title: Analysis of Delta-Notch interaction by molecular modeling and molecular dynamic simulation studies.
abstract: Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch1 extracellular ligand binding domain shows the presence of 11th and 12th EGF-like repeats. Here a portion of the Drosophila Delta protein, known to interact with Notch extracellular domain, has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein-docking method using GRAMM. Molecular dynamic simulations of the modeled structures were performed. The probable structures for Delta-Notch complex have been proposed based on interaction energy parameter and planarity studies.
authors.affiliation: West Bengal State University , Berunanpukuria, P.O. Malikapur, Barasat , Kolkata, 700126, India.
authors.forename: Riddhi
authors.initials: R
authors.lastname: Majumder
authors.forename: Sujata
authors.initials: S
authors.lastname: Roy
authors.forename: Ashoke Ranjan
authors.initials: AR
authors.lastname: Thakur
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry* / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D051880:Receptors, Notch / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D051880:Receptors, Notch; C064045:delta protein