR chain sequences limits the… read more here.
Keywords: cell; air; binding specificity; air bert ... See more keywords
Trans-splicing facilitated by RNA pairing greatly expands sDscam isoform diversity but not homophilic binding specificity
Sign Up to like & getrecommendations! Published in 2022 at "Science Advances"
DOI: 10.1126/sciadv.abn9458
Abstract: The Down syndrome cell adhesion molecule 1 (Dscam1) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for nervous and immune functions. Chelicerates generate approximately 50 to 100 shortened Dscam… read more here.
Keywords: rna pairing; homophilic binding; binding specificity; trans splicing ... See more keywords
Intra-Domain Residue Coevolution in Transcription Factors Contributes to DNA Binding Specificity
Sign Up to like & getrecommendations! Published in 2023 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.03651-22
Abstract: While unraveling DNA-binding specificity of TFs is the key to understanding the basis and molecular mechanism of gene expression regulation, identifying the critical determinants that contribute to DNA binding specificity remains a major challenge. In… read more here.
Keywords: coevolving residues; dna; binding specificity; dna binding ... See more keywords
Structural insight to elucidate the binding specificity of the anti-cortisol Fab fragment with glucocorticoids.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of structural biology"
DOI: 10.2139/ssrn.4367514
Abstract: Cortisol is a steroid hormone that is produced by the adrenal gland. It is a primary stress hormone that increases glucose levels in the blood stream. High concentrations of cortisol in the body can be… read more here.
Keywords: cortisol fab; binding specificity; anti cortisol; cortisol ... See more keywords
Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.763750
Abstract: The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could,… read more here.
Keywords: ashh2 domain; binding specificity; specificity ashh2; toward h3k4me1 ... See more keywords
The Binding Specificity of PAB1 with Poly(A) mRNA, Regulated by Its Structural Folding
Sign Up to like & getrecommendations! Published in 2022 at "Biomedicines"
DOI: 10.3390/biomedicines10112981
Abstract: The poly(A)-binding protein cytoplasmic 1 (PAB1 or PABPC1) protein is associated with the long poly(A) mRNA tails, inducing stability. Herein, we investigated the dynamics of the PABPC1 protein, along with tracing its mRNA binding specificity.… read more here.
Keywords: poly; pab1; poly mrna; binding specificity ... See more keywords