Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein

被引:12
作者
Velmurugu, Yogambigai [1 ]
Vivas, Paula [1 ,4 ]
Connolly, Mitchell [1 ]
Kuznetsov, Serguei V. [1 ]
Rice, Phoebe A. [2 ]
Ansari, Anjum [1 ,3 ]
机构
[1] Univ Illinois, Dept Phys, Chicago, IL 60607 USA
[2] Univ Chicago, Dept Biochem & Mol Biol, 920 E 58th St, Chicago, IL 60637 USA
[3] Univ Illinois, Dept Bioengn, Chicago, IL 60607 USA
[4] ASK Chem, 5200 Blazer Pkwy, Dublin, OH 43017 USA
基金
美国国家科学基金会;
关键词
DIFFUSION-DRIVEN MECHANISMS; FACILITATED TARGET LOCATION; DAMAGE RECOGNITION; NUCLEIC-ACIDS; ECORV ENDONUCLEASE; NUCLEOSOMAL DNA; PROMOTER DNA; HU BINDING; BENT DNA; IHF;
D O I
10.1093/nar/gkx1215
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a mu s-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (similar to 100 mu s) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1-10 ms) step is accelerated similar to 5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is nonspecific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
引用
收藏
页码:1741 / 1755
页数:15
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