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Volumn 110, Issue 39, 2006, Pages 19652-19663

Characterization of nucleobase-amino acid stacking interactions utilized by a DNA repair enzyme

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; CRYSTAL STRUCTURE; DNA; ENZYMES; POTENTIAL ENERGY;

EID: 33750309040     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp061939v     Document Type: Article
Times cited : (77)

References (92)
  • 3
    • 0001473891 scopus 로고    scopus 로고
    • For a review of studies related to the DNA glycosylases, see, for example: (a) David, S. S.; Williams, S. D. Chem. Rev. 1998, 98, 1221-1261.
    • (1998) Chem. Rev. , vol.98 , pp. 1221-1261
    • David, S.S.1    Williams, S.D.2
  • 9
    • 33644639463 scopus 로고    scopus 로고
    • and references therein
    • (b) Mishina, Y.; Duguid, E. M.; He, Chuan, Chem. Rev. 2006, 106, 215-232, and references therein.
    • (2006) Chem. Rev. , vol.106 , pp. 215-232
    • Mishina, Y.1    Duguid, E.M.2    He, C.3
  • 22
    • 0000965687 scopus 로고    scopus 로고
    • For a review on the calculation of stacking interactions between the natural DNA nucleobases, see, for example: (a) Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247-3276.
    • (1999) Chem. Rev. , vol.99 , pp. 3247-3276
    • Hobza, P.1    Sponer, J.2
  • 66
    • 84906412092 scopus 로고    scopus 로고
    • note
    • Polarizabilities decrease with the surface area according to TRP (80.8) > TYR (57.6) > PHE (54.0) > HIS (36.4) (where the HF/6-31G-(d,p) polarizabilities are provided in brackets in units of bohr3).
  • 68
    • 84906412093 scopus 로고    scopus 로고
    • note
    • -1. Consideration of twist intervals smaller than 30° may yield better agreement.
  • 69
    • 84906368809 scopus 로고    scopus 로고
    • note
    • It should be noted that the centers of mass of adenine and 3-methyladenine are slightly different, which also leads to small changes in the preferred angle of rotation.
  • 70
    • 84906397646 scopus 로고    scopus 로고
    • note
    • We note that the tilt angle is not considered since the tilt dependence is only significant in the case of 3MeA:HIS dimer.
  • 85
    • 84906368807 scopus 로고    scopus 로고
    • note
    • The tilt angle was not further investigated for these modified bases since this consistently led to a very small, if any, increase in the stacking interaction for A and 3MeA complexes.
  • 89
    • 84906412091 scopus 로고    scopus 로고
    • note
    • It should be noted that εA was suggested to bind to MagIII in two different orientations (see ref 9).
  • 90
    • 84906412089 scopus 로고    scopus 로고
    • note
    • It should be noted that two atoms in hypoxanthine were mislabeled in the crystal structure of free hypoxanthine cocrystallized with AlkA (ref 8); however, this does not affect our overlay process.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.