scholarly journals S06A1 Mechanistic insight into RNA acetylation to maintain the decoding fidelity in bacteria(Structural Biology of ncRNA Processing and Function)

2007 ◽  
Vol 47 (supplement) ◽  
pp. S8
Author(s):  
Sarin Chimnaronk ◽  
Tateki Suzuki ◽  
Tetsuhiro Manita ◽  
Yoshiho Ikeuchi ◽  
Min Yao ◽  
...  
Keyword(s):  
Structural Biology ◽  
Mechanistic Insight ◽  
And Function ◽  
Insight Into ◽  
Decoding Fidelity

scholarly journals Transcription factors Foxo3a and Foxo1 couple the E3 ligase Cbl-b to the induction of Foxp3 expression in induced regulatory T cells

2010 ◽  
Vol 207 (7) ◽  
pp. 1381-1391 ◽  
Author(s):  
Yohsuke Harada ◽  
Yasuyo Harada ◽  
Chris Elly ◽  
Ge Ying ◽  
Ji-Hye Paik ◽  
...  
Keyword(s):  
T Cells ◽  
Ring Finger ◽  
Foxp3 Expression ◽  
Proximal Region ◽  
Binding Motif ◽  
Mechanistic Insight ◽  
T Cell Regulation ◽  
And Function ◽  
Deficient Mice ◽  
Insight Into

The transcription factor Foxp3 is essential for optimal regulatory T (T reg) cell development and function. Here, we show that CD4+ T cells from Cbl-b RING finger mutant knockin or Cbl-b–deficient mice show impaired TGF-β–induced Foxp3 expression. These T cells display augmented Foxo3a phosphorylation, but normal TGF-β signaling. Expression of Foxo3a rescues Foxp3 expression in Cbl-b–deficient T cells, and Foxo3a deficiency results in defective TGF-β–driven Foxp3 induction. A Foxo3a-binding motif is present in a proximal region of the Foxp3 promoter, and is required for Foxo3a association. Foxo1 exerts similar effects as Foxo3a on Foxp3 expression. This study reveals that Foxo factors promote transcription of the Foxp3 gene in induced T reg cells, and thus provides new mechanistic insight into Foxo-mediated T cell regulation.

Structural and mechanistic insight into alkane hydroxylation by Pseudomonas putida AlkB

2014 ◽  
Vol 460 (2) ◽  
pp. 283-293 ◽  
Author(s):  
Hernan Alonso ◽  
Oded Kleifeld ◽  
Adva Yeheskel ◽  
Poh C. Ong ◽  
Yu C. Liu ◽  
...  
Keyword(s):  
Ab Initio ◽  
Pseudomonas Putida ◽  
Structure And Function ◽  
Alkane Hydroxylation ◽  
Mechanistic Insight ◽  
Unknown Structure ◽  
And Function ◽  
Alkane Hydroxylases ◽  
Insight Into

Integral membrane non-haem di-iron alkane hydroxylases (AlkBs) are enzymes of unknown structure that allow bacteria to grow on alkanes. Catalysis-linked modifications with the inhibitor 1-octyne, mutagenesis studies and ab initio modelling provided novel insights into the structure and function of AlkB.

scholarly journals A nanobody-based molecular toolkit provides new mechanistic insight into clathrin-coat initiation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Linton M Traub
Keyword(s):  
Decisive Role ◽  
Subcellular Location ◽  
Combined Approach ◽  
Mechanistic Insight ◽  
Early Endosomes ◽  
The Stability ◽  
And Function ◽  
Insight Into ◽  
Complementarity Determining Region

Besides AP-2 and clathrin triskelia, clathrin coat inception depends on a group of early-arriving proteins including Fcho1/2 and Eps15/R. Using genome-edited cells, we described the role of the unstructured Fcho linker in stable AP-2 membrane deposition. Here, expanding this strategy in combination with a new set of llama nanobodies against EPS15 shows an FCHO1/2–EPS15/R partnership plays a decisive role in coat initiation. A nanobody containing an Asn-Pro-Phe peptide within the complementarity-determining region 3 loop is a function-blocking pseudoligand for tandem EPS15/R EH domains. Yet, in living cells, EH domains gathered at clathrin-coated structures are poorly accessible, indicating residence by endogenous NPF-bearing partners. Forcibly sequestering cytosolic EPS15 in genome-edited cells with nanobodies tethered to early endosomes or mitochondria changes the subcellular location and availability of EPS15. This combined approach has strong effects on clathrin coat structure and function by dictating the stability of AP-2 assemblies at the plasma membrane.

scholarly journals Insight into helicase mechanism and function revealed through single-molecule approaches

2010 ◽  
Vol 43 (2) ◽  
pp. 185-217 ◽  
Author(s):  
Jaya G. Yodh ◽  
Michael Schlierf ◽  
Taekjip Ha
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Magnetic Tweezers ◽  
Repetitive Behaviors ◽  
Helicase Activity ◽  
Step Size ◽  
Mechanistic Insight ◽  
Combination Of Methods ◽  
And Function ◽  
Insight Into

AbstractHelicases are a class of nucleic acid (NA) motors that catalyze NTP-dependent unwinding of NA duplexes into single strands, a reaction essential to all areas of NA metabolism. In the last decade, single-molecule (sm) technology has proven to be highly useful in revealing mechanistic insight into helicase activity that is not always detectable via ensemble assays. A combination of methods based on fluorescence, optical and magnetic tweezers, and flow-induced DNA stretching has enabled the study of helicase conformational dynamics, force generation, step size, pausing, reversal and repetitive behaviors during translocation and unwinding by helicases working alone and as part of multiprotein complexes. The contributions of these sm investigations to our understanding of helicase mechanism and function will be discussed.

scholarly journals Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1

2019 ◽  
Vol 48 (3) ◽  
pp. 1423-1434
Author(s):  
Yuichiro Nomura ◽  
Eric J Montemayor ◽  
Johanna M Virta ◽  
Samuel M Hayes ◽  
Samuel E Butcher
Keyword(s):  
Homo Sapiens ◽  
Structural Basis ◽  
Evolutionary Divergence ◽  
Sequence Identity ◽  
U6 Snrna ◽  
Mechanistic Insight ◽  
Substrate Analog ◽  
Cyclic Phosphate ◽  
And Function ◽  
Insight Into

Abstract U6 snRNA undergoes post-transcriptional 3′ end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3′ end of U6 and, in humans, leaves a 2′,3′ cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2′,3′ cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3′ phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5′-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Computational Approaches to Predict the Non-canonical DNAs

2019 ◽  
Vol 14 (6) ◽  
pp. 470-479 ◽  
Author(s):  
Nazia Parveen ◽  
Amen Shamim ◽  
Seunghee Cho ◽  
Kyeong Kyu Kim
Keyword(s):  
Computational Methods ◽  
Genetic Instability ◽  
Computational Prediction ◽  
Structure And Function ◽  
Sequence Motifs ◽  
Computational Approaches ◽  
Functional Roles ◽  
And Function ◽  
Genetic Events ◽  
Insight Into

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

Sign in / Sign up

Export Citation Format

Share Document