Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

BACKGROUND: Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which proteins operate. Despite recent advances in the development of new methods to model macromolecular assemblies, most current methodologies are designed to work with experimentally determined protein structures. However, because only computer-generated models are available for a large number of proteins in a given genome, computational tools should tolerate structural inaccuracies in order to perform the genome-wide modeling of PPIs. RESULTS: To address this problem, we developed eRank(PPI), an algorithm for the identification of near-native conformations generated by protein docking using experimental structures as well as protein models. The scoring function implemented in eRank(PPI) employs multiple features including interface probability estimates calculated by eFindSite(PPI) and a novel contact-based symmetry score. In comparative benchmarks using representative datasets of homo- and hetero-complexes, we show that eRank(PPI) consistently outperforms state-of-the-art algorithms improving the success rate by ~10 %. CONCLUSIONS: eRank(PPI) was designed to bridge the gap between the volume of sequence data, the evidence of binary interactions, and the atomic details of pharmacologically relevant protein complexes. Tolerating structure imperfections in computer-generated models opens up a possibility to conduct the exhaustive structure-based reconstruction of PPI networks across proteomes. The methods and datasets used in this study are available at www.brylinski.org/erankppi

CHAPTER 11: Molecular Docking Studies of Curcumin

Computation, such as high-throughput screening and virtual screening, which are essential tools of modern drug discovery research, has an important role in drug discovery. Molecular docking is an in silico method used to develop the homology model for a novel drug candidate. Due to the fact that curcumin is a well-known drug, molecular docking in that context can be performed either for investigating the binding capacities of curcumin with novel targeted molecules or for curcumin analogs. Molecular docking is very useful and reasonably reliable for predicting putative binding interactions, activities and affinities of drugs for macromolecules like proteins. © 2021 The Royal Society of Chemistry

CHAPTER 9: Biosynthesis of Curcumin and Molecular Targets and the Biological Mechanism of Curcumin

The biosynthesis of curcumin can be viewed from different perspectives, a natural pathway in Curcuma Longa (turmeric) and artificial pathways in Oryza sativa (rice) and rice bran pitch respectively, using Esterichia coli (E. Coli). The natural pathway for the synthesis of curcumin can be divided into two, an upstream and a downstream section. The transcription factor nuclear factor B (NF-B) governs several cellular signaling pathways associated with cancer, and targets various cytokines, proinflammatory molecules, growth factors, cell adhesion molecules, oncogenes and pro/anti-apoptotic proteins during carcinogenesis. Curcumin targets the transcription factors, protein kinases (PKs), angiogenesis, cell cycle regulators, sirtuins, NF-B signaling pathway, E-cadherin, vascular endothelial growth factor (VEGF), signal transducers and activators of the transcription 3 (STAT-3) signaling pathway, B-cell lymphoma (Bcl-2), p53, DNA, microRNA (miRNA), apoptosis and autophagy. The biological mechanism comprises different activities that are antioxidant, anticancer, antiviral, antifungal, antiproliferative, anti-immunomodulatory and anti-inflammatory. The main focus of this chapter is to provide valuable information on the biological synthesis, biological mechanism and molecular targets of curcumin. © 2021 The Royal Society of Chemistry

Penetration and release studies of positively and negatively charged nanoemulsions - Is there a benefit of the positive charge?

PubMed ID: 22486953The surface of all tissues, including the stratum corneum, carries a negative charge. Following that fact it is assumed that a positively charged topical formulation could lead to an enhanced penetration because of an increased interaction with the negative charge of the membrane. The intention of this study is to prove an enhanced penetration of a positively charged nanoemulsion compared to a negatively charged nanoemulsion, both containing prednicarbate. The release and penetration of these nanoemulsions, produced with the high pressure homogenization method, were investigated. Regarding these results reveals that the release of the negatively charged formulation is higher compared to the positively charged nanoemulsion, while the penetration of the positively charged nanoemulsion is enhanced compared to the negatively charged formulation. The results of the investigated positively charged nanoemulsion containing prednicarbate show that its topical use could be advantageous for the therapy of atopic dermatitis, especially regarding phytosphingosine, which was responsible for the positive charge. © 2012 Elsevier B.V. All rights reserved

Aleyrodidae

The adults of the Aleyrodidae (whiteflies) are small winged insects usually yellow-white in colour; some species bear grey marks on the wings or are darker, even brown-black. Immatures may be misidentified as aphids or scale insects, but the “vasiform orifice” will help in separating whiteflies from other groups in slide mounted and red-stained puparia. All instars secrete wax, in the shape of powder, curls, threads or as vitreous layers. They are called “whiteflies” due to their general whitish appearance. They are mostly bisexual, but several species or “strains” show both arrhenotokous and thelytokous parthenogenesis, usually in relation to insemination. The post-embryonic development is neometabolic, consisting of four larval instars, pupae (immotile and not-feeding) and adults. Whiteflies share with other Sternorrhyncha the piercing-sucking mouthparts and the specialized “filter chamber” mid gut. They suck plant sap, killing their host plants in heavy infestations and excreting abundant liquid faeces as honeydew drops. These drops cover infested plants, which then blacken because of colonization by sooty mold fungi. The blackened plants or products are untradeable due to the sooty mold. Whiteflies may also cause physiological changes and transmit viruses. In the Mediterranean Region whiteflies live mostly on woody perennial plants. Natural or classical biological control programmes have successfully controlled current or potential pest species by the introduction of effective natural enemies. Aleurocanthus spiniferus Quaintance is currently of major concern to citriculture in the Mediterranean Region because it was recently introduced and no indigenous natural enemies seem to control it. As in the past, unwanted, introduced whiteflies may become key pests of citrus in the Mediterranean Region

Co-encapsulation of curcumin and piperin in zein-chitosane nanocapsules by electrospray

41st FEBS Congress on Molecular and Systems Biology for a Better Life -- SEP 03-08, 2016 -- Kusadasi, TURKEYWOS: 000383616901145FEB

Aleyrodidae

The adults of the Aleyrodidae (whiteflies) are small winged insects usually yellow-white in colour; some species bear grey marks on the wings or are darker, even brown-black. Immatures may be misidentified as aphids or scale insects, but the "vasiform orifice" will help in separating whiteflies from other groups in slide mounted and red-stained puparia. All instars secrete wax, in the shape of powder, curls, threads or as vitreous layers. They are called "whiteflies" due to their general whitish appearance. They are mostly bisexual, but several species or "strains" show both arrhenotokous and thelytokous parthenogenesis, usually in relation to insemination. The post-embryonic development is neometabolic, consisting of four larval instars, pupae (immotile and not-feeding) and adults. Whiteflies share with other Sternorrhyncha the piercing-sucking mouthparts and the specialized "filter chamber" mid gut. They suck plant sap, killing their host plants in heavy infestations and excreting abundant liquid faeces as honeydew drops. These drops cover infested plants, which then blacken because of colonization by sooty mold fungi. The blackened plants or products are untradeable due to the sooty mold. Whiteflies may also cause physiological changes and transmit viruses. In the Mediterranean Region whiteflies live mostly on woody perennial plants. Natural or classical biological control programmes have successfully controlled current or potential pest species by the introduction of effective natural enemies. Aleurocanthus spiniferus Quaintance is currently of major concern to citriculture in the Mediterranean Region because it was recently introduced and no indigenous natural enemies seem to control it. As in the past, unwanted, introduced whiteflies may become key pests of citrus in the Mediterranean Region. © 2012 Bentham Science Publishers. All rights reserved