Complexes of HMO1 with DNA: Structure and Affinity

TL;DR

This paper investigates how the HMO1 protein binds to specific DNA sequences, revealing structural and affinity details that explain its sequence specificity.

Contribution

The study provides new structural and thermodynamic insights into HMO1's DNA binding mechanism and its preference for the IFHL motif.

Findings

HMO1 forms a complex with DNA without altering the structure of either component.

Molecular modeling shows two extended sites on HMO1 Box B stabilize DNA bending.

HMO1 binds IFHL sequences with twice the stability compared to randomized sequences.

Abstract

Saccharomyces cerevisiae HMO1 is an architectural nuclear DNA-binding protein that stimulates the activity of some remodelers and regulates the transcription of ribosomal protein genes, often binding to a DNA motif called IFHL. However, the molecular mechanism dictating this sequence specificity is unclear. Our circular dichroism spectroscopy studies show that the HMO1:DNA complex forms without noticeable changes in the structure of DNA and HMO1. Molecular modeling/molecular dynamics studies of the DNA complex with HMO1 Box B reveal two extended sites at the N-termini of helices I and II of Box B that are involved in the formation of the complex and stabilize the DNA bend induced by intercalation of the F114 side chain between base pairs. A comparison of the affinities of HMO1 for 24 bp DNA fragments containing either randomized or IFHL sequences reveals a twofold increase in the stability of the complex in the latter case, which may explain the selectivity in the recognition of the IFHL-containing promoter regions.

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