Facilitated DNA Search by Multidomain Transcription Factors: Cross Talk via a Flexible Linker

Abstract

More than 70% of eukaryotic proteins are composed of multiple domains. However, most studies of the search for DNA focus on individual protein domains and do not consider potential cross talk within a multidomain transcription factor. In this study, the molecular features of the DNA search mechanism were explored for two multidomain transcription factors: human Pax6 and Oct-1. Using a simple computational model, we compared a DNA search of multidomain proteins with a search of isolated domains. Furthermore, we studied how manipulating the binding affinity of a single domain to DNA can affect the overall DNA search of the multidomain protein. Tethering the two domains via a flexible linker increases their affinity to the DNA, resulting in a higher propensity for sliding along the DNA, which is more significant for the domain with the weaker DNA-binding affinity. In this case, the domain that binds DNA more tightly anchors the multidomain protein to the DNA and, via the linker, increases the local concentration of the weak DNA-binding domain (DBD). The tethered domains directly exchange between two parallel DNA molecules via a bridged intermediate, where intersegmental transfer is promoted by the weaker DBD. We found that, in general, the relative affinity of the two domains can significantly affect the cross talk between them and thus their overall capability to search DNA efficiently. The results we obtained by examining various multidomain DNA-binding proteins support the necessity of discrepancies between the DNA-binding affinities of the constituent domains.

Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble

“…To gain further insight into the role of the search modes, we also conducted coarse-grained molecular dynamics simulations for investigating the intersegment transfer processes. This computational approach is well established and was previously used for several proteins, including Egr-1 (28,(45)(46)(47). In these simulations, two B-form DNA duplexes (100 bp) were placed in parallel with an interaxial distance of 60 Å, and we monitored how protein translocates on DNA for the four types of Egr-1 ZF-DBD constructs.…”

“…Similar modeling scheme was used to model mutants types 2 and 3. Further details of the simulations and the analyses can be found in previous publications of Levy and coworkers (28,31,(45)(46)(47)60).…”

Isolating Contributions from Intersegmental Transfer to DNA Searching by Alkyladenine DNA Glycosylase*

“…It has been proposed that these basic tails enable efficient intersegmental transfer by allowing for transient formation of a bridging complex (23,24,36). AAG similarly has a positively charged amino terminus that decreases the rate of dissociation and thereby contributes to processive searching (11).…”

“…This region of human AAG is proteolytically sensitive and appears to be flexible (19). Many eukaryotic DNA-binding and DNA repair proteins also have disordered amino or carboxyl termini (20 -22), and it is proposed that one role of these flexible regions is to enable bridging interactions between two segments of DNA (23,24).…”

Interplay between Minor and Major Groove-binding Transcription Factors Sox2 and Oct1 in Translocation on DNA Studied by Paramagnetic and Diamagnetic NMR

“…Finally, a transcription factor can undergo direct transfer from one DNA site to either a distal site on the same DNA molecule or to another DNA molecule without ever dissociating into free solution. This involves a flycast mechanism (9) whereby a tail or domain is used to search for other DNA sites, resulting in the transient formation of a bridged complex, followed by the first order transfer of the remainder of the transcription factor to the new site (4,10,11).…”