The solution structure of a B-DNA undecamer comprising a portion of the specific target site for the cAMP receptor protein in the gal operon. Refinement on the basis of interproton distance data.
Open Access
- 1 March 1985
- journal article
- research article
- Published by Wiley in The EMBO Journal
- Vol. 4 (3) , 829-835
- https://doi.org/10.1002/j.1460-2075.1985.tb03705.x
Abstract
A restrained least squares refinement of the solution structure of the double‐stranded DNA undecamer 5′d(AAGTGT‐GACAT).5′d(ATGTCACACTT) comprising a portion of the specific target site of the cAMP receptor protein in the gal operon is presented. The structure is refined on the basis of both distance and planarity restraints, 2331 in all. The distance restraints comprise 150 interproton distances determined from pre‐steady state nuclear Overhauser enhancement measurements and 2159 other interatomic distances derived from idealized geometry (i.e., distances between covalently bonded atoms, between atoms defining fixed bond angles, and between atoms defining hydrogen bonding in AT and GC base pairs). Two refinements were carried out and in both cases the final RMS difference between the experimental and calculated interproton distances was 0.2 A. The difference between the two refined structures is small (overall RMS difference of 0.23 A) and represents the error in the refined coordinates. Although the refined structures have an overall B‐type conformation there are large variations in many of the local conformational parameters including backbone and glycosidic bond torsion angles, helical twist and propellor twist, base roll and base tilt angles.This publication has 29 references indexed in Scilit:
- Secondary structure in the solution conformation of the proteinase inhibitor IIA from bull seminal plasma by nuclear magnetic resonanceJournal of Molecular Biology, 1984
- Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methodsJournal of Molecular Biology, 1983
- Conformation of glucagon in a lipid-water interphase by 1H nuclear magnetic resonanceJournal of Molecular Biology, 1983
- Specific DNA binding of the cyclic AMP receptor protein to a synthetic oligodeoxyribonucleotideFEBS Letters, 1983
- Assignment of the 1H nuclear magnetic resonance spectrum of the proteinase inhibitor IIA from bull seminal plasma by two-dimensional nuclear magnetic resonance at 500 MHzJournal of Molecular Biology, 1983
- Base sequence and helix structure variation in B and A DNAJournal of Molecular Biology, 1983
- Mechanics of sequence-dependent stacking of bases in B-DNAJournal of Molecular Biology, 1982
- Structure of a B-DNA dodecamerJournal of Molecular Biology, 1981
- On the prediction of protein structure: The significance of the root-mean-square deviationJournal of Molecular Biology, 1980
- Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibers of biopolymersJournal of Molecular Biology, 1973