- Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome. [Journal Article]
- CONCLUSIONS: The bioinformatics approaches were efficient in generating three-dimensional models and to identify domains, thereby enabling to propose possible functions for the putative polypeptides produced by the ORFs wsv129, wsv178, wsv249, wsv463a, wsv477, wsv479, wsv492, and wsv497.
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- Effect of low complexity regions within the PvMSP3α block II on the tertiary structure of the protein and implications to immune escape mechanisms. [Journal Article]
- CONCLUSIONS: The findings indicate that PvMSP3α block II possesses LCRs which might confer a strong phenotypic plasticity. The phenomenon of phenotypic plasticity and implication of LCRs in malaria immunology in general and vaccine candidate genes in particular merits further exploration.
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- QRNAS: software tool for refinement of nucleic acid structures. [Journal Article]
- CONCLUSIONS: We demonstrate the ability of QRNAS to improve the quality of models generated with different methods. QRNAS was able to improve MolProbity scores of NMR structures, as well as of computational models generated in the course of the RNA-Puzzles experiment. The overall geometry improvement may be associated with increased model accuracy, especially on the level of correctly modeled base-pairs, but the systematic improvement of root mean square deviation to the reference structure should not be expected. The method has been integrated into a computational modeling workflow, enabling improved RNA 3D structure prediction.
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- Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region. [Journal Article]
- CONCLUSIONS: The identification of a predicted oligomerization region in the human THAP protein family opens new directions to investigate the members of this protein family.
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- A new technique for predicting intrinsically disordered regions based on average distance map constructed with inter-residue average distance statistics. [Journal Article]
- CONCLUSIONS: Our technique can predict the location of an intrinsically disordered region in a protein with an accuracy comparable to the best techniques proposed so far. Furthermore, it can also predict a core region of IDPs forming definite 3D structures through interactions, such as dimerization. The technique in our study may also serve as a means of predicting a disordered region which would become an ordered structure when binding to another protein.
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- Crystal structure of E. coli PRPP synthetase. [Journal Article]
- CONCLUSIONS: Overall, this study details key structural features of an enzyme that catalyzes a critical step in nucleotide metabolism. This work provides a framework for future studies of this important protein and, as nucleotides are critical for viability, may serve as a foundation for the development of novel anti-bacterial drugs.
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- The human transketolase-like proteins TKTL1 and TKTL2 are bona fide transketolases. [Journal Article]
- CONCLUSIONS: Our data support the hypothesis that TKTL1 and TKTL2 are functional transketolases and represent novel therapeutic targets for diabetes and cancer.
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- Deciphering evolution of immune recognition in antibodies. [Journal Article]
- CONCLUSIONS: The findings of this study highlight basic structural principles shaping the molecular evolution of a lineage for significantly diverse antigens. Antibodies of a lineage follow different developmental pathways while preserving the imprint of the germline. From the study, it can be generalized that structural diversification of the paratope is an outcome of natural selection of a conformation from an available ensemble, which is further optimized for antigen interaction. The study establishes that starting from a common lineage, antibodies can mature to recognize a wide range of antigens. This hypothesis can be further tested and validated experimentally.
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- Cryo-electron microscope image denoising based on the geodesic distance. [Journal Article]
- CONCLUSIONS: The main contribution of the proposed model is to apply the geodesic distance to measure the similarity of image blocks. We conclude that manifold learning methods can effectively eliminate the noise of the cryo-EM image and improve the accuracy of particle picking.
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- Novel features in the structure of P-glycoprotein (ABCB1) in the post-hydrolytic state as determined at 7.9 Å resolution. [Journal Article]
- CONCLUSIONS: The structural data imply that (i) a low basal ATPase activity is ensured by steric blockers of NBD dimerization and (ii) allocrite access to the central cavity may be structurally linked to NBD dimerization, giving insights into the mechanism of drug-stimulation of P-glycoprotein activity.
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- An improved protein structure evaluation using a semi-empirically derived structure property. [Journal Article]
- CONCLUSIONS: In this work, a semi-empirical methodological approach was provided for improving protein structure evaluation. It showed that, once structure models of a protein were obtained through homology technique, the problem of selection of a best model out of a confusion set of Pareto-optimal structures could be resolved by employing a structure agent directly obtainable through experiment with the same protein as experimental ingredient. Overall, in the backdrop of getting a reasonably accurate protein structure of pathogens causing epidemics or biological warfare, such approach could be of use as a plausible solution for fast drug design.
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- Comparative analysis of interactions between aryl hydrocarbon receptor ligand binding domain with its ligands: a computational study. [Journal Article]
- CONCLUSIONS: The data presented in this study provide a structural understanding of AhR with its ligands and set the basis for its functions in several pathways and their related diseases.
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- Crystal structure of carbonic anhydrase CaNce103p from the pathogenic yeast Candida albicans. [Journal Article]
- CONCLUSIONS: CaNce103p is a β-class homotetrameric metalloenzyme composed of two homodimers. Its structure closely resembles those of other β-type carbonic anhydrases, in particular CAS1 from Sordaria macrospora. The main differences occur in the N-terminal part and the substrate tunnel. Detailed knowledge of the CaNce103p structure and the properties of the substrate tunnel in particular will facilitate design of selective inhibitors of this enzyme.
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- Computational analysis of the interactions of a novel cephalosporin derivative with β-lactamases. [Journal Article]
- CONCLUSIONS: The detailed analysis of the complexes obtained by these simulations suggests possible hints to modulate the affinity of this compound towards these enzymes, in order to develop new derivatives with improved features to escape to degradation.
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