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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Models, Molecular

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Disease relevance of Models, Molecular


Psychiatry related information on Models, Molecular


High impact information on Models, Molecular

  • For the cadherins, protein zero, and CD2, additional experimental data support the insights obtained from structural analysis of their domains and molecular models of their adhesion complexes [8].
  • These findings provide a molecular model of how LTA expression may be genetically regulated by allele-specific recruitment of the transcriptional repressor ABF-1 [9].
  • Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast [10].
  • We suggest that GCN4 protein is a specific transcription factor, and we describe a molecular model for the general control of amino acid biosynthetic genes [11].
  • A molecular model of this interaction has been generated that should be useful in the design of candidate therapeutic inhibitors of CCP activation by amyloid beta-protein [12].

Chemical compound and disease context of Models, Molecular


Biological context of Models, Molecular

  • These data support a molecular model in which synaptotagmin triggers exocytosis through its interactions with membranes and the SNARE complex [18].
  • We propose the following molecular model of translocation: after the binding of EF-G.GTP, the P site-bound tRNA, by a movement of the 3'-terminal single-stranded ACCA tail, establishes an interaction with 23S rRNA in the adjacent E site, thereby initiating the tRNA transfer from the P site to the E site and promoting GTP hydrolysis [19].
  • The contributions to ligand binding by individual residues were determined in two designs by alanine-scanning mutagenesis, and are consistent with the molecular models [20].
  • A molecular model of Ca(V)1.2 indicates that Ser-1142 is unlikely to be phosphorylated, and thus we conclude that BayK binding stabilizes mode 2 gating allosterically by either protecting a phospho Ser/Thr on the alpha(1)C subunit or mimicking phosphorylation at that site [21].
  • Myosin-V stepping kinetics: a molecular model for processivity [22].

Anatomical context of Models, Molecular


Associations of Models, Molecular with chemical compounds

  • In this article, we propose a molecular model for NF2 protein (merlin) function in the light of these and related new findings [28].
  • This article reviews the basis for these molecular cysteine switches, drawing on the NMDA receptor as an exemplary protein, and proposes a molecular model for the action of S-nitrosylation based on recently derived crystal structures [29].
  • This relationship is consistent with more than two thirds of the energy yielded by glucose oxidation being used to support events associated with glutamate neurotransmission, and it supports a molecular model of a stoichiometric coupling between glutamate neurotransmission and functional glucose oxidation [30].
  • A molecular model of the excitatory postsynaptic membrane is given in terms of two biochemical cycles intimately associated: an acetylcholine cycle and a calcium cycle [31].
  • We used this specificity, and a molecular model of an integrin beta tail-PTB domain interaction to predict critical interacting residues [32].

Gene context of Models, Molecular

  • Extensive heterologous studies of homomeric CNGA2 channels have led to a molecular model of channel modulation based on the binding of calcium-calmodulin to a site on the cytoplasmic amino terminus of CNGA2 [33].
  • Genetic and molecular studies of touch avoidance in the nematode Caenorhabditis elegans have resulted in a molecular model for a mechanotransducing complex. mec-4 and mec-10 encode proteins hypothesized to be subunits of a mechanically gated ion channel that are related to subunits of the vertebrate amiloride-sensitive epithelial Na+ channel [34].
  • Our results support a molecular model in which bivalent NHERF PDZ domains regulate channel gating by crosslinking the C-terminal tails in a single dimeric CFTR channel, and the magnitude of this regulation is coupled to the stoichiometry of these interactions [35].
  • The molecular model suggests that a rotation of TM3 may be important for activation of the MC4R [36].
  • Based on the structure of the closely related lymphotoxin alpha-tumor necrosis factor receptor I complex, a molecular model of the FasL homotrimer bound to three Fas molecules was generated using knowledge-based protein modeling methods [37].

Analytical, diagnostic and therapeutic context of Models, Molecular


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  10. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Hecht, A., Laroche, T., Strahl-Bolsinger, S., Gasser, S.M., Grunstein, M. Cell (1995) [Pubmed]
  11. GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: implications for general control of amino acid biosynthetic genes in yeast. Hope, I.A., Struhl, K. Cell (1985) [Pubmed]
  12. Aspartate residue 7 in amyloid beta-protein is critical for classical complement pathway activation: implications for Alzheimer's disease pathogenesis. Velazquez, P., Cribbs, D.H., Poulos, T.L., Tenner, A.J. Nat. Med. (1997) [Pubmed]
  13. A molecular model of the inducer binding domain of the galactose repressor of Escherichia coli. Hsieh, M., Hensley, P., Brenowitz, M., Fetrow, J.S. J. Biol. Chem. (1994) [Pubmed]
  14. A detailed structural description of Escherichia coli succinyl-CoA synthetase. Fraser, M.E., James, M.N., Bridger, W.A., Wolodko, W.T. J. Mol. Biol. (1999) [Pubmed]
  15. Systematic site-directed mutagenesis of human protein SRP54: interactions with signal recognition particle RNA and modes of signal peptide recognition. Huang, Q., Abdulrahman, S., Yin, J., Zwieb, C. Biochemistry (2002) [Pubmed]
  16. Requirement of multiple phage displayed peptide libraries for optimal mapping of a conformational antibody epitope on CCR5. O'Connor, K.H., Königs, C., Rowley, M.J., Irving, J.A., Wijeyewickrema, L.C., Pustowka, A., Dietrich, U., Mackay, I.R. J. Immunol. Methods (2005) [Pubmed]
  17. Extracellular acidosis modulates drug block of Kv4.3 currents by flecainide and quinidine. Singarayar, S., Bursill, J., Wyse, K., Bauskin, A., Wu, W., Vandenberg, J., Breit, S., Campbell, T. J. Cardiovasc. Electrophysiol. (2003) [Pubmed]
  18. Kinetics of synaptotagmin responses to Ca2+ and assembly with the core SNARE complex onto membranes. Davis, A.F., Bai, J., Fasshauer, D., Wolowick, M.J., Lewis, J.L., Chapman, E.R. Neuron (1999) [Pubmed]
  19. Binding of the 3' terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation. Lill, R., Robertson, J.M., Wintermeyer, W. EMBO J. (1989) [Pubmed]
  20. Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Allert, M., Rizk, S.S., Looger, L.L., Hellinga, H.W. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  21. Modulation of cardiac Ca(V)1.2 channels by dihydropyridine and phosphatase inhibitor requires Ser-1142 in the domain III pore loop. Erxleben, C., Gomez-Alegria, C., Darden, T., Mori, Y., Birnbaumer, L., Armstrong, D.L. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  22. Myosin-V stepping kinetics: a molecular model for processivity. Rief, M., Rock, R.S., Mehta, A.D., Mooseker, M.S., Cheney, R.E., Spudich, J.A. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  23. Metaphyseal chondrodysplasia type Schmid mutations are predicted to occur in two distinct three-dimensional clusters within type X collagen NC1 domains that retain the ability to trimerize. Marks, D.S., Gregory, C.A., Wallis, G.A., Brass, A., Kadler, K.E., Boot-Handford, R.P. J. Biol. Chem. (1999) [Pubmed]
  24. Subtype-specific interactions of type C staphylococcal enterotoxins with the T-cell receptor. Deringer, J.R., Ely, R.J., Stauffacher, C.V., Bohach, G.A. Mol. Microbiol. (1996) [Pubmed]
  25. Enzymes of the mast cell granule. Schwartz, L.B., Austen, K.F. J. Invest. Dermatol. (1980) [Pubmed]
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  27. Short- and long-term effects of ciliary neurotrophic factor on androgen-sensitive motoneurons in the lumbar spinal cord. Bengston, L., Lopez, V., Watamura, S., Forger, N.G. J. Neurobiol. (1996) [Pubmed]
  28. Merlin: hanging tumor suppression on the Rac. Sherman, L.S., Gutmann, D.H. Trends Cell Biol. (2001) [Pubmed]
  29. Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation. Lipton, S.A., Choi, Y.B., Takahashi, H., Zhang, D., Li, W., Godzik, A., Bankston, L.A. Trends Neurosci. (2002) [Pubmed]
  30. In vivo NMR studies of the glutamate neurotransmitter flux and neuroenergetics: implications for brain function. Rothman, D.L., Behar, K.L., Hyder, F., Shulman, R.G. Annu. Rev. Physiol. (2003) [Pubmed]
  31. Molecular model of postsynaptic potential. Dubois, D.M., Schoffeniels, E. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  32. Integrin beta cytoplasmic domain interactions with phosphotyrosine-binding domains: a structural prototype for diversity in integrin signaling. Calderwood, D.A., Fujioka, Y., de Pereda, J.M., García-Alvarez, B., Nakamoto, T., Margolis, B., McGlade, C.J., Liddington, R.C., Ginsberg, M.H. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  33. Calmodulin permanently associates with rat olfactory CNG channels under native conditions. Bradley, J., Bönigk, W., Yau, K.W., Frings, S. Nat. Neurosci. (2004) [Pubmed]
  34. Molecular modeling of mechanotransduction in the nematode Caenorhabditis elegans. Tavernarakis, N., Driscoll, M. Annu. Rev. Physiol. (1997) [Pubmed]
  35. Regulation of cystic fibrosis transmembrane conductance regulator single-channel gating by bivalent PDZ-domain-mediated interaction. Raghuram, V., Mak, D.D., Foskett, J.K. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  36. High affinity agonistic metal ion binding sites within the melanocortin 4 receptor illustrate conformational change of transmembrane region 3. Lagerström, M.C., Klovins, J., Fredriksson, R., Fridmanis, D., Haitina, T., Ling, M.K., Berglund, M.M., Schiöth, H.B. J. Biol. Chem. (2003) [Pubmed]
  37. Characterization of Fas (Apo-1, CD95)-Fas ligand interaction. Schneider, P., Bodmer, J.L., Holler, N., Mattmann, C., Scuderi, P., Terskikh, A., Peitsch, M.C., Tschopp, J. J. Biol. Chem. (1997) [Pubmed]
  38. Structure comparison of human glioma pathogenesis-related protein GliPR and the plant pathogenesis-related protein P14a indicates a functional link between the human immune system and a plant defense system. Szyperski, T., Fernández, C., Mumenthaler, C., Wüthrich, K. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  39. Probing the ligand-binding domain of the mGluR4 subtype of metabotropic glutamate receptor. Hampson, D.R., Huang, X.P., Pekhletski, R., Peltekova, V., Hornby, G., Thomsen, C., Thøgersen, H. J. Biol. Chem. (1999) [Pubmed]
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