scholarly journals Conformational landscape of full-length Smad proteins

2021 ◽  
Author(s):  
Tiago Gomes ◽  
Pau Martin-Malpartida ◽  
Lidia Ruiz ◽  
Eric Aragon ◽  
Tiago N. Cordeiro ◽  
...  
Keyword(s):  
Transforming Growth Factor ◽  
Building Blocks ◽  
Full Length ◽  
Integrative Approach ◽  
Resonance Spectroscopy ◽  
Dynamic Simulations ◽  
X Ray ◽  
Intrinsically Disordered ◽  
Smad Proteins ◽  
Quaternary Structures

Smad transcription factors, the main effectors of the TGFβ (transforming growth factor β) network, have been shaped along the evolution of multicellular animals to regulate essential processes. Smad proteins have a mixed architecture of globular domains and flexible linkers and adopt distinct quaternary structures depending on their activation state and cellular context. Here we studied the structures of full-length Smad4 and Smad2 proteins through an integrative approach combining small-angle X-ray scattering and detailed atomic information obtained from Nuclear Magnetic Resonance spectroscopy, X-ray and molecular dynamic simulations. Both Smad4 and Smad2 populate ensembles of expanded/compact conformations, with the MH1 and MH2 domains tethered by intrinsically disordered linkers that provide conformational freedom to the proteins. In solution, Smad4 is monomeric, whereas Smad2 coexists as monomer-dimer-trimer association states, even without activation. Smad2 dimers, which were previously overlooked, are proposed as key building blocks that define the functional quaternary structures of Smad proteins.

scholarly journals Stability and flexibility of full-length human oligodendrocytic QKI6

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Arne Raasakka ◽  
Petri Kursula
Keyword(s):  
Rna Binding ◽  
Full Length ◽  
Rna Transport ◽  
Myelin Membrane ◽  
X Ray ◽  
Intrinsically Disordered ◽  
X Ray Scattering ◽  
The Central Nervous System ◽  
Sequential Unfolding

Abstract Objective Oligodendrocytes account for myelination in the central nervous system. During myelin compaction, key proteins are translated in the vicinity of the myelin membrane, requiring targeted mRNA transport. Quaking isoform 6 (QKI6) is a STAR domain-containing RNA transport protein, which binds a conserved motif in the 3′-UTR of certain mRNAs, affecting the translation of myelination-involved proteins. RNA binding has been earlier structurally characterized, but information about full-length QKI6 conformation is lacking. Based on known domains and structure predicitons, we expected full-length QKI6 to be flexible and carry disordered regions. Hence, we carried out biophysical and structural characterization of human QKI6. Results We expressed and purified full-length QKI6 and characterized it using mass spectrometry, light scattering, small-angle X-ray scattering, and circular dichroism spectroscopy. QKI6 was monodisperse, folded, and mostly dimeric, being oxidation-sensitive. The C-terminal tail was intrinsically disordered, as predicted. In the absence of RNA, the RNA-binding subdomain is likely to present major flexibility. In thermal stability assays, a double sequential unfolding behaviour was observed in the presence of phosphate, which may interact with the RNA-binding domain. The results confirm the flexibility and partial disorder of QKI6, which may be functionally relevant.

scholarly journals Dynamical Oligomerisation of Histidine Rich Intrinsically Disordered Proteins Is Regulated through Zinc-Histidine Interactions

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 168 ◽  
Author(s):  
Carolina Cragnell ◽  
Lasse Staby ◽  
Samuel Lenton ◽  
Birthe Kragelund ◽  
Marie Skepö
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Intrinsically Disordered Proteins ◽  
Divalent Cations ◽  
Disordered Proteins ◽  
Resonance Spectroscopy ◽  
Binding Motifs ◽  
Histatin 5 ◽  
X Ray ◽  
Intrinsically Disordered ◽  
X Ray Scattering

Intrinsically disordered proteins (IDPs) can form functional oligomers and in some cases, insoluble disease related aggregates. It is therefore vital to understand processes and mechanisms that control pathway distribution. Divalent cations including Zn2+ can initiate IDP oligomerisation through the interaction with histidine residues but the mechanisms of doing so are far from understood. Here we apply a multi-disciplinary approach using small angle X-ray scattering, nuclear magnetic resonance spectroscopy, calorimetry and computations to show that that saliva protein Histatin 5 forms highly dynamic oligomers in the presence of Zn2+. The process is critically dependent upon interaction between Zn2+ ions and distinct histidine rich binding motifs which allows for thermodynamic switching between states. We propose a molecular mechanism of oligomerisation, which may be generally applicable to other histidine rich IDPs. Finally, as Histatin 5 is an important saliva component, we suggest that Zn2+ induced oligomerisation may be crucial for maintaining saliva homeostasis.

Axially Chiral Bis(α-amino Acid)s and Their Deamino Analogues. Synthesis and Configurational Assignment

1998 ◽  
Vol 63 (2) ◽  
pp. 211-221 ◽  
Author(s):  
Miloš Tichý ◽  
Luděk Ridvan ◽  
Miloš Buděšínský ◽  
Jiří Závada ◽  
Jaroslav Podlaha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nmr Spectra ◽  
Building Blocks ◽  
X Ray Diffraction ◽  
Amino Groups ◽  
X Ray ◽  
Configurational Assignment ◽  
Symmetry Properties ◽  
Axially Chiral ◽  
Polymeric Structures

The axially chiral bis(α-amino acid)s cis-2 and trans-2 as possible building blocks for polymeric structures of novel type of helicity were prepared. Their configuration has been determined by NMR spectroscopy and, in the case of the trans-isomer, confirmed by single-crystal X-ray diffraction. Analogous pair of stereoisomeric diacids cis-3 and trans-3, devoid of the amino groups, was also prepared and their configuration assigned. The observed differences in the NMR spectra of cis- and trans-isomers of 2 and 3 are discussed from the viewpoint of their different symmetry properties.

scholarly journals Whole-Genome Doubling Affects Pre-miRNA Expression in Plants

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1004
Author(s):  
Salvatore Esposito ◽  
Riccardo Aversano ◽  
Pasquale Tripodi ◽  
Domenico Carputo
Keyword(s):  
Dna Repair ◽  
Mirna Expression ◽  
Building Blocks ◽  
Nucleotide Metabolism ◽  
Integrative Approach ◽  
Whole Genome ◽  
Solanum Commersonii ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Micro Rnas

Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.

scholarly journals Backbone and nearly complete side-chain chemical shift assignments reveal the human uncharacterized protein CXorf51A as intrinsically disordered

2021 ◽  
Vol 15 (2) ◽  
pp. 441-448
Author(s):  
Christoph Wiedemann ◽  
Kingsley Benjamin Obika ◽  
Sandra Liebscher ◽  
Jan Jirschitzka ◽  
Oliver Ohlenschlãger ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Intrinsically Disordered Protein ◽  
Genome Project ◽  
Side Chain ◽  
Resonance Spectroscopy ◽  
Chemical Shift Assignments ◽  
Uncharacterized Protein ◽  
Protein Coding ◽  
Intrinsically Disordered ◽  
Side Chain Chemical Shift

AbstractEven though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these “unknown” proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A. Both our bioinformatics analysis as well as the $$^1$$ 1 H, $$^{13}$$ 13 C, $$^{15}$$ 15 N backbone and near-complete side-chain chemical shift assignments indicate that it is an intrinsically disordered protein.

scholarly journals A Sustainable Biomineralization Approach for the Synthesis of Highly Fluorescent Ultra-Small Pt Nanoclusters

Biosensors ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 128 ◽  
Author(s):  
Rajkamal Balu ◽  
Robert Knott ◽  
Christopher M. Elvin ◽  
Anita J. Hill ◽  
Namita R. Choudhury ◽  
...  
Keyword(s):  
Quantum Yield ◽  
Photoelectron Spectroscopy ◽  
Photophysical Properties ◽  
Conformational Dynamics ◽  
Aqueous Media ◽  
Intrinsically Disordered Protein ◽  
X Ray ◽  
Pt Nanoclusters ◽  
Intrinsically Disordered ◽  
Green Fluorescent

Herein we report the first example of a facile biomineralization process to produce ultra-small-sized highly fluorescent aqueous dispersions of platinum noble metal quantum clusters (Pt-NMQCs) using a multi-stimulus responsive, biomimetic intrinsically disordered protein (IDP), Rec1-resilin. We demonstrate that Rec1-resilin acts concurrently as the host, reducing agent, and stabilizer of the blue-green fluorescent Pt-NMQCs once they are being formed. The photophysical properties, quantum yield, and fluorescence lifetime measurements of the synthesized Pt-NMQCs were examined using UV-Vis and fluorescence spectroscopy. The oxidation state of the Pt-NMQCs was quantitatively analyzed using X-ray photoelectron spectroscopy. Both a small angle X-ray scattering technique and a modeling approach have been attempted to present a detailed understanding of the structure and conformational dynamics of Rec1-resilin as an IDP during the formation of the Pt-NMQCs. It has been demonstrated that the green fluorescent Pt-NMQCs exhibit a high quantum yield of ~7.0% and a lifetime of ~9.5 ns in aqueous media. The change in photoluminescence properties due to the inter-dot interactions between proximal dots and aggregation of the Pt-NMQCs by evaporation was also measured spectroscopically and discussed.

Organic Crystals in the Tracheids of Torreya Yunnanensis

IAWA Journal ◽  
1996 ◽  
Vol 17 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Yuki Kondo ◽  
Tomoyuki Fujii ◽  
Yoshioki Hayashi ◽  
Atsushi Kato
Keyword(s):  
Phase Contrast ◽  
Growth Ring ◽  
Uv Spectra ◽  
Resonance Spectroscopy ◽  
Organic Crystals ◽  
X Ray Diffraction ◽  
Cinnamic Aldehyde ◽  
X Ray ◽  
Polarised Light ◽  
Contrast Microscopy

Organic crystals were found in tracheid lumina of some samples of Torreya yunnanensis Chen ' L. K. Fu imported from Yunnan, China. Tracheids with crystals were found in short to long tangential bands along the growth ring boundaries. Because the crystals were rapidly dissolved with ethanol and xylene, cross and tangential sections were mounted in de-ionized water without staining and observed by biological, polarised light, and phase-contrast microscopy. The crystals were sublimated under vacuum during routine sample preparation for conventional SEM and only the peripheral parts remained. With the aid of low vacuum-SEM and modified cryo-SEM procedure, the shape of the crystals was revealed. Some were styloid and large enough to fill tracheid lumina, while others were stacked appearing as slates filling tracheid lumina. X-ray diffraction applied to sections and isolated crystals showed that they were single crystals and orientated along the cell wall. UV spectra on isolated crystals and methanol dissolution of crystals suggested that they were composed of phenolic compounds. Crystals that were recrystallized from methanol were analysed by 1H and l3C nuclear magnetic resonance spectroscopy. These two techniques revealed that the major and minor components were o-methoxy cinnamic acid and o-methoxy cinnamic aldehyde.

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