Mechanistic insights into glycosidase chemistry

The enzymatic hydrolysis of the glycosidic bond continues to gain importance, reflecting the critically important roles complex glycans play in health and disease as well as the rekindled interest in enzymatic biomass conversion. Recent advances include the broadening of our understanding of enzyme reaction coordinates, through both computational and structural studies, improved understanding of enzyme inhibition through transition state mimicry and fascinating insights into mechanism yielded by physical organic chemistry approaches.     

Mechanistic insights into LDL nanoparticle-mediated siRNA delivery

Although small interfering RNA (siRNA) can silence the expression of disease-related genes, delivery of these highly charged molecules is challenging. Delivery approaches for siRNAs are actively being pursued, and improved strategies are required for nontoxic and efficient delivery for gene knockdown. Low density lipoprotein (LDL) is a natural and endogenous nanoparticle that has a rich history as a delivery vehicle. Here, we examine purified LDL nanoparticles as carriers for siRNAs. When siRNA was covalently conjugated to cholesterol, over 25 chol-siRNA could be incorporated onto each LDL without changing nanoparticle morphology. The resulting LDL-chol-siRNA nanoparticles were selectively taken up into cells via LDL receptor mediated endocytosis, resulting in enhanced gene silencing compared to free chol-siRNA (38% gene knock down versus 0% knock down at 100 nM). However, silencing efficiency was limited by the receptor-mediated entrapment of the LDL-chol-siRNA nanoparticles in endolysosomes. Photochemical internalization demonstrated that endolysosome disruption strategies significantly enhance LDL-mediated gene silencing (78% at 100 nM).     

Mechanistic insights into linear polyethylenimine-mediated gene transfer

We recently debuted a variety of linear polyethylenimines (LPEIs) with low molecular weight as carriers for gene delivery. The highest transfection efficiency (approximately 44%) was obtained with LPEI 6.6 kDa, while the cytotoxicity remained low (approximately 90% of CHO-K1 cells survived the transfection procedure). Here, we investigated various steps during the transfection process using LPEI 8.1, 5.0 and 1.8 kDa, in order to gain a more complete insight into LPEI-mediated gene transfer and to explore conceptual aspects for further optimization. The cellular uptake characterized by flow cytometry was similar for LPEI 8.1 and 5.0 kDa, while it was significantly lower for LPEI 1.8 kDa. The transfection efficacy in contrast was at NP 24 20.07% for LPEI 8.1 kDa and 39.71% for LPEI 5.0 kDa. This suggests that the endocytosis seems not to be a decisive parameter that determines the efficacy of a polymer in the transfection process. Real-time PCR investigations revealed that LPEI 1.8 kDa likewise or even better protected plasmid from degradation compared to LPEI 5.0 or 8.1 kDa. Furthermore, we found that 1/6 to 1/3 intact plasmid DNA reached the intracellular compartments after complexation with LPEI 1.8 kDa. Therefore, the amount of plasmid DNA available in the cytoplasm seems not to be a limiting factor in the transfection process. That LPEI 8.1-polyplexes built at NP 12 in glucose and transfected in serum-free culture conditions were superior to those built in sodium chloride or transfected in serum-containing conditions points at the structure as a decisive parameter deserving more attention in future studies.     

Mechanistic insights into protein precipitation by alcohol

Ethanol is used to precipitate proteins during various processes, including purification and crystallization. To elucidate the mechanism of protein precipitation by alcohol, we have investigated the solubility and structural changes of protein over a wide range of alcohol concentrations. Conformation of hen egg-white lysozyme was changed from native to α-helical rich structure in the presence of ethanol at concentrations above 60%. The solubility of lysozyme was reduced with increasing ethanol concentration, although gel formation at ethanol concentrations between 60% and 75% prevented accurate solubility measurements. SH-modified lysozyme showed largely unfolded structure in water and α-helical structure in the presence of ethanol. More importantly, solubility of the chemically modified lysozyme molecules decreased with increasing ethanol concentration. There is no indication of increased solubility upon unfolding of the lysozyme molecules by ethanol, indicating that any favorable interaction of ethanol with the hydrophobic side chains, if indeed occuring, is offset by the unfavorable interaction of ethanol with the hydrophilic side chains and peptide bonds.     

X-chromosome inactivation and the search for chromosome-wide silencers

X-chromosome inactivation leads to divergent fates for two homologous chromosomes. Whether one X remains active or becomes silenced depends on the activity of Xist, a gene expressed only from the inactive X and whose RNA product 'paints' the X in cis. Recent work argues that Xist RNA itself is the acting agent for initiating the silencing step. Xist RNA contains separable domains for RNA localization and chromosome silencing. While no Xist RNA-interacting factors have been identified, a growing collection of chromatin alterations have been identified on the inactive X, including variant histone H2A composition and histone H3 methylation. Some or all of these changes may be critical for chromosome-wide silencing. As none of the silencing proteins identified so far is unique to X chromosome inactivation, the specificity must partly reside in Xist RNA whose spread along the X orchestrates general silencing factors for this specific task.     

Mechanistic insights into Diels-Alder reactions in natural product biosynthesis

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Mechanistic insights into laccase-mediated functionalisation of lignocellulose material

Recent emerging studies on the grafting mechanisms of functional molecules onto complex lignocellulose moieties have shown useful insights and possibilities in opening new frontiers in the enzymatic development of multifunctional polymers. Thanks to these studies which have demonstrated in principle the ability of laccases to mediate the coupling of antimicrobial compounds, hydrophobic molecules, including application processes for the development of fibreboards, particle boards, laminates etc. Further, laccase mediated grafting strategies developed using small reactive molecules e.g. phenolic amines which impart reactive properties to an inert polymer demonstrates the remarkable opportunities of enzyme meditated functionalization of polymers. Therefore recent studies focusing on understanding the mechanistic basis of the coupling mechanisms in order to make meaningful contribution to the development of new processes and products are a welcome development.     

Mechanistic insights into fungal mitochondrial outer membrane protein biogenesis

The majority of mitochondrial proteins are nuclear-encoded and need to be transported into the mitochondria, including the proteins in the outer mitochondrial membrane. For β-barrel proteins, the preproteins are initially recognized and imported by the TOM complex, then shuttled to the SAM complex via small Tim proteins. For ⍺-helical proteins, some preproteins are recognized by the TOM complex and imported into the membrane by the MIM complex. In recent years multiple structures of the TOM complex and the SAM complex have been reported, increasing our understanding of the mechanism of protein biogenesis in the outer mitochondrial membrane.     

Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin

How aminoglycoside antibiotics limit bacterial growth and viability is not clearly understood. Here we employ fast kinetics to reveal the molecular mechanism of action of a clinically used, new-generation, semisynthetic aminoglycoside Arbekacin (ABK), which is designed to avoid enzyme-mediated deactivation common to other aminoglycosides. Our results portray complete picture of ABK inhibition of bacterial translation with precise quantitative characterizations. We find that ABK inhibits different steps of translation in nanomolar to micromolar concentrations by imparting pleotropic effects. ABK binding stalls elongating ribosomes to a state, which is unfavorable for EF-G binding. This prolongs individual translocation step from ∼50 ms to at least 2 s; the mean time of translocation increases inversely with EF-G concentration. ABK also inhibits translation termination by obstructing RF1/RF2 binding to the ribosome. Furthermore, ABK decreases accuracy of mRNA decoding (UUC vs. CUC) by ∼80 000 fold, causing aberrant protein production. Importantly, translocation and termination events cannot be completely stopped even with high ABK concentration. Extrapolating our kinetic model of ABK action, we postulate that aminoglycosides impose bacteriostatic effect mainly by inhibiting translocation, while they become bactericidal in combination with decoding errors.