Precise structural determination of weakly binding peptides by utilizing dihedral angle constraints

Journal of Biomolecular NMR

Volumn 46, Issue 4, 2010, Pages 299-305

  Mizukoshi, Yumiko ^a,b   Nagasu, Michiko ^a,b   Shimada, Ichio ^a,c   Takahashi, Hideo ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b Japan Biological Informatics Consortium   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Cross correlated relaxation; Dihedral angle; Peptide ligand; Structure determination; Weak binding

Indexed keywords

ACCURACY; ANALYTICAL PARAMETERS; ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DIHEDRAL ANGLE CONSTRAINT; DIPOLE; LIGAND BINDING; MOLECULAR INTERACTION; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN TARGETING; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

ANISOTROPY; BINDING SITES; LIGANDS; MACROMOLECULAR SUBSTANCES; MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 77951665253     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-010-9402-3     Document Type: Article

References (33)

1. MJJ Blommers W Stark CE Jones D Head CE Owen W Jahnke 1999 Transferred cross-correlated relaxation complements transferred NOE: structure of an IL-4R-derived peptide bound to STAT-6 J Am Chem Soc 121 1949 1953 10.1021/ja9836545 (Pubitemid 29132053)
2. MJJ Blommers A Strauss M Geiser P Ramage H Sparrer W Jahnke 2007 NMR-based strategies to elucidate bioactive conformations of weakly binding ligands Top Curr Chem 128 16
3. T Carlomagno C Griesinger 2000 Errors in the measurement of cross-correlated relaxation rates and how to avoid them J Magn Reson 144 280 287 10.1006/jmre.2000.2056 2000JMagR.144..280C
4. T Carlomagno IC Felli M Czech R Fischer M Sprinzl C Griesinger 1999 Transferred cross-correlated relaxation: application to the determination of sugar pucker in an aminoacylated tRNA-mimetic weakly bound to EF-Tu J Am Chem Soc 121 1945 1948 10.1021/ja9835887 (Pubitemid 29132052)
5. T Carlomagno VM Sánchez MJJ Blommers C Griesinger 2003 Derivation of dihedral angles from CH-CH dipolar-dipolar cross-correlated relaxation rates: a C-C torsion involving a quaternary carbon atom in epothilone A bound to tubulin Angew Chem Int Ed 42 2515 2517 10.1002/anie.200350950 (Pubitemid 36753424)
6. 13C- labeled biomolecules J Am Chem Soc 121 6876 6883 10.1021/ja984390p (Pubitemid 29374487)
7. GM Clore AM Gronenborn 1982 Theory and applications of the transferred nuclear Overhauser effect to the study of conformations of small ligands bound to proteins J Magn Res 48 402 417
8. SE Cwirla EA Peters RW Barrett WJ Dower 1990 Peptides on phage: a vast library of peptides for identifying ligands Proc Acad Sci Natl USA 87 6378 6382 10.1073/pnas.87.16.6378 1990PNAS...87.6378C (Pubitemid 20259021)
9. F Delaglio S Grzesiek GW Vuister G Zhu J Pfeifer A Bax 1995 NMRPipe: a multidimensional spectral processing system based on UNIX pipes J Biomol NMR 6 277 293 10.1007/BF00197809
10. EZ Eisenmesser APR Zabell CB Post 2000 Accuracy of bound peptide structures determined by exchange transferred nuclear Overhauser data: a simulation study J Biomol NMR 17 17 32 10.1023/A:1008311703619 (Pubitemid 30434835)
11. T Herrmann P Güntert K Wüthrich 2002 Protein NMR structure determination with automated NOE assignment using the new software CANDID and torsion angle dynamics algorithm DYANA J Mol Biol 319 209 227 10.1016/S0022-2836(02)00241-3 (Pubitemid 34729497)
12. VJ Hruby 2002 Designing peptide receptor agonists and antagonists Nat Rev Drug Discov 1 847 858 10.1038/nrd939 (Pubitemid 37361580)
13. α(i) multiple-quantum coherences J Biomol NMR 17 265 268 10.1023/A:1008393903160 (Pubitemid 30620724)
14. K Kloiber W Schüler R Konrat 2002 Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation J Biomol NMR 22 349 363 10.1023/A:1014936319712 (Pubitemid 34449946)
15. R Koradi M Billeter K Wüthrich 1996 MOLMOL: a program for display and analysis of macromolecular structures J Mol Graph 14 51-5 29 32
16. RA Laskowski JAC Rullmann 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 (Pubitemid 126706801)
17. K Loth P Pelupessy G Bodenhausen 2005 Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide protein nuclei in proteins through cross-correlated relaxation in NMR spectroscopy J Am Chem Soc 127 6062 6068 10.1021/ja042863o (Pubitemid 40577663)
18. PRL Markwick M Sattler 2004 Site-specific variations of carbonyl chemical shift anisotropies in proteins J Am Chem Soc 126 11424 11425 10.1021/ja047859r (Pubitemid 39244943)
19. Y Mizukoshi H Takahashi I Shimada 2006 Rapid preparation of stable isotope labeled peptides that bind to target proteins by a phage library system J Biomol NMR 34 23 30 10.1007/s10858-005-5054-0 (Pubitemid 43300225)
20. F Ni 1994 Recent developments in transferred NOE methods Prog NMR Spectrosc 26 517 606 10.1016/0079-6565(94)90000-0 (Pubitemid 124003834)
21. T Nisihara Y Ushio H Higuchi N Kayagaki N Yamaguchi K Soejima S Matsuo H Maeda Y Eda K Okumura H Yagita 2001 Humanization and epitope mapping of neutralizing anti-human Fas ligand monoclonal antibodies: structural insights into Fas/Fas ligand interaction J Immunol 167 3266 3275 (Pubitemid 32852567)
22. P Pelupessy E Chiarparin R Ghose G Bodenhausen 1999 Simultaneous determination of Ψ and Φ angles in proteins from measurements of cross-correlated relaxation effects J Biomol NMR 14 277 280 10.1023/A: 1008339928400 (Pubitemid 29396486)
23. S Ravindranathan JM Mallet P Sinay G Bodenhausen 2003 Transferred cross-relaxation and cross-correlation in NMR: effects of intermediate exchange on the determination of the conformation of bound ligands J Magn Reson 163 199 207 10.1016/S1090-7807(03)00156-3 2003JMagR.163..199R
24. B Reif M Hennig C Griesinger 1997 Direct measurement of angles between bond vectors in high-resolution NMR Science 276 1230 1233 10.1126/science.276. 5316.1230 (Pubitemid 27227354)
25. H Schwalbe T Carlomagno M Hennig J Junker B Reif C Richter C Griesinger 2001 Cross-correlated relaxation for measurement of angles between tensorial interactions Methods Enzymol 338 35 81 (Pubitemid 32666574)
26. JK Scott GP Smith 1990 Searching for peptide ligands with an epitope library Science 249 386 390 10.1126/science.1696028 1990Sci...249..386S (Pubitemid 20248864)
27. SS Sidhu WJ Fairbrother K Deshayes 2003 Exploring protein-protein interactions with phage display ChemBioChem 4 14 25 10.1002/cbic.200390008 (Pubitemid 36114206)
28. GP Smith 1985 Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface Science 228 1315 1317 10.1126/science.4001944 1985Sci...228.1315S
29. H Takahashi I Shimada 2007 Pairwise NMR experiments for the determination of protein backbone dihedral angle Φ based on cross-correlated spin relaxation J Biomol NMR 37 179 185 10.1007/s10858-006-9108-8 (Pubitemid 46476995)
30. 14N electric field gradient tensor orientations with respect to the molecular frame in a polypeptide J Am Chem Soc 114 5312 5321 10.1021/ja00039a048
31. 15N chemical shift anisotropy from quantitative measurement of relaxation interference effects J Am Chem Soc 118 6986 6991 10.1021/ja960510m (Pubitemid 26252043)
32. B Vögeli L Yao 2009 Correlated dynamics between protein HN and HC bonds observed by NMR cross relaxation J Am Chem Soc 131 3668 3678 10.1021/ja808616v
33. 13C' (carbonyl) chemical shift anisotropy mechanisms J Am Chem Soc 119 11938 11940 10.1021/ja972329z (Pubitemid 28012759)