subject:(Osmoprotectants)

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1. F. Dapiaggi. MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS.

Degree: 2018, Università degli Studi di Milano

In this PhD thesis computational methods have been employed in order to study different biologically relevant systems. In the first part of the thesis two Ebola virus proteins were studied, namely Viral Protein 24 (VP24) and Viral Protein 35 (VP35), responsible for the inhibition of the immune response . After a brief theoretical introduction to the main computational methods employed in the thesis, a study of VP35 in complex with small organic molecules is presented. These compounds are able to inhibit the interaction between VP35 and viral nucleoprotein. This study confirms the experimental findings highlighting new important key interactions between the protein the inhibitors. Moreover, an Essential Dynamics analysis points out an interesting collective motion of the apo-form that is hindered by the presence of the ligands. Afterwards, the protein-protein interaction VP24-Karyopherin (KPNA) is studied. An atomistic analysis of the interactions at the interface leads to the design of a nonapeptide with VP24 binding capability. The peptide is derived from a KPNA subsequence and could potentially inhibit the VP24-KPNA interaction. Subsequently an analysis on the pockets present on VP24 surface in different solvents is performed. Once the most promising pocket has been located, a virtual screening on a subset of ZINC database is carried out, leading to the identification of few classes of molecules potentially able to bind VP24. Finally the effect of the osmolytes on VP24 protein structure is studied, pointing out how osmoprotectants and urea have opposite effects on the protein, the former stabilizing the folded state and the latter shifting the equilibrium to the denatured state. In the second part of the manuscript the study of the interaction of an antimicrobial peptide with a lipid membrane is presented. This work was carried out in the University of Groningen under the supervision of Prof. Siewert Jan Marrink in order to deepen the Coarse Grain method. Advisors/Committee Members: tutor: M. Sironi, co-tutor: S. Pieraccini, coordinatore: E. Licandro, LICANDRO, EMANUELA.

Subjects/Keywords: Ebola; Virus; Computational; Chemistry; Molecular dynamics; Free energy; MMPBSA; Docking; Coarse Grain; VP24; VP35; Virtual Screening; Osmolytes; Protein; Osmoprotectants; Denaturants; Inhibitors; Peptide; Settore CHIM/02 - Chimica Fisica

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APA (6^th Edition):

Dapiaggi, F. (2018). MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/545872

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Dapiaggi, F.. “MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS.” 2018. Thesis, Università degli Studi di Milano. Accessed January 19, 2021. http://hdl.handle.net/2434/545872.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Dapiaggi, F.. “MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS.” 2018. Web. 19 Jan 2021.

Vancouver:

Dapiaggi F. MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS. [Internet] [Thesis]. Università degli Studi di Milano; 2018. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/2434/545872.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Dapiaggi F. MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS. [Thesis]. Università degli Studi di Milano; 2018. Available from: http://hdl.handle.net/2434/545872

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of the Western Cape

2. Yekwani, Khanyisa Yolanda. Physio-biochemical characterization of two wheat cultivars to Fusarium proliferatum infection .

Degree: 2019, University of the Western Cape

URL: http://hdl.handle.net/11394/7526

Wheat is a key global commodity in terms of acreage and tradeable value and as a staple in household diets. Many factors including biotic stress conditions have detrimental effects on global wheat production and yield. The increasing prevalence of biotic stress inflicted by fungal species such as Fusarium has significantly reduced yield and quality of cereal crops thus, threatening sustainable agriculture and food security. Interactions between wheat and Fusarium spp. such as Fusarium proliferatum triggers the accumulation of reactive oxygen species (ROS) to levels toxic to the plant thus leading to oxidative damage and ultimate cellular death. In order to maintain redox homeostasis, plants rely on ROS-scavenging antioxidants (enzymatic and non-enzymatic) to control ROS molecules to levels less toxic to plants. This study investigated the impact of F. proliferatum on the physio-biochemical responses of two wheat cultivars (SST 015 and SST 088). Changes in seed germination, growth, biomass, chlorophyll and mineral contents were monitored. Furthermore, changes in ROS accumulation and antioxidant enzyme activity was measured in the shoots of both wheat cultivars. Advisors/Committee Members: Klein, Ashwil (advisor), Bangani, Xolisa (advisor).

Subjects/Keywords: Mineral nutrients; Seed germination; Antioxidant enzymes; Cell death; Lipid peroxidation; Reactive oxygen species; Osmoprotectants; Photosynthetic metabolism; Plant growth parameters; Triticum aestivum L. (Wheat); Fusarium proliferatum; Biotic stress Fusarium

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Yekwani, K. Y. (2019). Physio-biochemical characterization of two wheat cultivars to Fusarium proliferatum infection . (Thesis). University of the Western Cape. Retrieved from http://hdl.handle.net/11394/7526

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yekwani, Khanyisa Yolanda. “Physio-biochemical characterization of two wheat cultivars to Fusarium proliferatum infection .” 2019. Thesis, University of the Western Cape. Accessed January 19, 2021. http://hdl.handle.net/11394/7526.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yekwani, Khanyisa Yolanda. “Physio-biochemical characterization of two wheat cultivars to Fusarium proliferatum infection .” 2019. Web. 19 Jan 2021.

Vancouver:

Yekwani KY. Physio-biochemical characterization of two wheat cultivars to Fusarium proliferatum infection . [Internet] [Thesis]. University of the Western Cape; 2019. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/11394/7526.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yekwani KY. Physio-biochemical characterization of two wheat cultivars to Fusarium proliferatum infection . [Thesis]. University of the Western Cape; 2019. Available from: http://hdl.handle.net/11394/7526

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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