Conformations and dynamics of Ets-1 ETS domain-DNA complexes.

ABSTRACT: Molecular dynamics studies have been performed for 3.5 ns on the ETS domain of Ets-1 transcription factor bound to the 14-bp DNA, d(AGTGCCGGAAATGT), comprising the core sequence of high-affinity (GGAA), ETS-GGAA. In like manner, molecular dynamics simulations have been carried out for 3.9 ns on the mutant low-affinity core sequence, GGAG (ETS-GGAG). Analyses of the DNA backbone of ETS-GGAG show conformational interconversions from BI to BII substates. Also, crank shaft motions are noticed at the mutated nucleotide base pair step after 1500 ps of dynamics. The corresponding nucleotide of ETS-GGAA is characteristic of a BI conformation and no crank shaft motions are observed. The single mutation of ETS-GGAA to ETS-GGAG also results in variations of helical parameters and solvent-accessible s

SUBMITTER: Reddy SY 

PROVIDER: S-EPMC307592 | biostudies-literature | 2003 Dec

REPOSITORIES: biostudies-literature