Combinatorial properties of RNA secondary structures.

The secondary structure of an RNA molecule is of great importance and possesses influence, e.g., on the interaction of tRNA molecules with proteins or on the stabilization of mRNA molecules. The classification of secondary structures by means of their order proved useful with respect to numerous applications. In 1978, Waterman, who gave the first precise formal framework for the topic, suggested to determine the number a(n,p) of secondary structures of size n and given order p. Since then, no satisfactory result has been found. Based on an observation due to Viennot et al., we will derive generating functions for the secondary structures of order p from generating functions for binary tree structures with Horton-Strahler number p. These generating functions enable us to compute a precise asymptotic equivalent for a(n,p). Furthermore, we will determine the related number of structures when the number of unpaired bases shows up as an additional parameter. Our approach proves to be general enough to compute the average order of a secondary structure together with all the r-th moments and to enumerate substructures such as hairpins or bulges in dependence on the order of the secondary structures considered.     

Generic properties of combinatory maps: Neutral networks of RNA secondary structures

Random graph theory is used to model and analyse the relationship between sequences and secondary structures of RNA molecules, which are understood as mappings from sequence space into shape space. These maps are non-invertible since there are always many orders of magnitude more sequences than structures. Sequences folding into identical structures formneutral networks. A neutral network is embedded in the set of sequences that arecompatible with the given structure. Networks are modeled as graphs and constructed by random choice of vertices from the space of compatible sequences. The theory characterizes neutral networks by the mean fraction of neutral neighbors (λ). The networks are connected and percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value (λ>λ*). Below threshold (λ<λ*), the networks are partitioned into a largest “giant” component and several smaller components. Structure are classified as “common” or “rare” according to the sizes of their pre-images, i.e. according to the fractions of sequences folding into them. The neutral networks of any pair of two different common structures almost touch each other, and, as expressed by the conjecture ofshape space covering sequences folding into almost all common structures, can be found in a small ball of an arbitrary location in sequence space. The results from random graph theory are compared to data obtained by folding large samples of RNA sequences. Differences are explained in terms of specific features of RNA molecular structures. Deicated to professor Manfred Eigen     

Developmentally regulated, combinatorial RNA processing modulates AMPA receptor biogenesis

The subunit composition determines AMPA receptor (AMPA-R) function and trafficking. Mechanisms underlying channel assembly are thus central to the efficacy and plasticity of glutamatergic synapses. We previously showed that RNA editing at the Q/R site of the GluR2 subunit contributes to the assembly of AMPA-R heteromers by attenuating formation of GluR2 homotetramers. Here we report that this function of the Q/R site depends on subunit contacts between adjacent ligand binding domains (LBDs). Changes of LBD interface contacts alter GluR2 assembly properties, forward traffic, and expression at synapses. Interestingly, developmentally regulated RNA editing within the LBD (at the R/G site) produces analogous effects. Our data reveal that editing to glycine reduces the self-assembly competence of this critical subunit and slows GluR2 maturation in the endoplasmic reticulum (ER). Therefore, RNA editing sites, located at strategic subunit interfaces, shape AMPA-R assembly and trafficking in a developmentally regulated manner.     

Pseudoknots in RNA secondary structures: representation, enumeration, and prevalence.

A number of non-coding RNA are known to contain functionally important or conserved pseudoknots. However, pseudoknotted structures are more complex than orthodox, and most methods for analyzing secondary structures do not handle them. I present here a way to decompose and represent general secondary structures which extends the tree representation of the stem-loop structure, and use this to analyze the frequency of pseudoknots in known and in random secondary structures. This comparison shows that, though a number of pseudoknots exist, they are still relatively rare and mostly of the simpler kinds. In contrast, random secondary structures tend to be heavily knotted, and the number of available structures increases dramatically when allowing pseudoknots. Therefore, methods for structure prediction and non-coding RNA identification that allow pseudoknots are likely to be much less powerful than those that do not, unless they penalize pseudoknots appropriately.     

Ferrocenesuccinate-bridged lanthanide polymeric complexes: Syntheses, structures and properties

One-dimensional lanthanide-ferrocenesuccinate polymeric complexes [M(η²-FcCOC₂H₄COO)(μ₂-η²-FcCOC₂H₄COO)₂(H₂O)₂]_n (Fc = (η⁵-C₅H₄)Fe(η⁵-C₅H₄), M = Pr, 1; Ce, 2; La, 3) have been synthesized and structurally characterized by single-crystal X-ray crystallography. The three polymers are isomorphous, in which each Ln(III) ion is 10-coordinated and connects with two water molecules and eight oxygen atoms from ferrocenesuccinate units in two kinds of coordination modes: bidentate-chelating mode and tridentate-bridging mode. The variable-temperature magnetic susceptibility in the temperature range 5-300 K for 1 and 2 shows that both of them display weak antiferromagnetic interaction. In addition, the redox and fluorescent properties have been investigated. The redox properties are different from the previous results of transition metal compounds containing ferrocenyl systems. Compared with sodium ferrocenesuccinate, polymers 1 and 3, the fluorescent intensities of 2 are markedly enhanced in the solid state.     

Insect antimicrobial peptides: structures, properties and gene regulation

Antimicrobial peptides (AMPs) are part of the armament that insects have developed to fight off pathogens. Insect AMPs are typically cationic and often made of less than 100 amino acid residues. Although their structures are diverse, most of the AMPs can be assigned to a limited number of families. The most common structures are represented by peptides assuming a alpha-helical conformation in organic solutions or disulfide-stabilized beta-sheets with or without alpha-helical domains present. The diverse activity spectrum of these peptides may indicate different modes of action. Genetic analysis in the Drosophila model evidenced that multiple signal transduction pathways are activating the genes coding AMPs.     

m-Terphenylphosphines: Synthesis, structures and coordination properties

A series of m-terphenylphosphines TerphPCl₂, TerphPH₂ and TerphPMe₂ (Terph = 2,6-Mes₂C₆H₃-, 2,6-(4-t-BuC₆H₄)₂C₆H₃-, 2,6-(3,5-Me₂C₆H₃)₂C₆H₃-, 2,6-(2,6-Et₂C₆H₃)₂C₆H₃-, and 2,6-(2,6-i-Pr₂C₆H₃)₂C₆H₃-; Mes = 2,4,6-Me₃C₆H₂-) was prepared and fully characterized. The structural investigation by X-ray crystallography and density functional theory revealed significant distortions in the environment of the ipso carbon and phosphorus centers. These can be traced back to steric interactions and repulsions of the chlorine and methyl substituents on phosphorus with one of the flanking arenes of the m-terphenyl substituents. The primary phosphine 2,6-Mes₂C₆H₃PH₂, 6, and the dimethylphosphine 2,6-(3,5-Me₂C₆H₃)₂C₆H₃PMe₂, 9, readily form complexes with the Cl₂Ru(p-cymene) complex fragment, whereas the larger phosphine 2,6-Mes₂C₆H₃PMe₂, 8, does not. Heating of the complexes TerphPR₂Ru(Cl₂)(p-cymene) 11 and 12 and the mixture of 8 and {(p-cymene)RuCl₂}₂ lead to expulsion of the p-cymene ligand and intramolecular η⁶ coordination of one of the flanking arene rings to the ruthenium center to afford the complexes Cl₂RuP(H₂)C₆H₃-2-η⁶-Mes-6-Mes, 13, Cl₂RuP(Me₂)C₆H₃-2-η⁶-Mes-6-Mes, 14, and Cl₂RuP(H₂)C₆H₃-2-η⁶-(3,5-Me₂C₆H₃)-6-(3,5-Me₂C₆H₃), 15. All complexes were characterized by NMR spectroscopy and complexes 14 and 15 also by X-ray crystallography.     

Two heterometal-organic coordination polymers with chelidamic acid: Syntheses, structures and optical properties

Two heterometal-organic coordination polymers with chelidamic acid ligands, [AgNd(C₇H₃NO₅)₂·3H₂O]_n (1) and 0.75H₃O·[K_0.25Nd(C₇H₃NO₅)₂·3H₂O]·1.75H₂O (2), have been synthesized and characterized by X-ray single-crystal diffraction. The crystal structure of 1 features that chelating units composed of one Nd(III) ion and two tridentate chelating chelidamic acid ligands are connected by the Ag(I) ions to form a one-dimensional chain, further linked by hydrogen bonds into a 3D network. As for 2, discrete independent molecules, made up of Nd(III) and K(I) ions and chelidamic acid ligands, are linked through the hydrogen bonds to form a 1D chain, which are further inter-linked through the complex hydrogen bonds to form a 3D network. The optical properties of 1 and 2 were investigated in terms of fluorescent spectra, which both exhibit good luminescence.     

Correlating SHAPE signatures with three-dimensional RNA structures

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a facile technique for quantitative analysis of RNA secondary structure. In general, low SHAPE signal values indicate Watson-Crick base-pairing, and high values indicate positions that are single-stranded within the RNA structure. However, the relationship of SHAPE signals to structural properties such as non-Watson-Crick base-pairing or stacking has thus far not been thoroughly investigated. Here, we present results of SHAPE experiments performed on several RNAs with published three-dimensional structures. This strategy allows us to analyze the results in terms of correlations between chemical reactivities and structural properties of the respective nucleotide, such as different types of base-pairing, stacking, and phosphate-backbone interactions. We find that the RNA SHAPE signal is strongly correlated with cis-Watson-Crick/Watson-Crick base-pairing and is to a remarkable degree not dependent on other structural properties with the exception of stacking. We subsequently generated probabilistic models that estimate the likelihood that a residue with a given SHAPE score participates in base-pairing. We show that several models that take SHAPE scores of adjacent residues into account perform better in predicting base-pairing compared with individual SHAPE scores. This underscores the context sensitivity of SHAPE and provides a framework for an improved interpretation of the response of RNA to chemical modification.     

Common structures of the 5' non-coding RNA in enteroviruses and rhinoviruses. Thermodynamical stability and statistical significance

A total of 4051 suboptimal secondary structures are predicted by folding the 5' non-coding region of ten polioviruses, five human rhinoviruses and three coxsackieviruses using our new suboptimal folding algorithm for the prediction of both optimal and suboptimal RNA secondary structures. A comparative analysis of these RNA secondary structures reveals the conservation of common secondary structure that can be supported by phylogenetic data. The thermodynamic stability and statistical significance of these predicted, conserved helical elements are assessed and significant structure motifs in the 5' non-coding region are proposed. The possible roles of these structure motifs in the virus life cycle are discussed.     

ROTAS: a rotamer-dependent,atomic statistical potential for assessment and prediction of protein structures

Background

Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures.

Results

In this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named “rotamer-dependent atomic statistical potential” (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality.

Conclusions

A new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-307) contains supplementary material, which is available to authorized users.     

Dual antioxidant structures with potent anti-inflammatory,hypolipidemic and cytoprotective properties

Novel amide derivatives of trolox, 3,5-di-tert-butyl-4-hydroxybenzoic acid, (E)-3-(3,5-di-tert-butyl-4-hydroxyphenyl)acrylic acid and cinnamic acid with cysteamine and l-cysteine ethyl ester were synthesised. In four cases, the disulfide derivatives were also isolated and tested. All compounds were examined for antioxidant activity, expressed as their ability to inhibit lipid peroxidation and to scavenge free radicals. They were found to demonstrate up to 17-fold better activity than that of the parent antioxidant acids. They could reduce acute inflammation up to 87%. The most active antioxidant compounds were further tested for their in vivo hypolipidemic effect, which ranged from 47% to 73%, and for their ability to protect the liver against oxidative toxicity caused by high paracetamol dose. The disulfide derivatives of 3,5-di-tert-butyl-4-hydroxybenzoic acid and cinnamic acid had no antioxidant activity and presented equal or lower anti-inflammatory effect than their thiol analogues, indicating that their molecular characteristics may not permit biological barrier penetration.     

Polyproline helices in protein structures: A statistical survey

A statistical survey of polyproline II (PPII) helices extracted from protein crystal structures is here reported. The average hydrophobicity of these helices is intermediate between those displayed by beta-strands and coil regions and is similar to that of alpha-helices. PPII helices with amphipathic properties have been identified and classified. Amino acid propensities for PPII helices derived in this study differ significantly from those previously reported. They show a little albeit significant correlation with propensities for alpha-helices whereas they are fully non-correlated to propensities for beta-sheets. Finally, PPII propensities have been correlated with amino acid frequencies in structural proteins, such as collagen and extensins.     

Two cadmium-thiocyanate coordination polymers with organic cations: Synthesis, crystal structures and luminescent properties

Two new inorganic-organic hybrid polymers [ClBzQl]₂[Cd(SCN)_3.5Br_0.5]·0.25H₂O (1) and [ClBzMePy][Cd(SCN)₃] (2) (ClBzQl = 1-(4′-Cl-benzyl)quinolinium cation and ClBzMePy = 1-(4′-Cl-benzyl)-2-methylpyridinium cation) have been synthesized and characterized by IR, UV, elemental analysis and X-ray crystallography. Crystal structure analyses show that two polymers belong to the monoclinic space group P2/n (1) and P2₁/c (2) with a = 18.548(2) Å, b = 9.526(1) Å, c = 20.689(2) Å, β = 94.008(1)°, V = 3646.6(5) Å³ for 1, and a = 11.195(2) Å, b = 16.415(3) Å, c = 10.751(2) Å, β = 102.930(3)°, V = 1925.7(7) Å³ for 2. The Cd atom exhibits a distorted octahedral coordination geometry for 1 and 2. For 1, a pair of 1,1-μ-SCN⁻ anions and a pair of 1,3-μ-SCN⁻ anions are alternately bridge adjacent Cd centers to form infinite polymeric chains. For 2, adjacent Cd atoms are linked by three 1,3-μ-SCN⁻ anions to form infinite [Cd(SCN)₃⁻]_∞ polymeric chains. The luminescent properties of the two polymers in the solid state at room temperature were investigated.     

RNA targeting by small molecules: Binding of protoberberine, benzophenanthridine and aristolochia alkaloids to various RNA structures

Studies on RNA targeting by small molecules to specifically control certain cellular functions is an area of remarkable current interest. For this purpose, a basic understanding of the molecular aspects of the interaction of small molecules with various RNA structures is essential. Alkaloids are a group of natural products with potential therapeutic utility, and very recently, their interaction with many RNA structures have been reported. Especially noteworthy are the protoberberines and aristolochia alkaloids distributed widely in many botanical families. Many of the alkaloids of these group exhibit excellent binding affinity to many RNA structures that may be exploited to develop RNA targeted therapeutics. This review attempts to present the current status on the understanding of the interaction of these alkaloids with various RNA structures, mainly highlighting the biophysical aspects.     

Artificial ribonucleases: from combinatorial libraries to efficient catalysts of RNA cleavage

Combinatorial libraries of small organic compounds capable of cleaving RNA were synthesized. The compounds contain benzene ring substituted with two residues of bis quaternary salt of diazabicyclo[2.2.2]octane (DABCO) bearing hydrophobic fragments of different length and structure, attached to DABCO at the bridge position. These compounds, lacking traditional functionalities involved in transesterification reaction, exhibit pronounced RNA cleavage activity. To identify the most active artificial ribonucleases, sublibraries and truncated libraries, containing compounds lacking one of substituents were synthesized. Analysis of ribonuclease activity of truncated libraries resulted in identification of the most active compounds, which are characterized by the presence of at least one long oligomethylene substituent.     

Cobalt and cadmium complexes with N-heterocyclic dicarboxylic acid ligands: Syntheses, structures, magnetic and fluorescent properties

Two new complexes, [Co(Himdc)₂(H₂O)₂] (1) and {[Cd(pzdc)(H₂O)]·H₂O}_n (2) (H₂imdc = imidazole-4, 5-dicarboxylic acid, H₂pzdc = pyrazine-2, 3-dicarboxylic acid), have been synthesized and structurally characterized. Compound 1 is a new triclinic mononuclear complex formed by two Himdc⁻ ligands trans coordinated to the Co^II center in bidentate chelate mode and two water ligands. Compound 2 shows a two dimensional layer structure in which pzdc²⁻ dianion ligand adopts unique doubly bridging bis-bidentate μ₄ coordination mode. Temperature-dependent magnetic susceptibilities and thermal stability for 1 and solid-state fluorescent properties for 2 have been discussed in detail.     

Radiation hybrid mapping: statistical criteria and their properties

Statistical tests specially developed for radiation hybrid (RH) mapping, modified likelihood-ratio test and Akaike's information content, are proposed. They allow several most likely gene orders to be identified to a certain accuracy. The properties of the proposed tests that characterize the accuracy of gene ordering as dependent on the number of genes mapped, the position of the selective gene, and the sample size have been studied. Recommendations as to the practical use of these tests are presented.