• sequence
  • Based on the sequence alignment results of canonical EF-hand motifs, especially the conserved side chains directly involved in Ca2+ binding, a pattern PS00018 has been generated to predict canonical EF-hand sites. (wikipedia.org)
  • The 12-residue canonical EF-hand loop binds Ca2+ mainly via sidechain carboxylates or carbonyls (loop sequence positions 1, 3, 5, 12). (wikipedia.org)
  • The consensus sequence of this motif was more recently reported by Hanson and Whiteheart (2005) to be hhhhDE, where E denotes a glutamate residue. (wikipedia.org)
  • This structure is similar to canonical Ca 2+ -CaM-peptide complexes, although TRPV1 contains no classical CaM recognition sequence motif. (rupress.org)
  • Historically motifs were identified and analysed in an effort to understand the relationship between protein sequence and structure, to improve prediction methods. (slideserve.com)
  • It is rare to find less than five interacting parallel strands in a motif, suggesting that a smaller number of strands may be unstable, however it is also fundamentally more difficult for parallel β-sheets to form because strands with N and C termini aligned necessarily must be very distant in sequence. (wikipedia.org)
  • James D. Watson and Francis Crick described this structure as a double helix with a radius of 10 Å and pitch of 34 Å, making one complete turn about its axis every 10 bp of sequence. (wikipedia.org)
  • Genes
  • In the human genome, Myc is located on chromosome 8 and is believed to regulate expression of 15% of all genes through binding on enhancer box sequences (E-boxes) and recruiting histone acetyltransferases (HATs). (wikipedia.org)
  • Myc protein is a transcription factor that activates expression of many genes through binding enhancer box sequences (E-boxes) and recruiting histone acetyltransferases (HATs). (wikipedia.org)
  • By binding Miz-1 transcription factor and displacing the p300 co-activator, it inhibits expression of Miz-1 target genes. (wikipedia.org)
  • residue
  • Although the coordination properties remain similar with the canonical 29-residue helix-loop-helix EF-hand motif, the EF-hand-like motifs differ from EF-hands in that they contain deviations in the secondary structure of the flanking sequences and/or variation in the length of the Ca2+-coordinating loop. (wikipedia.org)
  • The 14-residue pseudo EF-hand loop chelates Ca2+ primarily via backbone carbonyls (positions 1, 4, 6, 9). (wikipedia.org)
  • For example, the semi-continuous Ca2+-binding site in D-galactose-binding protein (GBP) contains a nine-residue loop. (wikipedia.org)
  • This domain has a conserved 10-residue Ca2+-binding loop strikingly similar to the canonical 12-residue EF-hand loop. (wikipedia.org)
  • The lysine (K) residue in the Walker A motif, together with the main chain NH atoms, are crucial for nucleotide-binding. (wikipedia.org)
  • citation needed] PTPs (protein tyrosine phosphatases) that catalyse the hydrolysis of an inorganic phosphate from a phosphotyrosine residue (the reverse of a tyrosine kinase reaction) contain a motif which folds into a P-loop-like structure with an arginine in the place of the conserved lysine. (wikipedia.org)
  • Upon cleavage, the C-terminus of Myc (containing the DNA binding domain) is degraded, while Myc-nick, the N-terminal segment 298-residue segment remains in the cytoplasm. (wikipedia.org)
  • nest
  • since such a short peptide does not form an alpha helix, this suggests that it is the nest, rather than being at the N-terminus of a helix, that is the main phosphate binding feature. (wikipedia.org)
  • affinities
  • The NMR studies support our hypothesis that both ligand arrangement and dynamic properties play essential role in tuning Ca(II) binding affinities. (gsu.edu)
  • We have shown that our developed grafting approach can be applied to probe intrinsic Ca(II) binding affinities of different Ca(II) binding sites. (gsu.edu)
  • Interactions
  • The goal of this research project is to probe key determinants for calcium binding properties and pairing interactions at the site specific level using a grafting approach and high resolution NMR. (gsu.edu)
  • Because interactions with the minor groove are often mediated by the 2'-OH of the ribose sugar, this RNA motif looks very different from its DNA equivalent. (wikipedia.org)
  • structures
  • While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structure motifs that serve as molecular building blocks. (wikipedia.org)
  • Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. (wikipedia.org)
  • pathway
  • The AAV infective pathway involves the binding of the virus to a cell-surface receptor and subsequent clathrin-mediated endocytosis. (ufl.edu)
  • family
  • Secreted modular calcium binding protein-1 ( Smoc -1) belongs to the BM-40 family which has been implicated with tissue remodeling, angiogenesis and bone mineralization. (biomedcentral.com)
  • Buffalo Smoc -1 was found to encode a secreted matricellular glycoprotein containing two EF-hand calcium binding motifs homologous to that of BM-40/SPARC family. (biomedcentral.com)
  • Most members of the family are made of two homologous clusters of three transmembrane spans, separated by a central loop and assembled with an opposite orientation in the membrane. (uclouvain.be)
  • site
  • In electrophysiology studies, mutation of the Ca 2+ -CaM-binding site on TRPV1-ARD abolished desensitization in response to repeated application of capsaicin, whereas mutation of the Ca 2+ -CaM-binding site in TRPV1-CT led to a more subtle phenotype of slowed and reduced TRPV1 desensitization. (rupress.org)
  • atoms
  • The Ca2+ ion is coordinated by seven protein oxygen atoms, five of which are from the loop mimicking the canonical EF-loop whereas the other two are from the carboxylate group of a distant Glu. (wikipedia.org)
  • Additionally
  • Additionally, when treated with ParvE101Q, calcium sparks (spontaneous releases of Ca2+ from the sarcoplasmic reticulum) are not different from normal. (wikipedia.org)
  • structure
  • For example, a helix-loop-strand instead of the helix-loop-helix structure is in periplasmic galactose-binding protein (Salmonella typhimurium, PDB: 1gcg​) or alginate-binding protein (Sphingomonas sp. (wikipedia.org)
  • Here, we present the crystal structure of calcium-bound CaM (Ca 2+ -CaM) in complex with the TRPV1-CT segment, determined to 1.95-Å resolution. (rupress.org)
  • The double helix is the dominant tertiary structure for biological DNA, and is also a possible structure for RNA. (wikipedia.org)
  • Because minor groove triples are capable of stably packing a free loop and helix, they are key elements in the structure of large ribonucleotides, including the group I intron, the group II intron, and the ribosome. (wikipedia.org)
  • common
  • The most common example of a minor loop triple is the A-minor motif, or the insertion of adenosine bases into the minor groove (see above). (wikipedia.org)
  • activation
  • The influx of calcium after channel activation serves as a negative feedback mechanism leading to TRPV1 desensitization. (rupress.org)
  • However
  • However, this motif is not restricted to adenosines, as other nucleobases have also been observed to interact with the RNA minor groove. (wikipedia.org)