Premium
Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants
Author(s) -
Arthanari Haribabu,
McConnell Kevin J.,
Beger Richard,
Young Matthew A.,
Beveridge D. L.,
Bolton Philip H.
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10263
Subject(s) - chemistry , dihedral angle , two dimensional nuclear magnetic resonance spectroscopy , molecular dynamics , nuclear magnetic resonance spectroscopy , j coupling , nuclear magnetic resonance spectroscopy of nucleic acids , crystallography , nuclear overhauser effect , nmr spectra database , force field (fiction) , carbon 13 nmr satellite , computational chemistry , stereochemistry , spectral line , fluorine 19 nmr , transverse relaxation optimized spectroscopy , molecule , hydrogen bond , organic chemistry , physics , quantum mechanics
To assess the accuracy of the molecular dynamics (MD) models of nucleic acids, a detailed comparison between MD‐calculated and NMR‐observed indices of the dynamical structure of DNA in solution has been carried out. The specific focus of our comparison is the oligonucleotide duplex, d(CGCGAATTCGCG) 2 , for which considerable structural data have been obtained from crystallography and NMR spectroscopy. An MD model for the structure of d(CGCGAATTCGCG) 2 in solution, based on the AMBER force field, has been extended with a 14 ns trajectory. New NMR data for this sequence have been obtained in order to allow a detailed and critical comparison between the calculated and observed parameters. Observable two‐dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY) volumes and scalar coupling constants were back‐calculated from the MD trajectory and compared with the corresponding NMR data. The comparison of these results indicate that the MD model is in generally good agreement with the NMR data, and shows closer accord with experiment than back‐calculations based on the crystal structure of d(CGCGAATTCGCG) 2 or the canonical A or B forms of the sequence. The NMR parameters are not particularly sensitive to the known deficiency in the AMBER MD model, which is a tendency toward undertwisting of the double helix when the parm.94 force field is used. The MD results are also compared with a new determination of the solution structure of d(CGCGAATTCGCG) 2 using NMR dipolar coupling data. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 3–15, 2003