Mapping of protein structural ensembles by chemical shifts

Journal of Biomolecular NMR

Volumn 48, Issue 2, 2010, Pages 71-83

  Baskaran, Kumaran ^a   Brunner, Konrad ^a   Munte, Claudia E ^a   Kalbitzer, Hans Robert ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

Chemical shift; Solution structure; Structural ensemble

Indexed keywords

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; ENERGY TRANSFER; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE;

ALGORITHMS; CARBON; HYDROGEN; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; TEMPERATURE;

EID: 78149361854     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-010-9438-4     Document Type: Article

References (26)

1. Arun K, Langmead CJ (2004) Large-scale testing of chemical shift prediction algorithms and improved machine learning-based approaches to shift prediction. Computational Systems Bioinformatics Conference (CSB'04) 712-713
2. AT Brunger 2007 Version 1.2 of the crystallography and NMR system Nat Protoc 2 2728 2733 10.1038/nprot.2007.406
3. AT Brunger PD Adams GM Clore WL DeLano P Gros RW Grosse-Kunstleve JS Jiang J Kuszewski M Nilges NS Pannu RJ Read LM Rice T Simonson GL Warren 1998 Crystallography & NMR System: a new software suite for macromolecular structure determination Acta Crystallogr D Biol Crystallogr 54 905 921 10.1107/S0907444998003254 (Pubitemid 28443603)
4. M Geyer T Schweins C Herrmann T Prisner A Wittinghofer HR Kalbitzer 1996 Conformational transition in p21ras and its complexes with effector protein Raf-RBD and the GTPase activating protein GAP Biochemistry 35 10308 10320 10.1021/bi952858k (Pubitemid 26277289)
5. M Hahmann T Maurer M Lorenz W Glaser W Hengstenberg HR Kalbitzer 1998 Structural studies of the Histidine-Containing Phosphocarrier Protein (HPr) from Enterococcus faecalis Eur J Biochem 252 51 58 10.1046/j.1432-1327.1998.2520051. x (Pubitemid 28089957)
6. 31P NMR spectroscopy of microcrystals of the Ras protein and its effector loop mutants: comparison of solution and crystal structures J Mol Biol 342 1033 1040 10.1016/j.jmb.2004.07.077 (Pubitemid 39165665)
7. Z Jia M Vandonselaar W Hengstenberg JW Quail LTJ Delbaere 1994 The 1.6 structure of the histidine containing phosphocarrier protein HPr from Streptococcus faecalis J Mol Biol 236 1341 1355 10.1016/0022-2836(94)90062-0
8. WL Jorgensen J Tirado-Rives 1988 The OPLS force field for proteins. Energy minimizations for crystals of cyclic peptides and crambin J Am Chem Soc 110 1657 1666 10.1021/ja00214a001
9. WL Jorgensen J Chandrasekhar JD Madura RW Impey ML Klein 1983 Comparison of simple potential functions for simulating liquid water J Chem Phys 79 926 935 10.1063/1.445869 1983JChPh..79..926J
10. HR Kalbitzer M Spoerner P Ganser C Hosza W Kremer 2009 Fundamental link between folding states and functional states of proteins J Am Chem Soc 131 16714 16719 10.1021/ja904314q
11. R Koradi M Billeter K Wuthrich 1996 MOLMOL: a program for display and analysis of macromolecular structures J Mol Graph 14 51 55 10.1016/0263-7855(96) 00009-4 (Pubitemid 26152976)
12. RA Laskowski JA Rullmannn MW MacArthur R Kaptein JM Thornton 1996 AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR J Biomol NMR 8 477 486 10.1007/BF00228148
13. 1H chemical shifts J Biomol NMR 45 413 426 10.1007/s10858-009-9384-1
14. JP Linge MA Williams CAEM Spronk AMJJ Bonvin M Nilges 2003 Refinement of protein structures in explicit solvent Proteins Struct Funct Genet 50 496 506 10.1002/prot.10299 (Pubitemid 36158461)
15. T Maurer S Meier N Kachel CE Munte S Hasenbein B Koch W Hengstenberg HR Kalbitzer 2004 High-resolution structure of the histidine-containing phosphocarrier protein (HPr) from Staphylococcus aureus and characterization of its interaction with the bifunctional HPr kinase/phosphorylase J Bacteriol 186 5906 5918 10.1128/JB.186.17.5906-5918.2004 (Pubitemid 39128664)
16. J Meiler 2003 PROSHIFT: protein chemical shift prediction using artificial neural networks J Biomol NMR 26 25 37 10.1023/A:1023060720156 (Pubitemid 36553450)
17. 15N chemical shifts J Biomol NMR 2 215 240 10.1023/A:1023812930288 (Pubitemid 36758442)
18. EF Pai U Krengel GA Petsko RS Goody W Kabsch A Wittinghofer 1990 Refined crystal structure of the triphosphate conformation of H-Ras p21 at 1.35 resolution: implications for the mechanism of GTP hydrolysis EMBO J 9 2351 2359
19. SJ Perkins LN Johnson DC Philipps RA Dwek 1977 Conformational changes, dynamics and assignments in 1H NMR studies of proteins using ring current calculations. Hen egg white lysozyme FEBS Lett 82 17 22 10.1016/0014-5793(77) 80876-4 (Pubitemid 8201727)
20. FH Schumann H Riepl T Maurer W Gronwald K-P Neidig HR Kalbitzer 2007 Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions J Biomol NMR 39 275 289 10.1007/s10858-007-9197- z (Pubitemid 350055750)
21. Y Shen A Bax 2007 Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology J Biomol NMR 38 289 302 10.1007/s10858-007-9166-6 (Pubitemid 47108511)
22. M Spoerner C Herrmann IR Vetter HR Kalbitzer A Wittinghofer 2001 Dynamic properties of the Ras switch I region and its importance for binding to effectors Proc Natl Acad Sci 98 4944 4949 10.1073/pnas.081441398 2001PNAS...98.4944S (Pubitemid 32397062)
23. 31P solid state NMR spectroscopy J Mol Biol 323 899 907 10.1016/S0022-2836(02)01010-0 (Pubitemid 35341063)
24. Y Wang 2004 Secondary structural effects on protein NMR chemical shifts J Biomol NMR 30 233 244 10.1007/s10858-004-3098-1 (Pubitemid 40069140)
25. Y Wang O Jardetzky 2002 Probability-based protein secondary structure identification using combined NMR chemical-shift data Protein Sci 11 852 861 10.1110/ps.3180102 (Pubitemid 34241293)
26. 13C chemical shifts in proteins using a density functional database J Biomol NMR 21 321 333 10.1023/A:1013324104681 (Pubitemid 34071387)