Oxidative dissolution of synthetic vivianites as a method for the crystallization of molecular structural motifs

Structural Chemistry - Isolation of structural motifs from minerals can be used to improve the understanding of fundamental processes such as catalytic mechanisms and spectroscopic vibrations. In...     

Designing structural motifs for clickamers: exploiting the 1,2,3-triazole moiety to generate conformationally restricted molecular architectures

Noncovalent interactions, especially hydrogen-bonding interactions as well as electrostatic forces, confined within one macromolecule are the key to designing foldamers that adopt well-defined conformations in solution. In the context of significant recent activities in the area of triazole-connected foldamers, so-called clickamers, we present a fundamental study that compares various model compounds that bear adjacent N-, O-, or F-heteroatom substituents. The interplay of attractive and repulsive interactions leads to rotational constraints around the single bonds attached to both the 1- and 4-positions of the 1,2,3-triazole moiety and should therefore be able to induce well-defined conformational preferences in higher oligomers and polymers, that is, foldamers. Various compounds were synthesized and characterized with regard to their preferred conformations in all three aggregation states--that is, in the gas phase, in solution as well as in the solid state--by employing DFT calculations, NMR spectroscopic experiments, and X-ray crystallography, respectively. On the basis of the thus-obtained general understanding of the conformational behavior of the individual connection motifs, heterostructures were prepared from different motifs without affecting their distinct folding characteristics. Therefore, this work provides a kind of foldamer construction kit, which should enable the design of various clickamers with specific shape and incorporated functionality.     

Intramolecular cyclization to fused pyranoisoxazoles and molecular packing motifs identification through X-ray structural studies

The present work describes intramolecular cyclization of 4-(hydroxyamino)-2-oxo-6-aryl-N-(substituted)-2H-pyran-3-carboxamides (1a-e) under the basic condition to yield fused pyranoisoxazoles (2a-e). The X-ray structural studies delineate a network of non-covalent forces that provided a molecular packing motif to generate a reproducible stacking pattern towards column scaffold formation in the pyranoisoxazole crystal system.     

Orthogonal addressable monolayers for integrating molecular logic

Plug and play: The mimicking of integrated circuits by using two individual monolayers (molecular chips) is shown. These monolayers can be individually addressed using identical inputs. Upon combination of their optical outputs, the input/output characteristics of a molecular encoder is obtained. Since the encoder functionality is only displayed when both chips are active, the device behaves according to a plug-and-play principle (In=input; see picture).     

Novel structural motifs consisting of chiral thiazolines: synthesis, molecular recognition, and anticancer activity

The facile synthesis of linear and cyclic chiral oligo(4-alpha/beta-methyl)thiazolines is described. Linear oligothiazolines have been efficiently synthesized by the iterative formation of thiazoline rings and two-directional block condensation. The construction of 24- to 36-membered cyclic oligothiazolines was achieved through the head-to-tail cyclo-oligomerization of doubly deprotected linear fragments. Studies of the interactions of both the linear and cyclic oligomers with chiral compounds revealed that cyclic oligomers displayed a strong binding affinity towards mandelic acid, whereas linear oligomers showed a poor affinity. Linear oligomers have been proven to inhibit the cell growth of the cancer cell lines HPAC, PC-3, and HCT-116. Studies of the structure-activity relationships showed that the IC50 values are clearly dependent on both the length and the terminal functionalities of the linear oligomers. Longer derivatives showed more potent activity (e.g., hexi- and octithiazolines exhibit IC50<1 microM) against all three cancer cell lines. In sharp contrast, cyclic oligomers were inactive to all three cell lines.     

A novel structural class of photoswitchable oligonucleotide

Directed Michaelis-Arbuzov reactions of support-bound internucleotide O-benzyl- or O-methyl-phosphite triesters with meta-phenylazobenzylamine or alkane-/glycol-linked α,ω-diamines were effected in the presence of iodine. The corresponding tritylated phosphoramidate-linked 11-mers were fully deprotected and released from the support under standard conditions and the fast- and slow-diastereoisomers of both the E- and the Z-meta-phenylazobenzyl-appended oligomers were readily resolved by RP-HPLC. The primary amine-functionalised oligonucleotides were either purified, detritylated and then finally treated with N-hydroxysuccinimidyl carboxylic acid ester derivatives of photoswitchable moieties (Route A) or first derivatised and then subsequently purified and detritylated (Route B). This latter route enabled resolution of fast- and slow-isomers of the trityl-on oligomers bearing novel photoswitchable azopyridine or 9-alkoxyanthracene moieties using RP-HPLC, following which the pure diastereoisomers were detritylated and characterised by MALDI-MS.     

Monitoring genomic alterations with a panel of oligonucleotide probes specific for various simple repeat motifs

Germline and somatic instability of the human genome was studied, using synthetic oligonucleotides specific for simple repeat motifs. The following probes were used: (GTG)5, (GACA)4, (GATA)4, (CT)8, (TTAGGG)3, (GT)8, (GAA)6 and (GGAT)4. Each of them is unique with respect to the target regions recognized in the genome. Thus compilation of the various fingerprint data provides a complex map of the genome (and its deviations). While the fingerprints of differentiated somatic tissues never showed any alterations, in tumor tissues (namely gliomas) many changes could be detected. Most of the latter reflect secondary karyological aberrations. In nearly one third of the gliomas, drastically amplified and apparently monomorphic DNA fragments were identified. This marker should make it possible to deal with causal pathogenetic mechanisms as well as novel diagnostic strategies.     

The structural modeling of EF-hand motifs in parvalbumin

Parvalbumin (Parv) is a typical protein with EF-hand motifs that play an important role in many physiological processes. We present a novel free energy to model the skeletal C\(_\alpha \) chain of the protein from the basic principle of mathematics and physics. Starting from the crystal structure of Parv (PDB code 2PVB), we first analyze the profile of the C\(_\alpha \) bond and torsion angles over the segment that contains the secondary structures. Then the parameters in the energy function are evaluated for the helix ABCD fragment that contains two EF-hand domains in Parv. Meanwhile an eight-soliton configuration at the energy minimum is constructed to model the conformation of ABCD fragment. The deviation of the conformation constructed from the model away from the crystal structure is as small as 1.28 Å. The structural modeling stems from the physical energy, which is a benefit relative to the statistics-based or knowledge-based technologies.     

Importance of structural motifs in liquid hydrogen fluoride

The investigation of liquid phases by means of accurate electronic structure methods is a demanding task due to the high computational effort. We applied second-order M?ller-Plesset perturbation theory and high-level quantum chemical calculations using the coupled-cluster method with single, double and perturbative triple excitations in combination with Dunnings correlation-consistent basis sets up to quintuple ζ quality. Based on these calculations, we extrapolated the correlation energy to the basis set limit in order to improve the results even further. For comparison to the correlated electronic structure methods, density functional calculations employing different functionals are presented as well. The investigated species are a cyclic pentamer as well as a set of branched structures. The quantum cluster equilibrium method is employed for the investigation of the liquid-phase structure of hydrogen fluoride. The pentamer is found to be present to a high extent and in the case of the MP2/QZVP data, its presence improves the results significantly. Accounting for branched structures slightly improves results, so that they are found to be present but not to dominate in liquid hydrogen fluoride. Concerning both the interaction energy and the result of the quantum cluster equilibrium calculation the basis set has a major influence, whereas the difference between M?ller-Plesset perturbation theory and coupled-cluster calculations is less pronounced.     

SiteBinder: an improved approach for comparing multiple protein structural motifs

There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.     

Spin-counting NMR experiments for the spectral editing of structural motifs in solids

Scalar couplings, recoupled or full dipolar interactions can be used to characterize multinuclear structural molecular motifs in solids, by counting the neighbouring spins in solid-state NMR, opening new ways for the differentiation of overlapping spectral responses which is a limiting factor in many high resolution experiments carried out on disordered systems.     

The structural basis for induction of VanB resistance

Because teicoplanin and vancomycin are the last line of defense for many bacterial infections, the emergence of resistance to glycopeptide antibiotics in enterococci and streptococci has aroused concern. Despite their similarity in terms of structure and mechanism of action, vancomycin induces the expression of genes that leads to bacterial resistance, and teicoplanin does not. We have used a combination of chemical and enzymatic methods to produce sets of vancomycin and teicoplanin analogues that allow us to consider whether the aglycon, the carbohydrate, or other parts of these molecules stimulate VanB resistance. We show that the teicoplanin and vancomycin aglycons are the structural elements that lead to induction of resistance. We think that lipid-containing analogues of vancomycin, like teicoplanin itself, circumvent resistance because the lipid chain changes the periplasmic distribution of the glycopeptide and, therefore, changes the biosynthetic step that it blocks.     

Chemical approaches to molecular logic elements for addition and subtraction

Molecular and supramolecular logic gates are candidates for computation at the nanoscale level. Nowadays all common logic operations can be mimicked with molecular devices based on chemical approaches. One step further towards molecular systems with increased logic capabilities is the addition or subtraction of binary digits. This Minireview describes recent developments to attain this goal, including bioinspired systems based on DNA and enzymes. Furthermore, chemical molecular logic gates are discussed and compared critically with regard to alternative concepts.     

The importance of short structural motifs in protein structure analysis

Summary Proteins tend to use recurrent structural motifs on all levels of organization. In this paper we first survey the topics of recurrent motifs on the local secondary structure level and on the global fold level. Then, we focus on the intermediate level which we call the short structural motifs. We were able to identify a set of structural building blocks that are very common in protein structure. We suggest that these building blocks can be used as an important link between the primary sequence and the tertiary structure. In this framework, we present our latest results on the structural variability of the extended strand motifs. We show that extended strands can be divided into three distinct structural classes, each with its own sequence specificity. Other approaches to the study of short structural motifs are reviewed.     

Systematic investigation of sequence and structural motifs that recognize ATP

Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs. The five motifs define five distinct ATP–protein interaction modes which concern over 5% of known protein structures. We demonstrate that although these motifs share a common GXG tripeptide they recognize ATP through different functional groups. The p-loop motif recognizes ATP through phosphates, class II aminoacyl-tRNA synthetase motif targets adenosine and the other three motifs recognize both phosphates and adenosine. We show that some motifs are shared by different enzyme types. Statistical tests demonstrate that the five sequence motifs are significantly associated with the nucleotide binding proteins. Large-scale test on PDB reveals that about 98% of proteins that include one of the structural motifs are confirmed to bind ATP.     

Reusable amine-based structural motifs for green house gas (CO2) fixation

A series of compounds with an amine based structural motif (ASM) have been synthesized for efficient atmospheric CO(2) fixation. The H-bonded ASM-bicarbonate complexes were formed with an in situ generated HCO(3)(-) ion. The complexes have been characterized by IR, (13)C NMR, and X-ray single-crystal structural analysis. ASM-bicarbonate salts have been converted to pure ASMs in quantitative yield under mild conditions for recycling processes.     

Diastereoselective synthesis of highly functionalized tetrahydroxanthenols--unprecedented access to privileged structural motifs

Tetrahydroxanthenones, which can be easily prepared by a domino oxa-Michael aldol condensation, offer various possibilities for diastereoselective functionalization, giving access to the stereocontrolled synthesis of stereochemical triades or tetrades, which represent privileged structural motifs. In most cases, the relative stereochemistry was unequivocally established by crystal structure analysis.     

Determination of oligonucleotide composition from mass spectrometrically measured molecular weight

Extensive calculations for molecular mass versus subunit composition have been made for oligonucleotides from RNA and DNA to determine the extent to which base compositions might be derived from mass spectrometrically determined molecular weights. In the absence of compositional constraints (e.g., any numbers of A, U, G, C), measurement of molecular weight leads to only modest restrictions in allowable number of base compositions; however, if the compositional value for any one residue is known, such as from selective chemical modification or enzymatic cleavage, the number of allowable base compositions becomes unexpectedly low. For example, hydrolysis of RNA by ribonuclease T₁ produces oligonucleotides for which G=1, for which all base compositions can be uniquely specified up to the 14-mer level, solely by measurement of mass to within ±0,01%. The effects of methylation, phosphorylation state of nucleotide termini, and knowledge of chain length on the determination of subunit composition are discussed.