Silylated Sugars – Synthesis and Properties

Silicon has been used in carbohydrate chemistry for half a century, but mostly as a protective group for sugar alcohols. Recently, the use of silicon has expanded to functionalization via C–H activation, conformational arming of glycosyl donors, and conformational alteration of carbohydrates. Silicon has proven useful as more than a protective group and during the last one and a half decades we have demonstrated how it influences both the reactivity of glycosyl donors and stereochemical outcome of glycosylations. Silicon can also be attached directly to the sugar C-backbone, which has even more pronounced effects on the chemistry and properties of the molecules. In this Account, we will give a tour through our work involving silicon and carbohydrates.1 Introduction2 Conformational Arming of Glycosyl Donors with Silyl Groups3 Silyl Protective Groups for Tethering Glycosyl Donors4. Si–C Glycosides via C–H Activation4.1 C–H Activation and Oxidation of Methyl 6-Deoxy-l-glycosides4.2 Synthesis of All Eight 6-Deoxy-l-sugars4.3 Synthesis of All Eight l-Sugars by C–H Activation4.4 Modification of the Oxasilolane Ring5 C–Si in Glycosyl Donors – Activating or Not?6 Si–C-Substituted Pyranosides7 Perspective

Interactions of a small molecule configuration mimetic the interactions found in α-synuclein aggregation

Parkinson’s disease (PD) is an increasingly prevalent and currently incurable neurodegenerative disorder. The aggregation of the amyloid disordered protein α-synuclein (Syn) has been implicated in the development of PD. Syn aggregation has been widely investigated but information concerning the conformational alterations in the diverse protein aggregated species at the molecular level is still scarce. To address this issue, it was here developed a comparative study involving the known parent N-acetyl-L-tyrosinamide (NAYA) compound and the Syn protein by using spectroscopic techniques. At least two different configurations of the NAYA compound were found to exist in solution. One configuration, known as the NAYA closed shape configuration, involves an amide intramolecular hydrogen-bonded interaction and was found to be a model interaction for the hydrophilic core of β-sheets, which are the most common conformational alteration found in Syn aggregated species. Since the spectroscopic techniques used herein also differentiate between tyrosyl and peptide bond groups and both NAYA and Syn possess such groups it was possible to assign these groups interactions in the β-sheets formed. This study retrieves the importance of using model compounds with spectroscopic characteristics similar to those found in proteins to access the complex interactions network existing in the amyloid aggregated species.

Vibrational spectroscopy analysis of ligand efficacy in M2R

The intrinsic efficacy of ligand binding to G protein-coupled receptors (GPCRs) reflects the ability of the ligand to differentially activate its receptor to cause a physiological effect. Here we use attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy to examine the ligand-dependent conformational changes in the human M2 muscarinic acetylcholine receptor (M2R). We show that different ligands affect conformational alteration appearing at the C=O stretch of amide-I band in M2R. Notably, ATR-FTIR signals strongly correlated with G-protein activation levels in cells. Together, we propose that amide-I band serves as an infrared probe to distinguish the ligand efficacy in M2R and paves the path to rationally design ligands with varied efficacy towards the target GPCR.

Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB

RNA conformational alteration has significant impacts on cellular processes and phenotypic variations. An emerging genetic factor of RNA conformational alteration is a new class of single nucleotide variant (SNV) named riboSNitch. RiboSNitches have been demonstrated to be involved in many genetic diseases. However, identifying riboSNitches is notably difficult as the signals of RNA structural disruption are often subtle. Here, we introduce a novel computational framework–RIboSNitch Predictor based on Robust Analysis of Pairing probabilities (Riprap). Riprap identifies structurally disrupted regions around any given SNVs based on robust analysis of local structural configurations between wild-type and mutant RNA sequences. Compared to previous approaches, Riprap shows higher accuracy when assessed on hundreds of known riboSNitches captured by various experimental RNA structure probing methods including the parallel analysis of RNA structure (PARS) and the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). Further, Riprap detects the experimentally validated riboSNitch that regulates human catechol-O-methyltransferase haplotypes and outputs structurally disrupted regions precisely at base resolution. Riprap provides a new approach to interpreting disease-related genetic variants. In addition, we construct a database (RiboSNitchDB) that includes the annotation and visualization of all presented riboSNitches in this study as well as 24 629 predicted riboSNitches from human expression quantitative trait loci.

MON-522 In Silico Analysis of Polymorphism rs2228638 in Neuropillin-1 Demonstrated That This Variant May Hinder EBV Entry into Epithelial Cells

The Epstein-Barr virus (EBV) is the first herpesvirus identified to be associated with human cancers and our group has demonstrated its association to thyroid cancer. It infects the vast majority of the world population causing latent and persistent infection, interfering in the metabolism of the host cells and triggering tumorigenic processes. Neuropillin-1 (NRP-1) is a type I transmembrane glycoprotein distributed on the cell surface of the virus, and considered vital for tumorigenesis. It has been demonstrated that EBV infection was increased by NRP1 expression. However, a conformational alteration of NRP1 could interfere with virus internalization into epithelial cells. The rs2228638 polymorphism of NRP1 may modify the molecule tridimensional configuration. In order to better understand the role of this polymorphism, based on NCBI dbSNP and UniProt databases, we evaluated the effect of the amino acid change in the protein structure using bioinformatics tools including SIFT, Align GVGD, PolyPhen-2, SNAP, PANTHER, PredictSNP, nsSNPAnalyzer, PROVEAN, SNP&GO, PMut and MuPRO. PANTHER prediction indicated that the polymorphic variant could produce a change in function. MuPRO indicated that the amino acid exchange produced by the polymorphism decreases protein stability. However, none of these tools showed conformational alteration. In conclusion, the presence of the rs2228638 polymorphism of NRP-1 may cause functional but not morphological changes that hinder EBV entry into the epithelial cells.

A unique conformational escape reaction of HIV-1 against an allosteric integrase inhibitor

HIV-1 integrase (IN) contributes to HIV-1 RNA binding, which is required for viral maturation. Non-catalytic site integrase inhibitors (NCINIs) have been developed as allosteric IN inhibitors, which perform anti-HIV-1 activity by disrupting IN multimerization. Here, we show that IN undergoes a novel conformational alteration to escape from NCINIs. We observed that NCINI-resistant HIV-1 variants have accumulated amino acid (AA) mutations in the IN-encoding region. We employed HPLC and thermal stability assays to show that the AA mutations affect the folding and dimerization interface of the IN catalytic core domains, resulting in severely decreased multimerization of full-length IN proteins (IN under-multimerization). The under-multimerization of IN was finally restored by HIV-1 RNA in the viral particles. Our study demonstrates that HIV-1 countervails NCINIs by IN under-multimerization as a novel escape mechanism. Our findings provide information on the understanding of IN multimerization and influence the development of unique anti-HIV-1 strategies.

Solution and crystal phase resonance Raman spectroscopy: Valuable tools to unveil the structure and function of heme proteins

In the present review, examples are provided illustrating the application of resonance Raman microscopy to heme protein single crystals to highlight the artifacts induced by the crystallization process or the conformational alteration induced by cooling. Moreover, the structural information determined from the RR spectra of heme proteins in solution and crystals is compared to that obtained from their X-ray structures to show how the combined spectroscopic/crystallographic approach is a powerful weapon in the structural biologist’s armamentarium.