Experimental snapshots of a protein-DNA binding landscape

Abstract

Protein recognition of DNA sites is a primary event for gene function. Its ultimate mechanistic understanding requires an integrated structural, dynamic, kinetic, and thermodynamic dissection that is currently limited considering the hundreds of structures of protein-DNA complexes available. We describe a protein-DNA-binding pathway in which an initial, diffuse, transition state ensemble with some nonnative contacts is followed by formation of extensive nonnative interactions that drive the system into a kinetic trap. Finally, nonnative contacts are slowly rearranged into native-like interactions with the DNA backbone. Dissimilar protein-DNA interfaces that populate along the DNA-binding route are explained by a temporary degeneracy of protein-DNA interactions, centered on "dual-role" residues. The nonnative species slow down the reaction allowing for extended functionality.energy landscape | human papillomavirus E2 protein | kinetic trap | kinetics | protein-DNA interaction

Mammalian Testis-determining Factor SRY and the Enigma of Inherited Human Sex Reversal

“…8E); (b) the transition states between coupled funnels and to the unbound state, and (c) the breadth or ruggedness of the native-like ground state. Whereas Sanchez et al (93) envisaged that frustration is widespread even in wild-type protein-DNA complexes, our studies of V60L SRY suggest that introduction of a single newly frustrated site can give rise to nonlocal changes in DNA bending.…”

“…Mutations V60L and V60A accelerate inferred rates of association; as a seeming paradox, perturbation of the minor wing enhances the apparent efficiency of a conformational search. In a related context, Sanchez et al (93) have developed a theoretical formalism for visualizing frustration based on coupled energy landscapes. By analogy to theories of nascent protein folding, the essential idea invokes a minimally frustrated free energy landscape for sequence recognition.…”

Mapping the Transition State for DNA Bending by IHF

“…The spirit of these measurements is analogous to the φ-value analysis pioneered by Fersht to probe the transition-state ensemble for protein folding. 53 Although similar approaches have been used to examine the encounter complex in stopped-flow studies of protein-DNA interactions, 23,24,[54][55][56] this study provides the first snapshot of the transitionstate ensemble separating the nonspecific encounter complex and the final, fully bent complex for a DNA-bending protein.…”

“…[22][23][24] For these and other DNA-bending proteins, there is ample evidence that DNA sequences that are more easily deformed into the conformation adopted by the DNA in the complex bind to the protein with a higher affinity. [25][26][27][28][29][30][31][32][33] The question remains: is the enhanced affinity reflected in an increase in the DNA bending rate or a decrease in the unbending/dissociation rate?…”

Frustration in protein–DNA binding influences conformational switching and target search kinetics

“…For example, following the arrival of the protein at the target site, additional events may be required for specific DNA recognition to occur (3). This transition from the encounter complex that is stabilized by nonspecific interactions to the specific protein-DNA complex may involve conformational changes to one or both biomolecules.…”