• The Drosophila extra sex combs (esc) protein, a member of the Polycomb group (PcG), is a transcriptional repressor of homeotic genes. (umn.edu)
  • Studies on post-translational modification of PXR indicate how this protein is converted from a positive regulator in drug metabolism into a transcriptional repressor in inflammatory response. (ku.edu)
  • Thus, in B cells HDAC7 is a transcriptional repressor of undesirable genes. (eur.nl)
  • In differentiating neuroblastoma cells, HASH-1 is down-regulated, and there is coincident up-regulation of the transcriptional repressor HES-1, which is known to bind the HASH-1 promoter. (lu.se)
  • We used diethylnitrosamine (DEN) injection to initiate liver cancer in mice and assessed the extent of liver cancer in JDP2-transgenic and wild type control mice by biochemical and molecular biology techniques. (biomedcentral.com)
  • Journal of Molecular Biology 2008, 381 (2), 373-382. (ncl.ac.uk)
  • The team led by Dr. Kuo-Chiang Hsia (Institute of Molecular Biology, Academia Sinica) and Dr. Wei-Yi Chen (Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University) presents a cryo-EM structure of Kap114p, one of the Kap-βs, in complex with TATA box binding protein and reveals a non-canonical function beyond nuclear transport that modulates TBP-dependent transcription. (sinica.edu.tw)
  • Molecular and cellular biology , 17 (11), 6663-6672. (umn.edu)
  • One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. (cshlpress.com)
  • Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. (cshlpress.com)
  • Graduate students in my lab enter through the new Biophysical Sciences Graduate Program , in addition to the Programs in Biochemistry & Molecular Biology , Chemistry , and Physics . (openwetware.org)
  • American Society for Biochemistry and Molecular Biology, Inc. (ncl.ac.uk)
  • He then moved to the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany where he performed his postdoctoral studies in the lab of Dr. Thomas Graf from 1991 to 1996. (ubc.ca)
  • A growing number of studies are finding diverse and essential roles for molecular recognition events in mediating information transfer and complex assembly in biology. (mtu.edu)
  • Additionally, Klaus Schulten will be honored at the Meeting's Awards Ceremony as a 2012 Society Fellow during the Biophysical Society's on Monday February 27, 2012 for his groundbreaking effort to develop computational molecular biology as an important tool to solve problems in biophysics. (memprotein.org)
  • Currently, with the application of molecular biology resources in human identification, it became possible to identify a person even without physical ante-mortem data or with deteriorated biological material in negligible amounts, which are actually relatively common conditions in forensic analyses 7,12,16,19 . (bvsalud.org)
  • But a mutation in the citrate-eaters allowed them to make an "antiporter" protein, CitT, that allows citrate to cross the membrane and enter the cell. (evolutionnews.org)
  • MDM2 is a multidomain protein that functions as an E3 ubiquitin ligase, transcription repressor, mRNA-binding protein, translation factor, and molecular chaperone. (ed.ac.uk)
  • lambda 6-85, a truncated, monomeric form of the N-terminal domain of lambda repressor, refolds with a lifetime of approximately 250 microseconds. (duke.edu)
  • molecular and genetic decoding. (cdc.gov)
  • Genetic studies have shown that esc protein is required in early embryos at about the time that other PcG proteins become engaged in homeotic gene repression. (umn.edu)
  • However, the existence of specific transcriptional repressors responsible for the silencing of lineage inappropriate genes remains elusive. (eur.nl)
  • In principle, development of small molecule inhibitors of interactions of specific transcriptional activators (or repressors) with DNA or with the basal transcription machinery could provide highly selective regulators of gene expression and thus highly selective therapeutic agents (e.g., antiviral agents based on disabling essential viral gene expression). (mtu.edu)
  • DELLA proteins play a central role in these processes via direct protein-protein interactions with key transcription factors. (duke.edu)
  • As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis. (springer.com)
  • Similarly, the PXR protein also forms the molecular basis of an important class of drug-drug interactions in the clinical setting. (ku.edu)
  • Since the mid-20th century, from discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. (cshlpress.com)
  • A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create a unified view of the field and a fuller understanding of protein-DNA interactions. (cshlpress.com)
  • This binding of Nutlin-3 has two consequences: (i) antagonistic effects through competitive disruption of the MDM2-p53 complex and (ii) agonist effects that allosterically stabilize MDM2 protein-protein interactions that increase p53 ubiquitination as well as nucleophosmin deoligomerization. (ed.ac.uk)
  • These tend to fall roughly into two categories: validation of putative or suspected interactions and identification of unknown associated proteins. (aacrjournals.org)
  • The classic method for analysis of protein-protein interactions is the co-immunoprecipitation (co-IP), also known as a "pull down" ( 1, 2 ), which constitutes the gold standard in the field. (aacrjournals.org)
  • Unlike immunofluorescence microscopy approaches, which provide correlative information about proteins sharing cellular space, co-IP can confirm direct often high-affinity physical interactions between two proteins or protein complexes of equal or better affinity. (aacrjournals.org)
  • The validity of co-IP approaches can quickly deteriorate when forced expression of tagged proteins are used to investigate possible interactions, yet this approach, particularly when endogenous factors are assessed, can provide useful information about potential protein associations. (aacrjournals.org)
  • In fact, biological outcomes are often due to physical interactions between proteins that are so highly selective that seemingly minor chemical modifications (i.e. methylation, acetylation or phosphorylation) can completely abolish biomolecular recognition processes and redirect signaling pathways. (mtu.edu)
  • water-mediated interactions resulted in severely [email protected] reduced af®nities for trp repressor (Joachimi ak et al. (lu.se)
  • Studying interactions, we noted that all four Id proteins could dimerize with E47 or E2-2, but not with HASH-1 or dHAND. (lu.se)
  • His laboratory has followed two primary interests: 1) the transcription factor networks that regulate fate determination in various cells that make blood, and 2) the cell surface proteins expressed by hematopoietic stem cells that and allow them to communicate with their microenvironment. (ubc.ca)
  • Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)
  • PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. (springer.com)
  • In S. cerevisiae , this interaction is at least in part provided by Spp1 that directly interacts with both methylated H3K4 near DSB sites and the axis-localized protein Mer2 (Acquaviva et al. (springer.com)
  • The esc protein consists primarily of multiple copies of the WD repeat, a motif that has been implicated in protein-protein interaction. (umn.edu)
  • We suggest that these regions might mediate physical interaction with esc partner proteins. (umn.edu)
  • The number of studies that have used protein interaction discovery approaches for identification of associated factors is overwhelming. (aacrjournals.org)
  • On top of the elastic rods, one shows fitted all-atom DNA structures, electric field profiles, forces of protein-DNA interaction, and the CAP protein bound within the short loops. (uiuc.edu)
  • Over the past decade, it has been well established that PXR functions as a master-regulator of xenobiotic- and drug-inducible expression and activity of numerous genes that encode key members of the phase I and phase II metabolic enzymes, as well as several membrane transporter proteins. (ku.edu)
  • Here we addressed the molecular mechanism behind repression of non-lymphoid genes in B cells. (eur.nl)
  • Transcription factor Nrf2 is a key regulator of genes encoding phase II detoxification enzymes and antioxidant proteins in response to environmental chemical insults. (cdc.gov)
  • It has been demonstrated that the bolting and flowering signals from internal or external factors usually converge on a few integrator genes which serve as flowering inducers or repressors during floral transition. (frontiersin.org)
  • A transcriptional co-repressor is a protein that interacts with other DNA-binding proteins to suppress the activity of certain genes, although it cannot attach (bind) to DNA by itself. (medlineplus.gov)
  • Like Rb protein, many of the proteins encoded by tumor suppressor genes act at specific points in the cell cycle. (medscape.com)
  • DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)
  • For example, the TP53 gene, located on chromosome 17, encodes a 53-kd nuclear protein that functions as a cell cycle checkpoint. (medscape.com)
  • Click molecule labels to explore molecular sequence information. (nih.gov)
  • It is assumed that the Id helix-loop-helix (HLH) proteins act by associating with ubiquitously expressed basic HLH (bHLH) transcription factors, such as E47 and E2-2, which prevents these factors from forming functional hetero- or homodimeric DNA binding complexes. (lu.se)
  • The p16INK4A protein is a cell-cycle inhibitor that acts by inhibiting activated cyclin D:CDK4/6 complexes, which play a crucial role in the control of the cell cycle by phosphorylating Rb protein. (medscape.com)
  • PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
  • For example, MVs from E. coli under envelope stress contain multiple misfolded proteins, whose release enhances bacterial survival [ 9 ]. (nature.com)
  • The remaining two proteins obtained after HPLC separation were identified as homologues of bacterial repressor-like proteins. (ox.ac.uk)
  • Typically, OMVs are dominated by outer membrane proteins, while the cytoplasmic membrane proteins and cytoplasmic proteins are the primary contents of MVs. (nature.com)
  • Cd did not affect the protein levels of Keap1, which is a repressor of the cytoplasmic Nrf2, or Cul-3, an E3 ligase involved in the proteasomal degradation of Nrf2. (cdc.gov)
  • It did this by making more of a transporter protein called DctA, which imports - at a small energy cost - succinate and other molecules exported by the citrate-eating strain. (evolutionnews.org)
  • One source of confusion may be that proxy measures of protein synthesis, such as mGluR-LTD or phosphorylation of signaling molecules, have been used in intact hippocampal slice preparations, whereas metabolic labeling experiments have been performed in synaptoneurosome preparations of cortex that are not easily related to altered hippocampal synaptic plasticity. (jneurosci.org)
  • Binding of the repressor complex REST-mSIN3b by small molecules restores neuronal gene transcription in Huntington's disease models. (ox.ac.uk)
  • To see how the scripts work, go to that directory, and start the main presentation: vmd -e present.tcl DATA: ~~~~~ The main directory contains the TcL scripts, UNIX utility scripts for file copying, etc., the PSF files for the presented molecules, the PDB files for the lac repressor and the water bath, and the BMP icons for the menu panels. (uiuc.edu)
  • The over-all goal of my research program is to understand how complex biological molecules adopt their functional, 3-dimensional conformations: The Protein and RNA Folding Problem. (openwetware.org)
  • Through gene knockout studies he has shown that these molecules act as a type of molecular "Teflon" to make cells more mobile and invasive and also facilitate chemotaxis. (ubc.ca)
  • Most of the important insights regarding the specific function of AP-1 proteins have been established through the use of mice with either loss- or gain-of-function manipulations of various members of the bZIP protein family [ 13 ]. (biomedcentral.com)
  • Here, we use an in vitro assay of protein synthesis in the hippocampus of male Fmr1 knock-out (KO) mice to explore the molecular mechanisms involved in this core biochemical phenotype under conditions where aberrant synaptic physiology has been observed. (jneurosci.org)
  • We find that elevated basal protein synthesis in Fmr1 KO mice is selectively reduced to wild-type levels by acute inhibition of mGluR5 or ERK1/2, but not by inhibition of mTOR (mammalian target of rapamycin). (jneurosci.org)
  • One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
  • In humans and mice, hotspots are specified by PRDM9, a meiosis-specific PRDM family protein (Baudat et al. (springer.com)
  • We identified the nuclear transcriptional regulators DELLA proteins, which function as master growth repressors by inhibiting all aspects of GA responses. (duke.edu)
  • Liver-enriched nuclear receptor (NR) proteins regulate the expression and activity of several pivotal hepatic biochemical pathways including the uptake, metabolism and excretion of cholesterol, bile acids, glucose, and xenobiotic compounds from the body. (ku.edu)
  • In particular, quinolone-like compound 91 (C91) at a non-toxic nanomolar concentration reduced mSIN3b nuclear entry and occupancy at the RE1/NRSE within the Bdnf locus, and restored brain-derived neurotrophic factor (BDNF) protein levels in HD cells. (ox.ac.uk)
  • This involves purification of a specific protein from the pool of cellular proteins, followed by Western blotting of a suspected interacting protein ( 1 ). (aacrjournals.org)
  • Summary Progress Tideglusib continues in understanding the breadth of molecular and cellular players in HIT. (immune-source.com)
  • Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes and we discuss one such case, the diffusion of lac repressor in a packed cellular nucleoid. (lu.se)
  • Sulfur deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants. (mpg.de)
  • By multi-faceted approaches using the reference plant Arabidopsis, my lab has made major breakthroughs in elucidating the sites and regulatory mechanisms of GA biosynthesis, and the conserved molecular events of GA perception and the early GA signaling pathway. (duke.edu)
  • To understand the role of the epigenetic co-repressor protein TRIM28 in the control of transposable elements (TEs) and how TEs control gene regulation in the developing and adult brain. (lu.se)
  • Although the exact function of this protein is unknown, it appears to play an important role in nerve cells (neurons) in many areas of the brain. (medlineplus.gov)
  • This altered protein accumulates in neurons and interferes with normal cell functions. (medlineplus.gov)
  • Surprisingly, we recently found that DELLA directly interacts with multiple classes of key regulatory proteins in other signaling pathways. (duke.edu)
  • The extended CAG region changes the structure of atrophin 1 and how the protein interacts with other proteins to control gene function. (medlineplus.gov)
  • 2013 ). Interestingly, the molecular mechanisms underlying the patterning of meiotic DSBs are quite distinct in different species with apparently two major pathways. (springer.com)
  • We are also predicting protein structures by simulating folding pathways, taking advantage of our experimental results and an approach that dynamically integrates local and global information. (openwetware.org)
  • What pathways are this gene/protein implicaed in? (cancerindex.org)
  • Taken together, the data represent a likely mechanism and provides initial molecular details for the connection between the PXR signaling pathway and inflammation. (ku.edu)
  • The molecular mechanism of Cd action is currently unclear. (cdc.gov)
  • However, the molecular mechanism that controls lettuce bolting and flowering upon thermal treatments is largely unknown. (frontiersin.org)
  • There he worked with Dr. Max D. Cooper (Howard Hughes Medical Institute, National Academy of Sciences) and his research focused on cell surface proteins expressed by preB cells that regulate B cell maturation and homing. (ubc.ca)
  • We also elucidated the conserved molecular events of GA perception and the early GA signaling pathway. (duke.edu)
  • These results suggest that the ERK1/2 pathway, and other neurotransmitter systems that stimulate protein synthesis via ERK1/2, represent additional therapeutic targets for FXS. (jneurosci.org)
  • It has provided one of the most accurate descriptions of a protein folding pathway yet obtained. (openwetware.org)
  • The sequence comparisons and modeling suggest that there are seven WD repeats in esc protein which together form a seven-bladed β-propeller. (umn.edu)
  • Beyond aiding in the prediction of structure from sequence, the relevance of folding studies is underscored by the involvement of misfolded conformers in a variety of human diseases and the role of "natively-unfolded" proteins in regulation, recognition, and binding. (openwetware.org)
  • Our multi-disciplinary research program aims to understand the molecular architecture and recognition features of the early events in transcription initiation, and to use these insights to develop inhibitors of transcriptional assembly. (mtu.edu)
  • Chemistry Department be a major determinant of trp repressor/operator recognition. (lu.se)
  • Rett syndrome (RTT) is a severe neurodevelopmental disorder caused, in most classic cases, by mutations in the X-linked methyl-CpG-binding protein 2 gene (MECP2). (nih.gov)
  • RS is related to various mutations on the MECP2 gene, which codes for methyl-CpG binding protein-2 (MECP2). (medscape.com)
  • To gain insight into the molecular mechanisms mediating HDAC7 repression in pre-B cells, we undertook co-immunoprecipitation and chromatin immunoprecipitation experimental approaches. (eur.nl)
  • In MEF cells with wild type Nrf2 and mouse hepa 1c1c7 cells, Cd increased the Nrf2 protein level but not the Nrf2 mRNA level dose-dependently. (cdc.gov)
  • We demonstrated that 1,25(OH)2 D3 treatment suppressed transcript levels, protein levels, and activity of NHE1 in LLC cells. (bvsalud.org)
  • We found that the three Id proteins expressed in neuroblastoma cells (Id1, Id2, and Id3) were down-regulated during induced differentiation, indicating that Id proteins help keep the tumor cells in an undifferentiated state. (lu.se)
  • The ability of Id proteins to affect HES-1 activity is of particular interest in neuronal cells, where regulation of HES-1 is essential for the timing of neuronal differentiation. (lu.se)
  • [ 1 ] His prediction was subsequently supported by the cloning of the retinoblastoma tumor suppressor gene ( RB1 ) and by functional studies of the retinoblastoma protein, Rb. (medscape.com)
  • There are numerous methods for the discovery of unknown associated protein networks, with purification of the bait (the protein of interest) followed by mass spectrometry as a common theme. (aacrjournals.org)
  • A strong rationale for taking this approach is that slice has been shown to accurately reproduce the in vivo phenotype of elevated basal protein synthesis in the Fmr1 KO hippocampus (cf. (jneurosci.org)
  • Thus, the existence of repressor-like proteins was demonstrated at the protein level in archaea, raising the question of structural and functional consequences of these proteins on the otherwise eukaryotic-like basal transcriptional machinery in archaea. (ox.ac.uk)
  • Although it is now clear that mGluR5 participates in the pathogenesis of FXS, at least in animal models, it is still poorly understood how Gp1 mGluRs trigger protein synthesis and how this process is altered in the absence of FMRP to disrupt synaptic function. (jneurosci.org)
  • Site-directed mutagenesis of specific loops, predicted to extend from the propeller surface, identifies conserved parts of esc protein required for function in vivo. (umn.edu)
  • Significant insight into the function of proteins can be delineated by discovering and characterizing interacting proteins. (aacrjournals.org)
  • In addition to continuing the experimental protein and RNA folding studies, new research areas in the Sosnick lab involve the rational design of proteins and RNAs to control their structure and function, and the expansion of the computational component. (openwetware.org)
  • In addition, he identified a number of novel hematopoietic stem cell surface proteins and began analyzing their function. (ubc.ca)
  • As a result, the protein is altered and cannot function normally, though it is unclear how these changes lead to the specific features of CHEDDA syndrome. (medlineplus.gov)
  • When comparing proteomes of MVs between iron-limiting and iron-rich conditions, we found that under iron-limiting conditions, heme-binding proteins are enriched. (nature.com)
  • The transcription factor TATA-box binding protein (TBP) modulates gene expression in nuclei. (sinica.edu.tw)
  • Transcriptional dysregulation is a hallmark of Huntington's disease (HD) and one cause of this dysregulation is enhanced activity of the REST-mSIN3a-mSIN3b-CoREST-HDAC repressor complex, which silences transcription through REST binding to the RE1/NRSE silencer. (ox.ac.uk)
  • Methyl-histone binding analysis of the yeast double chromodomain protein Chd1. (mtu.edu)
  • However, the Id proteins did complex with HES-1, and increased levels of Id2 reduced the DNA binding activity of HES-1. (lu.se)
  • Fragile X syndrome (FXS) is caused by loss of the FMR1 gene product FMRP (fragile X mental retardation protein), a repressor of mRNA translation. (jneurosci.org)
  • Our data suggest that elevated protein synthesis in the Fmr1 KO is due to saturation of mRNA translation downstream of the MAP kinase ERK1/2 which is basally activated by mGluR5. (jneurosci.org)
  • In this regard, his lab has identified a novel family of hematopoietic cell surface proteins, called the CD34 family, and shown that these are essential for a number of developmentally important processes. (ubc.ca)
  • An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. (lu.se)
  • The ATN1 gene variants that cause CHEDDA syndrome occur in one of the two copies of the gene in each cell and lead to a change in single protein building blocks (amino acids) in atrophin 1. (medlineplus.gov)
  • In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
  • dnademos.tar.gz (5MB) AUTHOR: Alexander Balaeff [email protected] From the README file included with the demos GOAL: ~~~~~ The scripts set up a menu to present the protein-DNA complex of the lac repressor, solvated in a water bath, with different elastic rod loops attached to the protein-bound DNA segments. (uiuc.edu)
  • 17-mer used in this work and for the crystal structure of the 2:1 trp repressor/operator complex by Lawson & Carey (1993). (lu.se)
  • 1988) for the d-(ACT)Ád-(AGT) halfsites contacting the repressor in the 1:1 complex. (lu.se)
  • Modulation of Basic Helix-Loop-Helix Transcription Complex Formation by Id Proteins during Neuronal Differentiation. (lu.se)
  • The CDK4-cyclinD complex normally phosphorylates the retinoblastoma protein (Rb protein), leading to release of the E2F transcription factor and cell cycle progression. (medscape.com)
  • Data presented here reveal that activation of the inflammatory response modulates the SUMOylation and ubiquitination status of ligand-bound PXR protein. (ku.edu)
  • SCRIPTS: ~~~~~~~~ present.tcl -- the master script, which sets up sets up the VMD presentation styles and colors, loads lac repressor + water, calls the other scripts (which create the Tk menus and load the PDB data for the elastic loop molecular sets), and resets the presentation to its initial state. (uiuc.edu)
  • Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. (cancerindex.org)
  • The TM-4 d set, composed of 30 experimental enthalpies of formation, is employed for the second row transition metal study, while the LP80 set, composed of atomic ionization potentials and electron affinities and molecular dissociation energies and enthalpies of formation, is utilized for the lower p -block study. (acscomp.org)
  • In this work, we evaluate four novel sulfur-containing polymers of intrinsic microporosity (PIMs) for use in CO 2 /CH 4 gas separation membranes through the use of molecular simulations. (acscomp.org)
  • Various mouse models for HCC were developed to study the molecular mechanisms involved in various stages of liver cancer [ 5 ]. (biomedcentral.com)
  • Finally, detailed protocols for purification of mammalian proteins necessary to perform in vitro SUMOylation reactions are presented. (ku.edu)
  • In recent years, advances have permitted the purification of endogenous proteins and methods for scaling down starting material. (aacrjournals.org)
  • 2) a study of the SUMOylation and ubiquitination of PXR protein. (ku.edu)
  • The SUMOylation and ubiquitination of the PXR protein functions to feedback-repress the inflammatory and xenobiotic responses, respectively. (ku.edu)
  • Cd stabilized the Nrf2 protein by inhibiting the Keap1/CuI3dependent ubiquitination and 26S proteasomal turnover of Nrf2. (cdc.gov)
  • also known as ASH1), neurogenic differentiation factor 1 (NeuroD1), yes-associated protein 1 (YAP1) and POU class 2 homeobox 3 (POU2F3). (cancerindex.org)