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Nuclear Factor of Activated T cells 5 (NFAT5) is a transcription factor (TF) that mediates protection from adverse effects of hypertonicity by increasing transcription of genes, including those that lead to cellular accumulation of protective organic osmolytes. NFAT5 has three intrinsically ordered (ID) activation domains (ADs). Using the NFAT5 N-terminal domain (NTD), which contains AD1, as a model, we demonstrate by biophysical methods that the NTD senses osmolytes and hypertonicity, resulting in stabilization of its ID regions. In the presence of sufficient NaCl or osmolytes, trehalose and sorbitol, the NFAT5 NTD undergoes a disorder-to-order shift, adopting higher average secondary and tertiary structure. Thus, NFAT5 is activated by the stress that it protects against. In its salt and/or osmolyte-induced more ordered conformation, the NTD interacts with several proteins, including HMGI-C, which is known to protect against apoptosis. These findings raise the possibility that the increased intracellular ionic strength and elevated osmolytes caused by hypertonicity activate and stabilize NFAT5., Competing Interests: The authors declare no competing interest.

Pathological retinal neovascularization is the most common cause of vision loss. PKCθ has been shown to play a role in type 2 diabetes, which is linked to retinal neovascularization. Based on these clues, we have studied the role of PKCθ and its downstream target genes JunB and VEGFR3 in retinal neovascularization using global and tissue-specific knockout mouse models along with molecular biological approaches. Here, we show that vascular endothelial growth factor A (VEGFA) induces PKCθ phosphorylation in human retinal microvascular endothelial cells (HRMVECs) and downregulation of its levels attenuates VEGFA-induced HRMVECs migration, sprouting and tube formation. Furthermore, the whole body deletion of PKCθ or EC-specific deletion of its target gene JunB inhibited hypoxia-induced retinal EC proliferation, tip cell formation and neovascularization. VEGFA also induced VEGFR3 expression via JunB downstream to PKCθ in the regulation of HRMVEC migration, sprouting, and tube formation in vitro and OIR-induced retinal EC proliferation, tip cell formation and neovascularization in vivo. In addition, VEGFA-induced VEGFR3 expression requires VEGFR2 activation upstream to PKCθ-JunB axis both in vitro and in vivo. Depletion of VEGFR2 or VEGFR3 levels attenuated VEGFA-induced HRMVEC migration, sprouting and tube formation in vitro and retinal neovascularization in vivo and it appears that these events were dependent on STAT3 activation. Furthermore, the observations using soluble VEGFR3 indicate that VEGFR3 mediates its effects on retinal neovascularization in a ligand dependent and independent manner downstream to VEGFR2. Together, these observations suggest that PKCθ-dependent JunB-mediated VEGFR3 expression targeting STAT3 activation is required for VEGFA/VEGFR2-induced retinal neovascularization.

The failure of the Integrase Strand Transfer Inhibitors (INSTIs) due to the mutations occurring at the catalytic site of HIV integrase (IN) has led to the design of allosteric integrase inhibitors (ALLINIs). Lens epithelium derived growth factor (LEDGF/p75) is the host cellular cofactor which helps chaining IN to the chromatin. The protein-protein interactions (PPIs) were observed at the allosteric site (LEDGF/p75 binding domain) between LEDGF/p75 of the host cell and IN of virus. In recent years, many small molecules such as CX04328, CHIBA-3053 and CHI-104 have been reported as LEDGF/p75-IN interaction inhibitors (LEDGINs). LEDGINs have emerged as promising therapeutics to halt the PPIs by binding at the interface of both the proteins. In the present work, we correlated the docking scores for the reported LEDGINs containing quinoline scaffold with the in vitro biological data. The hierarchal clustering method was used to divide the compounds into test and training set. The robustness of the generated model was validated by q2 and r2 for the predicted set of compounds. The generated model between the docking score and biological data was assessed to predict the activity of the hits (quinoline scaffold) obtained from virtual screening of LEDGINs providing their structureactivity relationships to aim for the generation of potent agents., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Transcription factors (TFs) orchestrate multiple cellular processes through tight regulation via post-translational modifications (PTMs). Thus, decoding the combinations of PTMs should provide critical layer of information that can be integrated into highly specific cellular outputs to reveal a network of genes and their target-specific regulation. Protein modifications play a decisive role in various drug responses and eventually in prognosis for many life-threatening diseases, and recent studies demonstrate that TF-based drug designing must consider structural and functional changes due to PTMs, yet we are just beginning to grasp this enormity and the impact on normal development and disease pathophysiology.

The N-terminal domains (NTDs) of many members of the nuclear hormone receptor (NHR) family contain potent transcription-activating functions (AFs). Knowledge of the mechanisms of action of the NTD AFs has lagged, compared with that concerning other important domains of the NHRs. In part, this is because the NTD AFs appear to be unfolded when expressed as recombinant proteins. Recent studies have begun to shed light on the structure and function of the NTD AFs. Recombinant NTD AFs can be made to fold by application of certain osmolytes or when expressed in conjunction with a DNA-binding domain by binding that DNA-binding domain to a DNA response element. The sequence of the DNA binding site may affect the functional state of the AFs domain. If properly folded, NTD AFs can bind certain cofactors and primary transcription factors. Through these, and/or by direct interactions, the NTD AFs may interact with the AF2 domain in the ligand binding, carboxy-terminal portion of the NHRs. We propose models for the folding of the NTD AFs and their protein-protein interactions.

Molecularly targeted cancer therapies substantially improve patient outcomes, although the durability of their effectiveness can be limited. Resistance to these therapies is often related to adaptive changes in the target oncoprotein which reduce binding affinity. The arsenal of targeted cancer therapies, moreover, lacks coverage of several notorious oncoproteins with challenging features for inhibitor development. Degraders are a relatively new therapeutic modality which deplete the target protein by hijacking the cellular protein destruction machinery. Degraders offer several advantages for cancer therapy including resiliency to acquired mutations in the target protein, enhanced selectivity, lower dosing requirements, and the potential to abrogate oncogenic transcription factors and scaffolding proteins. Herein, we review the development of proteolysis targeting chimeras (PROTACs) for selected cancer therapy targets and their reported biological activities. The medicinal chemistry of PROTAC design has been a challenging area of active research, but the recent advances in the field will usher in an era of rational degrader design. [ABSTRACT FROM AUTHOR]

The level of CD40 expression on dendritic cells (DCs) plays a decisive role in disease protection during Leishmania donovani (LD) infection. However, current understanding of the molecular regulation of CD40 expression remains elusive. Using molecular, cellular and functional approaches, we identified a role for Runx1 and Runx3 transcription factors in the regulation of CD40 expression in DCs. In response to lipopolysaccharide (LPS), tumor necrosis factor alpha (TNFα) or antileishmanial drug sodium antimony gluconate (SAG), both Runx1 and Runx3 translocated to the nucleus, bound to the CD40 promoter and upregulated CD40 expression on DCs. These activities of Runx proteins were mediated by the upstream phosphatidylinositol 3-kinase (PI3K)-Akt pathway. Notably, LD infection attenuated LPS- or TNFα-induced CD40 expression in DCs by inhibiting PI3K-Akt-Runx axis via protein tyrosine phosphatase SHP-1. In contrast, CD40 expression induced by SAG was unaffected by LD infection, as SAG by blocking LD-induced SHP-1 activation potentiated PI3K-Akt signaling to drive Runx-mediated CD40 upregulation. Adoptive transfer experiments further showed that Runx1 and Runx3 play a pivotal role in eliciting antileishmanial immune response of SAG-treated DCs in vivo by promoting CD40-mediated type-1 T cell responses. Importantly, antimony-resistant LD suppressed SAG-induced CD40 upregulation on DCs by blocking the PI3K-Akt-Runx pathway through sustained SHP-1 activation. These findings unveil an immunoregulatory role for Runx proteins during LD infection. Author summary: Visceral leishmaniasis (VL), caused by Leishmania donovani, is the second most deadly parasitic disease in the world after malaria. The protective immunity against this disease largely depends on the level of CD40 (a cell surface protein) expression on a specialized group of immune cells called "dendritic cells" (DCs), which play a central role in initiating antileishmanial immune responses. Accordingly, to develop an improved immunological approach for the treatment/prevention of VL, it is important to understand the molecular events that favor the induction of CD40 expression on DCs. However, the molecular mechanisms controlling CD40 expression are not yet fully understood. Our work describes, for the first time, that the transcription factors Runx1 and Runx3 promote CD40 expression on DCs, which thereby potentiate the ability of DCs to induce antileishmanial immune responses in vivo. Our study thus provides new insights into the molecular mechanism required for an immune response to combat VL. [ABSTRACT FROM AUTHOR]

Abstract: Botulinum neurotoxins (BoNTs), produced by Clostridium botulinum are the most toxic substances known to the mankind. BoNTs (seven serotypes, A–G) are produced along with a group of neurotoxin associated proteins (NAPs) in a physiologically coordinated manner, regulated by a common transcription factor for the gene cluster that encodes for the BoNT and NAPs. Hemagglutinin-33 (Hn-33) is a 33kDa subcomponent of NAPs, which is resistant to protease digestion, and accounts for about half of the NAPs molecules in the BoNT/A complex. Natural exposures to BoNT in food poisoning cases as well as in the medical applications of BoNT as a therapeutic agent, humans are exposed to the BoNT/A complex. The toxin itself is known to block neurotransmitter release from presynaptic nerves, but the effect of NAPs is unexplored. In this article, we report an important observation of the anti-apoptotic effect of Hn-33 in Hn-33-preincubated human neuroblastoma SH-SY5Y cells. Activity of caspases, which are the central executioners of apoptosis, was substantially (78%) reduced by Hn-33. Degradation of chromosomal DNA, another biochemical hallmark of apoptosis, was blocked in Hn-33 incubated SH-SY5Y cells. Interestingly, purified BoNT/A also showed substantial anti-apoptotic activity. These findings may have significant implications to the use of BoNT as a therapeutic agent, and to devise counter measures to botulinum poisoning. [Copyright &y& Elsevier]

Intrinsically disordered (ID) regions of proteins commonly exist within transcription factors, including the N-terminal domain (NTD) of steroid hormone receptors (SHRs) that possesses a powerful activation function, AF1 region. The mechanisms by which SHRs pass signals from a steroid hormone to control gene expression remain a central unresolved problem. The role of N-terminal activation function AF1, which exists in an intrinsically disordered (ID) conformation, in this process is of immense importance. It is hypothesized that under physiological conditions, ID AF1 undergoes disorder/order transition via inter- and intra-molecular communications, which allows AF1 surfaces to interact with specific co-regulatory proteins, critical for the final outcome of target gene expression regulated by SHRs. However, the means by which AF1 acquires functionally folded conformations is not well understood. In this study, we tested whether binding of jun dimerization protein 2 (JDP2) within the DNA binding domain (DBD) of the glucocorticoid receptor (GR) leads to acquisition of functionally active structure in its AF1/NTD. Our results show that signals mediated from GR DBD:JDP2 interactions in a two domain GR fragment, consisting of the entire NTD and little beyond DBD, significantly increased secondary/tertiary structure formation in the NTD/AF1. This increased structure formation facilitated AF1's interaction with specific co-regulatory proteins and subsequent glucocorticoid response element-mediated AF1 promoter:reporter activity. These results support the hypothesis that inter- and intra-molecular signals give a functionally active structure(s) to the GR AF1, which is important for its transcriptional activity. [ABSTRACT FROM AUTHOR]

Intrinsically disordered (ID) regions are frequently found in the activation domains of many transcription factors including nuclear hormone receptors. It is believed that these ID regions promote molecular recognition by creating large surfaces suitable for interactions with their specific protein binding partners, which is a critical component of gene regulation by transcription factors. It has been hypothesized that conditional folding of these activation domains may be a prerequisite for their efficient interaction with specific coregulatory proteins, and subsequent transcriptional activity leading to the regulation of target gene(s). In this study, we tested whether a naturally occurring osmolyte, trehalose can promote functionally ordered conformation in glucocorticoid receptor's major activation function domain, AF1, which is found to exist as an ID protein, and requires an efficient interaction with coregulatory proteins for optimal activity. Our data show that trehalose induces an ordered conformation in AF1 such that its interaction with steroid receptor coactivator-1 (SRC-1), a critical coregulator of glucocorticoid receptor's activity, is greatly enhanced. [ABSTRACT FROM AUTHOR]

Abstract: The steroid hormone receptors (SHRs) are ligand-dependent intracellular transcription factors that are known to influence the development and growth of many human cancers. SHRs pass signals from a steroid/hormone to the target genes by interacting with specific response element DNA sequences and various coregulatory proteins that consists of activators and/or corepressors. Disruptions in physiological functions of SHRs leads to several types of malignancies such as breast cancer, leukemia and lymphoma, prostate cancer, ovarian cancer, and lung cancer among others. Steroids/hormones/SHRs and their coregulators have opened up a unique window for novel steroid-based targeted therapies for cancer. Thus, dysregulation of SHR signaling in cancers compared with normal tissues can be exploited to target drugs that prevent and treat human cancers. In recent years, hormonal therapy has made a major contribution to the treatment of several cancers including reduced recurrence rates and longer survival rates. Development of various steroid receptor modulators and their potential therapeutic efficacies has provided us a great opportunity to effectively manage diseases like cancer in future. In this review article, we have summarized up-to-date knowledge of the role of SHRs in the development and progression of cancers, and potential endocrine-based therapeutic approaches to tackle these diseases. [ABSTRACT FROM AUTHOR]

Osmolytes are naturally occurring organic compounds, which represent different chemical classes including amino acids, methylamines, and polyols. By accumulating high concentrations of osmolytes, organisms adapt to perturbations that can cause structural changes in their cellular proteins. Osmolytes shift equilibrium toward natively-folded conformations by raising the free energy of the unfolded state. As osmolytes predominantly affect the protein backbone, the balance between osmolyte-backbone interactions and amino acid side chain-solvent interactions determines protein folding. Abnormal cell volume regulation significantly contributes to the pathophysiology of several disorders, and cells respond to these changes by importing, exporting, or synthesizing osmolytes to maintain volume homeostasis. In recent years, it has become quite evident that cells regulate many biological processes such as protein folding, protein disaggregation, and protein-protein interactions via accumulation of specific osmolytes. Many genetic diseases are attributed to the problems associated with protein misfolding/aggregation, and it has been shown that certain osmolytes can protect these proteins from misfolding. Thus, osmolytes can be utilized as therapeutic targets for such diseases. In this review article, we discuss the role of naturally occurring osmolytes in protein stability, underlying mechanisms, and their potential use as therapeutic molecules. © 2010 IUBMB IUBMB Life, 62(12): 891-895 [ABSTRACT FROM AUTHOR]

Abstract: Steroid hormone receptors are members of a family of ligand inducible transcription factors, and regulate the transcriptional activation of target genes by recruiting coregulatory proteins to the pre-initiation machinery. The binding of these coregulatory proteins to the steroid hormone receptors is often mediated through their two activation functional domains, AF1, which resides in the N-terminal domain, and the ligand-dependent AF2, which is localized in the C-terminal ligand-binding domain. Compared to other important functional domains of the steroid hormone receptors, our understanding of the mechanisms of action of the AF1 are incomplete, in part, due to the fact that, in solution, AF1 is intrinsically disordered (ID). However, recent studies have shown that AF1 must adopt a functionally active and folded conformation for its optimal activity under physiological conditions. In this review, we summarize and discuss current knowledge regarding the molecular mechanisms of AF1-mediated gene activation, focusing on AF1 conformation and coactivator binding. We further propose models for the binding/folding of the AF1 domains of the steroid hormone receptors and their protein:protein interactions. The population of ID AF1 can be visualized as a collection of many different conformations, some of which may be assuming the proper functional folding for other critical target binding partners that result in the ultimate assembly of AF1:coactivator complexes and subsequent gene regulation. Knowledge of the mechanisms involved therein will significantly help in understanding how signals from a steroid to a specific target gene are conveyed. [Copyright &y& Elsevier]

A number of proteins with intrinsically disordered (ID) regions/domains are reported to be found disproportionately higher in transcription factors. Available evidences suggest that presence of ID region/domain within a transcription factor plays an important role in its biological functions. These ID sequences provide large flexible surfaces that can allow them to make more efficient physical and functional interactions with their target partners. Since transcription factors regulate expression of target genes by interacting with specific coregulatory proteins, these ID regions/domains can be used as a platform for such large macromolecular interactions, and may represent a mechanism for regulation of cellular processes. The precise structural basis for the function of these ID regions/domains of the transcription factors remains to be determined. In the recent years there has been growing evidence suggesting that an induced fit-like process leads to imposition of folded functional structure in these ID domains on which large multiprotein complexes are built. These multiprotein complexes may eventually dictate the final outcome of the gene regulation by the transcription factors. [ABSTRACT FROM AUTHOR]

Abstract: The glucocorticoid receptor (GR) belongs to the superfamily of ligand-activated transcription factors, the nuclear hormone receptors. Like other members of the family, the GR possesses a modular structure consisting of three major domains—the N-terminal (NTD), DNA binding (DBD), and ligand binding (LBD). Although the structures of independently expressed GR DBD and LBD are known, the structures of the NTD and of full-length GR are lacking. Both DBD and LBD possess overall globular structures. Not much is known about the structure of the NTD, which contains the powerful AF1/tau1/enh2 transactivation region. Several studies have shown that AF1 region is mostly unstructured and that it can acquire folded functional conformation under certain potentially physiological conditions, namely in the presence of osmolytes, when the GR DBD is bound to glucocorticoid response element (GRE), and when AF1 binds other transcription factor proteins. These conditions are discussed here. The functions of the GR will be fully understood only when its working three-dimensional structure is known. Based on the available data, we propose a model to explain data which are not adequately accounted for in the classical models of GR action. In this review, we summarize and discuss current information on the structure of the GR in the context of its functional aspects, such as protein:DNA and protein:protein interactions. Because of the close similarities in modular organization among the members of the nuclear hormone receptors, the principles discussed here for the GR should be applicable to many other receptors in the family as well. [Copyright &y& Elsevier]

In recent years, it has become clear that in many proteins, significant regions are encoded by amino acid sequences that do not automatically fold into their fully condensed, functional structures. Characterization of the conformational propensities and function of the nonglobular protein sequences represents a major challenge. Striking among proteins with unfolded regions are numbers of transcription factors, including steroid receptors. In many cases, the unfolded or partially folded regions of such proteins take shape when the protein interacts with its proper binding partner(s), that is, the molecules to which it must bind to carry out its function. The AF1 domain of the androgen receptor (AR) shows little structure, when expressed as a recombinant peptide. It has been shown previously that AF1 interacts with transcription factor TFIIF in vitro. Using Fourier transform infrared (FTIR), we tested whether this interaction can induce structure in the AR AF1. Our results demonstrate that the recombinant AR AF1 can acquire significantly higher helical content after interacting with RAP74, a subunit of the TFIIF complex. We further show that this induced conformation in the AR AF1 is well-suited for its interaction with SRC-1. [ABSTRACT FROM AUTHOR]

• Steroid hormone receptor (SHR)-coregulator (CoR) complexes are critical in SHR action. • SHR-CoR complexes are highly dynamic and rapidly include or exclude CoRs in genome. • Structural flexibilities within proteins create binding surfaces as and when needed. Understanding of the mechanisms of actions of the steroid hormone receptor (SHR)-coregulator (CoR) protein complexes in the gene regulations has revolutionized the field of molecular endocrinology and endocrine-related oncology. The discovery and characterization of steroid receptor coactivators (SRCs) and their ability to bind various transcription factors including SHRs to coordinate the regulation of multiple target genes highlights their importance as key coregulators in various cellular signaling crosstalks as well as therapeutic target for various endocrine-related disorders specifically endocrine cancers. The dynamic nature of the SHR-CoR multi-protein complexes indicate the critical role of conformational flexibilities within specific protein(s). In recent years, the importance of conformational dynamics of the SHRs in the intramolecular and intermolecular allosteric regulations mediated via their intrinsically disordered (ID) surfaces has been highlighted. In this review article, we have discussed the importance of ID conformations within the SRCs that may also be playing an important role in the formation/deformation of multi protein complexes involving SHRs and CoRs and subsequent target gene regulation. [ABSTRACT FROM AUTHOR]

The fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for downstream analysis. To facilitate this choice, we designed a novel tool for comparing alignment results of user data based on the relative reliability of uniquely aligned reads (CADBURE). CADBURE can easily evaluate different aligners, or different parameter sets using the same aligner, and selects the best alignment result for any RNA-Seq dataset. Strengths of CADBURE include the ability to compare alignment results without the need for synthetic data such as simulated genomes, alignment regeneration and randomly subsampled datasets. The benefit of a CADBURE selected alignment result was supported by differentially expressed gene (DEG) analysis. We demonstrated that the use of CADBURE to select the best alignment from a number of different alignment results could change the number of DEGs by as much as 10%. In particular, the CADBURE selected alignment result favors fewer false positives in the DEG analysis. We also verified differential expression of eighteen genes with RT-qPCR validation experiments. CADBURE is an open source tool (http://cadbure.sourceforge.net/). [ABSTRACT FROM AUTHOR]

c-Jun is one of the major component of the transcription factor AP-1 and involved in regulation of the expression of genes indispensable for cell proliferation and differentiation. Earlier reports from our laboratory have identified a positive regulatory element located between -148 to -124 (Jun25) region of the c-jun that is differentially recognized in normal and proliferating rat liver. The factor interacting with this region is present in the cytosol and undergoes post-translational modification and nuclear translocation upon growth stimulus. To identify the factors interacting with this region, EMSA using rat liver cytosolic extract (RCE) and nuclear extract (RNE) was performed. A slow-migrating complex was obtained with RCE when compared with that obtained with RNE. DNA-affinity purification of factors from the RCE and RNE, and their identification by MALDI were carried out. Two protein bands of ∼42 and 70 kDa in the affinity purified RCE were identified to be γactin and HSP70, respectively. Western blot analysis using anti-actin antibody confirmed the ∼42 kDa band to be actin. A single band of ∼40 kDa obtained in the affinity purified RNE was identified to be nuclear actin. Southwestern blot analysis of the affinity purified RCE showed that only ∼42 kDa band was recognized with the Jun-25 oligonucleotides. Thus, actin directly interacts with the positive regulatory element Jun25 of the c-jun and is likely to be involved in its positive regulation. [ABSTRACT FROM AUTHOR]

Highlights: [•] GC/GR trans-activates NFkB in luminal subtype breast cancer cell MCF7. [•] GC treatment increases the nuclear localization of p65/RelA. [•] The interaction between p65/RelA and GR is decreased in response to GC/GR signaling. [•] c-Myc as one of NFkB target genes is enhanced by GC/GR. [•] GC/GR promotes MCF7 cell proliferation, different from the pro-apoptotic effect in hematopoietic cancers. [Copyright &y& Elsevier]

Abstract: In recent years, it has become quite evident that numerous proteins exist as an ensemble of conformers that collectively appears to be intrinsically disordered (ID). Of particular significance is the growing body of evidence that intrinsic disorder is found in disproportionately higher amounts in cell signaling proteins and transcription factors, suggesting an important role in their regulatory capacity. Since these proteins are known to possess specific regions/domains that interact with specific coregulatory proteins for their efficient functioning, the large flexible regions in this class of proteins may have an advantage over fully folded proteins that can allow them to make more efficient physical functional interactions with their target partners, which may represent a mechanism for regulation of cellular processes. In fact, recent studies from several laboratories have reported existence of ID sequences in such regions in signaling proteins that play a critical role in regulating their functions. There are reports showing that ID regions/domains commonly exist within proteins with modular structures such as transcription factors, and are often located in their transactivation domain. Therefore, it is important to find out their existence and functional roles in transcriptional regulations by transcription factors. In recent years there has been growing evidence suggesting that an induced fit process leads to imposition of folded functional structure in these ID protein regions/domains. In most cases such binding and folding events have been found to occur when ID region encounters its specific binding partner(s). [Copyright &y& Elsevier]