Molecular Dynamics Analysis of Glucose Oxidase Stability against Temperature

Glucose oxidase (GOD) from local isolated Aspergillus niger IPBCC.08.610 shows a widespread application, specifically as a bioanode in glucose-based biofuel cells. Enzymes with adequate thermal stability are necessary for enhancing product efficiency. Also, evaluating the structural dynamics to improve temperature helps to determine the residue. The molecular dynamics simulation of GOD_IPBCC_1CF3 at temperatures of 300, 400, and 500 K was carried out to analyze important amino acid residues for thermal stability. The results showed that the amino acid residues responsible for thermal stability were dispersed into several essential regions, including D576 at the C terminal, E266-R250, and E38-R237 in the FAD-binding domain E485-R470 in the substrate-binding antiparallel beta system. However, the FAD molecular flexibility against temperature depends on conserve E48 by stabilizing the ribose sugar moiety.

Advances in the synthesis and antisense technology applications of bridged nucleic acid monomers

: Bridged nucleic acids (BNA) or locked nucleic acids (LNA) are a class of nucleic acids modification, which is obtained by connecting the 2'-O and 4'-C of ribose sugar using a methylene bridge. This ‘bridging or locking’ (hence the name) of ribose sugar has a tremendous impact both on the biological and biophysical properties of therapeutic nucleic acids. They have enhanced stability against nucleases and also have higher binding affinity for the target RNA. Owing to these advantages, BNA is one of the most preferred nucleic acid modifications of antisense oligonucleotides (ASOs). However, the synthesis of BNA monomers which are lengthy and low-yielding, requires extensive protection and deprotection of the sugar functionalities. In this article, we aim to review challenges associated with their synthesis, and discuss recent chemical, chemo-enzymatic, and transglycosylation strategies employed for efficient and cost-effective synthesis of BNA monomers and selected BNA analogues.

2′-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states

2′-O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3′-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of flexible RNAs containing bulges and internal loops. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of low-populated short-lived excited states by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi-value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.

Enhanced differentiation of isomeric RNA modifications by reducing the size of ions in ion mobility mass spectrometric measurements

With the ability to differentiate different molecular sizes, ion mobility spectrometry (IMS) has great potentials in the analysis of isomeric compounds. However, due to the lack of sensitivity and resolution, IMS has not been commonly used. To address the issue on resolution, the goals of this study are to explore a more effective way to perform IMS by reducing the size of ions prior to the IM measurements, and apply the new approach to the differentiation of isomeric RNA modifications. The size reduction of ribonucleoside ions was effectively accomplished by using the collision-induced dissociation process, in which the N-glycosidic bond in ribonucleoside was cleaved and split the ions into two parts—a smaller nucleobase ion and a neutral molecule of ribose sugar. Since the chemical group that corresponds to most of the RNA modifications makes up a relatively small part of the molecular structure of nucleobases, the differentiation of the dissociated nucleobase ions is expected to require a lower ion mobility resolution than the differentiation of bigger isomeric ribonucleoside ions. By using RNA methylation as a model in this study, the proposed method lowered the required resolution by 16% for the differentiation of 1-methyladenosine and N6-methyladenosine. Similar results were also obtained from the differentiation of methylated cytidine isomers. In comparison to the results obtained from using the conventional tandem mass spectrometric method, there was no significant loss of signals when the proposed method was used. The proposed method is expected to be applicable to other types of isomeric compounds. Also, the same approach is applicable on other IMS platforms.

2’-O-methylation alters the RNA secondary structural ensemble

ABSTRACT2’-O-methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3’-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of non-canonical RNA motifs. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of a low-populated short-lived excited state by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi (Φ) value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.

Structural Basis of RNA Cap Modification by SARS-CoV-2 Coronavirus

The novel severe acute respiratory syndrome coronoavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused over 2 million infections worldwide in four months. In SARS coronaviruses, the non-structural protein 16 (nsp16) methylates the 5’-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of full-length nsp16 and nsp10 of SARS-CoV-2 in the presence of cognate RNA substrate and a methyl donor, S-adenosyl methionine. The nsp16/nsp10 heterodimer was captured in the act of 2’-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We reveal large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This structure provides new mechanistic insights into the 2’-O methylation of the viral mRNA cap. We also discovered a distantly located ligand-binding site unique to SARS-CoV-2 that may serve as an alternative target site for antiviral development.

Environmentally benign pH-responsive cytidine-5′-monophosphate molecule-mediated akaganeite (5′-CMP-β-FeOOH) soft supramolecular hydrogels induced by the puckering of ribose sugar with efficient loading/release capabilities

A novel synthetic protocol for environmentally benign 5′-CMP-β-FeOOH soft hydrogels exhibiting a rapid pH-responsive reversible sol–gel transition, efficient adsorption and slow release capabilities is reported.

Carbocyclodipeptides as modified nucleosides: synthesis and anti-HIV activities

A new class of nucleoside analogues were synthesized using cyclic dipeptides and modified 2′-deoxyfuranoribose sugars to introduce flexibility by peptides in place of common nucleoside bases and to determine their biological properties. The synthesis was carried out by coupling of a protected ribose sugar with synthesized dipeptides in the presence of hexamethyldisilazane and trimethylsilyltriflate. The final products were characterized by NMR and high-resolution MS-TOF spectroscopy. The compounds were evaluated for anti-HIV activities. 1-(4-Azido-5-(hydroxymethyl)tetrahydrofuran-2-yl)-3,6-diisopropylpiperazine-2,5-dione (compound 14) containing 3- and 6-isopropyl groups in the base and 3′-azide (EC50 = 1.96 μmol/L) was the most potent compound among all of the synthesized analogs.

Role of Poly(ADP-Ribose) Polymerase during Vascular Reconstruction

Open vascular repair of ischemic myocardium and aortic aneurysms results in a systemic inflammatory response that influences the mortality and morbidity of these procedures. Recent studies in animal models of complex vascular reconstruction indicate that the activity of poly(ADP-ribose) polymerase (PARP) may influence the mortality and morbidity of these kinds of reconstructions. PARP's activity, localized to nuclei and mitochondria, is stimulated by deoxyribonucleic acid (DNA) strand breaks. Activation of PARP results in synthesis of poly(ADP-ribose) sugar moieties, whose primary role is to protect DNA from degradation during cytotoxic stress. Paradoxically, when stressful conditions similar to those experienced during vascular reconstructions result in overactivation of PARP, depletion of cellular levels of adenosine triphosphate and nicotinamide adenine dinucleotide can result in exacerbation of tissue injury. Herein we review the role of PARP in inflammation and its relevance to cardiovascular reconstructions.