Automated alignment-based curation of gene models in filamentous fungi
Burgt, A. van der; Severing, E.I. ; Collemare, J.A.R. ; Wit, P.J.G.M. de - \ 2014
BMC Bioinformatics 15 (2014). - ISSN 1471-2105 - 13 p.
pathogen fusarium-graminearum - ab-initio - genome - prediction - introns
Background Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming process that requires skilled biologists and is only marginally performed. The wealth of available fungal genomes has not yet been exploited by an automated method that applies quality control of gene models in order to obtain more accurate genome annotations. Results We provide a novel method named alignment-based fungal gene prediction (ABFGP) that is particularly suitable for plastic genomes like those of fungi. It can assess gene models on a gene-by-gene basis making use of informant gene loci. Its performance was benchmarked on 6,965 gene models confirmed by full-length unigenes from ten different fungi. 79.4% of all gene models were correctly predicted by ABFGP. It improves the output of ab initio gene prediction software due to a higher sensitivity and precision for all gene model components. Applicability of the method was shown by revisiting the annotations of six different fungi, using gene loci from up to 29 fungal genomes as informants. Between 7,231 and 8,337 genes were assessed by ABFGP and for each genome between 1,724 and 3,505 gene model revisions were proposed. The reliability of the proposed gene models is assessed by an a posteriori introspection procedure of each intron and exon in the multiple gene model alignment. The total number and type of proposed gene model revisions in the six fungal genomes is correlated to the quality of the genome assembly, and to sequencing strategies used in the sequencing centre, highlighting different types of errors in different annotation pipelines. The ABFGP method is particularly successful in discovering sequence errors and/or disruptive mutations causing truncated and erroneous gene models. Conclusions The ABFGP method is an accurate and fully automated quality control method for fungal gene catalogues that can be easily implemented into existing annotation pipelines. With the exponential release of new genomes, the ABFGP method will help decreasing the number of gene models that require additional manual curation.
Improving the Capture of Co2 by Substituted Monoethanolamines: Electronic Effects of Fluorine and Methyl Substituents
Gangarapu, S. ; Marcelis, A.T.M. ; Zuilhof, H. - \ 2012
ChemPhysChem 13 (2012)17. - ISSN 1439-4235 - p. 3973 - 3980.
main-group thermochemistry - free-energy perturbations - gas-phase basicities - ab-initio - noncovalent interactions - carbon-dioxide - amines - molecules - absorption - accuracy
The influence of electronic and steric effects on the reaction between CO(2) and monoethanolamine (MEA) absorbents is investigated using computational methods. The pK(a) of the alkanolamine, the reaction enthalpy for carbamate formation, and the hydrolytic carbamate stability are important factors for the efficiency of CO(2) capture. The steric and electronic effects of CH(3), CH(2)F, CHF(2), CF(3), F, dimethyl, difluoro, and bis(2-trifluoromethyl) substituents at the a carbon of MEA on this reaction are investigated. Density functional theory (DFT) (B3LYP, M06-2X, M08-HX and M11-L) and ab initio methods [spin component-scaled second-order Møller-Plesset theory (SCS-MP2), G3], each coupled with solvent models [conductor-like polarizable continuum model (CPCM) and universal solvation models (SM8 and SMD)], are shown to yield accurately calculated pK(a) values of the substituted MEAs. Specifically, G3, SCS-MP2, and M11-L methods coupled with the SMD and SM8 solvation models perform well with a mean unsigned error (MUE) of only 0.15, 0.24 and 0.25 pK(a) units, respectively. SCS-MP2 is used to calculate the reaction enthalpy for carbamate formation and the carbamate stability towards hydrolysis. With the introduction of ß-fluoro substituents (especially the CH(2) F moiety) the reaction enthalpy for the formation of carbamates can be fine-tuned to be less exothermic than that using the unsubstituted MEA. This implies a reduced energy requirement for the solvent-regeneration step in the post-combustion carbon-capture method, which is currently the energy-limiting step in efficient CO(2) capture. ß-Fluoro-substituted MEAs are also shown to form less stable carbamates than MEA. Thus, ß-fluoro-substituted MEAs display a great potential for the use in the post-combustion carbon-capture process. Finally, a clear correlation is observed between the gas-phase basicity and the tendency to form carbamates. This allows for the rapid prediction of which species will be formed experimentally, and thus the CO(2)-absorbing capacities of alkanolamines can be estimated
Quantum chemical calculation of infrared spectra of acidic groups in chabazite in the presence of water
Mihaleva, V.V. ; Santen, R.A. ; Jansen, A.P.J. - \ 2004
Journal of Chemical Physics 120 (2004)19. - ISSN 0021-9606 - p. 9212 - 9221.
neutron inelastic-scattering - hydrogen-bonded complexes - initio molecular-dynamics - density-functional theory - ab-initio - hydroxyl-groups - ft-ir - (h2o)-o-18 adsorption - h-mordenite - zeolite
The changes in the spectra of the acidic group in chabazite are studied by quantum chemical calculations. The zeolite is modeled by two clusters consisting of eight tetrahedral atoms arranged in a ring and seven tetrahedral atoms coordinated around the zeolite OH group. The potential energy and dipole surfaces were constructed from the zeolite OH stretch, in-plane and out-of-plane bending coordinates, and the intermolecular stretch coordinate that corresponds to a movement of the water molecule as a whole. Both the anharmonicities of the potential energy and dipole were taken into account by calculation of the frequencies and intensities. The matrix elements of the vibrational Hamiltonian were calculated within the discrete variable representation basis set. We have assigned the experimentally observed frequencies at ~2900, ~2400, and ~1700 cm¿1 to the strongly perturbed zeolite OH vibrations caused by the hydrogen bonding with the water molecule. The ABC triplet is a Fermi resonance of the zeolite OH stretch mode with the overtone of the in-plane bending (the A band) and the overtone of the out-of-plane bending (the C band). In the B band the stretch is also coupled with the second overtone of the out-of-plane bending. The frequencies at ~3700 and ~3550 cm¿1 we have assigned to the OH stretch frequencies of a slightly perturbed water molecule.
pi-Stacked Quadruply Hydrogen-Bonded Dimers: pi-Stacking Influences H-Bonding
Guo, D. ; Zuilhof, H. ; Sijbesma, R.P. - \ 2004
Organic Letters 6 (2004)21. - ISSN 1523-7060 - p. 3667 - 3670.
density-functional theory - ab-initio - supramolecular polymers - guanine-cytosine - base-pairs - complexes - model - systems - thymine
The effects of pi-stacking on the stability of multiply hydrogen-bonded systems are investigated using hybrid DFT calculations on pi-stacked quadruply H-bonded dimers of ureidopyrimidinone in its different tautomeric forms. Both the strengths of the hydrogen bonds and the relative occurrence of tautomers are influenced by pi-stacking; electrostatics and natural bond orbital analysis are used to explain these observations. Finally, these conclusions are independent of the precise nature of the multiply hydrogen-bonded systems, including the DNA base pairs.
The heterogeneity of the hydroxyl groups in chabazite
Mihaleva, V.V. ; Santen, R.A. ; Jansen, A.P.J. - \ 2003
Journal of Chemical Physics 119 (2003)24. - ISSN 0021-9606 - p. 13053 - 13060.
density-functional theory - initio molecular-dynamics - hydrogen-bonded complexes - bronsted acidic sites - ab-initio - methanol adsorption - zeolite catalysts - infrared-spectrum - embedded-cluster - first-principles
Two different clusters that have the topology of chabazite but different shapes have been used as a model for the Brønsted sites in chabazite. One of the clusters consists of eight tetrahedral atoms (8T) arranged in a ring and the other represents an intersection of two 8T rings. The adsorption of water and methanol on the two stable proton positions in chabazite has been studied using the B3LYP functional. The coordination of water and methanol with respect to the zeolite fragments were found to be similar, but with methanol situated closer to the acid site than water. The anharmonic zeolite OH stretch frequencies were found to be in the range of 2170¿2500 cm¿1 and 1457¿2074 cm¿1 in the presence of water and methanol, respectively. As a measure of the acidity of the bridging hydroxyl groups in chabazite the shift of the zeolite OH stretch frequency upon adsorption has been used. We have found that the proton attached to the oxygen atom O1 to be more acidic than the proton attached to the oxygen atom O3. Also, in the closed ring clusters the zeolite hydroxyl groups are more acidic than in the open clusters. This is not due to a steric effect as the orientation of the adsorbates with respect to the zeolite site is very similar for both clusters. The anharmonicities of the zeolite O¿H bond account for about 40% in the redshift upon the adsorption of water or methanol
A DFT study of methanol adsorption in 8T rings of chabazite
Mihaleva, V.V. ; Santen, R.A. ; Jansen, A.P.J. - \ 2001
The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 105 (2001)29. - ISSN 1520-6106 - p. 6874 - 6879.
initio molecular-dynamics - density-functional theory - bronsted acid sites - first-principles - ab-initio - catalytic activation - oh groups - zeolites - complexes - zsm-5
Hybrid B3LYP and gradient-corrected PW91 functionals were used for studying methanol adsorption on a zeolite cluster consisting of an 8T ring of chabazite. The comparison of the results obtained with PW91 with periodic calculations has shown that the adopted ring is an adequate approximation for the Brnsted sides in chabazite. Both physisorbed and chemisorbed methanol were found to be a minimum on the potential energy surface, with an energy difference up to 10 kJ/mol in favor of the hydrogen-bonded complex. It has been shown that compared to B3LYP, the PW91 functional overestimates the hydroxyl bond distance and underestimates the hydrogen bond distance. In the physisorbed mode, the methanol oxygen atom is strongly bonded to the zeolite proton, whereas the distance between the methanol proton and the framework oxygen atoms is 1.912-2.090 Å. We have calculated for hydrogen bonded methanol hydroxyl stretch frequencies in the intervals 3677-3582 and 2358-2187 cm-1 for the methanol and the zeolite OH bonds, respectively