Effect of Osmolytes on the Binding of EGR1 Transcription Factor to DNA

ABSTRACT: Osmolytes play a key role in maintaining protein stabilit

Physicochemical Insights Into the EGR1-DNA Interaction

Early growth response 1 (EGR1) transcription factor orchestrates a plethora of signaling cascades in response to a wide variety of stimuli such as growth factors and hormones. Herein, using a battery of biophysical tools, I explore the molecular basis of binding of EGR1 to its cognate gene promoters. My data show that the binding of EGR1 to DNA is tightly regulated by solution pH. The binding affinity undergoes an enhancement of more than an order of magnitude with increasing pH from 5 to 8, implying that the deprotonation of an ionizable residue accounts for such behavior. This ionizable residue is identified as H382 by virtue of the fact that its substitution to nonionizable residues abolishes pH-dependence of the binding of EGR1 to DNA. Notably, H382 inserts into the major groove of DNA and stabilizes the EGR1-DNA interaction via both hydrogen bonding and van der Waals contacts. I also provide evidence that the binding of EGR1 transcription factor to DNA displays virtually zero dependence on ionic strength under physiological salt concentrations and that such feat is accomplished via favorable enthalpic contributions. Importantly, I unearth the molecular origin of such favorable enthalpy and attribute it to the ability of H382 residue to stabilize the EGR1-DNA interaction via both intermolecular hydrogen bonding and van der Waals contacts against the backdrop of salt. Consistent with this notion, the substitution of H382 residue with other amino acids faithfully restores salt-dependent binding of EGR1 to DNA in a canonical fashion. Finally, my biophysical analysis reveals that DNA sequence variations within the target gene promoters tightly modulate the energetics of binding of EGR1 and that nucleotide substitutions at certain positions are much more detrimental to EGR1-DNA interaction than others. In particular, the reduction in binding affinity poorly correlates with the loss of enthalpy and gain of entropy—a trend indicative of a complex interplay between underlying thermodynamic factors due to the differential role of water solvent upon nucleotide substitution. In sum, my findings uncover an unexpected but a key protonation-deprotonation step in the molecular recognition of EGR1 and suggest that it may act as a sensor of pH within the intracellular environment. This study reports the first example of a eukaryotic protein-DNA interaction capable of overriding the polyelectrolye effect. The work presented herein also bears important implications on understanding the molecular determinants of a key protein-DNA interaction at the cross-roads of human health and disease

Biophysical basis of the promiscuous binding of B‐cell lymphoma protein 2 apoptotic repressor to BH3 ligands

B‐cell lymphoma protein 2 (Bcl2) apoptotic repressor carries out its function by virtue of its ability to bind to BH3 domains of various pro‐apoptotic regulators in a highly promiscuous manner. Herein, we investigate the biophysical basis of such promiscuity of Bcl2 toward its cognate BH3 ligands. Our data show that although the BH3 ligands harboring the LXXXAD motif bind to Bcl2 with submicromolar affinity, those with the LXXX[G/S]D motif afford weak interactions. This implies that the replacement of alanine at the fourth position (A + 4)—relative to the N‐terminal leucine (L0) within the LXXXAD motif—to glycine/serine results in the loss of free energy of binding. Consistent with this notion, the A + 4 residue within the BH3 ligands harboring the LXXXAD motif engages in key intermolecular van der Waals contacts with A149 lining the ligand binding groove within Bcl2, whereas A + 4G/S substitution results in the disruption of such favorable binding interactions. Of particular interest is the observation that although increasing ionic strength has little or negligible effect on the binding of high‐affinity BH3 ligands harboring the LXXXAD motif, the binding of those with the LXXX[G/S]D motif in general experiences a varying degree of enhancement. This salient observation is indicative of the fact that hydrophobic forces not only play a dominant but also a universal role in driving the Bcl2‐BH3 interactions. Taken together, our study sheds light on the molecular basis of the factors governing the promiscuous binding of Bcl2 to pro‐apoptotic regulators and thus bears important consequences on the development of rational therapeutic approaches. Copyright © 2013 John Wiley & Sons, Ltd. BH3 ligands can be divided into two distinct LXXXAD and LXXX[G/S]D motifs. BH3 ligands harboring LXXXAD motifs bind to B‐cell lymphoma protein 2 with high affinity. Increasing ionic strength generally results in binding enhancement of BH3 ligands. Hydrophobic interactions predominantly govern the formation of B‐cell lymphoma protein 2‐BH3 complexes

Energetic coupling along an allosteric communication channel drives the binding of Jun-Fos heterodimeric transcription factor to DNA

Although allostery plays a central role in driving protein-DNA interactions, the physical basis of such cooperative behavior remains poorly understood. In the present study, using isothermal titration calorimetry in conjunction with site-directed mutagenesis, we provide evidence that an intricate network of energetically-coupled residues within the basic regions of the Jun-Fos heterodimeric transcription factor accounts for its allosteric binding to DNA. Remarkably, energetic coupling is prevalent in residues that are both close in space, as well as residues distant in space, implicating the role of both short- and long-range cooperative interactions in driving the assembly of this key protein-DNA interaction. Unexpectedly, many of the energetically-coupled residues involved in orchestrating such a cooperative network of interactions are poorly conserved across other members of the basic zipper family, emphasizing the importance of basic residues in dictating the specificity of basic zipper-DNA interactions. Collectively, our thermodynamic analysis maps an allosteric communication channel driving a key protein-DNA interaction central to cellular functions in health and disease

Grb2 Directly Interacts with HGAL and Ameliorates Its Effects on B-Cell Receptor Signaling

Abstract Human Germinal center Associated Lymphoma (HGAL) is specifically expressed in germinal center (GC) B-cells and GC-derived lymphomas. High expression of HGAL is an independent predictor of prolonged survival of Diffuse Large B-Cell (DLBCL) and classical Hodgkin (cHL) lymphoma patients. HGAL is a unique adaptor protein that regulates both cell motility and B-cell receptor (BCR) signaling, processes that are central for the successful completion of the GC reaction. HGAL increases BCR signaling by binding to and enhancing Syk kinase activity. However, our previous studies also suggested that other proteins may be involved in HGAL-mediated regulation of BCR signaling. In vitro kinase assays demonstrated that both Syk and Lyn can phosphorylate HGAL. Mass spectrometry (μ LC/MS/MS) demonstrated that these kinases can phosphorylate HGAL's tyrosines Y80, Y86, Y106Y107, Y128 and Y148. The HGAL Y106Y107 comprise a YYENV motif (aa 106-110) similar to the phosphopeptide motif pYXNX frequently used as a binding site to the SH2 domain of Growth Factor Receptor bound protein 2 (Grb2). Grb2 signaling in B cells controls lymphoid follicle organization and the GC reaction. Specifically, Grb2 is an integral component of the BCR signalosome and decreases BCR-induced Ca2+influx. The presence of the phosphorylated YYENV motif in HGAL raised the hypothesis that HGAL-Grb2 interactions may play a role in HGAL -mediated regulation of BCR signaling. To address this possibility, we performed reciprocal coimmunoprecipitations (Co-IPs) of endogenous HGAL and Grb2 in Raji and VAL lymphoma cell lines. These studies demonstrated that HGAL Co-IPs with Grb2. The interaction between these two proteins is dependent on the presence and phosphorylation of tyrosines in the YYENV motif, since an HGAL mutant in which these tyrosines were mutated to phenylalanine (FFENV) failed to Co-IP with Grb2. Isothermal titration calorimetry confirmed that phosphorylated (pYEN) but not unphosphorylated (YEN) HGAL-derived 12-mer peptides bind to the SH2 domain of Grb2 with an affinity of 5µM. GST-Grb2 pull down assays with recombinant Trx-HGAL(FFENV) and Trx-HGAL proteins confirmed that the HGAL-Grb2 interaction is direct and occurs only if the HGAL tyrosines are phosphorylated. Concordantly, addition of phosphatase to cellular lysates decreased the HGAL-Grb2 interaction. Furthermore, CO-IP studies demonstrated that HGAL's interaction with Grb2 increases following BCR stimulation-induced HGAL phosphorylation. Concordantly, confocal microscopy studies demonstrated HGAL-Grb2 colocalization in the cell membrane following BCR signaling activation. We next examined the functional significance of the HGAL-Grb2 interaction on BCR activation as measured by intracellular and transmembrane Ca2+ mobilization and phosphorylation of proximal BCR effectors (Syk (Y352), BLNK (Y84), BTK (Y551) and PLCγ2 (Y753) in several lymphoma cell lines (U2942, TMD8 and Mino) stablly transfected to express HGAL protein. HGAL expression markedly increased Ca2+ influx and phosphorylation of these proteins, while Grb2 knockdown only slightly increased transmembrane Ca2+ mobilization. Of note, concomitant HGAL expression and Grb2 knockdown further increased intracellular and transmembrane Ca2+ influx and phosphorylation of BCR effectors in comparison to HGAL expression alone. Expression of the HGAL (FFENV) mutant also enhanced Ca2+ influx and phosphorylation of BCR effectors in comparison to wild type HGAL. Concordantly, expression of the dominant negative Grb2 (W193K) mutant also enhanced HGAL's effects on BCR signaling. These observations suggest that Grb2's interaction with HGAL ameliorates HGAL's effects on BCR signaling. We previously showed that HGAL interacts with Syk and enhances Syk kinase activity. We now demonstrate that Grb2 Co-IPs with both Syk and HGAL and thus may potentially interfere with HGAL-Syk interaction. Indeed, knockdown of Grb2 increased HGAL Co-IP with the Syk kinase and this was associated with increased BCR signaling. These findings indicate that Grb2 ameliorates HGAL-mediated enhancement of BCR signaling by decreasing HGAL binding to Syk. In summary, out data demonstrates that Grb2 directly interacts with HGAL and ameliorates HGAL-enhanced BCR signaling. These interactions may play an important function in regulating the magnitude of BCR signaling during the GC reaction. Disclosures No relevant conflicts of interest to declare

Structural and thermodynamic consequences of the replacement of zinc with environmental metals on estrogen receptor α–DNA interactions

Estrogen receptor α (ERα) acts as a transcription factor by virtue of the ability of its DNA‐binding (DB) domain, comprised of a tandem pair of zinc fingers, to recognize the estrogen response element within the promoters of target genes. Herein, using an array of biophysical methods, we probe the structural consequences of the replacement of zinc within the DB domain of ERα with various environmental metals and their effects on the thermodynamics of binding to DNA. Our data reveal that whereas the DB domain reconstituted with divalent ions of zinc, cadmium, mercury, and cobalt binds to DNA with affinities in the nanomolar range, divalent ions of barium, copper, iron, lead, manganese, nickel, and tin are unable to regenerate DB domain with DNA‐binding potential, although they can compete with zinc for coordinating the cysteine ligands within the zinc fingers. We also show that the metal‐free DB domain is a homodimer in solution and that the binding of various metals only results in subtle secondary and tertiary structural changes, implying that metal coordination may only be essential for binding to DNA. Collectively, our findings provide mechanistic insights into how environmental metals may modulate the physiological function of a key nuclear receptor involved in mediating a plethora of cellular functions central to human health and disease. Copyright © 2011 John Wiley & Sons, Ltd

Ligand Binding and Membrane Insertion Compete with Oligomerization of the BclXL Apoptotic Repressor

B-cell lymphoma extra large (BclXL) apoptotic repressor plays a central role in determining the fate of cells to live or die during physiological processes such as embryonic development and tissue homeostasis. Herein, using a myriad of biophysical techniques, we provide evidence that ligand binding and membrane insertion compete with oligomerization of BclXL in solution. Of particular importance is the observation that such oligomerization is driven by the intermolecular binding of its C-terminal transmembrane (TM) domain to the canonical hydrophobic groove in a domain-swapped trans fashion, whereby the TM domain of one monomer occupies the canonical hydrophobic groove within the other monomer and vice versa. Binding of BH3 ligands to the canonical hydrophobic groove displaces the TM domain in a competitive manner, allowing BclXL to dissociate into monomers upon hetero-association. Remarkably, spontaneous insertion of BclXL into DMPC/DHPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine/1,2-dihexanoyl-sn-glycero-3-phosphocholine) bicelles results in a dramatic conformational change such that it can no longer recognize the BH3 ligands in what has come to be known as the “hit-and-run” mechanism. Collectively, our data suggest that oligomerization of a key apoptotic repressor serves as an allosteric switch that fine-tunes its ligand binding and membrane insertion pertinent to the regulation of apoptotic machinery. [Display omitted] ► BclXL oligomerizes in solution. ► BclXL oligomerization is driven by the C-terminal TM domain through domain swapping. ► Binding of BH3 ligands triggers the dissociation of BclXL oligomers into monomers. ► Membrane insertion of BclXL is coupled with displacement of BH3 ligands

pH modulates the binding of early growth response protein 1 transcription factor to DNA

The transcription factor early growth response protein (EGR)1 orchestrates a plethora of signaling cascades involved in cellular homeostasis, and its downregulation has been implicated in the development of prostate cancer. Herein, using a battery of biophysical tools, we show that the binding of EGR1 to DNA is tightly regulated by solution pH. Importantly, the binding affinity undergoes an enhancement of more than an order of magnitude with an increase in pH from 5 to 8, implying that the deprotonation of an ionizable residue accounts for such behavior. This ionizable residue is identified as His382 by virtue of the fact that its replacement by nonionizable residues abolishes the pH dependence of the binding of EGR1 to DNA. Notably, His382 inserts into the major groove of DNA, and stabilizes the EGR1-DNA interaction via both hydrogen bonding and van der Waals contacts. Remarkably, His382 is mainly conserved across other members of the EGR family, implying that histidine protonation-deprotonation may serve as a molecular switch for modulating the protein-DNA interactions that are central to this family of transcription factors. Collectively, our findings reveal an unexpected but a key step in the molecular recognition of the EGR family of transcription factors, and suggest that they may act as sensors of pH within the intracellular environment

Discovery and Biological Evaluation of Potent and Selective N-Methylene Saccharin-Derived Inhibitors for Rhomboid Intramembrane Proteases

Rhomboids are intramembrane serine proteases and belong to the group of structurally and biochemically most comprehensively characterized membrane proteins. They are highly conserved and ubiquitously distributed in all kingdoms of life and function in a wide range of biological processes, including epidermal growth factor signaling, mitochondrial dynamics, and apoptosis. Importantly, rhomboids have been associated with multiple diseases, including Parkinson's disease, type 2 diabetes, and malaria. However, despite a thorough understanding of many structural and functional aspects of rhomboids, potent and selective inhibitors of these intramembrane proteases are still not available. In this study, we describe the computer-based rational design, chemical synthesis, and biological evaluation of novel N-methylene saccharin-based rhomboid protease inhibitors. Saccharin inhibitors displayed inhibitory potency in the submicromolar range, effectiveness against rhomboids both in vitro and in live Escherichia coli cells, and substantially improved selectivity against human serine hydrolases compared to those of previously known rhomboid inhibitors. Consequently, N-methylene saccharins are promising new templates for the development of rhomboid inhibitors, providing novel tools for probing rhomboid functions in physiology and disease.status: publishe