Premium
DNA bending studied by MD and 2D NMR NOESY simulations: Role of the junction sequence between the A/T tracts
Author(s) -
Luo Jia,
Sarma Mukti H.,
Gupta Goutam,
Sarma Ramaswamy H.
Publication year - 1991
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560400722
Subject(s) - two dimensional nuclear magnetic resonance spectroscopy , chemistry , molecular dynamics , spectral line , nmr spectra database , nuclear overhauser effect , nuclear magnetic resonance spectroscopy , computational chemistry , crystallography , stereochemistry , physics , quantum mechanics
We have performed all‐atom constant temperature ( T = 285 K) molecular dynamics ( MD ) simulations on d (GA 4 T 4 C) 2 and d (GT 4 A 4 C) 2 for 200 ps using the NMR ‐derived structures as the starting points. The major purpose of MD simulation is to search the conformational space so that we can construct an ensemble of conformations that will reproduce the experimentally observed 2D NMR NOESY spectra. Analyses of the ensemble of duplex structures reveal that in both oligomers constituent nucleotides predominantly display B I conformations. A simple two‐parameter analysis shows that the nature of the long‐range collective bending motion is different in the two duplexes. The conformations obtained by use of molecular dynamics are very similar to each other for the same molecule, the root mean square deviation ( RMSD ) being 1.6 Å for d (GA 4 T 4 C) 2 and 1.1 Å for d (GT 4 A 4 C) 2 . We have computed theoretical 2D NOESY spectra for an ensemble of a large library of 1200 structures in the MD trajectory for d (GA 4 T 4 C) 2 . Theoretical MD ‐derived 2D NOESY spectra, averaged through an automated loop computation procedure over the 1200 timewise additivity NOESY simulation spectra, are compared with the corresponding experimental spectra. The agreement between the theoretical and experimental NOESY spectra is good. The results suggest that there is no longer any need to interpret NMR data on the basis of a “nonexistent” time‐average structure and that worthwhile information about the realistic composition of the ensemble of conformations that are present in solution can be obtained by interconnecting MD simulations and NMR data.