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1.
Genes Dev ; 30(18): 2106-2118, 2016 Sep 15.
Article in English | MEDLINE | ID: mdl-27798851

ABSTRACT

Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II). A "step-wise" preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, we established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Here we performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB-promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II-TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions.


Subject(s)
Promoter Regions, Genetic/physiology , Protein Multimerization/physiology , Transcription Factors, TFII/metabolism , Transcriptional Activation/physiology , Cell Line, Tumor , Humans , Microscopy, Interference , Protein Binding , RNA Polymerase II/metabolism , Sequence Deletion , Time Factors
2.
J Biol Chem ; 298(10): 102428, 2022 10.
Article in English | MEDLINE | ID: mdl-36037972

ABSTRACT

The methyl-CpG-binding domain 2 and 3 proteins (MBD2 and MBD3) provide structural and DNA-binding function for the Nucleosome Remodeling and Deacetylase (NuRD) complex. The two proteins form distinct NuRD complexes and show different binding affinity and selectivity for methylated DNA. Previous studies have shown that MBD2 binds with high affinity and selectivity for a single methylated CpG dinucleotide while MBD3 does not. However, the NuRD complex functions in regions of the genome that contain many CpG dinucleotides (CpG islands). Therefore, in this work, we investigate the binding and diffusion of MBD2 and MBD3 on more biologically relevant DNA templates that contain a large CpG island or limited CpG sites. Using a combination of single-molecule and biophysical analyses, we show that both MBD2 and MBD3 diffuse freely and rapidly across unmethylated CpG-rich DNA. In contrast, we found methylation of large CpG islands traps MBD2 leading to stable and apparently static binding on the CpG island while MBD3 continues to diffuse freely. In addition, we demonstrate both proteins bend DNA, which is augmented by methylation. Together, these studies support a model in which MBD2-NuRD strongly localizes to and compacts methylated CpG islands while MBD3-NuRD can freely mobilize nucleosomes independent of methylation status.


Subject(s)
DNA Methylation , DNA-Binding Proteins , CpG Islands , DNA-Binding Proteins/metabolism , Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Nucleosomes , Protein Binding , Transcription Factors/metabolism , Humans , Single Molecule Imaging
3.
Nature ; 545(7653): 234-237, 2017 05 11.
Article in English | MEDLINE | ID: mdl-28467818

ABSTRACT

Wnt proteins modulate cell proliferation and differentiation and the self-renewal of stem cells by inducing ß-catenin-dependent signalling through the Wnt receptor frizzled (FZD) and the co-receptors LRP5 and LRP6 to regulate cell fate decisions and the growth and repair of several tissues. The 19 mammalian Wnt proteins are cross-reactive with the 10 FZD receptors, and this has complicated the attribution of distinct biological functions to specific FZD and Wnt subtype interactions. Furthermore, Wnt proteins are modified post-translationally by palmitoylation, which is essential for their secretion, function and interaction with FZD receptors. As a result of their acylation, Wnt proteins are very hydrophobic and require detergents for purification, which presents major obstacles to the preparation and application of recombinant Wnt proteins. This hydrophobicity has hindered the determination of the molecular mechanisms of Wnt signalling activation and the functional importance of FZD subtypes, and the use of Wnt proteins as therapeutic agents. Here we develop surrogate Wnt agonists, water-soluble FZD-LRP5/LRP6 heterodimerizers, with FZD5/FZD8-specific and broadly FZD-reactive binding domains. Similar to WNT3A, these Wnt agonists elicit a characteristic ß-catenin signalling response in a FZD-selective fashion, enhance the osteogenic lineage commitment of primary mouse and human mesenchymal stem cells, and support the growth of a broad range of primary human organoid cultures. In addition, the surrogates can be systemically expressed and exhibit Wnt activity in vivo in the mouse liver, regulating metabolic liver zonation and promoting hepatocyte proliferation, resulting in hepatomegaly. These surrogates demonstrate that canonical Wnt signalling can be activated by bi-specific ligands that induce receptor heterodimerization. Furthermore, these easily produced, non-lipidated Wnt surrogate agonists facilitate functional studies of Wnt signalling and the exploration of Wnt agonists for translational applications in regenerative medicine.


Subject(s)
Signal Transduction , Wnt Proteins/agonists , Wnt Proteins/metabolism , Wnt Signaling Pathway , beta Catenin/metabolism , Animals , Cell Differentiation , Cell Lineage , Cell Proliferation , Frizzled Receptors/metabolism , HEK293 Cells , Hepatocytes/cytology , Hepatomegaly/metabolism , Hepatomegaly/pathology , Humans , Hydrophobic and Hydrophilic Interactions , Intestines/cytology , Ligands , Liver/metabolism , Liver/pathology , Low Density Lipoprotein Receptor-Related Protein-5/metabolism , Low Density Lipoprotein Receptor-Related Protein-6/metabolism , Mesenchymal Stem Cells/cytology , Mesenchymal Stem Cells/metabolism , Mice , Models, Molecular , Organoids/cytology , Organoids/metabolism , Protein Multimerization , Solubility , Tissue Culture Techniques
4.
Nucleic Acids Res ; 49(22): 13000-13018, 2021 12 16.
Article in English | MEDLINE | ID: mdl-34883513

ABSTRACT

The telomere specific shelterin complex, which includes TRF1, TRF2, RAP1, TIN2, TPP1 and POT1, prevents spurious recognition of telomeres as double-strand DNA breaks and regulates telomerase and DNA repair activities at telomeres. TIN2 is a key component of the shelterin complex that directly interacts with TRF1, TRF2 and TPP1. In vivo, the large majority of TRF1 and TRF2 are in complex with TIN2 but without TPP1 and POT1. Since knockdown of TIN2 also removes TRF1 and TRF2 from telomeres, previous cell-based assays only provide information on downstream effects after the loss of TRF1/TRF2 and TIN2. Here, we investigated DNA structures promoted by TRF2-TIN2 using single-molecule imaging platforms, including tracking of compaction of long mouse telomeric DNA using fluorescence imaging, atomic force microscopy (AFM) imaging of protein-DNA structures, and monitoring of DNA-DNA and DNA-RNA bridging using the DNA tightrope assay. These techniques enabled us to uncover previously unknown unique activities of TIN2. TIN2S and TIN2L isoforms facilitate TRF2-mediated telomeric DNA compaction (cis-interactions), dsDNA-dsDNA, dsDNA-ssDNA and dsDNA-ssRNA bridging (trans-interactions). Furthermore, TIN2 facilitates TRF2-mediated T-loop formation. We propose a molecular model in which TIN2 functions as an architectural protein to promote TRF2-mediated trans and cis higher-order nucleic acid structures at telomeres.


Subject(s)
DNA/metabolism , Telomere-Binding Proteins/metabolism , Telomere/metabolism , Telomeric Repeat Binding Protein 2/metabolism , Animals , DNA/chemistry , DNA/genetics , HeLa Cells , Humans , Mice, Inbred C57BL , Microscopy, Atomic Force , Nucleic Acid Conformation , Protein Binding , Shelterin Complex/genetics , Shelterin Complex/metabolism , Telomere/genetics , Telomere-Binding Proteins/genetics , Telomeric Repeat Binding Protein 2/genetics
5.
Int Wound J ; 20(8): 3140-3147, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37194335

ABSTRACT

A meta-analysis was conducted to measure hepatic and pancreatic tumour resection (HPTR) risk factors (RFs) for surgical site wound infections (SSWIs). A comprehensive literature inspection was conducted until February 2023, and 2349 interrelated investigations were reviewed. The nine chosen investigations included 22 774 individuals who were in the chosen investigations' starting point, 20 831 of them were with pancreatic tumours (PTs), and 1934 with hepatic tumours (HTs). Odds ratio (OR) and 95% confidence intervals (CIs) were used to compute the value of the HPTR RFs for SSWIs using dichotomous and continuous approaches, and a fixed or random model. HT patients with biliary reconstruction had significantly higher SSWI (OR, 5.81; 95% CI, 3.42-9.88, P < .001) than those without biliary reconstruction. Nevertheless, there was no significant difference between individuals with PT who underwent pancreaticoduodenectomy and those who underwent distal pancreatectomy in SSWI (OR, 1.63; 95% CI, 0.95-2.77, P = .07). HT individuals with biliary reconstruction had significantly higher SSWI compared with those without biliary reconstruction. Nevertheless, there was no significant difference between PT individuals who underwent pancreaticoduodenectomy and those who underwent distal pancreatectomy in SSWI. However, owing to the small number of selected investigations for this meta-analysis, care must be exercised when dealing with its values.


Subject(s)
Liver Neoplasms , Pancreatic Neoplasms , Humans , Pancreas/surgery , Pancreatectomy/adverse effects , Pancreatic Neoplasms/surgery , Pancreatic Neoplasms/etiology , Pancreatic Neoplasms/pathology , Surgical Wound Infection/epidemiology , Surgical Wound Infection/etiology , Surgical Wound Infection/surgery , Liver Neoplasms/surgery
6.
J Biol Chem ; 297(3): 101080, 2021 09.
Article in English | MEDLINE | ID: mdl-34403696

ABSTRACT

TIN2 is a core component of the shelterin complex linking double-stranded telomeric DNA-binding proteins (TRF1 and TRF2) and single-strand overhang-binding proteins (TPP1-POT1). In vivo, the large majority of TRF1 and TRF2 exist in complexes containing TIN2 but lacking TPP1/POT1; however, the role of TRF1-TIN2 interactions in mediating interactions with telomeric DNA is unclear. Here, we investigated DNA molecular structures promoted by TRF1-TIN2 interaction using atomic force microscopy (AFM), total internal reflection fluorescence microscopy (TIRFM), and the DNA tightrope assay. We demonstrate that the short (TIN2S) and long (TIN2L) isoforms of TIN2 facilitate TRF1-mediated DNA compaction (cis-interactions) and DNA-DNA bridging (trans-interactions) in a telomeric sequence- and length-dependent manner. On the short telomeric DNA substrate (six TTAGGG repeats), the majority of TRF1-mediated telomeric DNA-DNA bridging events are transient with a lifetime of ~1.95 s. On longer DNA substrates (270 TTAGGG repeats), TIN2 forms multiprotein complexes with TRF1 and stabilizes TRF1-mediated DNA-DNA bridging events that last on the order of minutes. Preincubation of TRF1 with its regulator protein Tankyrase 1 and the cofactor NAD+ significantly reduced TRF1-TIN2 mediated DNA-DNA bridging, whereas TIN2 protected the disassembly of TRF1-TIN2 mediated DNA-DNA bridging upon Tankyrase 1 addition. Furthermore, we showed that TPP1 inhibits TRF1-TIN2L-mediated DNA-DNA bridging. Our study, together with previous findings, supports a molecular model in which protein assemblies at telomeres are heterogeneous with distinct subcomplexes and full shelterin complexes playing distinct roles in telomere protection and elongation.


Subject(s)
Cell Adhesion Molecules/metabolism , Telomere-Binding Proteins/metabolism , Telomeric Repeat Binding Protein 2/metabolism , Cell Adhesion Molecules/physiology , DNA/metabolism , DNA-Binding Proteins/metabolism , Humans , Microscopy, Atomic Force/methods , Models, Molecular , Multiprotein Complexes/metabolism , Protein Binding , Protein Isoforms/metabolism , Shelterin Complex/metabolism , Shelterin Complex/physiology , Telomere/metabolism , Telomere-Binding Proteins/physiology , Telomeric Repeat Binding Protein 1/metabolism , Telomeric Repeat Binding Protein 1/physiology , Telomeric Repeat Binding Protein 2/physiology
7.
Small ; 18(50): e2203723, 2022 12.
Article in English | MEDLINE | ID: mdl-36266931

ABSTRACT

Qualitative and quantitative analysis of transient signaling platforms in the plasma membrane has remained a key experimental challenge. Here, biofunctional nanodot arrays (bNDAs) are developed to spatially control dimerization and clustering of cell surface receptors at the nanoscale. High-contrast bNDAs with spot diameters of ≈300 nm are obtained by capillary nanostamping of bovine serum albumin bioconjugates, which are subsequently biofunctionalized by reaction with tandem anti-green fluorescence protein (GFP) clamp fusions. Spatially controlled assembly of active Wnt signalosomes is achieved at the nanoscale in the plasma membrane of live cells by capturing the co-receptor Lrp6 into bNDAs via an extracellular GFP tag. Strikingly, co-recruitment is observed of co-receptor Frizzled-8 as well as the cytosolic scaffold proteins Axin-1 and Disheveled-2 into Lrp6 nanodots in the absence of ligand. Density variation and the high dynamics of effector proteins uncover highly cooperative liquid-liquid phase separation (LLPS)-driven assembly of Wnt "signalodroplets" at the plasma membrane, pinpointing the synergistic effects of LLPS for Wnt signaling amplification. These insights highlight the potential of bNDAs for systematically interrogating nanoscale signaling platforms and condensation at the plasma membrane of live cells.


Subject(s)
Wnt Proteins , beta Catenin , Wnt Proteins/metabolism , beta Catenin/metabolism , Phosphorylation , Wnt Signaling Pathway , Cell Membrane/metabolism
8.
Opt Express ; 30(22): 40265-40276, 2022 Oct 24.
Article in English | MEDLINE | ID: mdl-36298962

ABSTRACT

The development of a CMOS manufactured THz sensing platform could enable the integration of state-of-the-art sensing principles with the mixed signal electronics ecosystem in small footprint, low-cost devices. To this aim, in this work we demonstrate a label-free protein sensing platform using highly doped germanium plasmonic antennas realized on Si and SOI substrates and operating in the THz range of the electromagnetic spectrum. The antenna response to different concentrations of BSA shows in both cases a linear response with saturation above 20 mg/mL. Ge antennas on SOI substrates feature a two-fold sensitivity as compared to conventional Si substrates, reaching a value of 6 GHz/(mg/mL), which is four-fold what reported using metal-based metamaterials. We believe that this result could pave the way to a low-cost lab-on-a-chip biosensing platform.


Subject(s)
Germanium , Ecosystem , Lab-On-A-Chip Devices , Electronics , Metals
9.
Nucleic Acids Res ; 48(10): 5639-5655, 2020 06 04.
Article in English | MEDLINE | ID: mdl-32352519

ABSTRACT

Cohesin SA1 (STAG1) and SA2 (STAG2) are key components of the cohesin complex. Previous studies have highlighted the unique contributions by SA1 and SA2 to 3D chromatin organization, DNA replication fork progression, and DNA double-strand break (DSB) repair. Recently, we discovered that cohesin SA1 and SA2 are DNA binding proteins. Given the recently discovered link between SA2 and RNA-mediated biological pathways, we investigated whether or not SA1 and SA2 directly bind to RNA using a combination of bulk biochemical assays and single-molecule techniques, including atomic force microscopy (AFM) and the DNA tightrope assay. We discovered that both SA1 and SA2 bind to various RNA containing substrates, including ssRNA, dsRNA, RNA:DNA hybrids, and R-loops. Importantly, both SA1 and SA2 localize to regions on dsDNA that contain RNA. We directly compared the SA1/SA2 binding and R-loops sites extracted from Chromatin Immunoprecipitation sequencing (ChIP-seq) and DNA-RNA Immunoprecipitation sequencing (DRIP-Seq) data sets, respectively. This analysis revealed that SA1 and SA2 binding sites overlap significantly with R-loops. The majority of R-loop-localized SA1 and SA2 are also sites where other subunits of the cohesin complex bind. These results provide a new direction for future investigation of the diverse biological functions of SA1 and SA2.


Subject(s)
Cell Cycle Proteins/metabolism , Chromosomal Proteins, Non-Histone/metabolism , R-Loop Structures , RNA-Binding Proteins/metabolism , Binding Sites , DNA/metabolism , RNA/metabolism , Cohesins
10.
Anal Bioanal Chem ; 412(14): 3413-3422, 2020 May.
Article in English | MEDLINE | ID: mdl-32198532

ABSTRACT

Localized surface plasmon resonance (LSPR) detection offers highly sensitive label-free detection of biomolecular interactions. Simple and robust surface architectures compatible with real-time detection in a flow-through system are required for broad application in quantitative interaction analysis. Here, we established self-assembly of a functionalized gold nanoparticle (AuNP) monolayer on a glass substrate for stable, yet reversible immobilization of Histidine-tagged proteins. To this end, one-step coating of glass substrates with poly-L-lysine graft poly(ethylene glycol) functionalized with ortho-pyridyl disulfide (PLL-PEG-OPSS) was employed as a reactive, yet biocompatible monolayer to self-assemble AuNP into a LSPR active monolayer. Site-specific, reversible immobilization of His-tagged proteins was accomplished by coating the AuNP monolayer with tris-nitrilotriacetic acid (trisNTA) PEG disulfide. LSPR spectroscopy detection of protein binding on these biocompatible functionalized AuNP monolayers confirms high stability under various harsh analytical conditions. These features were successfully employed to demonstrate unbiased kinetic analysis of cytokine-receptor interactions. Graphical abstract.


Subject(s)
Gold/chemistry , Metal Nanoparticles/chemistry , Protein Interaction Mapping/methods , Surface Plasmon Resonance/methods , Animals , Humans , Immobilized Proteins/metabolism , Interferon-alpha/metabolism , Models, Molecular , Protein Binding , Receptor, Interferon alpha-beta/metabolism , Refractometry/methods
11.
Cell Mol Biol (Noisy-le-grand) ; 66(2): 111-117, 2020 May 15.
Article in English | MEDLINE | ID: mdl-32415936

ABSTRACT

To detect the expression of metastasis-associated colon cancer gene 1 (MACC1) protein in gastric cancer tissues, and analyze its relationship with clinicopathological parameters of gastric cancer and its effect on proliferation and invasion of gastric cancer cells. METHODS: 71 patients with gastric cancer in Fifth Hospital in Wuhan from June 2014 to March 2018 were selected as research subjects. Western blot was used to detect the expression of MACC1 in gastric cancer tissue and normal gastric mucosa tissue, and gastric cancer cell SGC7901 was transfected. Transfection group (transfected with MACC1-siRNA), negative control group (transfected with siRNA-NC) and blank control group (untreated cells) were set up. After transfection, the expressions of MACC1 protein and mRNA in the 3 groups were detected by Western blot and qRT-PCR methods, the cell proliferation was detected by MTT method, and the invasion ability of cells in vitro was detected by Transwell chamber. RESULTS: The expression of MACC1 protein in gastric cancer tissue was higher than the control group (P< 0.05). The expression of MACC1 protein in gastric cancer was related to the differentiation degree, infiltration depth, lymph node metastasis and different stages of gastric cancer (P< 0.05). After transfection, the expressions of MACC1 protein and mRNA in the transfection group was significantly lower than the negative control group and blank group (P< 0.05). There was no significant difference in cell viability between the blank group and negative control group at each time point (P> 0.05). CONCLUSION: MACC1 was highly expressed in gastric cancer tissues. The expression of MACC1 was related to the differentiation degree, infiltration depth, lymph node metastasis and staging of gastric cancer. Down-regulation of MACC1 could inhibit the proliferation and invasion of gastric cancer cells. This study provided a certain biological basis for early clinical prediction, diagnosis and treatment of gastric cancer.


Subject(s)
Stomach Neoplasms/pathology , Trans-Activators/metabolism , Aged , Cell Line, Tumor , Cell Movement , Cell Proliferation , Female , Gastric Mucosa/metabolism , Humans , Lymphatic Metastasis , Male , Middle Aged , RNA Interference , RNA, Messenger/metabolism , RNA, Small Interfering/metabolism , Stomach Neoplasms/metabolism , Trans-Activators/antagonists & inhibitors , Trans-Activators/genetics
12.
J Biol Chem ; 293(3): 1054-1069, 2018 01 19.
Article in English | MEDLINE | ID: mdl-29175904

ABSTRACT

Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids, mediated by the cohesin protein complex, which also plays crucial roles in diverse genome maintenance pathways. Current models attribute DNA binding by cohesin to entrapment of dsDNA by the cohesin ring subunits (SMC1, SMC3, and RAD21 in humans). However, the biophysical properties and activities of the fourth core cohesin subunit SA2 (STAG2) are largely unknown. Here, using single-molecule atomic force and fluorescence microscopy imaging as well as fluorescence anisotropy measurements, we established that SA2 binds to both dsDNA and ssDNA, albeit with a higher binding affinity for ssDNA. We observed that SA2 can switch between the 1D diffusing (search) mode on dsDNA and stable binding (recognition) mode at ssDNA gaps. Although SA2 does not specifically bind to centromeric or telomeric sequences, it does recognize DNA structures often associated with DNA replication and double-strand break repair, such as a double-stranded end, single-stranded overhang, flap, fork, and ssDNA gap. SA2 loss leads to a defect in homologous recombination-mediated DNA double-strand break repair. These results suggest that SA2 functions at intermediate DNA structures during DNA transactions in genome maintenance pathways. These findings have important implications for understanding the function of cohesin in these pathways.


Subject(s)
Cell Cycle Proteins/metabolism , Chromosomal Proteins, Non-Histone/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Cell Cycle Proteins/chemistry , Chromosomal Proteins, Non-Histone/chemistry , DNA Repair/genetics , DNA Repair/physiology , DNA Replication/physiology , Fluorescence Polarization , Genomic Instability/genetics , Genomic Instability/physiology , Microscopy, Atomic Force , Microscopy, Fluorescence , Protein Binding/genetics , Protein Binding/physiology , Cohesins
13.
Nucleic Acids Res ; 44(13): 6363-76, 2016 07 27.
Article in English | MEDLINE | ID: mdl-27298259

ABSTRACT

Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids. Cohesion is thought to occur through the entrapment of DNA within the tripartite ring (Smc1, Smc3 and Rad21) with enforcement from a fourth subunit (SA1/SA2). Surprisingly, cohesin rings do not play a major role in sister telomere cohesion. Instead, this role is replaced by SA1 and telomere binding proteins (TRF1 and TIN2). Neither the DNA binding property of SA1 nor this unique telomere cohesion mechanism is understood. Here, using single-molecule fluorescence imaging, we discover that SA1 displays two-state binding on DNA: searching by one-dimensional (1D) free diffusion versus recognition through subdiffusive sliding at telomeric regions. The AT-hook motif in SA1 plays dual roles in modulating non-specific DNA binding and subdiffusive dynamics over telomeric regions. TRF1 tethers SA1 within telomeric regions that SA1 transiently interacts with. SA1 and TRF1 together form longer DNA-DNA pairing tracts than with TRF1 alone, as revealed by atomic force microscopy imaging. These results suggest that at telomeres cohesion relies on the molecular interplay between TRF1 and SA1 to promote DNA-DNA pairing, while along chromosomal arms the core cohesin assembly might also depend on SA1 1D diffusion on DNA and sequence-specific DNA binding.


Subject(s)
Chromosome Segregation/genetics , Nuclear Proteins/genetics , Telomere-Binding Proteins/genetics , Telomere/genetics , Telomeric Repeat Binding Protein 1/genetics , AT-Hook Motifs/genetics , Chromatids/genetics , Chromatids/ultrastructure , DNA-Binding Proteins/genetics , Humans , Microscopy, Atomic Force , Mitosis/genetics , Nuclear Proteins/metabolism , Telomere/ultrastructure , Telomere-Binding Proteins/metabolism , Telomeric Repeat Binding Protein 1/metabolism
14.
J Biol Chem ; 291(47): 24735-24746, 2016 Nov 18.
Article in English | MEDLINE | ID: mdl-27729449

ABSTRACT

Single-molecule photobleaching has emerged as a powerful non-invasive approach to extract the stoichiometry of multimeric membrane proteins in their native cellular environment. However, this method has mainly been used to determine the subunit composition of ion channels and receptors at the plasma membrane. Here, we applied single-molecule photobleaching to analyze the oligomeric state of an endoplasmic reticulum (ER) resident candidate ceramide sensor protein, SMSr/SAMD8. Co-immunoprecipitation and chemical cross-linking studies previously revealed that the N-terminal sterile alpha motif (or SAM) domain of SMSr drives self-assembly of the protein into oligomers and that SMSr oligomerization is promoted by curcumin, a drug known to perturb ER ceramide and calcium homeostasis. Application of cell spreading surface-active coating materials in combination with total internal reflection fluorescence (TIRF) microscopy allowed us to image GFP-tagged SMSr proteins as single fluorescent spots in the ER of HeLa cells in which expression of endogenous SMSr was abolished. In line with our biochemical analysis, we find that the number of bleaching steps in SMSr-GFP-positive spots displays a substantial drop after removal of the SAM domain. In contrast, treatment of cells with curcumin increased the number of bleaching steps. Our results document the first successful application of single-molecule photobleaching to resolve drug-induced and domain-dependent changes in the oligomeric state of an ER-resident membrane protein, hence establishing a complementary method to unravel the mechanism by which SMSr controls ceramide levels in the ER.


Subject(s)
Ceramides/metabolism , Endoplasmic Reticulum/metabolism , Membrane Proteins/metabolism , Photobleaching , Ceramides/chemistry , Endoplasmic Reticulum/chemistry , HeLa Cells , Humans , Membrane Proteins/chemistry , Microscopy, Fluorescence
15.
Nucleic Acids Res ; 42(4): 2493-504, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24271387

ABSTRACT

Human telomeres are maintained by the shelterin protein complex in which TRF1 and TRF2 bind directly to duplex telomeric DNA. How these proteins find telomeric sequences among a genome of billions of base pairs and how they find protein partners to form the shelterin complex remains uncertain. Using single-molecule fluorescence imaging of quantum dot-labeled TRF1 and TRF2, we study how these proteins locate TTAGGG repeats on DNA tightropes. By virtue of its basic domain TRF2 performs an extensive 1D search on nontelomeric DNA, whereas TRF1's 1D search is limited. Unlike the stable and static associations observed for other proteins at specific binding sites, TRF proteins possess reduced binding stability marked by transient binding (∼ 9-17 s) and slow 1D diffusion on specific telomeric regions. These slow diffusion constants yield activation energy barriers to sliding ∼ 2.8-3.6 κ(B)T greater than those for nontelomeric DNA. We propose that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA. This 'tag-team proofreading' represents a more general mechanism to ensure a specific set of proteins interact with each other on long repetitive specific DNA sequences without requiring external energy sources.


Subject(s)
DNA/metabolism , Telomere/metabolism , Telomeric Repeat Binding Protein 1/metabolism , Telomeric Repeat Binding Protein 2/metabolism , DNA/chemistry , Diffusion , Protein Binding , Protein Structure, Tertiary , Repetitive Sequences, Nucleic Acid , Telomere/chemistry , Telomeric Repeat Binding Protein 2/chemistry
16.
Nano Lett ; 15(5): 3610-5, 2015 May 13.
Article in English | MEDLINE | ID: mdl-25901412

ABSTRACT

We developed in situ single cell pull-down (SiCPull) of GFP-tagged protein complexes based on micropatterned functionalized surface architectures. Cells cultured on these supports are lysed by mild detergents and protein complexes captured to the surface are probed in situ by total internal reflection fluorescence microscopy. Using SiCPull, we quantitatively mapped the lifetimes of various signal transducer and activator of transcription complexes by monitoring dissociation from the surface and defined their stoichiometry on the single molecule level.


Subject(s)
Cytosol/chemistry , Multiprotein Complexes/chemistry , Single-Cell Analysis , Cytosol/metabolism , Humans , Microscopy, Fluorescence , Multiprotein Complexes/isolation & purification , Multiprotein Complexes/metabolism , Surface Properties
17.
Small ; 11(44): 5912-8, 2015 Nov 25.
Article in English | MEDLINE | ID: mdl-26421417

ABSTRACT

Triggered immobilization of proteins in the plasma membrane of living cells into functional micropatterns is established by using an adaptor protein, which is comprised of an antiGFP nanobody fused to the HaloTag protein. Efficient in situ reorganization of the type I interferon receptor subunits as well as intact, fully functional signaling complexes in living cells are achieved by this method.


Subject(s)
Cell Membrane/metabolism , Signal Transduction , Cell Survival , HeLa Cells , Humans , Immobilized Proteins/metabolism , Membrane Proteins/metabolism , Microtechnology , Receptors, Cell Surface/metabolism
18.
Nano Lett ; 14(4): 2189-95, 2014.
Article in English | MEDLINE | ID: mdl-24655019

ABSTRACT

On the basis of a protein cage scaffold, we have systematically explored intracellular application of nanoparticles for single molecule studies and discovered that recognition by the autophagy machinery plays a key role for rapid metabolism in the cytosol. Intracellular stealth nanoparticles were achieved by heavy surface PEGylation. By combination with a generic approach for nanoparticle monofunctionalization, efficient labeling of intracellular proteins with high fidelity was accomplished, allowing unbiased long-term tracking of proteins in the outer mitochondrial membrane.


Subject(s)
Autophagy , Cytosol/metabolism , Mitochondria/metabolism , Nanoparticles/metabolism , Proteins/metabolism , Fluorescent Dyes/chemistry , Fluorescent Dyes/metabolism , HeLa Cells , Humans , Microscopy, Fluorescence , Mitochondrial Proteins/analysis , Mitochondrial Proteins/metabolism , Nanoparticles/chemistry , Polyethylene Glycols/chemistry , Polyethylene Glycols/metabolism , Proteins/analysis
19.
Anal Chem ; 86(17): 8593-602, 2014 Sep 02.
Article in English | MEDLINE | ID: mdl-25148216

ABSTRACT

Unraveling the spatiotemporal organization of signaling complexes within the context of plasma membrane nanodomains has remained a highly challenging task. Here, we have applied super-resolution image correlation based on tracking and localization microscopy (TALM) for probing transient confinement as well as ligand binding and intracellular effector recruitment of the type I interferon (IFN) receptor in the plasma membrane of live cells. Ligand and receptor were labeled with monofunctional quantum dots, thus allowing long-term tracking with very high spatial and temporal resolution without an artificial receptor cross-linking at the cell surface. Dual-color TALM was employed for visualizing protein-protein interactions involved in IFN signaling at both sides of the plasma membrane with high spatial and temporal resolution. By pair correlation analyses based on time-lapse TALM images (pcTALM), complex assembly within dynamic submicroscopic zones was identified. Strikingly, recruitment of the IFN effector protein signal transducer and activator of transcription 2 (STAT2) into these dynamic signaling zones could be observed. The results suggest that confined diffusion zones in the plasma membrane are employed as transient platforms for the assembly of signaling complexes.


Subject(s)
Microscopy, Fluorescence , Receptor, Interferon alpha-beta/metabolism , Signal Transduction , Biotin/chemistry , Biotin/metabolism , Cell Membrane/metabolism , HeLa Cells , Humans , Oligopeptides/chemistry , Oligopeptides/metabolism , Protein Interaction Maps , Quantum Dots/chemistry , Receptor, Interferon alpha-beta/genetics , STAT2 Transcription Factor/metabolism , Time-Lapse Imaging
20.
Anal Bioanal Chem ; 406(14): 3345-57, 2014 May.
Article in English | MEDLINE | ID: mdl-24770786

ABSTRACT

Site-specific protein modification-e.g. for immobilization or labelling-is a key prerequisite for numerous bioanalytical applications. Although modification by use of short peptide tags is particularly attractive, efficient and bio-orthogonal systems are still lacking. Here, we review the application of multivalent chelators (MCH) for high-affinity yet reversible recognition of oligohistidine (His)-tagged proteins. MCH are based on multiple nitrilotriacetic acid (NTA) moieties grafted on to molecular scaffolds suitable for conjugation to surfaces, probes or other biomolecules. Reversible interaction with the His-tag is mediated via transition metal ions chelated by the NTA moieties. The small size and biochemical compatibility of these recognition units and the possibility of rapid dissociation of the interaction with His-tagged proteins despite sub-nanomolar binding affinity, enable distinct and versatile handling and modification of recombinant proteins. In this review, we briefly introduce the key principles and features of MCH-His-tag interactions and recapitulate the broad spectrum of bioanalytical applications with a focus on quantitative protein interaction analysis on micro or nano-patterned solid surfaces and specific protein labelling in living cells.


Subject(s)
Biosensing Techniques , Chelating Agents/chemistry , Animals , Histidine/chemistry , Humans , Ions , Lipids/chemistry , Nanotechnology , Nitrilotriacetic Acid/chemistry , Oxygen/chemistry , Protein Interaction Mapping , Proteins/chemistry , Recombinant Proteins/chemistry , Spectrophotometry , Surface Properties
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