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Volumn 41, Issue 2, 2008, Pages 77-88

Density functional calculations of 15N chemical shifts in solvated dipeptides

Author keywords

Chemical shielding tensor; Chemical shift calculation; Density functional calculation; Dipeptides; Nitrogen 15; Solvent effect

Indexed keywords

DIPEPTIDE; N METHYLACETAMIDE;

EID: 44949219081     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-008-9241-7     Document Type: Article
Times cited : (22)

References (53)
  • 1
    • 84962432238 scopus 로고    scopus 로고
    • Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches
    • Aidas K, Mogelhoj A, Kjaer H, Nielsen CB, Mikkelsen KV, Ruud K, Christiansen O, Kongsted J (2007) Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches. J Phys Chem A 111:4199-4210
    • (2007) J Phys Chem A , vol.111 , pp. 4199-4210
    • Aidas, K.1    Mogelhoj, A.2    Kjaer, H.3    Nielsen, C.B.4    Mikkelsen, K.V.5    Ruud, K.6    Christiansen, O.7    Kongsted, J.8
  • 2
    • 84961985847 scopus 로고    scopus 로고
    • Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model
    • Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995-2001
    • (1998) J Phys Chem A , vol.102 , pp. 1995-2001
    • Barone, V.1    Cossi, M.2
  • 3
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic-behavior
    • Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic-behavior. Phys Rev A 38:3098-3100
    • (1988) Phys Rev A , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 4
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. 3. The role of exact exchange
    • Becke AD (1993) Density-functional thermochemistry. 3. the role of exact exchange. J Chem Phys 98:5648-5652
    • (1993) J Chem Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 5
    • 12344331148 scopus 로고    scopus 로고
    • Reliable NMR chemical shifts for molecules in solution by methods rooted in density functional theory
    • Benzi C, Crescenzi O, Pavone M, Barone V (2004) Reliable NMR chemical shifts for molecules in solution by methods rooted in density functional theory. Magn Reson Chem 42:S57-S67
    • (2004) Magn Reson Chem , vol.42
    • Benzi, C.1    Crescenzi, O.2    Pavone, M.3    Barone, V.4
  • 7
    • 0034684181 scopus 로고    scopus 로고
    • Measurement of proton, nitrogen, and carbonyl chemical shielding anisotropies in a protein dissolved in a dilute liquid crystalline phase
    • Cornilescu G, Bax A (2000) Measurement of proton, nitrogen, and carbonyl chemical shielding anisotropies in a protein dissolved in a dilute liquid crystalline phase. J Am Chem Soc 122:10143-10154
    • (2000) J Am Chem Soc , vol.122 , pp. 10143-10154
    • Cornilescu, G.1    Bax, A.2
  • 8
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • 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
    • (1999) J Biomol NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 9
    • 84962349001 scopus 로고    scopus 로고
    • Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model
    • Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669-681
    • (2003) J Comput Chem , vol.24 , pp. 669-681
    • Cossi, M.1    Rega, N.2    Scalmani, G.3    Barone, V.4
  • 11
    • 0027308278 scopus 로고
    • Secondary and tertiary structural effects on protein nmr chemical-shifts-an abinitio approach
    • de Dios AC, Pearson JG, Oldfield E (1993) Secondary and tertiary structural effects on protein nmr chemical-shifts-an abinitio approach. Science 260:1491-1496
    • (1993) Science , vol.260 , pp. 1491-1496
    • de Dios, A.C.1    Pearson, J.G.2    Oldfield, E.3
  • 12
    • 0028080176 scopus 로고
    • The 3Rd Igg-binding domain from streptococcal protein-G-an analysis by X-ray crystallography of the structure alone and in a complex with fab
    • Derrick JP, Wigley DB (1994) The 3Rd Igg-binding domain from streptococcal protein-G-an analysis by X-ray crystallography of the structure alone and in a complex with fab. J Mol Biol 243:906-918
    • (1994) J Mol Biol , vol.243 , pp. 906-918
    • Derrick, J.P.1    Wigley, D.B.2
  • 13
    • 40749094858 scopus 로고
    • Self-consistent perturbation-theory of diamagnetism. 1. Gauge-invariant lcao method for nmr chemical-shifts
    • Ditchfield R (1974) Self-consistent perturbation-theory of diamagnetism. 1. Gauge-invariant lcao method for nmr chemical-shifts. Mol Phys 27:789-807
    • (1974) Mol Phys , vol.27 , pp. 789-807
    • Ditchfield, R.1
  • 15
    • 0032587511 scopus 로고    scopus 로고
    • The effect of noncollinearity of N-15-H-1 dipolar and N-15 CSA tensors and rotational anisotropy on N-15 relaxation, CSA/dipolar cross-correlation, and TROSY
    • Fushman D, Cowburn D (1999) The effect of noncollinearity of N-15-H-1 dipolar and N-15 CSA tensors and rotational anisotropy on N-15 relaxation, CSA/dipolar cross-correlation, and TROSY. J Biomol NMR 13:139-147
    • (1999) J Biomol NMR , vol.13 , pp. 139-147
    • Fushman, D.1    Cowburn, D.2
  • 16
    • 0034927324 scopus 로고    scopus 로고
    • 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
    • In: James T, Schmitz U, Doetsch V (eds)
    • 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. In: James T, Schmitz U, Doetsch V (eds) Methods in enzymology. Nuclear magnetic resonance of biological macromolecules, Pt B 339:109-126
    • (2001) Methods in Enzymology. Nuclear Magnetic Resonance of Biological Macromolecules , vol.339 , Issue.PART B , pp. 109-126
    • Fushman, D.1    Cowburn, D.2
  • 17
    • 0032576119 scopus 로고    scopus 로고
    • Direct measurement of N-15 chemical shift anisotropy in solution
    • Fushman D, Tjandra N, Cowburn D (1998) Direct measurement of N-15 chemical shift anisotropy in solution. J Am Chem Soc 120:10947-10952
    • (1998) J Am Chem Soc , vol.120 , pp. 10947-10952
    • Fushman, D.1    Tjandra, N.2    Cowburn, D.3
  • 18
    • 0033595535 scopus 로고    scopus 로고
    • 15N chemical shift anisotropy and chemical exchange contributions
    • 15N chemical shift anisotropy and chemical exchange contributions. J Am Chem Soc 121:8577-8582
    • (1999) J Am Chem Soc , vol.121 , pp. 8577-8582
    • Fushman, D.1    Tjandra, N.2    Cowburn, D.3
  • 19
    • 33745362452 scopus 로고    scopus 로고
    • 15N relaxation measurements at several fields. Implications for backbone order parameters
    • 15N relaxation measurements at several fields. Implications for backbone order parameters. J Am Chem Soc 128:7855-7870
    • (2006) J Am Chem Soc , vol.128 , pp. 7855-7870
    • Hall, J.B.1    Fushman, D.2
  • 23
    • 0035742784 scopus 로고    scopus 로고
    • Separating structure and dynamics in CSA/DD cross-correlated relaxation: A case study on trehalase and ubiquitin
    • Kover KE, Batta G (2001) Separating structure and dynamics in CSA/DD cross-correlated relaxation: A case study on trehalase and ubiquitin. J Magn Reson 150:137-146
    • (2001) J Magn Reson , vol.150 , pp. 137-146
    • Kover, K.E.1    Batta, G.2
  • 24
    • 0033520723 scopus 로고    scopus 로고
    • 15N chemical shift anisotropy in Escherichia coli ribonuclease H in solution
    • 15N chemical shift anisotropy in Escherichia coli ribonuclease H in solution. J Am Chem Soc 121:10119-10125
    • (1999) J Am Chem Soc , vol.121 , pp. 10119-10125
    • Kroenke, C.D.1    Rance, M.2    Palmer, A.G.3
  • 25
    • 0042494538 scopus 로고    scopus 로고
    • 15N chemical shift anisotropy in a protein dissolved in a dilute liquid crystalline medium with the application of magic angle sample spinning
    • 15N chemical shift anisotropy in a protein dissolved in a dilute liquid crystalline medium with the application of magic angle sample spinning. J Magn Reson 163:163-173
    • (2003) J Magn Reson , vol.163 , pp. 163-173
    • Kurita, J.1    Shimahara, H.2    Utsunomiya-Tate, N.3    Tate, S.4
  • 26
    • 0001204696 scopus 로고    scopus 로고
    • Ab initio studies of amide-N-15 chemical shifts in dipeptides: Applications to protein NMR spectroscopy
    • 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
    • (1996) J Phys Chem , vol.100 , pp. 16423-16428
    • Le, H.B.1    Oldfield, E.2
  • 27
    • 0345491105 scopus 로고
    • Development of the colle-salvetti correlation-energy formula into a functional of the electron-density
    • 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
    • (1988) Phys Rev B , vol.37 , pp. 785-789
    • Lee, C.T.1    Yang, W.T.2    Parr, R.G.3
  • 28
    • 0041466424 scopus 로고    scopus 로고
    • 15N chemical shift anisotropy in protein structure refinement and comparison with NH residual dipolar couplings
    • 15N chemical shift anisotropy in protein structure refinement and comparison with NH residual dipolar couplings. J Magn Reson 164:171-176
    • (2003) J Magn Reson , vol.164 , pp. 171-176
    • Lipsitz, R.S.1    Tjandra, N.2
  • 29
    • 17744366182 scopus 로고    scopus 로고
    • Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy
    • Loth K, Pelupessy P, Bodenhausen G (2005) Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy. J Am Chem Soc 127:6062-6068
    • (2005) J Am Chem Soc , vol.127 , pp. 6062-6068
    • Loth, K.1    Pelupessy, P.2    Bodenhausen, G.3
  • 30
    • 0027503130 scopus 로고
    • Orientational constraints as 3-dimensional structural constraints from chemical-shift anisotropy - The polypeptide backbone of gramicidin-a in a lipid bilayer
    • Mai W, Hu W, Wang C, Cross TA (1993) Orientational constraints as 3-dimensional structural constraints from chemical-shift anisotropy - the polypeptide backbone of gramicidin-a in a lipid bilayer. Protein Sci 2:532-542
    • (1993) Protein Sci , vol.2 , pp. 532-542
    • Mai, W.1    Hu, W.2    Wang, C.3    Cross, T.A.4
  • 31
    • 0142087939 scopus 로고    scopus 로고
    • An ab initio study of solvent polarity and hydrogen bonding effects on - The nitrogen NMR shieldings of N, N-dimethylacetamidine
    • Manalo MN, de Dios AC (2002) An ab initio study of solvent polarity and hydrogen bonding effects on - the nitrogen NMR shieldings of N, N-dimethylacetamidine. Magn Reson Chem 40:781-785
    • (2002) Magn Reson Chem , vol.40 , pp. 781-785
    • Manalo, M.N.1    de Dios, A.C.2
  • 32
    • 84962426744 scopus 로고    scopus 로고
    • 17O nuclear shielding in water and in acetone
    • 17O nuclear shielding in water and in acetone. J Phys Chem B 109:9830-9838
    • (2005) J Phys Chem B , vol.109 , pp. 9830-9838
    • Mennucci, B.1    Martinez, J.M.2
  • 33
    • 0035797751 scopus 로고    scopus 로고
    • Solvent effects on nuclear shieldings: Continuum or discrete solvation models to treat hydrogen bond and polarity effects?
    • Mennucci B, Martinez JM, Tomasi J (2001) Solvent effects on nuclear shieldings: Continuum or discrete solvation models to treat hydrogen bond and polarity effects? J Phys Chem A 105:7287-7296
    • (2001) J Phys Chem A , vol.105 , pp. 7287-7296
    • Mennucci, B.1    Martinez, J.M.2    Tomasi, J.3
  • 35
    • 0029283884 scopus 로고
    • Chemical-shifts and 3-dimensional protein structures
    • Oldfield E (1995) Chemical-shifts and 3-dimensional protein structures. J Biomol NMR 5:217-225
    • (1995) J Biomol NMR , vol.5 , pp. 217-225
    • Oldfield, E.1
  • 36
    • 0036025444 scopus 로고    scopus 로고
    • Chemical shifts in amino acids, peptides, and proteins: From quantum chemistry to drug design
    • Oldfield E (2002) Chemical shifts in amino acids, peptides, and proteins: From quantum chemistry to drug design. Annu Rev Phys Chem 53:349-378
    • (2002) Annu Rev Phys Chem , vol.53 , pp. 349-378
    • Oldfield, E.1
  • 38
    • 3042524732 scopus 로고    scopus 로고
    • Molecular modeling of dipeptide and its analogous systems with water
    • Selvarengan P, Kolandaivel PG (2004) Molecular modeling of dipeptide and its analogous systems with water. J Mol Model 10:198-203
    • (2004) J Mol Model , vol.10 , pp. 198-203
    • Selvarengan, P.1    Kolandaivel, P.G.2
  • 39
    • 34547179849 scopus 로고    scopus 로고
    • Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology
    • 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
    • (2007) J Biomol NMR , vol.38 , pp. 289-302
    • Shen, Y.1    Bax, A.2
  • 41
    • 0029900275 scopus 로고    scopus 로고
    • 15N chemical shift anisotropy from quantitative measurement of relaxation interference effects
    • 15N chemical shift anisotropy from quantitative measurement of relaxation interference effects. J Am Chem Soc 118:6986-6991
    • (1996) J Am Chem Soc , vol.118 , pp. 6986-6991
    • Tjandra, N.1    Szabo, A.2    Bax, A.3
  • 42
    • 84961980477 scopus 로고    scopus 로고
    • Quantum mechanical continuum solvation models
    • Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999-3093
    • (2005) Chem Rev , vol.105 , pp. 2999-3093
    • Tomasi, J.1    Mennucci, B.2    Cammi, R.3
  • 43
    • 33749169843 scopus 로고    scopus 로고
    • 15N relaxation in deuterated amide groups in proteins using direct nitrogen detection
    • 15N relaxation in deuterated amide groups in proteins using direct nitrogen detection. J Biomol NMR 36:27-36
    • (2006) J Biomol NMR , vol.36 , pp. 27-36
    • Vasos, P.R.1    Hall, J.B.2    Kummerle, R.3    Fushman, D.4
  • 44
    • 0036129107 scopus 로고    scopus 로고
    • Probability-based protein secondary structure identification using combined NMR chemical-shift data
    • Wang YJ, Jardetzky O (2002) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861
    • (2002) Protein Sci , vol.11 , pp. 852-861
    • Wang, Y.J.1    Jardetzky, O.2
  • 45
    • 1442281993 scopus 로고    scopus 로고
    • 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from phi, psi(-1), and chi(1) torsion angles
    • 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from phi, psi(-1), and chi(1) torsion angles. J Biomol NMR 28:327-340
    • (2004) J Biomol NMR , vol.28 , pp. 327-340
    • Wang, Y.J.1    Jardetzky, O.2
  • 46
    • 0032454094 scopus 로고    scopus 로고
    • Protein chemical shift analysis: A practical guide
    • Wishart DS, Nip AM (1998) Protein chemical shift analysis: A practical guide. Biochem Cell Biol 76:153-163
    • (1998) Biochem Cell Biol , vol.76 , pp. 153-163
    • Wishart, D.S.1    Nip, A.M.2
  • 47
    • 0031302286 scopus 로고    scopus 로고
    • Automated H-1 and C-13 chemical shift prediction using the BioMagResBank
    • Wishart DS, Watson MS, Boyko RF, Sykes BD (1997) Automated H-1 and C-13 chemical shift prediction using the BioMagResBank. J Biomol NMR 10:329-336
    • (1997) J Biomol NMR , vol.10 , pp. 329-336
    • Wishart, D.S.1    Watson, M.S.2    Boyko, R.F.3    Sykes, B.D.4
  • 48
    • 11744305193 scopus 로고
    • Efficient implementation of the gauge-independent atomic orbital method for NMR chemical-shift calculations
    • Wolinski K, Hinton JF, Pulay P (1990) Efficient implementation of the gauge-independent atomic orbital method for NMR chemical-shift calculations. J Am Chem Soc 112:8251-8260
    • (1990) J Am Chem Soc , vol.112 , pp. 8251-8260
    • Wolinski, K.1    Hinton, J.F.2    Pulay, P.3
  • 49
    • 0001125152 scopus 로고
    • 15N chemical-shift interaction tensors in a peptide-bond by 3-dimensional solid-state NMR-spectroscopy
    • 15N chemical-shift interaction tensors in a peptide-bond by 3-dimensional solid-state NMR-spectroscopy. J Am Chem Soc 117:6148-6149
    • (1995) J Am Chem Soc , vol.117 , pp. 6148-6149
    • Wu, C.H.1    Ramamoorthy, A.2    Gierasch, L.M.3    Opella, S.J.4
  • 50
    • 33745465576 scopus 로고    scopus 로고
    • Determinations of N-15 chemical shift anisotropy magnitudes in a uniformly N-15, C-13-labeled microcrystalline protein by three-dimensional magic-angle spinning nuclear magnetic resonance spectroscopy
    • Wylie BJ, Franks WT, Rienstra CM (2006) Determinations of N-15 chemical shift anisotropy magnitudes in a uniformly N-15, C-13-labeled microcrystalline protein by three-dimensional magic-angle spinning nuclear magnetic resonance spectroscopy. J Phys Chem B 110:10926-10936
    • (2006) J Phys Chem B , vol.110 , pp. 10926-10936
    • Wylie, B.J.1    Franks, W.T.2    Rienstra, C.M.3
  • 51
    • 41449101270 scopus 로고    scopus 로고
    • Multidimensional solid state NMR of anisotropic interactions in peptides and proteins
    • Wylie BJ, Rienstra CM (2008) Multidimensional solid state NMR of anisotropic interactions in peptides and proteins. J Chem Phys 128:052207
    • (2008) J Chem Phys , vol.128 , pp. 052207
    • Wylie, B.J.1    Rienstra, C.M.2
  • 52
    • 0035544152 scopus 로고    scopus 로고
    • Automated prediction of N-15, C-13(alpha), C-13(beta) and C-13′ chemical shifts in proteins using a density functional database
    • 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
    • (2001) J Biomol NMR , vol.21 , pp. 321-333
    • Xu, X.P.1    Case, D.A.2
  • 53
    • 0037114648 scopus 로고    scopus 로고
    • 13C′ chemical shifts in peptides using density functional theory
    • 13C′ chemical shifts in peptides using density functional theory. Biopolymers 65:408-423
    • (2002) Biopolymers , vol.65 , pp. 408-423
    • Xu, X.P.1    Case, Da.2


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