NMR elucidation of the role of Mg2+ in the structure and stability of the conserved RNA motifs of the EMCV IRES element

2014 ◽  
Vol 12 (9) ◽  
pp. 1495 ◽  
Author(s):  
Sadia Mohammed ◽  
Marie M. Phelan ◽  
Usman Rasul ◽  
Vasudevan Ramesh
Keyword(s):  
Rna Motifs ◽  
Structure And Stability ◽  
Ires Element

scholarly journals Role of the N-terminus in the structure and stability of chicken annexin V

FEBS Letters ◽  
1997 ◽  
Vol 416 (2) ◽  
pp. 217-220 ◽  
Author(s):  
David Arboledas ◽  
Nieves Olmo ◽  
Mª Antonia Lizarbe ◽  
Javier Turnay
Keyword(s):  
Annexin V ◽  
Structure And Stability ◽  
N Terminus

scholarly journals Influence of Magnesium Ions on the Preparation and Storage of DNA Tetrahedrons in Micromolar Ranges

Molecules ◽  
2019 ◽  
Vol 24 (11) ◽  
pp. 2091 ◽  
Author(s):  
Yue Hu ◽  
Zhou Chen ◽  
Zheng Hou ◽  
Mingkai Li ◽  
Bo Ma ◽  
...  
Keyword(s):  
The Novel ◽  
Magnesium Ions ◽  
Dna Nanostructures ◽  
Structure And Stability ◽  
Dna Concentration ◽  
Factors Influencing ◽  
Dna Tetrahedron ◽  
And Storage

The DNA tetrahedron (Td), as one of the novel DNA-based nanoscale biomaterials, has been extensively studied because of its excellent biocompatibility and increased possibilities for decorating precisely. Although the use of Td in laboratories is well established, knowledge surrounding the factors influencing its preparation and storage is lacking. In this research, we investigated the role of the magnesium ions, which greatly affect the structure and stability of DNA. We assembled 1, 2, 5, 10 and 20 μM Td in buffers containing different Mg2+ concentrations, demonstrating that 2 and 5 mM Mg2+ is optimal in these conditions, and that yields decrease dramatically once the DNA concentration reaches 20 μM or the Mg2+ concentration is lower than 0.5 mM. We also verified that the Td structure is retained better through freeze-thawing than lyophilization. Furthermore, a lower initial Mg2+ (≤2 mM) benefited the maintenance of Td structure in the process of lyophilization. Hence, our research sheds light on the influence of Mg2+ in the process of preparing and storing Td, and also provides some enlightenment on improving yields of other DNA nanostructures.

scholarly journals Decisive Role of 5f-Orbital Covalence in the Structure and Stability of Pentavalent Transuranic Oxo [M6O8] Clusters

2020 ◽  
Vol 59 (24) ◽  
pp. 18068-18077
Author(s):  
Shu-Xian Hu ◽  
Peng Zhang ◽  
Erli Lu ◽  
Ping Zhang
Keyword(s):  
Decisive Role ◽  
Structure And Stability

Elucidating the Role of Val-Asn 95 and Arg-Gly 52 Mutations on Structure and Stability of Fibroblast Growth Factor Homologous Factor 2

2019 ◽  
Vol 26 (11) ◽  
pp. 848-859
Author(s):  
Vidyalatha Kolli ◽  
Subhankar Paul ◽  
Praveen Kumar Guttula ◽  
Nandini Sarkar
Keyword(s):  
Amino Acids ◽  
Growth Factor ◽  
Fibroblast Growth Factor ◽  
Signal Sequence ◽  
Fibroblast Growth ◽  
Structure And Stability ◽  
Secretion Signal ◽  
Acrylamide Quenching ◽  
Voltage Gated Sodium Channels

Background: Fibroblast growth Factor Homologous Factors (FHFs) belong to a subclass of Fibroblast Growth Factor (FGF) family owing to their high sequence and structural similarities with FGFs. However, despite these similarities, there are properties which set them apart from FGFs. FHFs lack the secretion signal sequence unlike other FGF members, except FGF1 and 2. Unlike FGFs, FHFs are not able to bind to FGF Receptors (FGFRs) and instead have been implicated in binding to Voltage-Gated Sodium Channels (VGSCs), neuronal MAP kinase scaffold protein and islet-brain-2 (IB2). The two amino acids Arg-52 and Val95 are conserved in all FHFs and mutation of these residues lead to its inability to bind with VGSC/IB2. However, it is not clear whether the loss of binding is due to destabilization of the protein on mutation or due to involvement of Arg52 and Val95 in conferring functionality to FHFs. Objective: In the present study, we have mutated these two conserved residues of FHF2 with its corresponding FGF counterpart amino acids and studied the effects of the mutations on the structure and stability of the protein. Methods: Several biophysical methods like isothermal equilibrium denaturation study, ANS fluorescence, intrinsic fluorescence, acrylamide quenching, circular dichroism studies as well as using computational approaches were employed. Results: The single mutations were found to affect the overall stability, conformation and functionality of the protein. Conclusion: Thus, the studies throw light on the role of specific amino acids in deciding the stability, structure and functionality of proteins and will be useful for development of therapeutically engineered proteins.

scholarly journals N6-methyladenosine modification of HCV RNA genome regulates cap-independent IRES-mediated translation via YTHDC2 recognition

2021 ◽  
Vol 118 (10) ◽  
pp. e2022024118 ◽  
Author(s):  
Geon-Woo Kim ◽  
Aleem Siddiqui
Keyword(s):  
Translation Initiation ◽  
Mutational Analysis ◽  
Rna Helicase ◽  
Hcv Rna ◽  
Helicase Domain ◽  
Entry Site ◽  
Ires Element ◽  
Rna Genome ◽  
Hcv Ires

Hepatitis C virus (HCV) infections are associated with the risk of progression to fibrosis, cirrhosis, and hepatocellular carcinoma. The HCV RNA genome is translated by an internal ribosome entry site (IRES)-dependent mechanism. The structure and function of the HCV IRES have been investigated by both biological and biophysical criteria. Recently, the role of N6-methyladenosine (m6A) in cellular RNA and viral transcripts has been intensely investigated. The HCV RNA genome is m6A-methylated, and this modification regulates the viral life cycle. In this study, we investigated the role of m6A modification of the HCV genome in the IRES-dependent translation function by mutating m6A consensus motifs (DRACH) within the IRES element in stem–loop III and IV regions and studied their effect on translation initiation. There are several DRACH motifs within the IRES element. Of these, the DRACH motif at nucleotide (nt) 329-333, located about 7 nt upstream of initiator AUG (iAUG) codon, regulates IRES-mediated translation initiation. Mutational analysis showed that m6A methylation of the adenosine at nt 331 is essential for the IRES-dependent translation. m6A reader protein YTHDC2, containing the RNA helicase domain, recognizes m6A-methylated adenosine at nt 331 and, in concert with the cellular La antigen, supports HCV IRES-dependent translation. The RNA helicase dead YTHDC2 (E332Q) mutant failed to stimulate HCV translation initiation. This report highlights the functional roles of m6A modification and YTHDC2 in the HCV IRES-dependent translation initiation, thus offering alternative therapeutic avenues to interfere with the infectious process.

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