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*  E-box - Wikipedia
These proteins usually contain the basic helix-loop-helix protein structural motif, which allows them to bind as dimers. This ... Ripperger, J A.; Schibler, U. (Mar 2006). "Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp ... Chaudhary, J; Skinner, M K. (May 1999). "Basic helix-loop-helix proteins can act at the E-box within the serum response element ... 2000). "Serine/Threonine Kinases 3pK and MAPK-activated Protein Kinase 2 Interact with the Basic Helix-Loop-Helix Transcription ...
  https://en.wikipedia.org/wiki/E-box
*  Basic helix-loop-helix - Wikipedia
A basic helix-loop-helix (bHLH) is a protein structural motif that characterizes one of the largest families of dimerizing ... 2009: Grove, De Masi et al., identified novel short DNA motifs, bound by a subset of bHLH proteins, which they defined as "E- ... helix-loop-helix". Protein Profile. 2 (6): 621-702. PMID 7553065. Massari ME, Murre C (January 2000). "Helix-loop-helix ... It should not be confused with the helix-turn-helix domain. The motif is characterized by two α-helices connected by a loop. In ...
  https://en.wikipedia.org/wiki/Basic_helix-loop-helix
*  Myc - Wikipedia
... basic helix-loop-helix) structural and LZ (leucine zipper) motifs. Through its bHLH DNA-binding motif, Myc interacts with DNA, ... Blackwood EM, Eisenman RN (March 1991). "Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding ... Blackwood EM, Eisenman RN (March 1991). "Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding ... while the leucine zipper TF-binding motif allows the dimerization with its partner Max, another bHLH transcription factor. Myc ...
  https://en.wikipedia.org/wiki/Myc
*  cTFbase: a database for comparative genomics of transcription factors in cyanobacteria | BMC Genomics | Full Text
... and Basic-helix-loop-helix, etc. Helix-turn-helix motif is the most common structure of DBD in prokaryotes [3, 4, 6]. ... Dodd IB, Egan JB: Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 1990, 18 ( ... Galperin MY: Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J ... The searches were iterated until no newly retrieved sequences belonged to TF; (3) Scanning for helix-turn-helix motif. This ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-104
*  Networks in Cell Biology | SpringerLink
Ledent, V., Paquet, O., and Vervoort, M. (2002). Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome ... Gangloff, Y. G., Romier, C., Thuault, S., Werten, S., and Davidson, I. (2001). The histone fold is a key structural motif of ... Solé, S.V. and Valverde, S. (2006). Are networks motifs the spandrels of cellular complexity? TREE, 21(8):419-422.PubMedGoogle ... Metabolic Network Betweenness Centrality Real Network Average Path Length Network Motif These keywords were added by machine ...
  https://link.springer.com/chapter/10.1007/978-0-387-47509-7_10
*  What's hot today: Current papers in developmental biology and gene function
Proneural genes encode basic helix-loop-helix transcription factors that promote the expression of 'core' and subtype-specific ... Structural basis for the Nanos-mediated recruitment of the CCR4-NOT complex and translational repression. Genes Dev 28: 888-901 ... The Dntf-2r regulatory region is similar to the known β2 tubulin 14 bp testis motif (β2-UE1). Comparative sequence analyses ... act as testis-specific regulatory motifs in these genes. The Dntf-2r regulatory region is similar to the known β2 tubulin 14 bp ...
  http://www.sdbonline.org/sites/fly/aimain/model-organisms-june2014.htm
*  Protein structure prediction - Wikipedia
An example is the helix-loop-helix motif. Structural motifs are also referred to as supersecondary structures and folds. ... the known protein structures have been classified into hierarchical levels of structural complexity with the fold as a basic ... Examples of sequence motif databases are the Prosite catalog and the Stanford Motifs Database. motif (structural context) a ... fold similar to structural motif, includes a larger combination of secondary structural units in the same configuration. Thus, ...
  https://en.wikipedia.org/wiki/Protein_structure_prediction
*  DNA-binding domain - Wikipedia
The basic helix-loop-helix (bHLH) domain is found in some transcription factors and is characterized by two alpha helices (α- ... A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that ... set of DNA-binding domains to predict transcription factors in all completely sequenced genomes Table of DNA-binding motifs DNA ... helixes) connected by a loop. One helix is typically smaller and due to the flexibility of the loop, allows dimerization by ...
  https://en.wikipedia.org/wiki/DNA-binding_domain
*  SMART: PTB domain annotation
It contains a peptide binding pocket (formed by the beta strand 5 and C-terminal alpha helix) and a highly basic phospholipid ... The structural bases of the interactions are well understood for the few domains now experimentally determined, and ligand- ... The Shc-like PID specifically binds to the Asn-Pro-Xaa-Tyr(P) motif found in many tyrosine-phosphorylated proteins including ... Specificity of the PTB domain of Shc for beta turn-forming pentapeptide motifs amino-terminal to phosphotyrosine. ...
  http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=PTB&BLAST=DUMMY
*  Heterogeneous Nuclear Ribonucleoprotein K Binds to the Cytosine-Rich Sequence of the Hypoxia Inducible Factor 1 Alpha Proximal...
Wang GL, Jiang BH, Rue EA, Semenza GL (1995) Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated ... or long-loop sizes, class II. Class I i-motif structures include the VEGF, RET and Rb i-motifs, which have loop size ... or the pH at which half the structural species consists of i-motif and the other half of non-i-motif folded species) of 5.8, ... Knowing that C15 is in the loop region of the i-motif and is highly brominated when folded in an i-motif and that hnRNP K does ...
  https://www.omicsonline.org/heterogeneous-nuclear-ribonucleoprotein-k-binds-to-the-cytosine-rich-sequence-of-the-hypoxia-inducible-factor-1-alpha-proximal-promoter-that-forms-a-stable-i-motif-at-neutral-ph-2161-0398.S5-001.php?aid=10995
*  CASK | SpringerLink
Therefore, although the structural information provides a basic framework to probe molecular and cellular function of CASK, ... and the LID region composed of a long loop and alpha helix. The LID region of CASK GuK domain has a structure distinct from ... The Hook motif that follows the SH3 domain has been shown to interact with protein 4.1 and effect actin filamentation (Biederer ... 1996); it has also been suggested that besides PDZ-binding motifs, neurexin and syndecan harbor secondary interaction sites for ...
  https://link.springer.com/referenceworkentry/10.1007/978-3-319-67199-4_101833
*  Quint Lab:papers of the month - OpenWetWare
cd- Yi et al.: A basic helix-loop-helix transcription factor controls cell growth and size in root hairs. Nat Gen 2010 ... mq - Yin et al.: Structural insights into the mechanism of abscisic acid signaling by PYL proteins. Nat Struct Mol Biol. 16: ... mq - Chung/Howe: A critical role for the TIFY motif in repression of jasmonate signaling by repression of a stabilized splice ... mq - Shoval & Alon: SnapShot: Network Motifs. Cell 143:326e1-2. *mq - Ruschaki et al.: The proteasome antechamber maintains ...
  https://openwetware.org/wiki/?title=Quint_Lab:papers_of_the_month&oldid=478841
*  The Light-Response BTB1 and BTB2 Proteins Assemble Nuclear Ubiquitin Ligases That Modify Phytochrome B and D Signaling in...
... molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix ... E3s recognize structural motifs in the target and then catalyze an isopeptide linkage between the C-terminal Gly of Ub and an ... basic helix-loop-helix. BACK. BTB-and-C-terminal-Kelch. NLS. nuclear localization sequence. RT. reverse transcription. Y2H. ... which belong to the basic helix-loop-helix (bHLH) superfamily of transcriptional regulators (Bae and Choi, 2008; Leivar and ...
  http://www.plantphysiol.org/content/160/1/118.full
*  Beta sheet - Wikipedia
A β-helix is formed from repeating structural units consisting of two or three short β-strands linked by short loops. These ... in which case it is called a β-α-β motif. A closely related motif called a β-α-β-α motif forms the basic component of the most ... a program to identify and analyze structural motifs in proteins". Protein Science. 5 (2): 212-20. doi:10.1002/pro.5560050204. ... Individual strands can also be linked in more elaborate ways with longer loops that may contain α-helices. The Greek key motif ...
  https://en.wikipedia.org/wiki/Beta_sheet
*  Protein Structure | Encyclopedia.com
It consists of two antiparallel helices at about a 60-degree angle to each other connected by a loop. This motif, which binds ... and loops). Tertiary structure is subdivided into certain portions that are termed motifs and domains. ... These may be ionic bonds between the charged acidic or basic groups of side chains of amino acids, or hydrogen bonds whereby a ... Recognition of two molecules for each other is termed "structural complementarity"; that is, the three-dimensional structures ...
  https://www.encyclopedia.com/plants-and-animals/zoology-and-veterinary-medicine/zoology-general/protein-structure
*  Structural And Molecular Dynamics Analysis Of The Super Secondary Motifs From TIM Barrel Proteins: Implications For Folding And...
The acquired complex three-dimensional structure of proteins is a culmination of simple structural fragments like α-α, β-Î ... The TIM barrel proteins are made up of a regular repeating βαβ motif resulting in the strands and helices in an alternating ... loop length, loop dynamics, residue preferences in loops, long range side chain main chain interactions etc., to shortlist βαβ ... Thus, tertiary structures can be seen as a combination of basic building block motifs implying that all complex protein ...
  https://www.omicsonline.org/proceedings/structural-and-molecular-dynamics-analysis-of-the-super-secondary-motifs-from-tim-barrel-proteins-implications-for-foldi-72403.html
*  protein facts, information, pictures | Encyclopedia.com articles about protein
The helix-loop-helix motif is a knobby structure, and the zinc finger projects outward like its name. These last two motifs ... Serving as the basic structural molecule of all the tissues in the body, protein makes up nearly 17 percent of the total body ... It is the amino acid sequence that determines the folding pattern, common motifs being the 'alpha helix' and the 'pleated beta ... Combinations of secondary structure form "motifs." A coiled-coil motif is common among proteins that associate with the DNA ...
  https://www.encyclopedia.com/science-and-technology/biochemistry/biochemistry/protein
*  G protein-coupled receptor - Mashpedia Free Video Encyclopedia
... common structural theme among GPCRs is palmitoylation of one or more sites of the C-terminal tail or the intracellular loops. ... the seven-transmembrane helices, is conserved, the relative orientation of the helices differ significantly from that of ... International Union of Basic and Clinical Pharmacology. Retrieved 11 August 2008.. *. "GPCRdb". Data, diagrams and web tools ... Ligand binding disrupts an ionic lock between the E/DRY motif of TM-3 and acidic residues of TM-6. As a result, the GPCR ...
  http://www.mashpedia.com/G-protein_coupled_receptor
*  Unicellular and multicellular Organisms are best explained through design
as illustrated by the basic helix-loophelix (bHLH) protein family involved in diverse cellular developmental processes in ... For example, what if any are the selection barriers to (and the drivers toward) it? Are the motifs in the morphological ... It is now widely accepted, on the basis of structural, biochemical, and molecular evidence, that the five major types of large ... This feature enables sometimes radically different variants of a developmental motif, such as cell-cell adhesion, to achieve ...
  http://reasonandscience.heavenforum.org/t2010-unicellular-and-multicellular-organisms-are-best-explained-through-design
*  HIF1A - Wikipedia
HIF1A contains a basic helix-loop-helix domain near the C-terminal, followed by two distinct PAS (PER-ARNT-SIM) domains, and a ... Freedman SJ, Sun ZY, Poy F, Kung AL, Livingston DM, Wagner G, Eck MJ (Apr 2002). "Structural basis for recruitment of CBP/p300 ... Hansson LO, Friedler A, Freund S, Rudiger S, Fersht AR (Aug 2002). "Two sequence motifs from HIF-1alpha bind to the DNA-binding ... The HIF1A polypeptide also contains a nuclear localization signal motif, two transactivating domains CTAD and NTAD, and an ...
  https://en.wikipedia.org/wiki/HIF1A
*  RNA-binding protein database - Wikipedia
These domains contain a few basic modular units. Comparing with a single motif, RBPs can recognize a much longer stretch of ... the flanking helices, the β-strand and the variable loop between β2 and β3 (type I) or between α2 and β2 (type II) play a very ... The weak interaction surface is largely increased by these motifs. As the result, RBPs can bind RNA with higher specificity and ... The strategy used by zinc figure to distinguish these two type of nucleotides may contain distinct structural arrangement of ...
  https://en.wikipedia.org/wiki/RNA-binding_protein_database
*  Histone acetyltransferase - Wikipedia
It should be noted that there is a seven-stranded β-sheet that is surrounded by α-helices as well as a loop that is involved in ... Human p300 contains a highly basic loop embedded in the middle of its HAT domain that is hyperacetylated in the active form of ... but there are many structural differences in the regions flanking this central core. Overall, the structural data is consistent ... The C motif is found in most GNATs, but it is not present in the majority of other known HATs. The yeast Gcn5 (general control ...
  https://en.wikipedia.org/wiki/Histone_acetyltransferase
*  Protein domain - Wikipedia
EF hand : a helix-turn-helix structural motif found in each structural domain of the signaling protein calmodulin and in the ... For example, the β-hairpin motif consists of two adjacent antiparallel β-strands joined by a small loop. It is present in most ... Structural alignment is an important tool for determining domains. Several motifs pack together to form compact, local, semi- ... Basic Leucine zipper domain (bZIP domain) : is found in many DNA-binding eukaryotic proteins. One part of the domain contains a ...
  https://en.wikipedia.org/wiki/Protein_domain
*  Major intrinsic proteins - Wikipedia
The two conserved D-P-A motifs in the loops between TMSs 2 and 3 and TMSs 5 and 6 form the interface between the two duplicated ... motif. Aquaporins generally have the NPA motif in both halves, the glycerol facilitators generally have an NPA motif in the ... Murata, K.; Mitsuoka, K.; Hirai, T.; Walz, T.; Agre, P.; Heymann, J. B.; Engel, A.; Fujiyoshi, Y. (2000-10-05). "Structural ... small basic (SIPs) and unclassified X (XIPs) intrinsic proteins. One of the plant clusters includes only tonoplast (TIP) ...
  https://en.wikipedia.org/wiki/Major_intrinsic_proteins