scholarly journals Corrigendum: CLIP (Cross-Linking and Immunoprecipitation) Identification of RNAs Bound by a Specific Protein

2022 ◽  
Vol 2022 (1) ◽  
pp. pdb.corr107811
Author(s):  
Robert B. Darnell
Keyword(s):  
Specific Protein ◽  
Cross Linking

scholarly journals Microtubule Actin Cross-Linking Factor (Macf)

1999 ◽  
Vol 147 (6) ◽  
pp. 1275-1286 ◽  
Author(s):  
Conrad L. Leung ◽  
Dongming Sun ◽  
Min Zheng ◽  
David R. Knowles ◽  
Ronald K.H. Liem
Keyword(s):  
Calcium Binding ◽  
Coiled Coil ◽  
Specific Protein ◽  
Binding Domain ◽  
Full Length ◽  
Actin Binding ◽  
Cross Linking ◽  
Actin Binding Domain

We cloned and characterized a full-length cDNA of mouse actin cross-linking family 7 (mACF7) by sequential rapid amplification of cDNA ends–PCR. The completed mACF7 cDNA is 17 kb and codes for a 608-kD protein. The closest relative of mACF7 is the Drosophila protein Kakapo, which shares similar architecture with mACF7. mACF7 contains a putative actin-binding domain and a plakin-like domain that are highly homologous to dystonin (BPAG1-n) at its NH2 terminus. However, unlike dystonin, mACF7 does not contain a coiled–coil rod domain; instead, the rod domain of mACF7 is made up of 23 dystrophin-like spectrin repeats. At its COOH terminus, mACF7 contains two putative EF-hand calcium-binding motifs and a segment homologous to the growth arrest–specific protein, Gas2. In this paper, we demonstrate that the NH2-terminal actin-binding domain of mACF7 is functional both in vivo and in vitro. More importantly, we found that the COOH-terminal domain of mACF7 interacts with and stabilizes microtubules. In transfected cells full-length mACF7 can associate not only with actin but also with microtubules. Hence, we suggest a modified name: MACF (microtubule actin cross-linking factor). The properties of MACF are consistent with the observation that mutations in kakapo cause disorganization of microtubules in epidermal muscle attachment cells and some sensory neurons.

scholarly journals Ca2+-dependent interaction of the growth-associated protein GAP-43 with the synaptic core complex

1997 ◽  
Vol 325 (2) ◽  
pp. 455-463 ◽  
Author(s):  
Tatsumi HARUTA ◽  
Noboru TAKAMI ◽  
Manami OHMURA ◽  
Yoshio MISUMI ◽  
Yukio IKEHARA
Keyword(s):  
Pc12 Cells ◽  
Synaptic Vesicles ◽  
Specific Protein ◽  
Cross Linking ◽  
Core Complex ◽  
Synaptic Vesicle Exocytosis ◽  
Kinase C ◽  
Vesicle Exocytosis ◽  
Chemical Cross Linking ◽  
Dependent Interaction

The synaptic vesicle exocytosis occurs by a highly regulated mechanism: syntaxin and 25 kDa synaptosome-associated protein (SNAP-25) are assembled with vesicle-associated membrane protein (VAMP) to form a synaptic core complex and then synaptotagmin participates as a Ca2+ sensor in the final step of membrane fusion. The 43 kDa growth-associated protein GAP-43 is a nerve-specific protein that is predominantly localized in the axonal growth cones and presynaptic terminal membrane. In the present study we have examined a possible interaction of GAP-43 with components involved in the exocytosis. GAP-43 was found to interact with syntaxin, SNAP-25 and VAMP in rat brain tissues and nerve growth factor-dependently differentiated PC12 cells, but not in undifferentiated PC12 cells. GAP-43 also interacted with synaptotagmin and calmodulin. These interactions of GAP-43 could be detected only when chemical cross-linking of proteins was performed before they were solubilized from the membranes with detergents, in contrast with the interaction of the synaptic core complex, which was detected without cross-linking. Experiments invitro showed that the interaction of GAP-43 with these proteins occurred Ca2+-dependently; its maximum binding with the core complex was observed at 100 μM Ca2+, whereas that of syntaxin with synaptotagmin was at 200 μM Ca2+. These values of Ca2+ concentration are close to that required for the Ca2+-dependent release of neurotransmitters. Furthermore we observed that the interaction invitro of GAP-43 with the synaptic core complex was coupled with protein kinase C-mediated phosphorylation of GAP-43. Taken together, our results suggest a novel function of GAP-43 that is involved in the Ca2+-dependent fusion of synaptic vesicles.

UV cross-linking identifies four polypeptides that require the TATA box to bind to the Drosophila hsp70 promoter

1990 ◽  
Vol 10 (8) ◽  
pp. 4233-4238
Author(s):  
D S Gilmour ◽  
T J Dietz ◽  
S C Elgin
Keyword(s):  
Specific Protein ◽  
Cross Linking ◽  
Dependent Manner ◽  
Hsp70 Promoter ◽  
Intimate Contact ◽  
Nuclear Extracts ◽  
Multicomponent Complex ◽  
Tata Sequence ◽  
Drosophila Embryos

A protein fraction that requires the TATA sequence to bind to the hsp70 promoter has been partially purified from nuclear extracts of Drosophila embryos. This TATA factor produces a large DNase I footprint that extends from -44 to +35 on the promoter. A mutation that changes TATA to TATG interferes both with the binding of this complex and with the transcription of the hsp70 promoter in vitro, indicating that this interaction is important for transcriptional activity. Using a highly specific protein-DNA cross-linking assay, we have identified four polypeptides that require the TATA sequence to bind to the hsp70 promoter. Polypeptides of 26 and 42 kilodaltons are in intimate contact with the TATA sequence. Polypeptides of 150 and 60 kilodaltons interact within the region from +24 to +47 in a TATA-dependent manner. Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex.

scholarly journals Mapping Precursor-binding Site on TatC Subunit of Twin Arginine-specific Protein Translocase by Site-specific Photo Cross-linking

2012 ◽  
Vol 287 (16) ◽  
pp. 13430-13441 ◽  
Author(s):  
Stefan Zoufaly ◽  
Julia Fröbel ◽  
Patrick Rose ◽  
Tobias Flecken ◽  
Carlo Maurer ◽  
...  
Keyword(s):  
Binding Site ◽  
Specific Protein ◽  
Cross Linking ◽  
Site Specific

scholarly journals Site-specific Protein Cross-Linking with Genetically Incorporated 3,4-Dihydroxy-L-Phenylalanine

ChemBioChem ◽  
2009 ◽  
Vol 10 (8) ◽  
pp. 1302-1304 ◽  
Author(s):  
Aiko Umeda ◽  
Gabrielle Nina Thibodeaux ◽  
Jie Zhu ◽  
YungAh Lee ◽  
Zhiwen Jonathan Zhang
Keyword(s):  
Specific Protein ◽  
Cross Linking ◽  
Site Specific ◽  
Protein Cross Linking

scholarly journals UV cross-linking identifies four polypeptides that require the TATA box to bind to the Drosophila hsp70 promoter.

1990 ◽  
Vol 10 (8) ◽  
pp. 4233-4238 ◽  
Author(s):  
D S Gilmour ◽  
T J Dietz ◽  
S C Elgin
Keyword(s):  
Specific Protein ◽  
Cross Linking ◽  
Dependent Manner ◽  
Hsp70 Promoter ◽  
Intimate Contact ◽  
Nuclear Extracts ◽  
Multicomponent Complex ◽  
Tata Sequence ◽  
Drosophila Embryos

A protein fraction that requires the TATA sequence to bind to the hsp70 promoter has been partially purified from nuclear extracts of Drosophila embryos. This TATA factor produces a large DNase I footprint that extends from -44 to +35 on the promoter. A mutation that changes TATA to TATG interferes both with the binding of this complex and with the transcription of the hsp70 promoter in vitro, indicating that this interaction is important for transcriptional activity. Using a highly specific protein-DNA cross-linking assay, we have identified four polypeptides that require the TATA sequence to bind to the hsp70 promoter. Polypeptides of 26 and 42 kilodaltons are in intimate contact with the TATA sequence. Polypeptides of 150 and 60 kilodaltons interact within the region from +24 to +47 in a TATA-dependent manner. Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex.

scholarly journals Engagement of the Lewis X Antigen (CD15) Results in Monocyte Activation

Blood ◽  
1997 ◽  
Vol 89 (1) ◽  
pp. 307-314 ◽  
Author(s):  
Siu K. Lo ◽  
Douglas T. Golenbock ◽  
Philip M. Sass ◽  
Azmat Maskati ◽  
Hong Xu ◽  
...  
Keyword(s):  
Nuclear Factor Κb ◽  
Specific Protein ◽  
Cross Linking ◽  
Blood Monocytes ◽  
Monocyte Activation ◽  
Lewis X ◽  
Sv40 Promoter ◽  
Monocytic Cell ◽  
Monocytic Cell Line ◽  
Tnf Α

Abstract We previously reported that monocyte adhesion to tumor necrosis factor-α (TNF-α)–treated endothelial cells increased expression of tissue factor and CD36 on monocytes. Using immunological cross-linking to mimic receptor engagement by natural ligands, we now show that CD15 (Lewis X), a monocyte counter-receptor for endothelial selectins may participate in this response. We used cytokine production as a readout for monocyte activation and found that CD15 cross-linking induced TNF-α release from peripheral blood monocytes and cells from the monocytic cell line MM6. Quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) showed an increase in steady-state TNF-α mRNA after 3 to 4 hours of cross-linking. CD15 cross-linking also concomitantly increased interleukin-1β (IL-1β) mRNA, while no apparent change was observed in the levels of β-actin mRNA, indicating specificity. To examine transcriptional regulation of cytokine genes by CD15 engagement, a CAT plasmid reporter construct containing IL-1β promoter/enhancer sequences was introduced into MM6. Subsequent cross-linking of CD15 increased CAT activity. CD15 engagement by monoclonal antibody also attenuated IL-1β transcript degradation, demonstrating that signaling via CD15 also had posttranscriptional effects. Nuclear extracts of anti-CD15 cross-linked cells demonstrated enhanced levels of the transcriptional factor activator protein-1, minimally changed nuclear factor-κB, and did not affect SV40 promoter specific protein-1. We conclude that engagement of CD15 on monocytes results in monocyte activation. In addition to its well-recognized adhesive role, CD15 may function as an important signaling molecule capable of initiating proinflammatory events in monocytes that come into contact with activated endothelium.

Sign in / Sign up

Export Citation Format

Share Document