3,966 results match your criteria dna-binding protein-interaction

NF-κB Rel Subunit Exchange on a Physiological Timescale.

Protein Sci 2021 Jun 4. Epub 2021 Jun 4.

Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.

The Rel proteins of the NF-κB complex comprise one of the most investigated transcription factor families, forming a variety of hetero- or homodimers. Nevertheless, very little is known about the fundamental kinetics of NF-κB complex assembly, or the inter-conversion potential of dimerised Rel subunits. Here, we examined an unexplored aspect of NF-κB dynamics, focusing on the dissociation and re-association of the canonical p50 and p65 Rel subunits and their ability to form new hetero- or homodimers. Read More

View Article and Full-Text PDF

DNA-Bound p53-DNA-Binding Domain Interconverts between Multiple Conformations: Implications for Partner Protein Recognition.

J Phys Chem B 2021 Jun 27;125(22):5832-5837. Epub 2021 May 27.

Department of Biophysics, Bose Institute, P1-12, C.I.T. Scheme VII M, Kolkata 700054, India.

Protein-protein interaction networks are critical components of cellular regulation. Hub proteins, defined by their ability to interact with numerous protein partners, are the pivots of these networks. A hypothesis that an ensemble of rapidly interconverting conformational states contributes significantly to the ability of hub proteins to interact with diverse partners has been proposed. Read More

View Article and Full-Text PDF

Oligomerization of THAP9 Transposase via Amino-Terminal Domains.

Biochemistry 2021 May 25. Epub 2021 May 25.

Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India.

Active DNA transposases like the Drosophila P element transposase (DmTNP) undergo oligomerization as a prerequisite for transposition. Human THAP9 (hTHAP9) is a catalytically active but functionally uncharacterized homologue of DmTNP. Here we report (using co-immunoprecipitation, pull down, colocalization, and proximity ligation assays) that both full length and truncated hTHAP9 (corresponding to amino-terminal DNA binding and predicted coiled coil domains) undergo homo-oligomerization, predominantly in the nuclei of HEK293T cells. Read More

View Article and Full-Text PDF

A division of labor between two biotin protein ligase homologs.

Mol Microbiol 2021 May 24. Epub 2021 May 24.

Department of Biochemistry, University of Illinois, Urbana, IL, USA.

Group I biotin protein ligases (BPLs) catalyze the covalent attachment of biotin to its cognate acceptor proteins. In contrast, Group II BPLs have an additional N-terminal DNA-binding domain and function not only in biotinylation but also in transcriptional regulation of genes of biotin biosynthesis and transport. Most bacteria contain only a single biotin protein ligase, whereas Clostridium acetobutylicum contains two biotin protein ligase homologs: BplA and BirA'. Read More

View Article and Full-Text PDF

Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin.

Nat Commun 2021 05 19;12(1):2953. Epub 2021 May 19.

Department of Pathology, University of Michigan, Ann Arbor, MI, USA.

Recent cryo-EM structures show the highly dynamic nature of the MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation of such dynamics remain unclear. Here we show that DPY30 and the intrinsically disordered regions (IDRs) of ASH2L work together in restricting the rotational dynamics of the MLL1 complex on the NCP. Read More

View Article and Full-Text PDF

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.

Nat Commun 2021 05 11;12(1):2702. Epub 2021 May 11.

Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.

Bacterial RNA polymerase (RNAP) holoenzyme initiates transcription by recognizing the conserved -35 and -10 promoter elements that are optimally separated by a 17-bp spacer. The MerR family of transcriptional regulators activate suboptimal 19-20 bp spacer promoters in response to myriad cellular signals, ranging from heavy metals to drug-like compounds. The regulation of transcription by MerR family regulators is not fully understood. Read More

View Article and Full-Text PDF

Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data.

Nat Commun 2021 05 10;12(1):2580. Epub 2021 May 10.

Stanley Center at Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Combining genetic and cell-type-specific proteomic datasets can generate biological insights and therapeutic hypotheses, but a technical and statistical framework for such analyses is lacking. Here, we present an open-source computational tool called Genoppi (lagelab.org/genoppi) that enables robust, standardized, and intuitive integration of quantitative proteomic results with genetic data. Read More

View Article and Full-Text PDF

How structural biology transformed studies of transcription regulation.

J Biol Chem 2021 May 3:100741. Epub 2021 May 3.

Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205. Electronic address:

The past four decades have seen remarkable advances in our understanding of the structural basis of gene regulation. Technological advances in protein expression, nucleic acid synthesis and structural biology made it possible to study the proteins that regulate transcription in the context of ever larger complexes containing proteins bound to DNA. This review, written on the occasion of the 50 anniversary of the founding of the Protein Data Bank (PDB) focuses on the insights gained from structural studies of protein-DNA complexes, and the role the PDB has played in driving this research. Read More

View Article and Full-Text PDF

Bootstrapping and Pinning down the Root Meristem; the Auxin-PLT-ARR Network Unites Robustness and Sensitivity in Meristem Growth Control.

Int J Mol Sci 2021 Apr 29;22(9). Epub 2021 Apr 29.

Theoretical Biology Group, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.

After germination, the meristem of the embryonic plant root becomes activated, expands in size and subsequently stabilizes to support post-embryonic root growth. The plant hormones auxin and cytokinin, together with master transcription factors of the PLETHORA (PLT) family have been shown to form a regulatory network that governs the patterning of this root meristem. Still, which functional constraints contributed to shaping the dynamics and architecture of this network, has largely remained unanswered. Read More

View Article and Full-Text PDF

Development of an Antigen-Antibody Co-Display System for Detecting Interaction of G-Protein-Coupled Receptors and Single-Chain Variable Fragments.

Int J Mol Sci 2021 Apr 29;22(9). Epub 2021 Apr 29.

Laboratory of Regeneromics, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.

G-protein-coupled receptors (GPCRs), especially chemokine receptors, are ideal targets for monoclonal antibody drugs. Considering the special multi-pass transmembrane structure of GPCR, it is often a laborious job to obtain antibody information about off-targets and epitopes on antigens. To accelerate the process, a rapid and simple method needs to be developed. Read More

View Article and Full-Text PDF

Live-Cell Analysis of Human Cytomegalovirus DNA Polymerase Holoenzyme Assembly by Resonance Energy Transfer Methods.

Microorganisms 2021 Apr 26;9(5). Epub 2021 Apr 26.

Department of Molecular Medicine, University of Padua, 35122 Padova, Italy.

Human cytomegalovirus (HCMV) genome replication is a complex and still not completely understood process mediated by the highly coordinated interaction of host and viral products. Among the latter, six different proteins form the viral replication complex: a single-stranded DNA binding protein, a trimeric primase/helicase complex and a two subunit DNA polymerase holoenzyme, which in turn contains a catalytic subunit, pUL54, and a dimeric processivity factor ppUL44. Being absolutely required for viral replication and representing potential therapeutic targets, both the ppUL44-pUL54 interaction and ppUL44 homodimerization have been largely characterized from structural, functional and biochemical points of view. Read More

View Article and Full-Text PDF

Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning.

Cancers (Basel) 2021 Apr 2;13(7). Epub 2021 Apr 2.

Laboratory of Pharmacology, Medical School, Democritus University of Thrace, GR-68100 Alexandroupolis, Greece.

DNA methylation plays an important role in breast cancer (BrCa) pathogenesis and could contribute to driving its personalized management. We performed a complete bioinformatic analysis in BrCa whole methylome datasets, analyzed using the Illumina methylation 450 bead-chip array. Differential methylation analysis vs. Read More

View Article and Full-Text PDF

Dissection of Functional Modules of AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 4 in the Development of the Root Xylem.

Front Plant Sci 2021 6;12:632078. Epub 2021 Apr 6.

School of Biological Sciences, College of Natural Science, Seoul National University, Seoul, South Korea.

Xylem development in the root apical meristem requires a complex cross talk between plant hormone signaling and transcriptional factors (TFs). The key processes involve fine-tuning between neighboring cells, mediated the intercellular movement of signaling molecules. As an example, we previously reported that AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN (AHL) 4 (AHL4), a member of the 29 AT-hook family TFs in , moves into xylem precursors from their neighbors to determine xylem differentiation. Read More

View Article and Full-Text PDF

[MutL Protein from the Neisseria gonorrhoeae Mismatch Repair System: Interaction with ATP and DNA].

Mol Biol (Mosk) 2021 Mar-Apr;55(2):289-304

Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991 Russia.

The mismatch repair system (MMR) ensures the stability of genetic information during DNA replication in almost all organisms. Mismatch repair is initiated after recognition of a non-canonical nucleotide pair by the MutS protein and the formation of a complex between MutS and MutL. Eukaryotic and most bacterial MutL homologs function as endonucleases that introduce a single-strand break in the daughter strand of the DNA, thus activating the repair process. Read More

View Article and Full-Text PDF

SAGA and SAGA-like SLIK transcriptional coactivators are structurally and biochemically equivalent.

J Biol Chem 2021 Apr 14:100671. Epub 2021 Apr 14.

Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia. Electronic address:

The SAGA-like complex SLIK is a modified version of the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. SLIK is formed through C-terminal truncation of the Spt7 SAGA subunit, causing loss of Spt8, one of the subunits that interacts with the TATA-binding protein (TBP). SLIK and SAGA are both coactivators of RNA polymerase II transcription in yeast and both SAGA and SLIK perform chromatin modifications. Read More

View Article and Full-Text PDF

Mediator subunit Med15 dictates the conserved "fuzzy" binding mechanism of yeast transcription activators Gal4 and Gcn4.

Nat Commun 2021 04 13;12(1):2220. Epub 2021 Apr 13.

Department of Biochemistry, University of Washington, Seattle, WA, USA.

The acidic activation domain (AD) of yeast transcription factor Gal4 plays a dual role in transcription repression and activation through binding to Gal80 repressor and Mediator subunit Med15. The activation function of Gal4 arises from two hydrophobic regions within the 40-residue AD. We show by NMR that each AD region binds the Mediator subunit Med15 using a "fuzzy" protein interface. Read More

View Article and Full-Text PDF

Generation of Fluorescent Versions of Saccharomyces cerevisiae RPA to Study the Conformational Dynamics of Its ssDNA-Binding Domains.

Methods Mol Biol 2021 ;2281:151-168

Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.

Replication protein A (RPA) is an essential single-stranded DNA (ssDNA)-binding protein that sequesters ssDNA and protects it from nucleolytic degradation. The RPA-ssDNA nucleoprotein acts as a hub to recruit over two dozen DNA metabolic enzymes onto ssDNA to coordinate DNA replication, repair, and recombination. RPA functions as a heterotrimer composed of RPA70, RPA32, and RPA14 subunits and has multiple DNA-binding and protein-interaction domains. Read More

View Article and Full-Text PDF
January 2021

Comparing SSB-PriA Functional and Physical Interactions in Gram-Positive and -Negative Bacteria.

Methods Mol Biol 2021 ;2281:67-80

School of Biomedical Sciences, Chung Shan Medical University, Taichung City, Taiwan.

Single-stranded DNA (ssDNA)-binding protein (SSB) is essential for DNA metabolic processes. SSB also binds to many DNA-binding proteins that constitute the SSB interactome. The mechanism through which PriA helicase, an initiator protein in the DNA replication restart process, is stimulated by SSB in Escherichia coli (EcSSB) has been established. Read More

View Article and Full-Text PDF
January 2021

A gene regulatory network for antenna size control in carbon dioxide-deprived Chlamydomonas reinhardtii cells.

Plant Cell 2021 May;33(4):1303-1318

Algae Biotechnology and Bioenergy, Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universit�tsstrasse 27, 33615, Bielefeld, Germany.

In green microalgae, prolonged exposure to inorganic carbon depletion requires long-term acclimation responses, involving modulated gene expression and the adjustment of photosynthetic activity to the prevailing supply of carbon dioxide. Here, we describe a microalgal regulatory cycle that adjusts the light-harvesting capacity at photosystem II (PSII) to the prevailing supply of carbon dioxide in Chlamydomonas (Chlamydomonas reinhardtii). It engages low carbon dioxide response factor (LCRF), a member of the squamosa promoter-binding protein (SBP) family of transcription factors, and the previously characterized cytosolic translation repressor nucleic acid-binding protein 1 (NAB1). Read More

View Article and Full-Text PDF

PIM-induced phosphorylation of Notch3 promotes breast cancer tumorigenicity in a CSL-independent fashion.

J Biol Chem 2021 Mar 25:100593. Epub 2021 Mar 25.

Faculty of Science and Engineering/ Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland; Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands. Electronic address:

Dysregulation of the developmentally important Notch signaling pathway is implicated in several types of cancer, including breast cancer. However, the specific roles and regulation of the four different Notch receptors have remained elusive. We have previously reported that the oncogenic PIM kinases phosphorylate Notch1 and Notch3. Read More

View Article and Full-Text PDF

Physiological, biochemical, and transcriptional regulation in a leguminous forage Trifolium pratense L. responding to silver ions.

Plant Physiol Biochem 2021 May 11;162:531-546. Epub 2021 Mar 11.

School of Resources and Civil Engineering, Northeastern University, 11 Wenhua Road, Heping District, Shenyang, 110819, China. Electronic address:

Trifolium pratense L. (red clover) is an important leguminous crop with great potential for Ag-contaminated environment remediation. Whereas, the molecular mechanisms of Ag tolerance in red clover are largely unknown. Read More

View Article and Full-Text PDF

Purine-rich element binding protein B attenuates the coactivator function of myocardin by a novel molecular mechanism of smooth muscle gene repression.

Mol Cell Biochem 2021 Mar 20. Epub 2021 Mar 20.

Department of Biochemistry, University of Vermont, Robert Larner, M.D. College of Medicine, Burlington, VT, 05405, USA.

Myocardin is a potent transcriptional coactivator protein, which functions as the master regulator of vascular smooth muscle cell differentiation. The cofactor activity of myocardin is mediated by its physical interaction with serum response factor, a ubiquitously expressed transactivator that binds to CArG boxes in genes encoding smooth muscle-restricted proteins. Purine-rich element binding protein B (Purβ) represses the transcription of the smooth muscle α-actin gene (Acta2) in fibroblasts and smooth muscle cells by interacting with single-stranded DNA sequences flanking two 5' CArG boxes in the Acta2 promoter. Read More

View Article and Full-Text PDF

Combined genomic and proteomic approaches reveal DNA binding sites and interaction partners of TBX2 in the developing lung.

Respir Res 2021 Mar 17;22(1):85. Epub 2021 Mar 17.

Institut Für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany.

Background: Tbx2 encodes a transcriptional repressor implicated in the development of numerous organs in mouse. During lung development TBX2 maintains the proliferation of mesenchymal progenitors, and hence, epithelial proliferation and branching morphogenesis. The pro-proliferative function was traced to direct repression of the cell-cycle inhibitor genes Cdkn1a and Cdkn1b, as well as of genes encoding WNT antagonists, Frzb and Shisa3, to increase pro-proliferative WNT signaling. Read More

View Article and Full-Text PDF

Caspase cleavage releases a nuclear protein fragment that stimulates phospholipid scrambling at the plasma membrane.

Mol Cell 2021 04 15;81(7):1397-1410.e9. Epub 2021 Mar 15.

Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Konoe-cho, Yoshida, Sakyoku, Kyoto 606-8501, Japan; AMED-FORCE, Japanese Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyodaku, Tokyo 100-0004, Japan; Center for Integrated Biosystems, Institute for Biomedical Sciences, Academia Sinica, Taipei, Taiwan. Electronic address:

Phospholipid scrambling in dying cells promotes phosphatidylserine exposure, a critical process for efferocytosis. We previously identified the Xkr family protein Xkr4 as a phospholipid-scrambling protein, but its activation mechanisms remain unknown. Here we show that Xkr4 is activated in two steps: dimer formation by caspase-mediated cleavage and structural change caused by activating factors. Read More

View Article and Full-Text PDF

Changes in gene expression of adipose tissue CD14 cells in patients with Type 2 diabetes mellitus and their relationship with environmental factors.

Zhong Nan Da Xue Xue Bao Yi Xue Ban 2021 Jan;46(1):1-10

School of Public Health, Shaanxi University of Chinese Medicine, Xianyang Shaanxi 712046.

Objectives: To study the gene expression of adipose tissue CD14 cells in patients with Type 2 diabetes mellitus (T2DM) based on chip data, screen differentially expressed genes, and analyze their relationship with the environmental factors.

Methods: The data of GSE54350 were obtained from the public database of gene expression profiling. The data were pre-processed by Network Analyst, String 11. Read More

View Article and Full-Text PDF
January 2021

A single amino acid substitution in the R2R3 conserved domain of the BrPAP1a transcription factor impairs anthocyanin production in turnip (Brassica rapa subsp. rapa).

Plant Physiol Biochem 2021 May 22;162:124-136. Epub 2021 Feb 22.

Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China. Electronic address:

The purple pigmentation in the epidermis of swollen roots of 'Tsuda' turnip (Brassica rapa subsp. rapa) is induced by light, providing a good system to investigate the genetic mechanism of light-dependent anthocyanin biosynthesis in B. rapa. Read More

View Article and Full-Text PDF

Blockage of glioma cell survival by truncated TEAD-binding domain of YAP.

J Cancer Res Clin Oncol 2021 Jun 2;147(6):1713-1723. Epub 2021 Mar 2.

Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, 710032, Shaanxi, China.

Background: Gliomas are highly aggressive and lack of efficient targeted therapy. YAP, as a Hippo pathway downstream effector, plays a key role in promoting tumor development through the interaction with transcription factor TEAD on the NH3-terminal proline-rich domain. Therefore, targeting TEAD-interacting domain of YAP may provide a novel approach for the treatment of gliomas. Read More

View Article and Full-Text PDF

Identification of key pathways and genes in polycystic ovary syndrome via integrated bioinformatics analysis and prediction of small therapeutic molecules.

Reprod Biol Endocrinol 2021 Feb 23;19(1):31. Epub 2021 Feb 23.

Department of Ayurveda, Rajiv Gandhi Education Society's Ayurvedic Medical College, Ron, Karanataka, 562209, India.

To enhance understanding of polycystic ovary syndrome (PCOS) at the molecular level; this investigation intends to examine the genes and pathways associated with PCOS by using an integrated bioinformatics analysis. Based on the expression profiling by high throughput sequencing data GSE84958 derived from the Gene Expression Omnibus (GEO) database, the differentially expressed genes (DEGs) between PCOS samples and normal controls were identified. We performed a functional enrichment analysis. Read More

View Article and Full-Text PDF
February 2021

Diving into Chromatin across Space and Time.

J Mol Biol 2021 03 20;433(6):166884. Epub 2021 Feb 20.

School of Medicine, Queen's University, ON, Canada. Electronic address:

View Article and Full-Text PDF

High expression of tumor susceptibility gene 101 (TSG101) is associated with more aggressive behavior in colorectal carcinoma.

J Cancer Res Clin Oncol 2021 Jun 22;147(6):1631-1646. Epub 2021 Feb 22.

Oncopathology Research Center, Department of Molecular Medicine, Iran University of Medical Sciences (IUMS), Hemmat Street (Highway), Tehran, 14496-14530, Iran.

Introduction: Identification of genetic determinants such as exosomal content that drives progression and metastasis of colorectal cancer (CRC) has received considerable attention. The present study aims to identify a suitable biomarker in CRC tissues and exosomes based on bioinformatics data to evaluate its expression patterns in CRC tissues as well as its clinicopathological significance.

Materials And Methods: Protein-protein interaction (PPI) network and enrichment analysis were applied to identify up-regulated genes that contributed in CRC exosomes to select the marker. Read More

View Article and Full-Text PDF