1thv Citations

Structures of three crystal forms of the sweet protein thaumatin.

Acta Crystallogr D Biol Crystallogr 50 813-25 (1994)
Related entries: 1thu, 1thw

Cited: 37 times
EuropePMC logo PMID: 15299348

Abstract

Three crystal forms of the sweet-tasting protein thaumatin from the African berry Thaumatococcus daniellii have been grown. These include two naturally occurring isoforms, A and B, that differ by a single amino acid, and a recombinant form of isoform B expressed in yeast. The crystals are of space groups C2 with a = 117.7, b = 44.9, c = 38.0 A, and beta = 94.0 degrees, P2(1)2(1)2(1) with a = 44.3, b = 63.7 and c = 72.7 A, and a tetragonal form P4(1)2(1)2 with a = b = 58.6 and c = 151.8 A. The structures of all three crystals have been solved by molecular replacement and subsequently refined to R factors of 0.184 for the monoclinic at 2.6 A, 0.165 for the orthorhombic at 1.75 A, and 0.181 for the tetragonal, also at 1.75 A resolution. No solvent was included in the monoclinic crystal while 123 and 105 water molecules were included in the higher resolution orthorhombic and tetragonal structures, respectively. A bound tartrate molecule was also clearly visible in the tetragonal structure. The r.m.s. deviations between molecular structures in the three crystals range from 0.6 to 0.7 A for Calpha atoms, and 1.1 to 1.3 A for all atoms. This is comparable to the r.m.s. deviation between the three structures and the starting model. Nevertheless, several peptide loops show particularly large variations from the initial model.

Articles - 1thv mentioned but not cited (9)

  1. A graph-theory algorithm for rapid protein side-chain prediction. Canutescu AA, Shelenkov AA, Dunbrack RL. Protein Sci 12 2001-2014 (2003)
  2. Side-chain modeling with an optimized scoring function. Liang S, Grishin NV. Protein Sci 11 322-331 (2002)
  3. Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library. Peterson RW, Dutton PL, Wand AJ. Protein Sci 13 735-751 (2004)
  4. Averaged kick maps: less noise, more signal... and probably less bias. Pražnikar J, Afonine PV, Guncar G, Adams PD, Turk D. Acta Crystallogr D Biol Crystallogr 65 921-931 (2009)
  5. One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Marshall SA, Vizcarra CL, Mayo SL. Protein Sci 14 1293-1304 (2005)
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  7. Predicting protein function from structure: unique structural features of proteases. Stawiski EW, Baucom AE, Lohr SC, Gregoret LM. Proc Natl Acad Sci U S A 97 3954-3958 (2000)
  8. A Saccharomyces cerevisiae assay system to investigate ligand/AdipoR1 interactions that lead to cellular signaling. Aouida M, Kim K, Shaikh AR, Pardo JM, Eppinger J, Yun DJ, Bressan RA, Narasimhan ML. PLoS One 8 e65454 (2013)
  9. A model for protein sequence evolution based on selective pressure for protein stability: application to hemoglobins. Marsh L. Evol Bioinform Online 5 107-118 (2009)


Reviews citing this publication (3)

  1. Protein folds in the all-beta and all-alpha classes. Chothia C, Hubbard T, Brenner S, Barns H, Murzin A. Annu Rev Biophys Biomol Struct 26 597-627 (1997)
  2. Developments in biotechnological production of sweet proteins. Masuda T, Kitabatake N. J Biosci Bioeng 102 375-389 (2006)
  3. Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology. Vergara A, Lorber B, Sauter C, Giegé R, Zagari A. Biophys Chem 118 102-112 (2005)

Articles citing this publication (25)

  1. Structural studies of the giant mimivirus. Xiao C, Kuznetsov YG, Sun S, Hafenstein SL, Kostyuchenko VA, Chipman PR, Suzan-Monti M, Raoult D, McPherson A, Rossmann MG. PLoS Biol 7 e92 (2009)
  2. Searching for silver bullets: an alternative strategy for crystallizing macromolecules. McPherson A, Cudney B. J Struct Biol 156 387-406 (2006)
  3. Solution structure of the thermostable sweet-tasting protein brazzein. Caldwell JE, Abildgaard F, Dzakula Z, Ming D, Hellekant G, Markley JL. Nat Struct Biol 5 427-431 (1998)
  4. Prediction of protein residue contacts with a PDB-derived likelihood matrix. Singer MS, Vriend G, Bywater RP. Protein Eng 15 721-725 (2002)
  5. Molecular resolution imaging of macromolecular crystals by atomic force microscopy. Kuznetsov YuG, Malkin AJ, Land TA, DeYoreo JJ, Barba AP, Konnert J, McPherson A. Biophys J 72 2357-2364 (1997)
  6. Atomic force microscopy investigation of vaccinia virus structure. Kuznetsov Y, Gershon PD, McPherson A. J Virol 82 7551-7566 (2008)
  7. Morphogenesis of mimivirus and its viral factories: an atomic force microscopy study of infected cells. Kuznetsov YG, Klose T, Rossmann M, McPherson A. J Virol 87 11200-11213 (2013)
  8. Structure, mechanistic action, and essential residues of a GH-64 enzyme, laminaripentaose-producing beta-1,3-glucanase. Wu HM, Liu SW, Hsu MT, Hung CL, Lai CC, Cheng WC, Wang HJ, Li YK, Wang WC. J Biol Chem 284 26708-26715 (2009)
  9. Correlation of the sweetness of variants of the protein brazzein with patterns of hydrogen bonds detected by NMR spectroscopy. Assadi-Porter FM, Abildgaard F, Blad H, Markley JL. J Biol Chem 278 31331-31339 (2003)
  10. Structure-sweetness relationship in egg white lysozyme: role of lysine and arginine residues on the elicitation of lysozyme sweetness. Masuda T, Ide N, Kitabatake N. Chem Senses 30 667-681 (2005)
  11. Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus. Kuznetsov YG, Dowell JJ, Gavira JA, Ng JD, McPherson A. Nucleic Acids Res 38 8284-8294 (2010)
  12. A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction. Pompidor G, Maury O, Vicat J, Kahn R. Acta Crystallogr D Biol Crystallogr 66 762-769 (2010)
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  14. cDNA sequences, MALDI-TOF analyses, and molecular modelling of barley PR-5 proteins. Reiss E, Schlesier B, Brandt W. Phytochemistry 67 1856-1864 (2006)
  15. Investigation of bacteriophage T4 by atomic force microscopy. Kuznetsov YG, Chang SC, McPherson A. Bacteriophage 1 165-173 (2011)
  16. The recognition mechanism of triple-helical β-1,3-glucan by a β-1,3-glucanase. Qin Z, Yang D, You X, Liu Y, Hu S, Yan Q, Yang S, Jiang Z. Chem Commun (Camb) 53 9368-9371 (2017)
  17. Glass-to-cryogenic-liquid transitions in aqueous solutions suggested by crack healing. Kim CU, Tate MW, Gruner SM. Proc Natl Acad Sci U S A 112 11765-11770 (2015)
  18. Structural analysis of a Synechococcus myovirus S-CAM4 and infected cells by atomic force microscopy. Kuznetsov YG, Martiny JB, McPherson A. J Gen Virol 91 3095-3104 (2010)
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  20. Efficient cryoprotection of macromolecular crystals using vapor diffusion of volatile alcohols. Farley C, Juers DH. J Struct Biol 188 102-106 (2014)
  21. Investigation into the binding of dyes within protein crystals. McPherson A, Larson SB. Acta Crystallogr F Struct Biol Commun 74 593-602 (2018)
  22. Use of dual polarization interferometry as a diagnostic tool for protein crystallization. Boudjemline A, Saridakis E, Swann MJ, Govada L, Mavridis IM, Chayen NE. Anal Chem 83 7881-7887 (2011)
  23. Nano-fibers produced by viral infection of amoeba visualized by atomic force microscopy. Kuznetsov YG, McPherson A. Biopolymers 95 234-239 (2011)
  24. Positive Charges on the Surface of Thaumatin Are Crucial for the Multi-Point Interaction with the Sweet Receptor. Masuda T, Kigo S, Mitsumoto M, Ohta K, Suzuki M, Mikami B, Kitabatake N, Tani F. Front Mol Biosci 5 10 (2018)
  25. Identification of the Active Principle Conferring Anti-Inflammatory and Antinociceptive Properties in Bamboo Plant. Araujo Sousa B, Nascimento Silva O, Farias Porto W, Lima Rocha T, Paulino Silva L, Ferreira Leal AP, Buccini DF, Oluwagbamigbe Fajemiroye J, de Araujo Caldas R, Franco OL, Grossi-de-Sá MF, de la Fuente Nunez C, Moreno SE. Molecules 26 3054 (2021)