Deconvolution of 1D NMR spectra: A deep learning-based approach.

The analysis of nuclear magnetic resonance (NMR) spectra to detect peaks and characterize their parameters, often referred to as deconvolution, is a crucial step in the quantification, elucidation, and verification of the structure of molecular systems. However, deconvolution of 1D NMR spectra is a challenge for both experts and machines. We propose a robust, expert-level quality deep learning-based deconvolution algorithm for 1D experimental NMR spectra. The algorithm is based on a neural network trained on synthetic spectra. Our customized pre-processing and labeling of the synthetic spectra enable the estimation of critical peak parameters. Furthermore, the neural network model transfers well to the experimental spectra and demonstrates low fitting errors and sparse peak lists in challenging scenarios such as crowded, high dynamic range, shoulder peak regions as well as broad peaks. We demonstrate in challenging spectra that the proposed algorithm is superior to expert results.

Influence of pH and Mg(ii) on the catalytic core domain 5 of a bacterial group II intron.

RNA molecules fold into complex structures that allow them to perform specific functions. To compensate the relative lack of diversity of functional groups within nucleotides, metal ions work as crucial co-factors. In addition, shifted pKas are observed in RNA, enabling acid-base reactions at ambient pH. The central catalytic domain 5 (D5) hairpin of the Azotobacter vinelandii group II intron undergoes both metal ion binding and pH dependence, presumably playing an important functional role in the ribozyme's reaction. By NMR spectroscopy we have here characterized the metal ion binding sites and affinities for the hairpin's internal G-A mismatch, bulge, and pentaloop. The influence of Mg(ii) and pH on the local conformation of the catalytically crucial region is also explored by fluorescence spectroscopy.

Characterization of the full-length btuB riboswitch from Klebsiella pneumoniae.

Riboswitches are cis-regulatory RNA elements on the mRNA level that control the expression of the downstream coding region. The interaction of the riboswitch with its specific metabolite, which is related to the function of the controlled gene, induces a structural change of the RNA architecture. Consequently, gene regulation is induced by un/masking of the ribosome binding site (RBS). In the genome of Klebsiella pneumoniae a sequence was identified by bioinformatics and proposed to be a B12 riboswitch regulated by coenzyme B12. Here we study this new coenzyme B12-dependent riboswitch system by in-line probing and ITC. The riboswitch sequence includes the whole expression platform as well as RBS. In-line probing experiments were performed to investigate the structural rearrangement of this 243-nt long RNA sequence while Isothermal Titration Calorimetry (ITC) yielded the thermodynamic parameters of the interaction between the riboswitch and its metabolite. The interaction of coenzyme B12 with the butB riboswitch of K. pneumoniae is an exothermic process with a 1:1 binding stoichiometry and binding affinities of log KA=6.73±0.02 at 15°C and log KA=6.00±0.09 at 30°C.

Dynamics at the air-water interface revealed by evanescent wave light scattering.

A new tool to study surface phenomena by evanescent wave light scattering is employed for an investigation of an aqueous surface through the water phase. When the angle of incidence passes the critical angle of total internal reflection, a high and narrow scattering peak is observed. It is discussed as an enhancement of scattering at critical angle illumination. Peak width and height are affected by the interfacial profile and the focusing of the beam. In addition, the propagation of capillary waves was studied at the surface of pure water and in the presence of latex particles and amphiphilic diblock copolymers. The range of the scattering vectors where propagating surface waves were detected is by far wider than standard surface quasi-elastic light scattering (SQELS) and comparable with those of X-ray photon correlation spectroscopy (XPCS).

Tilt angle of lipid acyl chains in unilamellar vesicles determined by ellipsometric light scattering.

Ellipsometric light scattering (ELS) at room temperature is applied to unilamellar vesicles (approximately 50 nm radius) of 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in the gel phase and of 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) in the liquid-crystaline phase. A high sensitivity of this technique to the local anisotropy is found. From the resulting local birefringence, a lower limit of (29 +/-0.5) degrees for the average tilt angle of the lipid chains of DPPC with respect to the membrane normal is estimated. This tilt angle value is slightly lower than literature values for the tilt angle in oriented lipid multi-bilayers on solid substrates.

The onset of amelogenin nanosphere aggregation studied by small-angle X-ray scattering and dynamic light scattering.

Proteins with predominantly hydrophobic character called amelogenins play a key role in the formation of the highly organized enamel tissue by forming nanospheres that interact with hydroxyapatite crystals. In the present investigation, we have studied the temperature and pH-dependent self-assembly of two recombinant mouse amelogenins, rM179 and rM166, the latter being an engineered version of the protein that lacks a 13 amino acid hydrophilic C-terminus. It has been postulated that this hydrophilic domain plays an important role in controlling the self-assembly behavior of rM179. By small-angle X-ray and neutron scattering, as well as by dynamic light scattering, we observed the onset of an aggregation of the rM179 protein nanospheres at pH 8. This behavior of the full-length recombinant protein is best explained by a core-shell model for the nanospheres, where hydrophilic and negatively charged side chains prevent the agglomeration of hydrophobic cores of the protein nanospheres at lower temperatures, while clusters consisting of several nanospheres start to form at elevated temperatures. In contrast, while capable of forming nanospheres, rM166 shows a very different aggregation behavior resulting in the formation of larger precipitates just above room temperature. These results, together with recent observations that rM179, unlike rM166, can regulate mineral organization in vitro, suggest that the aggregation of nanospheres of the full-length amelogenin rM179 is an important step in the self-assembly of the enamel matrix.

Collective dynamics of an end-grafted polymer brush in solvents of varying quality.

The dynamic structure of a chemically end-grafted polystyrene brush bathed in solvents of varying interactions was studied by evanescent wave dynamic light scattering. It reveals distinct behavior under good and poor solvent conditions. The cooperative diffusion is a generic feature of a good solvent environment, whereas a second slow relaxation mode appears in the theta solvent regime. Its characteristics resemble self-diffusion of clusters in a gel while weak concentration fluctuations in the polymer brush decay similarly to a semidilute polymer solution.

Pattern formation in homogeneous polymer solutions induced by a continuous-wave visible laser.

We report an unexpected nonphotothermal material organization induced by continuous-wave visible laser light at low power levels. This effect is observed along the laser beam propagation direction in fully transparent entangled solutions of common homopolymers featuring sufficiently high molecular mass and optical anisotropy along the chain backbone. The resulting formation of long-lived stringlike or dotlike patterns on the micrometer scale, probed by dark-field coherent imaging, depends on the molecular mass, architecture, solvent nature, and polymer concentration. Electrostrictive and alignment forces as well as chain cooperativity are responsible for the osmotic compression of the polymer solute. Subsequent waveguiding effects induce autoamplification and "pattern writing" upon prolonged illumination. This wave-medium coupling could potentially lead to photorefractive, microoptics, and nanotechnology applications.

Metal-modified nucleobase sextet: joining four linear metal fragments (trans-a2PtII) and six model nucleobases to an exceedingly stable entity.

Crosslinking of three different model nucleobases (9-ethyladenine, 9-EtA; 9-ethylguanine, 9-EtGH; 1-methyluracil, 1-MeU) by two linear trans-aPtII (a = NH3 or CH3NH2) entities leads to a flat metal-modified base triplet, trans,trans-[(NH3)2Pt(1-MeU-N3)(mu-9-EtA-N7,N1)Pt(CH3NH2)2(9-EtGH-N7)]3+ (4b). Upon hemideprotonation of the 9-ethylguanine base at the N1 position. 4b spontaneously dimerizes to the metalated nucleobase sextet 5, [(4b)(triple bond)(4b-H)]5+. In this dimeric structure a neutral and an anionic guanine ligand, which are complementary to each other, are joined through three H bonds and additionally by two H bonds between guanine and uracil nucleobases. Four additional interbase H bonds maintain the approximate coplanarity of all six bases. The two base triplets form an exceedingly stable entity (KD = 500 +/- 150 M(-1) in DMSO), which is unprecedented in nucleobase chemistry. The precursor of 4b and several related complexes are described and their structures and solution properties are reported.

Metal ion binding sites in a group II intron core.

Group II introns are catalytic RNA molecules that require divalent metal ions for folding, substrate binding, and chemical catalysis. Metal ion binding sites in the group II core have now been elucidated by monitoring the site-specific RNA hydrolysis patterns of bound ions such as Tb(3+) and Mg(2+). Major sites are localized near active site elements such as domain 5 and its surrounding tertiary interaction partners. Numerous sites are also observed at intron substructures that are involved in binding and potentially activating the splice sites. These results highlight the locations of specific metal ions that are likely to play a role in ribozyme catalysis.

Effects of N7-methylation, N7-platination, and C8-hydroxylation of guanine on H-bond formation with cytosine: platinum coordination strengthens the Watson-Crick pair.

The hydrogen bonding properties of 1-methylcytosine (1-MeC) with the following guanine base derivatives have been studied in DMSO-d6, applying concentration-dependent 1H NMR spectroscopy: 9-ethylguanine, 7,9-dimethylguanine (7,9-DimeGH+), and 7,8-dihydro-8-oxo-9-methylguanine (8-O-9-MeGH), as well as three 9-ethylguanine complexes carrying different Pt(II) moieties at the N7 position. The association constants K for the Watson-Crick pairing schemes are by a factor 2-3 higher in the cases of platinated guanine complexes compared to the Watson-Crick pair between 9-ethylguanine and 1-methylcytosine (K = 6.9 +/- 1.3 M(-1)). Similar enhanced stabilities are observed for the pairs formed between 1-MeC and 7,9-DimeGH+ or 8-O-9-MeGH. The increase in N1H acidity of the guanine derivative upon modification at the N7 or C8 positions can be correlated with the association constants K; the result is a bell-shaped curve meaning that acidification initially stabilizes hydrogen bond formation up to a certain maximum; further acidification then leads to a destabilization. For two of the examples studied in solution, hydrogen bonding according to Watson-Crick between N7-platinated 9-ethylguanine and 1-methylcytosine has also been established by X-ray crystallography.

Heavy metal mutagenicity: insights from bioinorganic model chemistry.

The mutagenicity of metal species may be the result of a direct interaction with the target molecule DNA. Possible scenarios leading to nucleobase mispairing are discussed, and selected examples are presented. They include changes in nucleobase selectivity as a consequence of alterations in acid-base properties of nucleobase atoms and groups involved in complementary H bond formation, guanine deprotonation, and stabilization of rare nucleobase tautomers by metal ions. Oxidative nucleobase damage brought about by metal species will not be considered.