Calicheamicin-DNA complexes: Warhead alignment and saccharide recognition of the minor groove Journal Article
| Authors: | Ikemoto, N.; Kumar, R. A.; Ling, T. T.; Ellestad, G. A.; Danishefsky, S. J.; Patel, D. J. |
| Article Title: | Calicheamicin-DNA complexes: Warhead alignment and saccharide recognition of the minor groove |
| Abstract: | The solution structures of calicheamicin γ1 1, its cycloaromatized analog (calicheamicin ε), and its aryl tetrasaccharide complexed to a common DNA hairpin duplex have been determined by NMR and distance-refined molecular dynamics computations. Sequence specificity is associated with carbohydrate- DNA recognition that places the aryl tetrasaccharide component of all three ligands in similar orientations in the minor groove at the d(T-C-C-T)·d(A- G-G-A) segment. The complementary fit of the ligands and the DNA minor groove binding site creates numerous van der Waals contacts as well as hydrogen bonding interactions. Notable are the iodine and sulfur atoms of calicheamicin that hydrogen bond with the exposed amino proton of the 5'- and 3'-guanines, respectively, of the d(A-G-G-A) segment. The sequence-specific carbohydrate binding orients the enediyne aglycone of calicheamicin γ1 1 such that its C3 and C6 proradical centers are adjacent to the cleavage sites. While the enediyne aglycone of calicheamicin γ1 1 is tilted relative to the helix axis and spans the minor groove, the cycloaromatized aglycone is aligned approximately parallel to the helix axis in the respective complexes. Specific localized conformational perturbations in the DNA have been identified from imino proton complexation shifts and changes in specific sugar pucker patterns on complex formation. The helical parameters for the carbohydrate binding site are comparable with corresponding values in B-DNA fibers while a widening of the groove is observed at the adjacent aglycone binding site. |
| Keywords: | comparative study; molecular dynamics; drug structure; dna; double stranded dna; molecular sequence data; magnetic resonance spectroscopy; binding site; dna sequence; hydrogen bond; models, molecular; solutions; nucleic acid conformation; antibiotics, antineoplastic; dna binding; nuclear magnetic resonance; molecular conformation; carbohydrate sequence; carbohydrate derivative; chemical bond; dna conformation; priority journal; article; calicheamicin gamma1; support, non-u.s. gov't; calicheamicin derivative; dna drug complex; antibiotics, aminoglycoside |
| Journal Title: | Proceedings of the National Academy of Sciences of the United States of America |
| Volume: | 92 |
| Issue: | 23 |
| ISSN: | 0027-8424 |
| Publisher: | National Academy of Sciences |
| Date Published: | 1995-11-07 |
| Start Page: | 10506 |
| End Page: | 10510 |
| Language: | English |
| DOI: | 10.1073/pnas.92.23.10506 |
| PUBMED: | 7479829 |
| PROVIDER: | scopus |
| PMCID: | PMC40640 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 28 August 2018 -- Source: Scopus |
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477Patel -
12Kumar
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