Facilitated Unbinding via Multivalency-Enabled Ternary Complexes: New Paradigm for Protein–DNA Interactions

Chen, Tai-Yen; Cheng, Yu‐Shan; Huang, Pei-San; Chen, Peng

doi:10.1021/acs.accounts.7b00541

Cited by 47 publications

(52 citation statements)

References 49 publications

(127 reference statements)

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“…2b). These deviations in the kinetics from the simple competition mechanism are a typical indication for the formation of ternary 8 complexes, a mechanism that has recently emerged as a paradigm for gene regulation and typically involves multivalent interactions [36][37][38][39][40] .Ternary complex formation immediately suggests itself for IDPs such as H1 and ProTα, whose interactions can be considered an extreme case of multivalency 8,36,40,41 : If the positively charged tails of H1 remain largely disordered and dynamic while bound to the nucleosome, as suggested by recent work on H1 bound to double-stranded DNA 6 and from simulations 26 , the negatively charged ProTα would still be able to invade the complex and bind to H1 while remaining disordered 5 . Intra-and intermolecular single-molecule FRET experiments show that ProTα binding indeed accelerates dissociation of H1 from the nucleosome (Fig.…”

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confidence: 99%

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Heidarsson

Mercadante

Sottini

et al. 2020

Preprint

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Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin α. Consequently, prothymosin α can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation. 3 A large fraction of the human genome codes for proteins that contain substantial disordered regions or even lack any well-defined three-dimensional structure 1 . These intrinsically disordered proteins are involved in many cellular processes and mediate key interactions with other proteins or nucleic acids 2 . DNA-and RNA-binding proteins often contain disordered regions highly enriched in positively charged residues 3,4 , which are expected to facilitate electrostatic interactions with their cellular targets, the highly negatively charged nucleic acids 3 . The affinities can be remarkably high, even if no structure is formed upon binding 5,6 . Such polyelectrolyte interactions have long been known in the field of soft matter physics 7 , but their importance in biology has only recently started to be recognized 5,6,[8][9][10][11] and is thus largely unexplored.A ubiquitous group of proteins with long disordered positively charged regions are the histones, which are responsible for packaging DNA into chromatin. Among these, the linker histones are particularly remarkable 12 : They are largely disordered and highly positively charged, with two disordered regions flanking a small folded globular domain. By binding to the linker DNA on the nucleosome (Fig. 1a), linker histones contribute to chromatin condensation and transcriptional regulation 12,13 . However, the role of protein disorder in the complex between nucleosome and linker histone and the functional consequences have remained unclear. Here, by integrating single-molecule experiments and simulations, we establish a molecular model of the linker histone-nucleosome complex and show that disorder enables an unexpected mechanism that regulates linker histone binding: The highly negatively charged and disordered human protein prothymosin α (ProTα), a histone chaperone 14-17 that forms a high-affinity disordered complex with linker histone H1 5 , can efficiently...

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confidence: 99%

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Heidarsson

Mercadante

Sottini

et al. 2020

Preprint

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“…Indeed, some proteins that undergo facilitated dissociation are architectural proteins, such as the bacterial protein Fis, which can DNA stabilize loops against applied forces (63,97). In addition, several recent studies suggest that facilitated dissociation may have important regulatory effects in living cells (23,29,30,36,98,99). Our model suggests that these facilitated dissociation kinetics may be modulated by mechanical stresses transmitted through DNA/chromatin, and more generally, the local conformation of the genome.…”

Section: Relevance To In Vivo Protein Kinetics and Functionmentioning

confidence: 86%

“…Non-fluorescing competitor proteins may be flowed in so that as competitors from solution exchange with the initially bound fluorescent proteins, the tethered DNA strand becomes darker. Using an approach with distinguishable sets of protein is essential because simply measuring the number of bound proteins is insufficient to determine the dissociation rate because proteins may exchange, i.e., when a protein vacates a DNA binding site, the binding site may nonetheless remain occupied by the competitor protein (21)(22)(23)30). However, with one species of "light" protein and one species of "dark" (competitor) protein, dissociation rates can be measured by observing the decay of the fluorescence signal along the tethered DNA.…”

Section: Single-molecule Experiments To Test the Modelmentioning

confidence: 99%

“…Recent work with a variety of biomolecules, such as transcription factors (20,22,(24)(25)(26)(27)(28)(29), metalloregulators (21,30), chromatin effectors (31), DNA polymerases (32)(33)(34)(35)(36), antibody-antigen complexes (37), and other biological complexes (23,(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48) has demonstrated that facilitated dissociation, in which protein dissociation rates depend on ambient protein or other biomolecule concentration, is a widespread phenomenon both in vitro and in vivo. Facilitated dissociation contrasts with classical kinetic models of bimolecular complexes that undergo a simple, binary on/off transitions, and have concentration-dependent association rates and concentration-independent dissociation rates.…”

Section: Introductionmentioning

confidence: 99%

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Force-dependent facilitated dissociation can generate protein-DNA catch bonds

Dahlke

Zhao

Sing

et al. 2019

Preprint

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Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry, and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip-and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. These force-dependent kinetics are broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor -competitor proteins -rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes. Statement of significanceMechanotransduction regulates chromatin structure and gene transcription. Forces may be transduced via biomolecular interaction kinetics, particularly, how molecular complexes dissociate under stress. Typically, molecules form "slip bonds" that dissociate more rapidly under tension, but some form "catch bonds" that dissociate more slowly under tension due to their internal structure. We develop a model for a distinct type of catch bond that emerges via an extrinsic factor: protein concentration in solution. Underlying this extrinsic catch bond is "facilitated dissociation," whereby competing proteins from solution accelerate protein-DNA unbinding by invading the DNA binding site. Forces may suppress invasion, inhibiting dissociation, as for catch bonds. Force-dependent facilitated dissociation can thus govern the kinetics of proteins sensitive to local DNA conformation and mechanical state.

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“…To measure the structural similarity of snapshots from the trajectories with respect to the binary-Fis reference structure, we used an order parameter Q , which compares the pairwise distances of C α atoms among the residues in a given instantaneous structure to those in the binary-Fis reference structure. The Q value ( Q binFis ) for all snapshots from the simulation trajectories was calculated using the following expression (3) where N is the total number of residues; r ij is the instantaneous distance between C α atoms of residue i and j in the Fis protein pair;…”

Section: Q Value Of Binary-fis Configuration ( Q Binfis )mentioning

confidence: 99%

Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation

Tsai

Zheng

Chen

et al. 2019

Preprint

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As a master transcription regulator, Fis protein influences over two hundred genes of E-coli . Fis protein's non-specific binding to DNA is widely acknowledged, and its kinetics of dissociation from DNA is strongly influenced by its surroundings: the dissociation rate increases as the concentration of Fis protein in the solution-phase increases. In this study, we use computational methods to explore the global binding energy landscape of the Fis1:Fis2:DNA ternary complex. The complex contains a binary-Fis molecular dyad whose formation relies on complex structural rearrangements. The simulations allow us to distinguish several different pathways for the dissociation of the protein from DNA with different functional outcomes, and involving different protein stoichiometries: 1. Simple exchange of proteins and 2. Cooperative unbinding of two Fis proteins to yield bare DNA. In the case of exchange, the protein on the DNA is replaced by solution-phase protein through competition for DNA binding sites. This process seen in fluorescence imaging experiments has been called facilitated dissociation. In the latter case of cooperative unbinding of pairs, two neighboring Fis proteins on DNA form a unique binary-Fis configuration via protein-protein interactions, which in turn leads to the co-dissociation of both molecules simultaneously, a process akin to the "molecular stripping" seen in the NFκB/IκB genetic broadcasting system. This simulation shows that the existence of multiple binding configurations of transcription factors can have a significant impact on the kinetics and outcome of transcription factor dissociation from DNA, with important implications for the systems biology of gene regulation by Fis.

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Facilitated Unbinding via Multivalency-Enabled Ternary Complexes: New Paradigm for Protein–DNA Interactions

Cited by 47 publications

References 49 publications

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Force-dependent facilitated dissociation can generate protein-DNA catch bonds

Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation

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