MCSS-based predictions of RNA binding sites

The diversity of RNA tertiary structures provides the basis for specific recognition by proteins or small molecules. To investigate the structural basis and the energetics which control RNA-ligand interactions, favorable RNA binding sites are identified using the MCSS method, which has been employed previously only for protein receptors. Two different RNAs for which the structures have been determined by NMR spectroscopy were examined: two structures of the TAR RNA which contains an arginine binding site, and the structure of the 16S rRNA which contains an aminoglycoside binding site (paromomycin). In accord with the MCSS methodology, the functional groups representing the entire ligand or only part of it (one residue in the case of the aminoglycosides) are first replicated and distributed with random positions and orientations around the target and then energy minimized in the force field of the target RNA. The Coulombic term and the dielectric constant of the force field are adjusted to approximate the effects of solvent-screening and counterions. Optimal force field parameters are determined to reproduce the binding mode of arginine to the TAR RNA. The more favorable binding sites for each residue of the aminoglycoside ligands are then calculated and compared with the binding sites observed experimentally. The predictability of the method is evaluated and refinements are proposed to improve its accuracy. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 7 December 1998     

Binding of erbium(III) and holmium(III) to native and chemically modified alfalfa biomass: a spectroscopic investigation

Traditional treatment methods used to clean-up heavy metal contamination of soils and waters are cost intensive whereas more cost effective methods need to be developed. The use of plant materials to remediate heavy contamination has been studied for the past two decades. This technique has shown much promise for many of the common heavy metal contaminants, but few studies have focused on the lanthanide series elements. By investigating the binding and interactions of the lanthanide elements to alfalfa biomass, a more complete understanding of the binding mechanisms and the interactions of heavy metals with biomaterials can be obtained. Different chemical functional groups on the alfalfa biomass, carboxyl, amino, sulfur, and ester groups, were modified to investigate the binding mechanisms of erbium(III) and holmium(III). Batch experiments were performed with native and chemically modified alfalfa biomass suggesting that the carboxyl groups play a major role in the binding of erbium(III) and holmium(III) to the alfalfa biomass. In addition, X-ray absorption spectroscopy (XAS) studies corroborated the data obtained from the batch experiments.     

A Benzophenone‐Based Photocaging Strategy for the N7 Position of Guanosine

Selective modification of nucleobases with photolabile caging groups enables the study and control of processes and interactions of nucleic acids. Numerous positions on nucleobases have been targeted, but all involve formal substitution of a hydrogen atom with a photocaging group. Nature, however, also uses ring‐nitrogen methylation, such as m⁷G and m¹A, to change the electronic structure and properties of RNA and control biomolecular interactions essential for translation and turnover. We report that aryl ketones such as benzophenone and α‐hydroxyalkyl ketone are photolabile caging groups if installed at the N7 position of guanosine or the N1 position of adenosine. Common photocaging groups derived from the ortho‐nitrobenzyl moiety were not suitable. Both chemical and enzymatic methods for site‐specific modification of N7G in nucleosides, dinucleotides, and RNA were developed, thereby opening the door to studying the molecular interactions of m⁷G and m¹A with spatiotemporal control.     

Functional group placement in protein binding sites: a comparison of GRID and MCSS

One approach to combinatorial ligand design begins by determining optimal locations (i.e., local potential energy minima) for functional groups in the binding site of a target macromolecule. MCSS and GRID are two methods, based on significantly different algorithms, which are used for this purpose. A comparison of the two methods for the same functional groups is reported. Calculations were performed for nonpolar and polar functional groups in the internal hydrophobic pocket of the poliovirus capsid protein, and on the binding surface of the src SH3 domain. The two approaches are shown to agree qualitatively; i.e., the global characteristics of the functional group maps generated by MCSS and GRID are similar. However, there are significant differences in the relative interaction energies of the two sets of minima, a consequence of the different functional form used to evaluate polar interactions (electrostatics and hydrogen bonding) in the two methods. The single sphere representation used by GRID affords only positional information, supplemented by the identification of hydrogen bonding interactions. By contrast, the multi-atom representation of most MCSS groups yields in both positional and orientational information. The two methods are most similar for small functional groups, while for larger functional groups MCSS yields results consistent with GRID but superior in detail. These results are in accord with the somewhat different purposes for which the two methods were developed. GRID has been used mainly to introduce functionalities at specific positions in lead compounds, in which case the orientation is predetermined by the structure of the latter. The orientational information provided by MCSS is important for its use in the de novo design of large, multi-functional ligands, as well as for improving lead compounds.     

Modelling protein-RNA interactions: an electron density study of the guanidinium and formate complexes with RNA bases

The complexes formed by the double interaction established between RNA bases and guanidinium and formate ions, as a model for the interacting groups of arginine and glutamic or aspartic amino acid side chains, have been theoretically studied. A density functional theory method (B3LYP/6-31 + G**) has been used for this study. The range of interaction energies obtained allowed for a distinction between bidentate and bifurcate hydrogen bond interactions. The analysis of the electron density and the natural bond orbital analysis shows that these complexes are bound by double hydrogen bonds established between the donor and acceptor groups of guanidinium and formate respectively and those of the RNA bases. Comparisons are made with the results obtained in some previous theoretical and experimental studies.     

New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis

The 2'-hydroxyl group contributes inextricably to the functional behavior of many RNA molecules, fulfilling numerous essential chemical roles. To assess how hydroxyl groups impart functional behavior to RNA, we developed a series of experimental strategies using an array of nucleoside analogs. These strategies provide the means to investigate whether a hydroxyl group influences function directly (via hydrogen bonding or metal ion coordination), indirectly (via space-filling capacity, inductive effects, and sugar conformation), or through interactions with solvent. The nucleoside analogs span a broad range of chemical diversity, such that quantitative structure activity relationships (QSAR) now become possible in the exploration of RNA biology. We employed these strategies to investigate the spliced exons reopening (SER) reaction of the group II intron. Our results suggest that the cleavage site 2'-hydroxyl may mediate an interaction with a water molecule.     

Methods for modified nucleotide identification in ribosomal RNA

Modified nucleotides are ubiquitous in all functional RNA, such as ribosomal RNA. The identification of modified nucleotides is essential for understanding the functional role of RNA in living cells. This review is devoted to methods used to identify modified nucleotides in ribosomal RNA.     

Carbohydrate Mimetics: A New Strategy for Tackling the Problem of Carbohydrate-Mediated Biological Recognition

Useful strategies for the design of molecules to mimic carbohydrates have been developed over the past few years. Mimics of the target may contain new functional groups, a new scaffold, or both (in the schematic representation the natural ligand is shown on the left and the modified version on the right). Many examples of successful carbohydrate mimetics that interfere with sugar–protein and sugar–nucleic acid interactions are known.     

An efficient thermally induced RNA conformational switch as a framework for the functionalization of RNA nanostructures

RNA offers a variety of interactions and dynamic conformational switches not available with DNA that may be exploited for the construction of nanomolecular structures. Here, we show how the RNA loop-loop, or "kissing", interaction can be used to construct specific circular RNA arrangements that are capable of thermal isomerization to alternative structures. We also show how this thermally induced structural rearrangement can be used to unmask a functional RNA structure, in this case, a peptide-binding RNA structure, the Rev-response element (RRE) of HIV, thereby acting as a functional peptide-binding switch. The relative ease with which the RRE could be engineered into the RNA substrates suggested that a variety of functional RNA structures may be introduced. In addition, the structural rearrangement was extremely efficient, showing that the "kissing" complexes described in this study may provide a useful framework for the construction of functional RNA-based nanostructures, as well as aid in our understanding of the way RNA functions in biological systems.     

Chirality-Embedded Nanographenes

The development of chiral nanographenes has mostly been carried out by bottom-up methods and examples of species developed by the post-modification of nanographenes prepared by top-down methods remain limited. We show that the attachment of chiral functional groups onto the edge of nanographenes generates chirality on the surface. X-ray diffraction analysis and DFT calculations indicate that the chirality of the functional groups is transferred to the surface via steric interactions from the chiral center through the five-membered cyclic imide to the nanographene edge. The exciton coupling between the p-bromophenyl groups confirms that the functional groups are arranged on the armchair edges at distances that permit exciton coupling, which provides information about their relative orientation. These pieces of information help to elucidate the edge structure of nanographenes prepared by top-down methods.     

Chirality‐Embedded Nanographenes

The development of chiral nanographenes has mostly been carried out by bottom‐up methods and examples of species developed by the post‐modification of nanographenes prepared by top‐down methods remain limited. We show that the attachment of chiral functional groups onto the edge of nanographenes generates chirality on the surface. X‐ray diffraction analysis and DFT calculations indicate that the chirality of the functional groups is transferred to the surface via steric interactions from the chiral center through the five‐membered cyclic imide to the nanographene edge. The exciton coupling between the p‐bromophenyl groups confirms that the functional groups are arranged on the armchair edges at distances that permit exciton coupling, which provides information about their relative orientation. These pieces of information help to elucidate the edge structure of nanographenes prepared by top‐down methods.     

Functional Xeno Nucleic Acids for Biomedical Application

Functional nucleic acids(FNAs) refer to a type of oligonucleotides with functions over the traditional genetic roles of nucleic acids, which have been widely applied in screening, sensing and imaging fields. However, the potential application of FNAs in biomedical field is still restricted by the unsatisfactory stability, biocompatibility, biodistribution and immunity of natural nucleic acids(DNA/RNA). Xeno nucleic acids(XNAs) are a kind of nucleic acid analogues with chemically modified sugar groups that possess improved biological properties, including improved biological stability, increased binding affinity, reduced immune responses, and enhanced cell penetration or tissue specificity. In the last two decades, scientists have made great progress in the research of functional xeno nucleic acids, which makes it an emerging attractive biomedical application material. In this review, we summarized the design of functional xeno nucleic acids and their applications in the biomedical field.     

The interaction of carbohydrates and amino acids with aromatic systems studied by density functional and semi-empirical molecular orbital calculations with dispersion corrections

Density functional theory (DFT-D) and semi-empirical (PM3-D) methods having an added dispersion correction have been used to study stabilising carbohydrate-aromatic and amino acid-aromatic interactions. The interaction energy for three simple sugars in different conformations with benzene, all give interaction energies close to 5 kcal mol(-1). Our original parameterization of PM3 (PM3-D) seriously overestimates this value, and has prompted a reparametrization which includes a modified core-core interaction term. With two additional parameters, the carbohydrate complexes, as well as the S22 data set, are well reproduced. The new PM3 scheme (PM3-D*) is found to describe the peptide bond-aromatic ring interactions accurately and, together with the DFT-D method, it is used to investigate the interaction of six amino acids with pyrene. Whilst the peptide backbone can adopt both stacked and T-shaped structures in the complexes with similar interaction energies, there is a preference for the unsaturated ring to adopt a stacked structure. Thus, peptides in which the latter interactions are maximised are likely to be the most effective for the functionalisation of carbon nanotubes.     

核糖核酸-蛋白质复合物规模化富集与鉴定技术的研究进展

核糖核酸(RNA)在细胞中并非单独存在,从它们产生到被降解的过程中与大量蛋白质发生相互作用,RNA结合蛋白(RNA-binding proteins, RBPs)能与RNA结合形成RNA-蛋白质复合物(RP复合物),并以这种复合物的形式发挥生理功能。RNAs或RBPs任一组分的异常与缺失都会影响RP复合物的正常生理功能,从而导致疾病的发生,如代谢异常、肌肉萎缩症、自身免疫性疾病和癌症。因此,定性定量分析RBPs及其在正常细胞和肿瘤细胞中与RNAs靶标之间的复杂相互作用网络有助于挖掘RP复合物在肿瘤发生发展中的作用,开发肿瘤生物标志物和新的治疗方式。要深入研究和理解RNAs与RBPs的相互作用网络,须依赖组学技术对RP复合物进行大规模鉴定。而作为在组学层面系统性解析RP复合物组成、含量和功能的第一步,大规模富集RP复合物极具挑战性。为了解决这一难题,研究者们发展了各种富集鉴定策略。该文针对RP复合物富集策略的最新进展进行了综述,包括紫外光交联和免疫沉淀(crosslinking and immunoprecipitation, CLIP)及其衍生技术、基于“点击化学”的富集策略和基于相分离的富集策略,比较分析了它们的技术原理、优缺点,以方便研究者们选择合适的策略来解决感兴趣的生物学问题。该文最后总结了当前的RP复合物富集方法仍然存在富集效率低和操作繁琐等亟需解决的技术挑战,为富集策略的发展提供了研究方向。     

Comparative study of NS(2)(S-aryl) pyridine-based dithia-containing ligands with different substituent groups. Reactivity toward Cu(II) and Ru(II)

Ligands LX of the type NS(2) with S-aryl substituents which incorporate the unit 2,6-bis(thiomethyl)pyridine modified with functional groups bonded to the aromatic moieties, either on the phenyl or on the pyridine, are produced. Electron-withdrawing groups, 3-chloro and 4-nitro, that reduce the pyridine basicity have been introduced. Methoxy or methoxycarbonyl substituents have been incorporated on the thiophenyl moieties. The comparative results from the reaction of these ligands with Cu(ClO(4))(2).6H(2)O and [RuCl(2)(PPh(3))(3)] have revealed that their coordination capacity has not been greatly modified as a result of the introduced groups. Complexes of general formulas [Cu(LX)][ClO(4)](2), except for L5, and [RuCl(2)(LX)(PPh(3))], have been obtained, respectively. The electronic characteristics of these complexes have been studied by cyclic voltammetry experiments. The structures of 2,6-bis[(2'-methoxycarbonyl)phenylthio-methyl]-4-nitropyridine (L5) and [RuCl(2)(L5)(PPh(3))].2CCl(4) have been characterized by single-crystal X-ray diffraction methods.     

Characterization of ESR active species on lithium chloride-modified mesoporous silica

The surface of mesoporous silica with regular nanometer-sized pores and high surface area has been modified by metal ions or functional groups to introduce specific interactions. We found that ESR active species were formed on lithium chloride (LiCl)-modified mesoporous silica after heat treatment. The structure and the surface properties of LiCl-modified mesoporous silica were characterized by XRD, ESR, nitrogen adsorption, UV-vis-NIR, and TPD. The results suggest that the ESR active species were generated on the surface in response to heat treatment above 673 K. Moreover, it was found for the first time that LiCl-modified mesoporous silica after the heat treatment has reversible adsorption properties for hydrogen under room temperature and atmospheric pressure.     

Aminoglycosides modified by resistance enzymes display diminished binding to the bacterial ribosomal aminoacyl-tRNA site

Understanding the basic principles that govern RNA binding by aminoglycosides is important for the design of new generations of antibiotics that do not suffer from the known mechanisms of drug resistance. With this goal in mind, we examined the binding of kanamycin A and four derivatives (the products of enzymic turnovers of kanamycin A by aminoglycoside-modifying enzymes) to a 27 nucleotide RNA representing the bacterial ribosomal A site. Modification of kanamycin A functional groups that have been directly implicated in the maintenance of specific interactions with RNA led to a decrease in affinity for the target RNA. Overall, the products of reactions catalyzed by aminoglycoside resistance enzymes exhibit diminished binding to the A site of bacterial 16S rRNA, which correlates well with a loss of antibacterial ability in resistant organisms that harbor these enzymes.     

Effects of functional groups on surface pressure-area isotherms of hydrophilic silicone polymers

Organic/inorganic hybrid silicone polymers are increasingly used in cosmetics, inks and paints, and fabric care applications owing to their special Si-O bond characteristics. Because of the presence of organic as well as inorganic groups, they show the properties of both, and the presence of hydrophobic as well as hydrophilic character makes them behave like a hybrid polymer. Though they are widely used, the utilization of hydrophilically modified silicones on a large scale has mainly been empirical due to lack of fundamental knowledge about variation in their properties with systematic change in their structure. The choice of moieties for hydrophilic modification of silicones in most of the earlier works has been nonionic based on ethylene oxide and propylene oxide groups, however, very little is known about their ionic counterparts. The current work focuses on understanding the behavior of functionally grafted silicone polymers with respect to the variation in the hydrophilic part of the grafting chain. Hydrophilically grafted silicone polymers form monolayers at the air-water interface, which are stabilized by interactions of functional groups with water. The present work examined the effects of functional group modifications on the conformational behavior of chains at the interface. It was observed that the shape of the chain depends on the available area at the interface (or surface pressure), and there are conformational changes with an increase in the number of molecules per unit area. While a poly(dimethylsiloxanes) (PDMS) chain may undergo stretched to helix transition as predicted earlier, this may not be the case for hydrophilically grafted chains. On the basis of the shape of the surface pressure-area isotherm and correlation with the scaling theory, a gradation in hydrophilicity of functional groups and hence modified silicone chains at the air-water interface is predicted.