Two distinct modes of protein-induced bending in DNA.
Two distinct modes of protein-induced bending in DNA.
Crystallised "naked" DNA oligomers in the B form show significant conformational mobility, particularly at CA/TG and TA/TA steps: there is a range in Roll angle of some 15 degrees between consecutive base-pairs, and Slide and Twist are directly coupled to Roll. We call such motions "mode I". They are sufficient to enable DNA to curve gently around proteins such as histone octamers in the nucleosome particle. When DNA bends around other proteins, such as CAP and TBP, its distortion is much more severe. Although the DNA in close contact with these proteins includes the CA/TG and TA/TA steps, respectively, the mode I flexibility is not deployed: instead, a more severe "mode II" manoeuvre is observed in DNA/protein co-crystals. Mode II has several distinctive physical features. First, its range of Roll angle is much wider than for mode I. Second, the major-groove width remains more-or-less constant as Roll increases, whereas it decreases significantly as Roll increases in mode I; and this enables the major groove of the DNA to accommodate a protein moiety in its severely bent conformation. Third, the value of Slide remains more-or-less constant as Roll increases, whereas it decreases in mode I. In general, in both modes I and II, the major-groove width appears to be closely related to the Slide between base-pairs. In mode II there appears to be a definite "point pivot" on the major-groove side of the two base-pairs that constitute a dinucleotide step, formed either by the steric interlocking of propeller-twisted base-pairs or by a bifurcated hydrogen bond. Distortion of DNA in mode II seems to be an intrinsic property of the double-helical structure, since it occurs whether protein is bound on the major-groove side (e.g. CAP) or on the minor-groove side (e.g. TBP). Mode II distortion occurs in a wider range of steps than those that show the largest mode-I variation; nevertheless, "access" to mode II deformation appears to be gained via mode I distortion at particular steps CA/TG and TA/TA.
- University of Cambridge United Kingdom
Nucleic Acid Conformation, Proteins, DNA, Mathematical Computing
Nucleic Acid Conformation, Proteins, DNA, Mathematical Computing
5 Research products, page 1 of 1
- 1998IsAmongTopNSimilarDocuments
- 2020IsAmongTopNSimilarDocuments
- 2013IsAmongTopNSimilarDocuments
- 2010IsAmongTopNSimilarDocuments
citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).133 popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.Top 10% influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).Top 10% impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.Top 10%
