Literature DB >> 8563464

Calibration of ring-current effects in proteins and nucleic acids.

D A Case1.   

Abstract

Density functional chemical shielding calculations are reported for methane molecules placed in a variety of positions near aromatic rings of the type found in proteins and nucleic acids. The results are compared to empirical formulas that relate these intermolecular shielding effects to magnetic anisotropy ('ring-current') effects and to electrostatic polarization of the C-H bonds. Good agreement is found between the empirical formulas and the quantum chemistry results, allowing a reassessment of the ring-current intensity factors for aromatic amino acids and nucleic acid bases. Electrostatic interactions contribute significantly to the computed chemical shift dispersion. Prospects for using this information in the analysis of chemical shifts in proteins and nucleic acids are discussed.

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Year:  1995        PMID: 8563464     DOI: 10.1007/bf00197633

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  12 in total

1.  Accurate and simple analytic representation of the electron-gas correlation energy.

Authors: 
Journal:  Phys Rev B Condens Matter       Date:  1992-06-15

2.  A relational database for sequence-specific protein NMR data.

Authors:  B R Seavey; E A Farr; W M Westler; J L Markley
Journal:  J Biomol NMR       Date:  1991-09       Impact factor: 2.835

3.  Resonance assignments of non-exchangeable protons in B type DNA oligomers, an overview.

Authors:  F J van de Ven; C W Hilbers
Journal:  Nucleic Acids Res       Date:  1988-07-11       Impact factor: 16.971

Review 4.  Quantum mechanical calculations of NMR chemical shifts in nucleic acids.

Authors:  C Giessner-Prettre; B Pullman
Journal:  Q Rev Biophys       Date:  1987-11       Impact factor: 5.318

5.  The impact of direct refinement against proton chemical shifts on protein structure determination by NMR.

Authors:  J Kuszewski; A M Gronenborn; G M Clore
Journal:  J Magn Reson B       Date:  1995-06

Review 6.  Use of chemical shifts and coupling constants in nuclear magnetic resonance structural studies on peptides and proteins.

Authors:  D A Case; H J Dyson; P E Wright
Journal:  Methods Enzymol       Date:  1994       Impact factor: 1.600

7.  Comparisons of ring-current shifts calculated from the crystal structure of egg white lysozyme of hen with the proton nuclear magnetic resonance spectrum of lysozyme in solution.

Authors:  S J Perkins; R A Dwek
Journal:  Biochemistry       Date:  1980-01-22       Impact factor: 3.162

8.  'Random coil' 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG.

Authors:  G Merutka; H J Dyson; P E Wright
Journal:  J Biomol NMR       Date:  1995-01       Impact factor: 2.835

Review 9.  Chemical shifts and three-dimensional protein structures.

Authors:  E Oldfield
Journal:  J Biomol NMR       Date:  1995-04       Impact factor: 2.835

10.  Relationship between nuclear magnetic resonance chemical shift and protein secondary structure.

Authors:  D S Wishart; B D Sykes; F M Richards
Journal:  J Mol Biol       Date:  1991-11-20       Impact factor: 5.469

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  43 in total

1.  Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations.

Authors:  M A McCoy; D F Wyss
Journal:  J Biomol NMR       Date:  2000-11       Impact factor: 2.835

2.  Prediction of proton chemical shifts in RNA. Their use in structure refinement and validation.

Authors:  J A Cromsigt; C W Hilbers; S S Wijmenga
Journal:  J Biomol NMR       Date:  2001-09       Impact factor: 2.835

3.  The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy.

Authors:  Heiko Patzelt; Bernd Simon; Antonius terLaak; Brigitte Kessler; Ronald Kühne; Peter Schmieder; Dieter Oesterhelt; Hartmut Oschkinat
Journal:  Proc Natl Acad Sci U S A       Date:  2002-07-15       Impact factor: 11.205

4.  Characterization of binding-induced changes in dynamics suggests a model for sequence-nonspecific binding of ssDNA by replication protein A.

Authors:  Shibani Bhattacharya; Maria-Victoria Botuyan; Fred Hsu; Xi Shan; A I Arunkumar; Cheryl H Arrowsmith; Aled M Edwards; Walter J Chazin
Journal:  Protein Sci       Date:  2002-10       Impact factor: 6.725

5.  Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements.

Authors:  Wim Vermeulen; Peter Vanhaesebrouck; Marleen Van Troys; Mieke Verschueren; Franky Fant; Marc Goethals; Christophe Ampe; José C Martins; Frans A M Borremans
Journal:  Protein Sci       Date:  2004-05       Impact factor: 6.725

6.  Analysis of (1)H chemical shifts in DNA: Assessment of the reliability of (1)H chemical shift calculations for use in structure refinement.

Authors:  S S Wijmenga; M Kruithof; C W Hilbers
Journal:  J Biomol NMR       Date:  1997-12       Impact factor: 2.835

7.  Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology.

Authors:  Yang Shen; Ad Bax
Journal:  J Biomol NMR       Date:  2007-07-04       Impact factor: 2.835

8.  Consistent blind protein structure generation from NMR chemical shift data.

Authors:  Yang Shen; Oliver Lange; Frank Delaglio; Paolo Rossi; James M Aramini; Gaohua Liu; Alexander Eletsky; Yibing Wu; Kiran K Singarapu; Alexander Lemak; Alexandr Ignatchenko; Cheryl H Arrowsmith; Thomas Szyperski; Gaetano T Montelione; David Baker; Ad Bax
Journal:  Proc Natl Acad Sci U S A       Date:  2008-03-07       Impact factor: 11.205

9.  Structure-based prediction of methyl chemical shifts in proteins.

Authors:  Aleksandr B Sahakyan; Wim F Vranken; Andrea Cavalli; Michele Vendruscolo
Journal:  J Biomol NMR       Date:  2011-07-12       Impact factor: 2.835

10.  Base pair opening in a deoxynucleotide duplex containing a cis-syn thymine cyclobutane dimer lesion.

Authors:  Belinda B Wenke; Leah N Huiting; Elisa B Frankel; Benjamin F Lane; Megan E Núñez
Journal:  Biochemistry       Date:  2013-12-11       Impact factor: 3.162

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