Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P54-55

Protein Science

Volumn 19, Issue 1, 2010, Pages 183-189

  Öhman, Anders ^a   Öman, Tommy ^a   Oliveberg, Mikael ^b  

^a UMEÅ UNIVERSITY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Backbone dynamics; Folding; NMR solution structure; Permutant; S6

Indexed keywords

LEUCINE; NUCLEAR PROTEIN; PERMUTANT PROTEIN; PHENYLALANINE; PROTEIN S6; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER MODEL; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; WILD TYPE;

BACTERIAL PROTEINS; MOLECULAR DYNAMICS SIMULATION; MUTATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN FOLDING; RIBOSOMAL PROTEIN S6; THERMODYNAMICS; THERMUS THERMOPHILUS;

THERMUS THERMOPHILUS;

EID: 75149193285     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.298     Document Type: Article

References (27)

1. Steitz TA (2008) A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol 9:242-253.
2. Agalarov SC, Sridhar Prasad G, Funke PM, Stout CD, Williamson JR (2000) Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science 288:107-113.
3. Lindahl M, Svensson LA, Liljas A, Sedelnikova SE, Eliseikina IA, Fomenkova NP, Nevskaya N, Nikonov SV, Garber MB, Muranova TA, Rykanova AI, Amons R (1994) Crystal structure of the ribosomal protein S6 from Thermus thermophilus. Embo J 13:1249-1254.
4. Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A (2000) Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell 102:615-623.
5. Wimberly BT, Brodersen DE, Clemons WM, Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V (2000) Structure of the 30S ribosomal subunit. Nature 407:327-339.
6. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF (2001) Crystal structure of the ribosome at 5.5 A resolution. Science 292: 883-896.
7. Otzen DE, Kristensen O, Proctor M, Oliveberg M (1999) Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry 38:6499-6511.
8. Otzen DE, Oliveberg M (2002) Conformational plasticity in folding of the split beta-alpha-beta protein S6: evidence for burst-phase disruption of the native state. J Mol Biol 317:613-627.
9. Lindberg M, Tangrot J, Oliveberg M (2002) Complete change of the protein folding transition state upon circular permutation. Nat Struct Biol 9:818-822.
10. Haglund E, Lindberg MO, Oliveberg M (2008) Changes of protein folding pathways by circular permutation. Overlapping nuclei promote global cooperativity. J Biol Chem 283:27904-27915.
11. Lindberg MO, Haglund E, Hubner IA, Shakhnovich EI, Oliveberg M (2006) Identification of the minimal protein-folding nucleus through loop-entropy perturbations. Proc Natl Acad Sci USA 103:4083-4088.
12. Ludvigsen S, Poulsen FM (1992) Positive theta-angles in proteins by nuclear magnetic resonance spectros-copy. J Biomol NMR 2:227-233.
13. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293.
14. Helgstrand M, Kraulis P, Allard P, Härd T (2000) Ansig for Windows: an interactive computer program for semiautomatic assignment of protein NMR spectra. J Biomol NMR 18:329-336.
15. Wüthrich K (1986) NMR of proteins and nucleic acids. New York: John Wiley & Sons.
16. Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog NMR Spectrosc 34:66.
17. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECKNMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477-486.
18. Padrta P, Sklenar V (2002) Program MULDER - a tool for extracting torsion angles from NMR data. J Biomol NMR 24:339-349.
19. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289-302.
20. Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14:51-55, 29-32.
21. Fletcher CM, Jones DNM, Diamond R, Neuhaus D (1996) Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures. J Biomol NMR 8:19.
22. Farrow NA, Muhandiram R, Singer AU, Pascal SM, Kay CM, Gish G, Shoelson SE, Pawson T, Forman-Kay JD, Kay LE (1994) Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33: 5984-6003.
23. Johnson BA, Blevins RA (1994) NMRView: a computer program for the visualization and analysis of NMR data. J Biomolecular NMR 4:603-614.
24. Lee LK, Rance M, Chazin WJ, Palmer AG, III (1997) Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C alpha nuclear spin relaxation. J Biomol NMR 9:287-298.
25. Mandel AM, Akke M, Palmer AG, III (1995) Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J Mol Biol 246:144-163.
26. Palmer AG, Rance M, Wright PE (1991) Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy. JACS 113:10.
27. Cole R, Loria JP (2003) FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data. J Biomol NMR 26:203-213.