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 1,500 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 surface area around the major and minor grooves of the DNA. The presence of water contacts during the entire simulation proximal to the fourth base pair step of core DNA sequence is a characteristic feature of ETS-GGAA. Such waters are more mobile in ETS-GGAG at 100 ps and distant after 1,500 ps. Anticorrelated motions between certain amino acids of Ets-1 protein are predominant in ETS-GGAA but less so or absent in the mutant. These motions are reflected in the flexibility of amino acid residues of the protein backbone. We consider that these conformational features and water contacts are involved in stabilizing the hydrogen bond interactions between helix-3 residues of Ets-1 and DNA during the transcription process. The Ets protein family of transcription factors includes species interacting with various genes that code for transcriptional activators and inhibitors involved in cell proliferation and differentiation (1, 2). The regulation of the initiation of gene transcription arises from the combined activity of different transcriptional regulators (2, 3). Ets family members found in species from invertebrates to humans share a conserved sequence of 85 amino acids, named the ETS domain. The ETS domain folds into a winged helix-turn-helix motif and binds to a consensus DNA sequence centered on the core GGAA motif, named the Ets-binding site. The sequences flanking this core motif (in the major groove) are variable and characterize the specificity of binding of the Ets transcription factor. Ets proteins have also been implicated in several types of cancer and other human diseases (4). Detailed conformational preferences that influence the sequence specificity of Ets proteins are essential for the design of anticancer drugs.The high-affinity DNA contains the GGAA core sequence, ETS-GGAA (Fig. 1). The low-affinity DNA is the single-base-pair mutant, ETS-GGAG. Recently we reported molecular dynamics (MD) studies (5) dealing with the binding of the ETS domain of Ets-1 protein to the high-and low-affinity 14-bp DNA structures. We have observed that the most conserved residues Arg-391, Arg-394, along with Tyr-395 of Ets-1, jointly contribute to recognize the GGAA or GGAG core DNA sequences (5). The differential hydrogen bond interact...

Sequence Discrimination by DNA-binding Domain of ETS Family Transcription Factor PU.1 Is Linked to Specific Hydration of Protein-DNA Interface

“…PU.1 is the most sequence-divergent member of the ETS family, a feature that may be correlated with its extensively hydrated protein-DNA interface. "Canonical" ETS-DNA complexes such as Ets-1 (11,12) and GABP␣ (42) feature a higher density of direct protein-to-nucleobase contacts than PU.1. Specific hydration might therefore evolve as compensatory mechanism to replace some of the "missing" anhydrous contacts.…”

Modulating the DNA Affinity of Elk-1 with Computationally Selected Mutations

“…Recently, Bruice and co-workers reported MD simulation results of Ets-1 bound to two different DNA sequences containing either GGAA or GGAG at the center, to understand how a single protein can differentiate two related DNA sequences. 38,39 They postulated that the binding affinity of Ets for the GGAG sequence is lower because of the alternate hydrogen bonds from Y395 (corresponding to Y66 of Elk) to either A3 or C4 0 , which destabilize the bidentate hydrogen bonds from R341 and R344 to DNA bases G2 and G1, respectively. When bound to a high-affinity site containing GGAA, the movement of Y395 is restricted by the C5 methyl group of T3 0 , which helps immobilize key hydrogen bonding networks.…”

Endothelial Transcriptional Networks in the Control of Angiogenesis: the ETS Factor

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