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

Models, Structural

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Disease relevance of Models, Structural


High impact information on Models, Structural


Chemical compound and disease context of Models, Structural


Biological context of Models, Structural

  • I-Abm12 differs from I-Ab by three amino acid replacements in the A beta chain, and the proposed structural model of the I-Abm12 molecule places these three amino acid substitutions along one of the alpha-helices where they may affect both antigen and TCR binding [16].
  • These results provide a focus for unraveling the many biochemical pathways implicated in integrin activation and suggest a general structural model for the connections between integrins and diverse cellular signal transduction pathways [17].
  • The 4,140-residue predicted amino acid sequence (466,481 D) is consistent with a three-domain structural model in which a long central rod domain, having mainly an alpha-helical coiled coil conformation, is flanked by globular NH2- and COOH-terminal domains [18].
  • A structural model of the UNC-86 POU domain, including base pairs and amino acid residues required for MEC-3 interaction, revealed that P145 and L195 are part of a hydrophobic pocket which is similar to the OCA-B-binding domain of the mammalian POU protein, Oct-1 [19].
  • A detailed structural model of cytotactin: protein homologies, alternative RNA splicing, and binding regions [20].

Anatomical context of Models, Structural


Associations of Models, Structural with chemical compounds

  • Structural models for the metal centers in the nitrogenase molybdenum-iron protein [26].
  • The following article reviews how the resemblance between these two protein families led to computer-assisted structural models of crucial elements involved in ligand binding by various glutamate receptors [27].
  • In structural models, this ectodomain is composed of two cysteine clusters flanking nine leucine-rich repeats (LRRs) [28].
  • A structural model of the bovine tRNA is presented based on the results of this chemical probing, on a comparison between nine homologous 'truncated cloverleaf' secondary structures and on analogies with the crystal structure of yeast phenylalanine tRNA [29].
  • Alignment of the functional results with the 3D structure of an acetylcholine receptor allowed us to generate structural models accounting for the closed and open pore conformations and for a gating mechanism of a Cys-loop receptor [30].

Gene context of Models, Structural

  • The structure was used to model the homologous domain 2, the other half of the GDNF-binding fragment, and to construct the first structural model of the GDNF-GFRalpha1 interaction [31].
  • These observations suggest a structural model of GCN4 protein in which a dimer binds to overlapping and non-identical half-sites, explaining why GCN4 recognition sites act bidirectionally in stimulating transcription [32].
  • When these residues are mapped on a structural model of hGH, they form a patch that overlaps but is not identical to that previously determined for the hGH receptor [33].
  • A structural model for this quaternary complex is presented in which the C-terminal sequence of p21 acts like double-sided tape and docks to both the PCNA and cyclin molecules [34].
  • Thus, a tertiary structural model of human GALNS was constructed from the X-ray crystal structure of N -acetylgalacto-samine-4-sulfatase and arylsulfatase A, using homology modeling, and 32 missense mutations were investigated [35].

Analytical, diagnostic and therapeutic context of Models, Structural


  1. A structural model for the HIV-1 Rev-RRE complex deduced from altered-specificity rev variants isolated by a rapid genetic strategy. Jain, C., Belasco, J.G. Cell (1996) [Pubmed]
  2. Proposed three-dimensional structure for the cellular prion protein. Huang, Z., Gabriel, J.M., Baldwin, M.A., Fletterick, R.J., Prusiner, S.B., Cohen, F.E. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  3. Characterization of a limited trypsin digestion form of eukaryotic elongation factor 1 alpha. Kinzy, T.G., Merrick, W.C. J. Biol. Chem. (1991) [Pubmed]
  4. Effects of zidovudine-selected human immunodeficiency virus type 1 reverse transcriptase amino acid substitutions on processive DNA synthesis and viral replication. Caliendo, A.M., Savara, A., An, D., DeVore, K., Kaplan, J.C., D'Aquila, R.T. J. Virol. (1996) [Pubmed]
  5. A structural model of rubredoxin from Desulfovibrio vulgaris at 2 A resolution. Adman, E.T., Sieker, L.C., Jensen, L.H., Bruschi, M., Le Gall, J. J. Mol. Biol. (1977) [Pubmed]
  6. Protein-protein communication: structural model of the repression complex formed by CytR and the global regulator CRP. Kallipolitis, B.H., Nørregaard-Madsen, M., Valentin-Hansen, P. Cell (1997) [Pubmed]
  7. Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Stark, H., Dube, P., Lührmann, R., Kastner, B. Nature (2001) [Pubmed]
  8. A copper cofactor for the ethylene receptor ETR1 from Arabidopsis. Rodríguez, F.I., Esch, J.J., Hall, A.E., Binder, B.M., Schaller, G.E., Bleecker, A.B. Science (1999) [Pubmed]
  9. Localization of an exchangeable GTP binding site at the plus end of microtubules. Mitchison, T.J. Science (1993) [Pubmed]
  10. Where plants make oxygen: a structural model for the photosynthetic oxygen-evolving manganese cluster. Yachandra, V.K., DeRose, V.J., Latimer, M.J., Mukerji, I., Sauer, K., Klein, M.P. Science (1993) [Pubmed]
  11. Selection and immunochemical analysis of lipooligosaccharide mutants of Neisseria gonorrhoeae. Dudas, K.C., Apicella, M.A. Infect. Immun. (1988) [Pubmed]
  12. Nucleotide sequence of bovine herpesvirus type 1 glycoprotein gIII, a structural model for gIII as a new member of the immunoglobulin superfamily, and implications for the homologous glycoproteins of other herpesviruses. Fitzpatrick, D.R., Babiuk, L.A., Zamb, T.J. Virology (1989) [Pubmed]
  13. Succinyl-CoA:3-ketoacid CoA transferase (SCOT): cloning of the human SCOT gene, tertiary structural modeling of the human SCOT monomer, and characterization of three pathogenic mutations. Fukao, T., Mitchell, G.A., Song, X.Q., Nakamura, H., Kassovska-Bratinova, S., Orii, K.E., Wraith, J.E., Besley, G., Wanders, R.J., Niezen-Koning, K.E., Berry, G.T., Palmieri, M., Kondo, N. Genomics (2000) [Pubmed]
  14. Effects of indomethacin in utero on the pulmonary vasculature of the newborn guinea pig. Demello, D.E., Murphy, J.D., Aronovitz, M.J., Davies, P., Reid, L.M. Pediatr. Res. (1987) [Pubmed]
  15. UMP kinase from the Gram-positive bacterium Bacillus subtilis is strongly dependent on GTP for optimal activity. Gagyi, C., Bucurenci, N., Sîrbu, O., Labesse, G., Ionescu, M., Ofiteru, A., Assairi, L., Landais, S., Danchin, A., Bârzu, O., Gilles, A.M. Eur. J. Biochem. (2003) [Pubmed]
  16. The contribution of mutant amino acids to alloantigenicity. Bill, J., Ronchese, F., Germain, R.N., Palmer, E. J. Exp. Med. (1989) [Pubmed]
  17. The talin-tail interaction places integrin activation on FERM ground. Campbell, I.D., Ginsberg, M.H. Trends Biochem. Sci. (2004) [Pubmed]
  18. Cloning and sequencing of rat plectin indicates a 466-kD polypeptide chain with a three-domain structure based on a central alpha-helical coiled coil. Wiche, G., Becker, B., Luber, K., Weitzer, G., Castañon, M.J., Hauptmann, R., Stratowa, C., Stewart, M. J. Cell Biol. (1991) [Pubmed]
  19. Protein interaction surface of the POU transcription factor UNC-86 selectively used in touch neurons. Röhrig, S., Röckelein, I., Donhauser, R., Baumeister, R. EMBO J. (2000) [Pubmed]
  20. A detailed structural model of cytotactin: protein homologies, alternative RNA splicing, and binding regions. Jones, F.S., Hoffman, S., Cunningham, B.A., Edelman, G.M. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  21. Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: a new interaction between old partners. Marintchev, A., Kolupaeva, V.G., Pestova, T.V., Wagner, G. Proc. Natl. Acad. Sci. U.S.A. (2003) [Pubmed]
  22. Existence of two heme B centers in cytochrome b561 from bovine adrenal chromaffin vesicles as revealed by a new purification procedure and EPR spectroscopy. Tsubaki, M., Nakayama, M., Okuyama, E., Ichikawa, Y., Hori, H. J. Biol. Chem. (1997) [Pubmed]
  23. A structural model of human erythrocyte protein 4.1. Leto, T.L., Marchesi, V.T. J. Biol. Chem. (1984) [Pubmed]
  24. Biogenesis of caveolae: a structural model for caveolin-induced domain formation. Parton, R.G., Hanzal-Bayer, M., Hancock, J.F. J. Cell. Sci. (2006) [Pubmed]
  25. The ring of the rhodopsin chromophore in a hydrophobic activation switch within the binding pocket. Spooner, P.J., Sharples, J.M., Goodall, S.C., Bovee-Geurts, P.H., Verhoeven, M.A., Lugtenburg, J., Pistorius, A.M., Degrip, W.J., Watts, A. J. Mol. Biol. (2004) [Pubmed]
  26. Structural models for the metal centers in the nitrogenase molybdenum-iron protein. Kim, J., Rees, D.C. Science (1992) [Pubmed]
  27. The macro- and microarchitectures of the ligand-binding domain of glutamate receptors. Paas, Y. Trends Neurosci. (1998) [Pubmed]
  28. Glycoprotein hormone receptors: determinants in leucine-rich repeats responsible for ligand specificity. Smits, G., Campillo, M., Govaerts, C., Janssens, V., Richter, C., Vassart, G., Pardo, L., Costagliola, S. EMBO J. (2003) [Pubmed]
  29. A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem. de Bruijn, M.H., Klug, A. EMBO J. (1983) [Pubmed]
  30. Pore conformations and gating mechanism of a Cys-loop receptor. Paas, Y., Gibor, G., Grailhe, R., Savatier-Duclert, N., Dufresne, V., Sunesen, M., de Carvalho, L.P., Changeux, J.P., Attali, B. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  31. The structure of GFRalpha1 domain 3 reveals new insights into GDNF binding and RET activation. Leppänen, V.M., Bespalov, M.M., Runeberg-Roos, P., Puurand, U., Merits, A., Saarma, M., Goldman, A. EMBO J. (2004) [Pubmed]
  32. GCN4, a eukaryotic transcriptional activator protein, binds as a dimer to target DNA. Hope, I.A., Struhl, K. EMBO J. (1987) [Pubmed]
  33. Rational design of receptor-specific variants of human growth hormone. Cunningham, B.C., Wells, J.A. Proc. Natl. Acad. Sci. U.S.A. (1991) [Pubmed]
  34. Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design. Kontopidis, G., Wu, S.Y., Zheleva, D.I., Taylor, P., McInnes, C., Lane, D.P., Fischer, P.M., Walkinshaw, M.D. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  35. Biochemical and structural analysis of missense mutations in N-acetylgalactosamine-6-sulfate sulfatase causing mucopolysaccharidosis IVA phenotypes. Sukegawa, K., Nakamura, H., Kato, Z., Tomatsu, S., Montaño, A.M., Fukao, T., Toietta, G., Tortora, P., Orii, T., Kondo, N. Hum. Mol. Genet. (2000) [Pubmed]
  36. Architecture of CRM1/Exportin1 suggests how cooperativity is achieved during formation of a nuclear export complex. Petosa, C., Schoehn, G., Askjaer, P., Bauer, U., Moulin, M., Steuerwald, U., Soler-López, M., Baudin, F., Mattaj, I.W., Müller, C.W. Mol. Cell (2004) [Pubmed]
  37. A novel heme protein, the Cu,Zn-superoxide dismutase from Haemophilus ducreyi. Pacello, F., Langford, P.R., Kroll, J.S., Indiani, C., Smulevich, G., Desideri, A., Rotilio, G., Battistoni, A. J. Biol. Chem. (2001) [Pubmed]
  38. Mechanism of membrane binding of the phospholipase D1 PX domain. Stahelin, R.V., Ananthanarayanan, B., Blatner, N.R., Singh, S., Bruzik, K.S., Murray, D., Cho, W. J. Biol. Chem. (2004) [Pubmed]
  39. Sequences required for the activity of PTOX (IMMUTANS), a plastid terminal oxidase: in vitro and in planta mutagenesis of iron-binding sites and a conserved sequence that corresponds to Exon 8. Fu, A., Park, S., Rodermel, S. J. Biol. Chem. (2005) [Pubmed]
  40. Neutron diffraction study of a phenol.nitroxide radical adduct: a structural model for hydrogen atom abstraction by peroxyl radicals from vitamin E and related phenolic antioxidants. Ahrens, B., Davidson, M.G., Forsyth, V.T., Mahon, M.F., Johnson, A.L., Mason, S.A., Price, R.D., Raithby, P.R. J. Am. Chem. Soc. (2001) [Pubmed]
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