scholarly journals Structure of the tripartite motif of KAP1/TRIM28 identifies molecular interfaces required for transcriptional silencing of retrotransposons

2018 ◽  
Author(s):  
Guido A. Stoll ◽  
Shun-ichiro Oda ◽  
Zheng-Shan Chong ◽  
Minmin Yu ◽  
Stephen H. McLaughlin ◽  
...  
Keyword(s):  
Self Assembly ◽  
Coiled Coil ◽  
Transcriptional Silencing ◽  
Higher Order ◽  
Significant Loss ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Krab Domain ◽  
Tripartite Motif ◽  
Self Association

AbstractTranscription of transposable elements is tightly regulated to prevent damage to the genome. The family of KRAB domain-containing zinc finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize specific retrotransposon sequences and recruit KAP1, which controls the assembly of an epigenetic silencing complex including histone H3K9 methyltransferase SETDB1. The chromatin remodeling activities of this complex repress transcription of the targeted transposable element and any adjacent genes. Here, we use biophysical and structural approaches to show that the tripartite motif (TRIM) of KAP1 forms antiparallel dimers, which further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevented higher-order oligomerization without a significant loss of retrotransposon silencing activity in a cell-based assay, indicating that, in contrast to other TRIM family members, self-assembly is not essential for the function of KAP1. The crystal structure of the KAP1 RBCC dimer identifies the KRAB domain binding site, in the coiled-coil domain near the dyad. Mutations at this site abolished KRAB binding and transcriptional silencing activity of KAP1. This work identifies the interaction interfaces in the KAP1 RBCC motif responsible for self-association and KRAB binding and establishes their role in retrotransposon silencing.

scholarly journals Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing

2019 ◽  
Vol 116 (30) ◽  
pp. 15042-15051 ◽  
Author(s):  
Guido A. Stoll ◽  
Shun-ichiro Oda ◽  
Zheng-Shan Chong ◽  
Minmin Yu ◽  
Stephen H. McLaughlin ◽  
...  
Keyword(s):  
Self Assembly ◽  
Coiled Coil ◽  
Structural Data ◽  
Higher Order ◽  
Significant Loss ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Krab Domain ◽  
Genome Damage ◽  
Tripartite Motif

Transcription of transposable elements is tightly regulated to prevent genome damage. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize specific retrotransposon sequences and recruit KAP1, inducing the assembly of an epigenetic silencing complex, with chromatin remodeling activities that repress transcription of the targeted retrotransposon and adjacent genes. Our biophysical and structural data show that the tripartite motif (TRIM) of KAP1 forms antiparallel dimers, which further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevent higher-order oligomerization without significant loss of retrotransposon silencing activity, indicating that, in contrast to other TRIM-family proteins, self-assembly is not essential for KAP1 function. The crystal structure of the KAP1 TRIM dimer identifies the KRAB domain binding site in the coiled-coil domain near the dyad. Mutations at this site abolished KRAB binding and transcriptional silencing activity of KAP1. This work identifies the interaction interfaces in the KAP1 TRIM responsible for self-association and KRAB binding and establishes their role in retrotransposon silencing.

scholarly journals The role of the main noncollagenous domain (NC1) in type IV collagen self-assembly.

1986 ◽  
Vol 103 (6) ◽  
pp. 2467-2473 ◽  
Author(s):  
E C Tsilibary ◽  
A S Charonis
Keyword(s):  
Self Assembly ◽  
Type Iv Collagen ◽  
Elevated Temperatures ◽  
Network Formation ◽  
Basement Membranes ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Amino Terminal ◽  
Type Iv ◽  
Self Association

Type IV collagen incubated at elevated temperatures in physiologic buffers self-associates (a) via its carboxy-terminal (NC1) domain, (b) via its amino-terminal (7S) domain, and (c) laterally; and it forms a network. When examined with the technique of rotary shadowing, isolated domain NC1 was found to bind along the length of type IV collagen to four distinct sites located at intervals of approximately 100 nm each. The same 100-nm distance was observed in domain NC1 of intact type IV collagen bound along the length of the collagen molecules during initial steps of network formation and in complete networks. The presence of anti-NC1 Fab fragments in type IV collagen solutions inhibited lateral association and network formation in rotary shadow images. During the process of self-association type IV collagen develops turbidity; addition of isolated domain NC1 inhibited the development of turbidity in a concentration-dependent manner. These findings indicate that domain NC1 of type IV collagen plays an important role in the process of self-association and suggest that alterations in the structure of NC1 may be partially responsible for impaired functions of basement membranes in certain pathological conditions.

scholarly journals Terminal short arm domains of basement membrane laminin are critical for its self-assembly.

1990 ◽  
Vol 110 (3) ◽  
pp. 825-832 ◽  
Author(s):  
J C Schittny ◽  
P D Yurchenco
Keyword(s):  
Self Assembly ◽  
Affinity Column ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Calcium Dependent ◽  
Domain Specific ◽  
Binding Domains ◽  
Individual Domain ◽  
The Individual

Laminin self-assembles into large polymers by a cooperative two-step calcium-dependent mechanism (Yurchenco, P. D., E. C. Tsilibary, A. S. Charonis, and H. Furthmayr. 1985. J. Biol. Chem. 260:7636-7644). The domain specificity of this process was investigated using defined proteolytically generated fragments corresponding to the NH2-terminal globule and adjacent stem of the short arm of the B1 chain (E4), a complex of the two short arms of the A and B2 chains attached to the proximal stem of a third short arm (E1'), a similar complex lacking the globular domains (P1'), and the distal half of the long arm attached to the adjacent portion of the large globule (E8). Polymerization, followed by an increase of turbidity at 360 nm in neutral isotonic TBS containing CaCl2 at 35 degrees C, was quantitatively inhibited in a concentration-dependent manner with laminin fragments E4 and E1' but not with fragments E8 and P1'. Affinity retardation chromatography was used for further characterization of the binding of laminin domains. The migration of fragment E4, but not of fragments E8 and P1', was retarded in a temperature- and calcium-dependent fashion on a laminin affinity column but not on a similar BSA column. These data are evidence that laminin fragments E4 and E1' possess essential terminal binding domains for the self-aggregation of laminin, while fragments E8 and P1' do not. Furthermore, the individual domain-specific interactions that contribute to assembly are calcium dependent and of low affinity.

scholarly journals Higher-order assembly of Sorting Nexin 16 controls tubulation and distribution of neuronal endosomes

2019 ◽  
Vol 218 (8) ◽  
pp. 2600-2618 ◽  
Author(s):  
ShiYu Wang ◽  
Zechuan Zhao ◽  
Avital A. Rodal
Keyword(s):  
Cell Body ◽  
Motor Neurons ◽  
Coiled Coil ◽  
Higher Order ◽  
Synaptic Growth ◽  
Sorting Nexin ◽  
Protein Receptors ◽  
Self Association ◽  
Signaling Receptors

The activities of neuronal signaling receptors depend heavily on the maturation state of the endosomal compartments in which they reside. However, it remains unclear how the distribution of these compartments within the uniquely complex morphology of neurons is regulated and how this distribution itself affects signaling. Here, we identified mechanisms by which Sorting Nexin 16 (SNX16) controls neuronal endosomal maturation and distribution. We found that higher-order assembly of SNX16 via its coiled-coil (CC) domain drives membrane tubulation in vitro and endosome association in cells. In Drosophila melanogaster motor neurons, activation of Rab5 and CC-dependent self-association of SNX16 lead to its endosomal enrichment, accumulation in Rab5- and Rab7-positive tubulated compartments in the cell body, and concomitant depletion of SNX16-positive endosomes from the synapse. This results in accumulation of synaptic growth–promoting bone morphogenetic protein receptors in the cell body and correlates with increased synaptic growth. Our results indicate that Rab regulation of SNX16 assembly controls the endosomal distribution and signaling activities of receptors in neurons.

scholarly journals Electric-Field-Directed Self-Assembly of Active Enzyme-Nanoparticle Structures

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Alexander P. Hsiao ◽  
Michael J. Heller
Keyword(s):  
Electric Field ◽  
Self Assembly ◽  
Microelectrode Array ◽  
Glucose Sensor ◽  
Directed Assembly ◽  
Passive Layer ◽  
Higher Order ◽  
Significant Loss ◽  
Layer By Layer ◽  
Multilayered Structures

A method is presented for the electric-field-directed self-assembly of higher-order structures composed of alternating layers of biotin nanoparticles and streptavidin-/avidin-conjugated enzymes carried out on a microelectrode array device. Enzymes included in the study were glucose oxidase (GOx), horseradish peroxidase (HRP), and alkaline phosphatase (AP); all of which could be used to form a light-emitting microscale glucose sensor. Directed assembly included fabricating multilayer structures with 200 nm or 40 nm GOx-avidin-biotin nanoparticles, with AP-streptavidin-biotin nanoparticles, and with HRP-streptavidin-biotin nanoparticles. Multilayered structures were also fabricated with alternate layering of HRP-streptavidin-biotin nanoparticles and GOx-avidin-biotin nanoparticles. Results showed that enzymatic activity was retained after the assembly process, indicating that substrates could still diffuse into the structures and that the electric-field-based fabrication process itself did not cause any significant loss of enzyme activity. These methods provide a solution to overcome the cumbersome passive layer-by-layer assembly methods to efficiently fabricate higher-order active biological and chemical hybrid structures that can be useful for creating novel biosensors and drug delivery nanostructures, as well as for diagnostic applications.

scholarly journals Fluorescein-Labeled Starch Maleate Nanoparticles as Sensitive Fluorescent Sensing Probes for Metal Ions

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Suk Fun Chin ◽  
Aressa Azman ◽  
Suh Cem Pang ◽  
Sing Muk Ng
Keyword(s):  
Particle Size ◽  
Metal Ions ◽  
Self Assembly ◽  
Detection Limits ◽  
Emission Wavelength ◽  
Dependent Manner ◽  
Ethanolic Solution ◽  
Concentration Dependent Manner ◽  
Maximum Emission ◽  
Fluorescent Sensing

Fluorescein 5(6)-isothiocyanate starch maleate (FISM) nanoparticles were prepared by covalently attached fluorescein 5(6)-isothiocyanate (FITC) with starch maleate. FISM nanoparticles with a mean particle size of 87 nm were formed via self-assembly upon precipitation in ethanolic solution. FISM nanoparticles were strongly fluorescent with maximum emission wavelength of 518 nm. The fluorescence of FISM nanoparticles can be quenched by silver (Ag+) and lead (Pb2+) ions in a concentration dependent manner. We have demonstrated the first use of FISM nanoparticles as cheap and effective fluorescent sensing probes for Ag+and Pb2+ions with detection limits as low as 2.55×10−5 M and 3.64×10−5 M, respectively.

Self-assembling triazolophanes: from croissants through donuts to spherical vesicles

2015 ◽  
Vol 51 (32) ◽  
pp. 6905-6908 ◽  
Author(s):  
V. Haridas ◽  
Appa Rao Sapala ◽  
Jerry P. Jasinski
Keyword(s):  
Crystal Structure ◽  
Self Assembly ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
X Ray ◽  
Self Assembling ◽  
Assembly Mechanism ◽  
Spherical Vesicles

A detailed ultramicroscopic analysis of three novel triazolophanes demonstrated a hierarchical self-assembly mechanism. These macrocycles self-assemble in a concentration dependent manner to hemi-toroids, toroids and finally to vesicles. The finding was supported by ultramicroscopy and X-ray crystal structure studies.

scholarly journals Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases

2020 ◽  
Vol 48 (6) ◽  
pp. 2615-2624
Author(s):  
Filippo Fiorentini ◽  
Diego Esposito ◽  
Katrin Rittinger
Keyword(s):  
Coiled Coil ◽  
E3 Ligase ◽  
Protein Family ◽  
Ring Domain ◽  
Cellular Functions ◽  
Protein Activity ◽  
Coiled Coil Region ◽  
Tripartite Motif ◽  
Large Protein Family ◽  
Self Association

TRIM proteins form a protein family that is characterized by a conserved tripartite motif domain comprising a RING domain, one or two B-box domains and a coiled-coil region. Members of this large protein family are important regulators of numerous cellular functions including innate immune responses, transcriptional regulation and apoptosis. Key to their cellular role is their E3 ligase activity which is conferred by the RING domain. Self-association is an important characteristic of TRIM protein activity and is mediated by homodimerization via the coiled-coil region, and in some cases higher order association via additional domains of the tripartite motif. In many of the TRIM family proteins studied thus far, RING dimerization is an important prerequisite for E3 ligase enzymatic activity though the propensity of RING domains to dimerize differs significantly between different TRIMs and can be influenced by other regions of the protein.

scholarly journals The TRIM5α B-Box 2 Domain Promotes Cooperative Binding to the Retroviral Capsid by Mediating Higher-Order Self-Association

2008 ◽  
Vol 82 (23) ◽  
pp. 11495-11502 ◽  
Author(s):  
Xing Li ◽  
Joseph Sodroski
Keyword(s):  
Virus Entry ◽  
Coiled Coil ◽  
Higher Order ◽  
Restriction Factor ◽  
Cooperative Binding ◽  
Specific Function ◽  
Retroviral Infection ◽  
Spry Domain ◽  
Dense Arrays ◽  
Self Association

ABSTRACT The retroviral restriction factor, TRIM5α, blocks infection of a spectrum of retroviruses soon after virus entry into the cell. TRIM5α consists of RING, B-box 2, coiled-coil, and B30.2(SPRY) domains. The B-box 2 domain is essential for retrovirus restriction by TRIM5α, but its specific function is unknown. We show here that the B-box 2 domain mediates higher-order self-association of TRIM5αrh oligomers. This self-association increases the efficiency of TRIM5α binding to the retroviral capsid, thus potentiating restriction of retroviral infection. The contribution of the B-box 2 domain to cooperative TRIM5α association with the retroviral capsid explains the conditional nature of the restriction phenotype exhibited by some B-box 2 TRIM5α mutants; the potentiation of capsid binding that results from B-box 2-mediated self-association is essential for restriction when B30.2(SPRY) domain-mediated interactions with the retroviral capsid are weak. Thus, B-box 2-dependent higher-order self-association and B30.2(SPRY)-dependent capsid binding represent complementary mechanisms whereby sufficiently dense arrays of capsid-bound TRIM5α proteins can be achieved.

scholarly journals In Vitro Inhibitory Mechanism Effect of TRAIP on the Function of TRAF2 Revealed by Characterization of Interaction Domains

2018 ◽  
Vol 19 (8) ◽  
pp. 2457 ◽  
Author(s):  
Eijaz Bhat ◽  
Chang Kim ◽  
Sunghwan Kim ◽  
Hyun Park
Keyword(s):  
Coiled Coil ◽  
Adaptor Protein ◽  
Direct Interaction ◽  
Negative Regulator ◽  
Dependent Manner ◽  
Inhibitory Mechanism ◽  
Concentration Dependent Manner ◽  
Critical Function

TRAF-interacting protein (TRAIP), a negative regulator of TNF-induced-nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation, inhibits adaptor protein TRAF2 by direct interaction and is critical in apoptosis, cell proliferation, antiviral response, and embryonic development. Although the critical function of TRAIP in NF-κB signaling is well-known, the molecular inhibitory mechanism of TRAIP remains unclear. We found that the TRAIP coiled-coil domain altered its stoichiometry between dimer and trimer in a concentration-dependent manner. Additionally, the TRAIP RING domain induced even higher-ordered assembly, which was necessary for interacting with the TRAF-N domain of TRAF2 but not TRAF1. Characterization of the TRAF-N domains of TRAF1 and TRAF2, the tentative TRAIP-binding region of TRAFs, suggested the molecular basis of the inhibitory effect of TRAIP on TRAF2 in NF-κB signaling.

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