Search results for "Bilin"
showing 10 items of 377 documents
UV‐Vis Spectroscopy Reveals a Correlation Between Y263 and BV Protonation States in Bacteriophytochromes
2019
Red-light photosensory proteins, phytochromes, link light activation to biological functions by interconverting between two conformational states. For this, they undergo large-scale secondary and tertiary changes which follow small-scale Z to E bond photoisomerization of the covalently bound bilin chromophore. The complex network of amino acid interactions in the chromophore-binding pocket plays a central role in this process. Highly conserved Y263 and H290 have been found to be important for the photoconversion yield, while H260 has been identified as important for bilin protonation and proton transfer steps. Here, we focus on the roles these amino acids are playing in preserving the chemi…
Site-by-site tracking of signal transduction in an azidophenylalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy
2021
Signal propagation in photosensory proteins is a complex and multidimensional event. Unraveling such mechanisms site-specifically in real time is an eligible but a challenging goal. Here, we elucidate the site-specific events in a red-light sensing phytochrome using the unnatural amino acid azidophenylalanine, vibrationally distinguishable from all other protein signals. In canonical phytochromes, signal transduction starts with isomerization of an excited bilin chromophore, initiating a multitude of processes in the photosensory unit of the protein, which eventually control the biochemical activity of the output domain, nanometers away from the chromophore. By implementing the label in pri…
Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes
2015
In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝn space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝn space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragme…
Atom-based Stochastic and non-Stochastic 3D-Chiral Bilinear Indices and their Applications to Central Chirality Codification
2006
Abstract Non-stochastic and stochastic 2D bilinear indices have been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. In order to evaluate the effectiveness of this novel approach in drug design we have modeled the angiotensin-converting enzyme inhibitory activity of perindoprilate's σ-stereoisomers combinatorial library. Two linear discriminant analysis models, using non-stochastic and stochastic linear indices, were obtained. The models had shown an accuracy of 95.65% for the training set and 100% for the external prediction set. Next the prediction of the σ-receptor antagonists of chiral 3-(3-hydroxypheny…
Nucleotide's bilinear indices: Novel bio-macromolecular descriptors for bioinformatics studies of nucleic acids. I. Prediction of paromomycin's affin…
2009
A new set of nucleotide-based bio-macromolecular descriptors are presented. This novel approach to bio-macromolecular design from a linear algebra point of view is relevant to nucleic acids quantitative structure-activity relationship (QSAR) studies. These bio-macromolecular indices are based on the calculus of bilinear maps on Re(n)[b(mk)(x (m),y (m)):Re(n) x Re(n)--Re] in canonical basis. Nucleic acid's bilinear indices are calculated from kth power of non-stochastic and stochastic nucleotide's graph-theoretic electronic-contact matrices, M(m)(k) and (s)M(m)(k), respectively. That is to say, the kth non-stochastic and stochastic nucleic acid's bilinear indices are calculated using M(m)(k)…
Phycocyanobilin in solution – a solvent triggered molecular switch
2014
We present a computational investigation of the conformational response of phycocyanobilin (PCB) to the ability of solvents to form hydrogen bonds. PCB is the chromophore of several proteins in light harvesting complexes. We determine the conformational distributions in different solvents (methanol and hexamethylphosphoramide HMPT) by means of ab initio molecular dynamics simulations and characterize them via ab initio calculations of NMR chemical shift patterns. The computed trajectories and spectroscopic fingerprints illustrate that the energy landscape is very complex and exhibits various conformations of similar energy. We elucidate the strong influence of the solvent characteristics on…
Divvalodības ietekme 5-7 gadus vecu bērnu valodas apguvē
2021
Maģistra darba nosaukums ir "Divvalodības ietekme 5-7 gadus vecu bērnu valodas apguvē". Divvalodība lēnām kļūst par normu visā pasaulē. Tāpēc autore šo maģistra darbu ir veltījusi divvalodībai un tās ietekmei uz valodas apguvi maziem bērniem. Šī pētījuma mērķis ir salīdzināt vienvalodu un divvalodu valodas apguvi un ieskicēt to līdzības un atšķirības, apsverot, vai bilingvisms pozitīvi vai negatīvi atspoguļo valodas apguves procesu. Lai sasniegtu šo mērķi, autore ir veikusi teorētisku pētījumu par galveno jautājumu, proti, vai divvalodība kaut kādā veidā atspoguļo valodas apguves procesu. Līdz ar to ir veikts empīriskais pētījums, lai teorētiskās atziņas aizstāvētu ar empīriskiem rezultātie…
Skolotāju pedagoģiskās darbības salīdzinoša analīze latviešu un mazākumtautību sākumskolu klasēs: sociālā pedagoģija
2006
Multivariate SPC of a sequencing batch reactor for wastewater treatment
2007
Data from a sequencing batch reactor (SBR) operated for enhanced biological phosphorus removal from wastewater have been analysed in order to propose an efficient MSPC scheme of the process. Different multivariate bilinear approaches have been applied and compared in terms of their capabilities for on-line and off-line fault detection and diagnosis. The typical three-way data structure from a batch process was unfolded batch-wise and variable-wise. In the latter case, two models were built: with (AT) and without (WKFH) removing the main non-linear behaviour of the process data. Since the process consists of several stages, the monitoring strategies tested include: one model for all stages a…