Machine learning methods for prediction of disulphide bonding states of cysteine residues in proteins

The goal of this thesis work is to develop a computational method based on machine learning techniques for predicting disulfide-bonding states of cysteine residues in proteins, which is a sub-problem of a bigger and yet unsolved problem of protein structure prediction. Improvement in the prediction of disulfide bonding states of cysteine residues will help in putting a constraint in the three dimensional (3D) space of the respective protein structure, and thus will eventually help in the prediction of 3D structure of proteins. Results of this work will have direct implications in site-directed mutational studies of proteins, proteins engineering and the problem of protein folding. We have used a combination of Artificial Neural Network (ANN) and Hidden Markov Model (HMM), the so-called Hidden Neural Network (HNN) as a machine learning technique to develop our prediction method. By using different global and local features of proteins (specifically profiles, parity of cysteine residues, average cysteine conservation, correlated mutation, sub-cellular localization, and signal peptide) as inputs and considering Eukaryotes and Prokaryotes separately we have reached to a remarkable accuracy of 94% on cysteine basis for both Eukaryotic and Prokaryotic datasets, and an accuracy of 90% and 93% on protein basis for Eukaryotic dataset and Prokaryotic dataset respectively. These accuracies are best so far ever reached by any existing prediction methods, and thus our prediction method has outperformed all the previously developed approaches and therefore is more reliable. Most interesting part of this thesis work is the differences in the prediction performances of Eukaryotes and Prokaryotes at the basic level of input coding when ‘profile’ information was given as input to our prediction method. And one of the reasons for this we discover is the difference in the amino acid composition of the local environment of bonded and free cysteine residues in Eukaryotes and Prokaryotes. Eukaryotic bonded cysteine examples have a ‘symmetric-cysteine-rich’ environment, where as Prokaryotic bonded examples lack it.

Scherhaftuntersuchung zu selbstkonditionierenden Adhäsiven an Schmelz und Dentin im Vergleich zu klassischen Adhäsivsystemen der vierten und fünften Generation

Mit einem Abscherverfahren wurde in vitro die Scherhaftung (SBS) von 4 kommerziell erhältlichen Adhäsiven der 4., 5. und 6. Generation (Optibond FL, Excite, Gluma Comfort Bond, Prompt L-Pop) und 7 experimentellen Einflaschen- (Capo E1, Capo E2, Capo Water, ENA) oder selbstkonditionierenden Adhäsiven (AC, AC+Desensitizer, Resulcin Aqua Prime N) an Schmelz/Dentin untersucht.Alle Adhäsive wurden entsprechend Herstellerangaben auf flache Schmelz-/Dentinflächen appliziert. Auf alle Adhäsivflächen wurden 3,5x2mm große Tetric Ceram Prüfkörper aufgebracht. Die Proben wurden vor Thermocycling 24h in Kochsalzlösung gelagert. Anschließend wurden die SBS-Werte gemessen.Das Mehrflaschensystem Optibond (33.2/34.4) zeigte signifikant (p<0.05) höhere Werte an Schmelz und Dentin als alle experimentellen Einflaschen- und alle selbstkonditionierenden Adhäsive. Die kommerziell erhältlichen 5. Generation Bondings tendieren zu höheren Werten als die selbstkonditionierenden Adhäsive, liegen aber unter denen der 4. Generation. AC (28.1/27.0)

Interplay of pi–pi stacking and hydrogen bonding in conjugated supramolecular systems studied by solid-state NMR

In this work supramolecular organic systems based on rigid pi-conjugated building blocks and flexible side chains were studied via solid-state NMR spectroscopy. Specifically, these studies focussed on phenylene ethynylene based macrocycles, polymer systems including polythiophenes, and rod-coil copolymers of oligo(p-benzamide) and poly(ethylene glycol). All systems were studied in terms of the local order and mobility. The central topic of this dissertation was to elucidate the role of the flexible side chains in interplay of different non-covalent interactions, like pi-pi-stacking and hydrogen bonding.Combining the results of this work, it can be concluded that the ratio of the rigid block and the attached alkyl side chains can be crucial for the design of an ordered pi-conjugated supramolecular system. Through alkyl side chains, it is also possible to introduce liquid-crystalline phases in the system, which can foster the local order of the system. Moreover in the studied system longer, unbranched alkyl side chains are better suited to stabilize the corresponding aggregation than shorter, branched ones.The combination of non-covalent interactions such as pi-pi-stacking and hydrogen bonding play an important role for structure formation. However, the effect of pi-pi-stacking interaction is much weaker than the effect of hydrogen bonding and is only observed in systems with a suitable local order. Hence, they are often not strong enough to control the local order. In contrast, hydrogen bonds predominantly influence the structural organization and packing. In comparison the size of the alkyl side chains is only of minor importance. The suppression of certain hydrogen bonds can lead to completely different structures and can induce a specific aggregation behavior. Thus, for the design of a supramolecular ordered system the presence of hydrogen bonding efficiently stabilizes the corresponding structure, but the ratio of hydrogen bond forming groups should be kept low to be able to influence the structure selectively.

Push-out bond strength of CAD/CAM-ceramic luted to dentin with self-adhesive resin cements

OBJECTIVES: This study evaluated the initial and the artificially aged push-out bond strength between ceramic and dentin produced by one of five resin cements. METHODS: Two-hundred direct ceramic restorations (IPS Empress CAD) were luted to standardized Class I cavities in extracted human molars using one of four self-adhesive cements (SpeedCEM, RelyX Unicem Aplicap, SmartCem2 and iCEM) or a reference etch-and-rinse resin cement (Syntac/Variolink II) (n=40/cement). Push-out bond strength (PBS) was measured (1) after 24h water storage (non-aged group; n=20/cement) or (2) after artificial ageing with 5000 thermal cycles followed by 6 months humid storage (aged group; n=20/cement). Nonparametrical ANOVA and pairwise Wilcoxon rank-sum tests with Bonferroni-Holm adjustment were applied for statistical analysis. The significance level was set at alpha=0.05. In addition, failure mode and fracture pattern were analyzed by stereomicroscope and scanning electron microscopy. RESULTS: Whereas no statistically significant effect of storage condition was found (p=0.441), there was a significant effect of resin cement (p<0.0001): RelyX Unicem showed significantly higher PBS than the other cements. Syntac/Variolink II showed significantly higher PBS than SmartCEM2 (p<0.001). No significant differences were found between SpeedCEM, SmartCem2, and iCEM. The predominant failure mode was adhesive failure of cements at the dentin interface except for RelyX Unicem which in most cases showed cohesive failure in ceramic. SIGNIFICANCE: The resin cements showed marked differences in push-out bond strength when used for luting ceramic restorations to dentin. Variolink II with the etch-and-rinse adhesive Syntac did not perform better than three of the four self-adhesive resin cements tested.

Hydrogen bonding of nucleotide base pairs: Application of the PM3 method

The ability of the pm3 semiempirical quantum mechanical method to reproduce hydrogen bonding in nucleotide base pairs was assessed. Results of pm3 calculations on the nucleotides 2′-deoxyadenosine 5′-monophosphate (pdA), 2′-deoxyguanosine 5′-monophosphate (pdG), 2′-deoxycytidine 5′-monophosphate (pdC), and 2′-deoxythymidine 5′-monophosphate (pdT) and the base pairs pdA–pdT, pdG–pdC, and pdG(syn)–pdC are presented and discussed. The pm3 method is the first of the parameterized nddo quantum mechanical models with any ability to reproduce hydrogen bonding between nucleotide base pairs. Intermolecular hydrogen bond lengths between nucleotides displaying Watson–Crick base pairing are 0.1–0.2 Å less than experimental results. Nucleotide bond distances, bond angles, and torsion angles about the glycosyl bond (χ), the C4′C5′ bond (γ), and the C5′O5′ bond (β) agree with experimental results. There are many possible conformations of nucleotides. pm3 calculations reveal that many of the most stable conformations are stabilized by intramolecular CHO hydrogen bonds. These interactions disrupt the usual sugar puckering. The stacking interactions of a dT–pdA duplex are examined at different levels of gradient optimization. The intramolecular hydrogen bonds found in the nucleotide base pairs disappear in the duplex, as a result of the additional constraints on the phosphate group when part of a DNA backbone. Sugar puckering is reproduced by the pm3 method for the four bases in the dT–pdA duplex. pm3 underestimates the attractive stacking interactions of base pairs in a B-DNA helical conformation. The performance of the pm3 method implemented in SPARTAN is contrasted with that implemented in MOPAC. At present, accurate ab initio calculations are too timeconsuming to be of practical use, and molecular mechanics methods cannot be used to determine quantum mechanical properties such as reaction-path calculations, transition-state structures, and activation energies. The pm3 method should be used with extreme caution for examination of small DNA systems. Future parameterizations of semiempirical methods should incorporate base stacking interactions into the parameterization data set to enhance the ability of these methods.

Ability of the PM3 Quantum Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules

The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-' suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-' imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-l. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and 0 predict that donor strength follows the order F > 0 > N and acceptor strength follows the order N > 0 > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H- - -N bond to be the strongest and the N-H- - -F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems.

N-H center dot center dot center dot pi hydrogen-bonding and large-amplitude tipping vibrations in jet-cooled pyrrole-benzene

The N-H center dot center dot center dot pi hydrogen bond is an important intermolecular interaction in many biological systems. We have investigated the infrared (IR) and ultraviolet (UV) spectra of the supersonic-jet cooled complex of pyrrole with benzene and benzene-d(6) (Pyr center dot Bz, Pyr center dot Bz-d(6)). DFT-D density functional, SCS-MP2 and SCS-CC2 calculations predict a T-shaped and (almost) C(s) symmetric structure with an N-H center dot center dot center dot pi hydrogen bond to the benzene ring. The pyrrole is tipped by omega(S(0)) = +/- 13 degrees relative to the surface normal of Bz. The N center dot center dot center dot ring distance is 3.13 angstrom. In the S(1) excited state, SCS-CC2 calculations predict an increased tipping angle omega(S(1)) = +/- 21 degrees. The IR depletion spectra support the T-shaped geometry: The NH stretch is redshifted by -59 cm(-1), relative to the "free" NH stretch of pyrrole at 3531 cm(-1), indicating a moderately strong N-H center dot center dot center dot pi interaction. The interaction is weaker than in the (Pyr)(2) dimer, where the NH donor shift is -87 cm(-1) [Dauster et al., Phys. Chem. Chem. Phys., 2008, 10, 2827]. The IR C-H stretch frequencies and intensities of the Bz subunit are very similar to those of the acceptor in the (Bz)(2) dimer, confirming that Bz acts as the acceptor. While the S(1) <- S(0) electronic origin of Bz is forbidden and is not observable in the gas-phase, the UV spectrum of Pyr center dot Bz in the same region exhibits a weak 0(0)(0) band that is red-shifted by 58 cm(-1) relative to that of Bz (38 086 cm(-1)). The origin appears due to symmetry-breaking of the p-electron system of Bz by the asymmetric pyrrole NH center dot center dot center dot pi hydrogen bond. This contrasts with (Bz)(2), which does not exhibit a 0(0)(0) band. The Bz moiety in Pyr center dot Bz exhibits a 6a(0)(1) band at 0(0)(0) + 518 cm(-1) that is about 20x more intense than the origin band. The symmetry breaking by the NH center dot center dot center dot pi hydrogen bond splits the degeneracy of the v(6)(e(2g)) vibration, giving rise to 6a' and 6b' sub-bands that are spaced by similar to 6 cm(-1). Both the 0(0)(0) and 6(0)(1) bands of Pyr center dot Bz carry a progression in the low-frequency (10 cm(-1)) excited-state tipping vibration omega', in agreement with the change of the omega tipping angle predicted by SCS-MP2 and SCS-CC2 calculations.

Micromorphology and adhesive performance of Er:YAG laser-treated dentin of primary teeth

This study evaluated (1) the micromorphology by scanning electron microscopy (SEM) and (2) the adhesive performance by microtensile bond strength (μTBS) of diamond bur-treated dentin compared to Er:YAG laser-treated dentin of human primary teeth. (1) For qualitative SEM evaluation, dentin of 18 second primary molars (n = 3/method) was treated with either diamond bur as a control (group 1a: 40 μm diamond bur only (clinical situation); group 1b: grinding + 40 μm diamond bur) or with Er:YAG laser (group 2a (clinical situation, manufacturer's settings): 200 mJ/25 Hz (5 W) + 100 mJ/35 Hz (3.5 W) laser only; group 2b (experimental setting "high"): grinding + 400 mJ/20 Hz (8 W); group 2c (manufacturer's setting "finishing"): grinding + 100 mJ/35 Hz (3.5 W); group 2d (experimental setting "low"): grinding + 50 mJ/35 Hz (1.75 W)). (2) For evaluation of adhesive performance, 64 second primary molars were divided into four groups and treated as described for group 1b and groups 2b/c/d (n = 16/method), and μTBS of Clearfil SE/Clearfil Majesty Esthetic to dentin was measured. The SEM micrographs were qualitatively analyzed. The μTBS values were compared with a Kruskal-Wallis test. The significance level was set at α = 0.05. SEM micrographs showed the typical micromorphologies with a smear layer for the diamond bur groups and open dentin tubules for all laser-treated groups. However, in group 2d, the laser beam had insufficiently irradiated the dentin area, rendering the underlying ground surface partly visible. There were no statistically significant differences between μTBS values of the four groups (p = 0.394). This suggests that Er:YAG laser treatment of dentin of primary molars provides bond strengths similar to those obtained following diamond bur treatment.

Irregularities below the Enamel-Dentin Junction May Predispose for Fissure Caries

This study investigated the structure of the fissure fundus on occlusal surfaces with respect to the detection of possible irregularities below the enamel-dentin junction (EDJ). Occlusal surfaces were examined by micro-computed tomography (µCT). In total, 203 third molars with clinically sound occlusal fissures or non-cavitated lesions were selected. All specimens were scanned with µCT. Subsequently, each tooth was sectioned, and each slice was investigated by stereomicroscopy. In 7 of 203 molars (3.4%), demarcated radiolucencies below the EDJ were detected by µCT. These defects were obviously of non-carious origin, because the µCT images revealed no gradient of demineralization in the dentin. In all cases, a direct pathway between the oral cavity and the dentin was evident. The comparison of the µCT sites with conventional histological images also revealed defects in the dentin. These results demonstrate that demarcated radiolucencies below the EDJ may not necessarily be caries lesions according to µCT images and may be classified as possible developmental irregularities. To avoid misinterpreting µCT data, dental researchers should carefully consider this condition when analyzing µCT images. The clinical significance of this finding is that these defects may predispose molar teeth to early-onset caries in occlusal pits and fissures.

Self-etch primers and conventional acid-etch technique for orthodontic bonding: a systematic review and meta-analysis

The use of self-etch primers has increased steadily because of their time savings and greater simplicity; however, overall benefits and potential disadvantages and harms have not been assessed systematically. In this study, we reviewed randomized controlled trials to assess the risk of attachment failure, bonding time, and demineralization adjacent to attachments between 1-stage (self-etch) and 2-stage (acid etch) bonding in orthodontic patients over a minimum follow-up period of 12 months.