Density functional calculations of chemical shielding of backbone 15N in helical residues of protein G

Journal of Biomolecular NMR

Volumn 45, Issue 3, 2009, Pages 245-253

  Cai, Ling ^a,c   Fushman, David ^a,c   Kosov, Daniel S ^a,b  

^a Bldg 142   (United States)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^c UNIVERSITY OF MARYLAND   (United States)

Author keywords

Abinitio; Chemical shielding calculation; Chemical shielding tensor; Density functional calculation; Nitrogen 15; Protein G

Indexed keywords

NITROGEN 16; NITROGEN DERIVATIVE; PROTEIN G; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; CHEMICAL REACTION; CHEMICAL SHIELDING; CONTROLLED STUDY; DENSITY FUNCTIONAL THEORY; DIPOLE; HYDROGEN BOND; IONIZATION; PRIORITY JOURNAL; PROTEIN INTERACTION; RESIDUE ANALYSIS;

GTP-BINDING PROTEINS; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, SECONDARY;

EID: 70350273076     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-009-9358-3     Document Type: Article

References (33)

1. Bader R (2009) Utilizing the charge field effect on amide N-15 chemical shifts for protein structure validation. J Phys Chem B 113:347-358
2. Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098-3100
3. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648-5652
4. Cai L, Fushman D, Kosov DS (2008) Density functional calculations of N-15 chemical shifts in solvated dipeptides. J Biomol NMR 41:77-88
5. Chesnut DB, Rusiloski BE, Moore KD, Egolf DA (1993) Use of locally dense basis-sets for nuclear magnetic resonance shielding calculations. J Comput Chem 14:1364-1375
6. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A second generation force-field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179-5197
7. 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
8. de Dios AC, Oldfield E (1993) Methods for computing nuclear magnetic resonance chemical shielding in large systems - multiple cluster and charge field approaches. Chem Phys Lett 205:108-116
9. de Dios AC, Pearson JG, Oldfield E (1993a) Chemical shifts in proteins - an ab initio study of C-13 nuclear magnetic resonance chemical shielding in glycine, alanine, and valine residues. J Am Chem Soc 115:9768-9773
10. de Dios AC, Pearson JG, Oldfield E (1993b) Secondary and tertiary structural effects on protein NMR chemical shifts: An ab initio approach. Science 260:1491-1496
11. de Dios AC, Laws DD, Oldfield E (1994) Predicting C-13 nuclear magnetic resonance chemical shielding tensors in zwitterionic L-threonine and L-tyrosine via quantum chemistry. J Am Chem Soc 116:7784-7786
12. Ditchfield R (1974) Self-consistent perturbation theory of diamagnetism. 1. Gauge-invariant LCAO method for NMR chemical shifts. Mol Phys 27:789-807
13. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, revision C.02. Gaussian Inc., Wallingford
14. Fushman D, Cowburn D (2001) Nuclear magnetic resonance relaxation in determination of residue-specific N-15 chemical shift tensors in proteins in solution: Protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy. Methods Enzymol 339:109-126
15. Fushman D, Tjandra N, Cowburn D (1998) Direct measurement of N-15 chemical shift anisotropy in solution. J Am Chem Soc 120:10947-10952
16. Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM (1991) A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253:657-661
17. Hall JB, Fushman D (2006) Variability of the 15N chemical shielding tensors in the B3 domain of protein G from 15N relaxation measurements at several fields. Implications for backbone order parameters. J Am Chem Soc 128:7855-7870
18. Humphrey W, Dalke A, Schulten K (1996) VMD - visual molecular dynamics. J Mol Graph 14:33-38
19. Le HB, Oldfield E (1996) Ab initio studies of amide-N-15 chemical shifts in dipeptides: Applications to protein NMR spectroscopy. J Phys Chem 100:16423-16428
20. Lee CT, Yang WT, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density. Phys Rev B 37:785-789
21. Lipsitz RS, Tjandra N (2003) 15N chemical shift anisotropy in protein structure refinement and comparison with NH residual dipolar couplings. J Magn Reson 164:171-176
22. Nadaud PS, Helmus JJ, Jaroniec CP (2007) C-13 and N-15 chemical shift assignments and secondary structure of the B3 immunoglobulin-binding domain of streptococcal protein G by magic-angle spinning solid-state NMR spectroscopy. Biomol NMR Assign 1:117-120
23. Shen Y, Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289-302
24. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu YB, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685-4690
25. Shen Y, Vernon R, Baker D, Bax A (2009) De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43:63-78
26. Ulmer TS, Ramirez BE, Delaglio F, Bax A (2003) Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. J Am Chem Soc 125:9179-9191
27. Vila JA, Scheraga HA (2007) Factors affecting the use of 13C(alpha) chemical shifts to determine, refine, and validate protein structures. Proteins 71:641-654
28. Wolinski K, Hinton JF, Pulay P (1990) Efficient implementation of the Gauge-independent toamic orbital method for NMR chemical-shift calculations. J Am Chem Soc 112:8251-8260
29. Wylie BJ, Sperling LJ, Frericks HL, Shah GJ, Franks WT, Rienstra CM (2007) Chemical-shift anisotropy measurements of amide and carbonyl resonances in a microcrystalline protein with slow magic-angle spinning NMR spectroscopy. J Am Chem Soc 129:5318-5319
30. Wylie BJ, Schwieters CD, Oldfield E, Rienstra CM (2009) Protein structure refinement using 13C alpha chemical shift tensors. J Am Chem Soc 131:985-992
31. Xu XP, Case DA (2001) Automated prediction of N-15, C-13(alpha), C-13(beta) and C-13 chemical shifts in proteins using a density functional database. J Biomol NMR 21:321-333
32. Xu XP, Case DA (2002) Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C chemical shifts in peptides using density functional theory. Biopolymers 65:408-423
33. Zuiderweg ERP (2002) Mapping protein-protein interactions in solution by NMR Spectroscopy. Biochemistry 41:1-7