Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations

BMC Structural Biology

Volumn 11, Issue , 2011, Pages

  Bernini, Andrea ^a   Spiga, Ottavia ^a   Consonni, Roberto ^b   Arosio, Ivana ^b   Fusi, Paola ^c   Cirri, Simone ^a   Guagliardi, Annamaria ^d   Niccolai, Neri ^a  

^a UNIVERSITY OF SIENA   (Italy)

^b CNR   (Italy)

^c UNIVERSITY OF MILANO BICOCCA   (Italy)

^d UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL PROTEIN; PROTEIN SSOD7; UNCLASSIFIED DRUG; DNA; DNA BINDING PROTEIN; SSO7D PROTEIN, SULFOLOBUS; WATER;

ARTICLE; HYDRATION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN LOCALIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE; SULFOLOBUS SOLFATARICUS; CHEMISTRY; HYDROGEN BOND; METABOLISM; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ARCHAEA;

ARCHAEAL PROTEINS; DATABASES, PROTEIN; DNA; DNA-BINDING PROTEINS; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; WATER;

EID: 80054725364     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-11-44     Document Type: Article

References (39)

1. Prion and water: tight and dynamical hydration sites have a key role in structural stability. De Simone A, Dodson GG, Verma CS, Zagari A, Fraternali F, Proceedings of the National Academy of Sciences of the United States of America 2005 102 21 7535 7540 10.1073/pnas.0501748102 15894615 (Pubitemid 40741006)
2. Dissection of complex protein dynamics in human thioredoxin. Qiu W, Wang L, Lu W, Boechler A, Sanders DA, Zhong D, Proceedings of the National Academy of Sciences of the United States of America 2007 104 13 5366 5371 10.1073/pnas.0608498104 17369362 (Pubitemid 47175686)
3. Adhesive water networks facilitate binding of protein interfaces. Ahmad M, Gu W, Geyer T, Helms V, Nat Commun 2011 2 261 21448160
4. A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment. Lounnas V, Pettitt BM, Proteins 1994 18 2 133 147 10.1002/prot.340180206 8159663 (Pubitemid 24055076)
5. Water: now you see it, now you don't. Levitt M, Park BH, Structure 1993 1 4 223 226 10.1016/0969-2126(93)90011-5 8081736 (Pubitemid 2031109)
6. Multiple solvent crystal structures: probing binding sites, plasticity and hydration. Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, Petsko GA, Ringe D, Journal of molecular biology 2006 357 5 1471 1482 10.1016/j.jmb.2006.01.039 16488429
7. Magnetic relaxation dispersion studies of biomolecular solutions. Halle B, Denisov VP, Methods in enzymology 2001 338 178 201 11460548 (Pubitemid 32666579)
8. Dynamics of protein and peptide hydration. Halle B, Modig K, Liepinsh E, Otting G, J Am Chem Soc 2004 126 1 102 114 10.1021/ja038325d 14709075 (Pubitemid 38090353)
9. NMR studies of water bound to biological molecules. Otting G, Progress in Nuclear Magnetic Resonance Spectroscopy 1997 31 259 285 10.1016/S0079-6565(97) 00012-5 (Pubitemid 127427696)
10. Homonuclear 1D and 2D NMR Experiments for the Observation of Solvent-Solute Interactions. Dalvit C, Journal of Magnetic Resonance, Series B 1996 112 3 282 288 10.1006/jmrb.1996.0143 (Pubitemid 126758736)
11. Water-protein NOEs: Optimized scheme for selective water excitation. Liepinsh E, Otting G, J Biomol Nmr 1999 13 1 73 76 10.1023/A:1008375214604 21080265 (Pubitemid 29089242)
12. High-resolution protein hydration NMR experiments: probing how protein surfaces interact with water and other non-covalent ligands. Huang H, Melacini G, Anal Chim Acta 2006 564 1 1 9 10.1016/j.aca.2005.10.049 17723356
13. Protein hydration in aqueous solution. Otting G, Liepinsh E, Wuthrich K, Science (New York, NY 1991 254 5034 974 980 10.1126/science.1948083 (Pubitemid 21917420)
14. Atomic and residue hydrophilicity in the context of folded protein structures. Kuhn LA, Swanson CA, Pique ME, Tainer JA, Getzoff ED, Proteins-Structure Function and Genetics 1995 23 4 536 547 10.1002/prot. 340230408 (Pubitemid 26009516)
15. NMR studies of protein hydration and TEMPOL accessibility. Niccolai N, Spiga O, Bernini A, Scarselli M, Ciutti A, Fiaschi I, Chiellini S, Molinari H, Temussi PA, Journal of molecular biology 2003 332 2 437 447 10.1016/S0022- 2836(03)00852-0 12948493 (Pubitemid 37013511)
16. MD and NMR studies of alpha-bungarotoxin surface accessibility. Venditti V, Bernini A, De Simone A, Spiga O, Prischi F, Niccolai N, Biochem Bioph Res Co 2007 356 1 114 117 10.1016/j.bbrc.2007.02.094 (Pubitemid 46413137)
17. NMR studies of protein surface accessibility. Niccolai N, Ciutti A, Spiga O, Scarselli M, Bernini A, Bracci L, Di Maro D, Dalvit C, Molinari H, Esposito G, et al. The Journal of biological chemistry 2001 276 45 42455 42461 10.1074/jbc.M107387200 11546818 (Pubitemid 37371157)
18. Probing protein surface accessibility with solvent and paramagnetic molecules. Bernini A, Venditti V, Spiga O, Niccolai N, Progress in Nuclear Magnetic Resonance Spectroscopy 2009 54 3-4 278 289 10.1016/j.pnmrs.2008.10.003
19. Toward the understanding of MNEI sweetness from hydration map surfaces. De Simone A, Spadaccini R, Temussi PA, Fraternali F, Biophys J 2006 90 9 3052 3061 10.1529/biophysj.105.073171 16461400
20. Structural characterization of the functional regions in the archaeal protein Sso7d. Renzone G, Vitale RM, Scaloni A, Rossi M, Amodeo P, Guagliardi A, Proteins 2007 67 1 189 197 10.1002/prot.21220 17243156 (Pubitemid 46340138)
21. Structural determinants responsible for the thermostability of Sso7d and its single point mutants. Consonni R, Arosio I, Recca T, Fusi P, Zetta L, Proteins 2007 67 3 766 775 10.1002/prot.21256 17340638 (Pubitemid 46625591)
22. Reversion of protein aggregation mediated by Sso7d in cell extracts of Sulfolobus solfataricus. Guagliardi A, Mancusi L, Rossi M, The Biochemical journal 2004 381 Pt 1 249 255 15025558 (Pubitemid 38932231)
23. The Sso7d protein of Sulfolobus solfataricus: in vitro relationship among different activities. Guagliardi A, Cerchia L, Rossi M, Archaea (Vancouver, BC 2002 1 2 87 93 (Pubitemid 38871650)
24. NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd(III)(DTPA-BMA) as paramagnetic probes. Bernini A, Venditti V, Spiga O, Ciutti A, Prischi F, Consonni R, Zetta L, Arosio I, Fusi P, Guagliardi A, et al. Biophys Chem 2008 137 2-3 71 75 10.1016/j.bpc.2008.07.003 18678440
25. Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs. Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH, J Mol Biol 2000 303 3 395 403 10.1006/jmbi.2000.4112 11031116
26. The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L, McCrary BS, Edmondson SP, Shriver JW, Wang AH, Nat Struct Biol 1998 5 9 782 786 10.1038/1822 9731772 (Pubitemid 28402081)
27. Solution Structure and DNA-Binding Properties of a Thermostable Protein from the Archaeon Sulfolobus-Solfataricus. Baumann H, Knapp S, Lundback T, Ladenstein R, Hard T, Nature Structural Biology 1994 1 11 808 819 10.1038/nsb1194-808 7634092 (Pubitemid 2151170)
28. A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core. Consonni R, Santomo L, Fusi P, Tortora P, Zetta L, Biochemistry 1999 38 39 12709 12717 10.1021/bi9911280 10504241 (Pubitemid 29463267)
29. The Protein Data Bank: a computer-based archival file for macromolecular structures. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M, J Mol Biol 1977 112 3 535 542 10.1016/S0022-2836(77)80200-3 875032 (Pubitemid 8109216)
30. Editing of chemical exchange-relayed NOEs in NMR experiments for the observation of protein-water interactions. Melacini G, Kaptein R, Boelens R, J Magn Reson 1999 136 2 214 218 10.1006/jmre.1998.1646 9986764 (Pubitemid 129608835)
31. The role of conserved water molecules in the catalytic domain of protein kinases. Knight JDR, Hamelberg D, McCammon JA, Kothary R, Proteins-Structure Function and Bioinformatics 2009 76 3 527 535 10.1002/prot.22451
32. GROMACS: A message-passing parallel molecular dynamics implementation. Berendsen HJC, van der Spoel D, van Drunen R, Comp Phys Comm 1995 91 43 56 10.1016/0010-4655(95)00042-E
33. Biomolecular Simulation: GROMOS96 Manual and User Guide. Van Gunsteren WF, Billeter S, Eising A, Hunenberger PH, Kruger P, Mark AE, Scott WRP, Tironi IG, BIOMOS bv, Zurich, Groningen 1996
34. The missing term in effective pair potentials. Berendsen HJC, Grigerra JR, Straatsma TP, Journal of Physical Chemistry 1987 91 6269-71
35. New tricks for modellers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Darden T, Perera L, Li L, Pedersen L, Struct Fold Des 1999 7 55 60 10.1016/S0969-2126(99)80009-4 (Pubitemid 29159182)
36. xdlMAPMAN and xdlDATAMAN-Programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Kleywegt GJ, Jones TA, Acta Crystallogr D 1996 52 826 828 10.1107/S0907444995014983 15299647 (Pubitemid 27064307)
37. Expression of a synthetic gene encoding P2 ribonuclease from the extreme thermoacidophilic archaebacterium Sulfolobus solfataricus in mesophylic hosts. Fusi P, Grisa M, Mombelli E, Consonni R, Tortora P, Vanoni M, Gene 1995 154 1 99 103 10.1016/0378-1119(94)00828-G 7867957
38. SPARKY 3. Goddard TD, Kneller DG, University of California, San Francisco
39. Water suppression that works. Excitation sculpting using arbitrary waveforms and pulsed field gradients. Hwang T, Shaka AJ, Journal of Magnetic Resonance, Series A 1995 112 2 275 279 10.1006/jmra.1995.1047