Rigid docking application to investigate sulfonylurea family members’ binding site with their receptor kir6.2sur1

Author(s):  
FARAH YOUSEF ◽  
OUSSAMA MANSOUR ◽  
JEHAD HERBALI
2003 ◽  
Vol 185 (23) ◽  
pp. 7001-7007 ◽  
Author(s):  
Susanne B. von Bodman ◽  
Jessica K. Ball ◽  
Marie A. Faini ◽  
Carmen M. Herrera ◽  
Timothy D. Minogue ◽  
...  

ABSTRACT Most LuxR homologues function as activators of transcription during the process of quorum sensing, but a few, including EsaR and ExpR Ecc , negatively impact gene expression. The LuxR-activated luxI promoter and LuxR binding site, the lux box, were used in artificial contexts to assess the potential for transcriptional activation and DNA binding by EsaR and ExpR Ecc . Although the acyl-homoserine lactone responsiveness of both proteins is the opposite of that shown by most LuxR family members, EsaR and ExpR Ecc have preserved the ability to interact with RNA polymerase and activate transcription despite their low affinity for the lux box DNA.


2002 ◽  
Vol 368 (2) ◽  
pp. 555-563 ◽  
Author(s):  
Dorina AVRAM ◽  
Andrew FIELDS ◽  
Thanaset SENAWONG ◽  
Acharawan TOPARK-NGARM ◽  
Mark LEID

Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting proteins 1 and 2 [CTIP1/Evi9/B cell leukaemia (Bcl) l1a and CTIP2/Bcl11b respectively] are highly related C2H2 zinc finger proteins that are abundantly expressed in brain and the immune system, and are associated with immune system malignancies. A selection procedure was employed to isolate high-affinity DNA binding sites for CTIP1. The core binding site on DNA identified in these studies, 5′-GGCCGG-3′ (upper strand), is highly related to the canonical GC box and was bound by a CTIP1 oligomeric complex(es) in vitro. Furthermore, both CTIP1 and CTIP2 repressed transcription of a reporter gene harbouring a multimerized CTIP binding site, and this repression was neither reversed by trichostatin A (an inhibitor of known class I and II histone deacetylases) nor stimulated by co-transfection of a COUP-TF family member. These results demonstrate that CTIP1 is a sequence-specific DNA binding protein and a bona fide transcriptional repressor that is capable of functioning independently of COUP-TF family members. These findings may be relevant to the physiological and/or pathological action(s) of CTIPs in cells that do not express COUP-TF family members, such as cells of the haematopoietic and immune systems.


2000 ◽  
Vol 113 (24) ◽  
pp. 4523-4531
Author(s):  
X.H. Lei ◽  
X. Shen ◽  
X.Q. Xu ◽  
H.S. Bernstein

G(2)/M progression requires coordinated expression of many gene products, but little is known about the transcriptional regulators involved. We recently identified human Cdc5, a positive regulator of G(2)/M in mammalian cells. We also demonstrated the presence of a latent activation domain in its carboxyl terminus, suggesting that human Cdc5 regulates G(2)/M through transcriptional activation. Despite the presence of a DNA binding domain, studies by others have failed to identify a preferential binding site for Cdc5 family members. In addition, Cdc5 recently has been associated with the splicesome in several organisms, suggesting that it may not act through DNA binding. We now report the identification of a 12 bp sequence to which human Cdc5 binds specifically and with high affinity through its amino terminus. We show that this DNA-protein interaction is capable of activating transcription. We also used a selection system in yeast to identify human genomic fragments that interact with human Cdc5. Several of these contained sequences similar to the binding site. We demonstrate that these bind human Cdc5 with similar specificity and affinity. These experiments provide the first evidence that Cdc5 family members can act as site-specific DNA binding proteins, and that human Cdc5 may interact with specific, low abundance sequences in the human genome. This raises the possibility that Cdc5 proteins may participate in more than one process necessary for regulated cell division.


Author(s):  
Farah Yousef ◽  
Oussama Mansour ◽  
Jehad Herbali

Sulfonylurea family members have been used as a second preferred line in the treatment of Type II Diabetes Mellitus (TIIDM) for decades. Only one crystal structure for its receptor Kir6.2\SUR1 binding with one of sulfonylurea member; Glibenclamide (GBM), is available in Protein Data Bank (PDB) database. The aim of this manuscript is to study in-silico other sulfonylurea family members’ interactions with their receptor Kir6.2\SUR1 using a docking software in the default settings. We have checked the validity of the software for the study. Then, we have applied a rigid docking on 14 compounds of sulfonyl urea group which they have anti-hyperglycemia activity. Next, we have compared their interactions to GBM interactions with Kir6.2\SUR1.  As a result, many compounds of this family had bound to Kir6.2\SUR1 receptor in the same pocket as GBM. These results confirmed a perspective we have discussed about sulfonylurea structure activity relationship.


1997 ◽  
Vol 272 (17) ◽  
pp. 11350-11355 ◽  
Author(s):  
Jose-Luis Diaz ◽  
Tilman Oltersdorf ◽  
William Horne ◽  
Michael McConnell ◽  
Gary Wilson ◽  
...  
Keyword(s):  

Biochemistry ◽  
2001 ◽  
Vol 40 (12) ◽  
pp. 3572-3582 ◽  
Author(s):  
Daniel Mamelak ◽  
Murugesapillai Mylvaganam ◽  
Heather Whetstone ◽  
Eva Hartmann ◽  
William Lennarz ◽  
...  

2015 ◽  
Vol 43 (5) ◽  
pp. 1095-1103 ◽  
Author(s):  
Daniel M. Foulkes ◽  
Dominic P. Byrne ◽  
Fiona P. Bailey ◽  
Patrick A. Eyers

Tribbles (TRIB) proteins are pseudokinase mediators of eukaryotic signalling that have evolved important roles in lipoprotein metabolism, immune function and cellular differentiation and proliferation. In addition, an evolutionary-conserved modulation of PI3K/AKT signalling pathways highlights them as novel and rather unusual pharmaceutical targets. The three human TRIB family members are uniquely defined by an acidic pseudokinase domain containing a ‘broken’ α C-helix and a MEK (MAPK/ERK)-binding site at the end of the putative C-lobe and a distinct C-terminal peptide motif that interacts directly with a small subset of cellular E3 ubiquitin ligases. This latter interaction drives proteasomal-dependent degradation of networks of transcription factors, whose rate of turnover determines the biological attributes of individual TRIB family members. Defining the function of individual Tribs has been made possible through evaluation of individual TRIB knockout mice, siRNA/overexpression approaches and genetic screening in flies, where the single TRIB gene was originally described 15 years ago. The rapidly maturing TRIB field is primed to exploit chemical biology approaches to evaluate endogenous TRIB signalling events in intact cells. This will help define how TRIB-driven protein–protein interactions and the atypical TRIB ATP-binding site, fit into cellular signalling modules in experimental scenarios where TRIB-signalling complexes remain unperturbed. In this mini-review, we discuss how small molecules can reveal rate-limiting signalling outputs and functions of Tribs in cells and intact organisms, perhaps serving as guides for the development of new drugs. We predict that appropriate small molecule TRIB ligands will further accelerate the transition of TRIB pseudokinase analysis into the mainstream of cell signalling.


2021 ◽  
Vol 220 (9) ◽  
Author(s):  
Andrew King On Wong ◽  
Barry Paul Young ◽  
Christopher J.R. Loewen

ER-plasma membrane (PM) contacts are proposed to be held together by distinct families of tethering proteins, which in yeast include the VAP homologues Scs2/22, the extended-synaptotagmin homologues Tcb1/2/3, and the TMEM16 homologue Ist2. It is unclear whether these tethers act redundantly or whether individual tethers have specific functions at contacts. Here, we show that Ist2 directly recruits the phosphatidylserine (PS) transport proteins and ORP family members Osh6 and Osh7 to ER–PM contacts through a binding site located in Ist2’s disordered C-terminal tethering region. This interaction is required for phosphatidylethanolamine (PE) production by the PS decarboxylase Psd2, whereby PS transported from the ER to the PM by Osh6/7 is endocytosed to the site of Psd2 in endosomes/Golgi/vacuoles. This role for Ist2 and Osh6/7 in nonvesicular PS transport is specific, as other tethers/transport proteins do not compensate. Thus, we identify a molecular link between the ORP and TMEM16 families and a role for endocytosis of PS in PE synthesis.


2002 ◽  
Vol 22 (1) ◽  
pp. 78-93 ◽  
Author(s):  
Jung-Kuang Hsieh ◽  
Damian Yap ◽  
Daniel J. O’Connor ◽  
Valentina Fogal ◽  
Lynn Fallis ◽  
...  

ABSTRACT We demonstrate here that the E2F1 induced by DNA damage can bind to and promote the apoptotic function of p53 via the cyclin A binding site of E2F1. This function of E2F1 does not require its DP-1 binding, DNA binding, or transcriptional activity and is independent of mdm2. All the cyclin A binding E2F family members can interact and cooperate with p53 to induce apoptosis. This suggests a novel role for E2F in regulating apoptosis in response to DNA damage. Cyclin A, but not cyclin E, prevents E2F1 from interacting and cooperating with p53 to induce apoptosis. However, in response to DNA damage, cyclin A levels decrease, with a concomitant increase in E2F1-p53 complex formation. These results suggest that the binding of E2F1 to p53 can specifically stimulate the apoptotic function of p53 in response to DNA damage.


1999 ◽  
Vol 277 (1) ◽  
pp. L79-L88 ◽  
Author(s):  
Zvjezdana Sever-Chroneos ◽  
Cindy J. Bachurski ◽  
Cong Yan ◽  
Jeffrey A. Whitsett

The regulatory role of activator protein-1 (AP-1) family members in mouse surfactant protein (SP) B (mSP-B) promoter function was assessed in the mouse lung epithelial cell line MLE-15. Expression of recombinant Jun B and c-Jun inhibited mSP-B promoter activity by 50–75%. Although c-Fos expression did not alter mSP-B transcription, Jun D enhanced mSP-B promoter activity and reversed inhibition of mSP-B by c-Jun or Jun B. A proximal AP-1 binding site (−18 to −10 bp) was identified that overlaps a thyroid transcription factor-1 binding site. Mutation of this proximal AP-1 site blocked both Jun B inhibition and Jun D enhancement and partially blocked c-Jun inhibition of promoter activity. Promoter deletion mutants were used to identify additional sequences mediating the inhibitory effects of c-Jun in the distal region from −397 to −253 bp. The AP-1 element in this distal site (−370 to −364 bp) is part of a composite binding site wherein AP-1, cAMP response element binding protein, thyroid transcription factor-1, and nuclear factor I interact. Point mutation of the distal AP-1 binding site partially blocked c-Jun-mediated inhibition of the SP-B promoter. Both stimulatory (Jun D) and inhibitory (c-Jun/Jun B) effects of AP-1 family members on mSP-B promoter activity are mediated by distinct cis-acting elements in the mSP-B 5′-flanking region.


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