Projects
Name
Computational analysis of interaction between Echinococcus granulosus lipid binding proteins (LBPs) with variants of vegetable oils using computational chemistry tools, exploring alternative therapies for Hydatid disease.
University
Universidad Catolica de Santa Maria
Domain
Biotechnologies and Informatics
Departement
Centro de Investigación en Ingeniería Molecular, Universidad Católica de Santa María Urb. San José, s/n, Umacollo, Arequipa.
Head
Badhin Gómez Valdez PhD.
Tutor
Badhin Gómez Valdez PhD.
Languages
Spanish, English, Portuguese, French.
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
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Type of Research Project
- Basic science
What is the background of the project?
Hydatid disease or echinococcosis is a health problem of global distribution, with greater impact in developing countries; so, it is considered within neglected or neglected diseases. The study of the metabolism of the parasites helps us to understand their relationship with the host in depth, thus contributing to the control and impact of the disease on health. There are fundamental components of metabolism without which the parasite could not live: carbohydrates, lipids and proteins. Lipids in E. granulosus fulfill the function of forming biological membranes that delimit the cells and their intra-cellular compartments; the limitation of these is that they do not can synthesize them, so they must acquire them from the host to supplement their absence. This project pretend to approach through theoretical chemistry, the physical chemistry information, kinetics and global and local chemical reactivity of different fatty acids from vegetable origin interacting with lipid binding proteins from E. granulosus. In addition, information related to the interaction with the binding proteins to lipids of Echinococcus granulosus, using quantum mechanical approaches in the context of the Density Functional Theory, Parr-Pearson theory of chemical reactivity and classical molecular dynamics simulations in a canonical ensemble. All structures of the lipid binding proteins will be optimized in the context of the solvent effect to obtain the most probable structure using Classical Mechanics techniques. The fatty acids will be stabilized using Quantum Mechanics techniques, making use of the Functional Theory of Density. The optimal structures will then be evaluated by Molecular Coupling.
What is the aim of the project?
This project pretend to approach through theoretical chemistry, the physical chemistry information, kinetics and global and local chemical reactivity of different fatty acids from vegetable origin interacting with lipid binding proteins from E. granulosus. In addition, information related to the interaction with the binding proteins to lipids of Echinococcus granulosus, using quantum mechanical approaches in the context of the Density Functional Theory, Parr-Pearson theory of chemical reactivity and classical molecular dynamics simulations in a canonical ensemble.
What techniques and methods are used?
All structures of the lipid binding proteins will be optimized in the context of the solvent effect to obtain the most probable structure using Classical Mechanics techniques. The fatty acids will be stabilized using Quantum Mechanics techniques, making use of the Functional Theory of Density. The optimal structures will then be evaluated by Molecular Coupling.
What is the role of the student?
- The student will observe the practical experiments but will be highly involved in the analysis of the results
- The tasks of the student will be performed on his/her own
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
The student is expected to learn techniques of molecular mechanics and quantum mechanics. At theoretical and practical level through its application using specialized software. The student will be in charge of a high-performance computing workstation. In which you can perform all the tests (in silico). Among these are: Molecular modeling, database alignment, protein prediction, molecular docking. Initially he will be under supervision to learn the techniques, but then the student can repeat them himself.
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
The student will read recent scientific articles about the topic, the student will have two exposition in the weekly journal club, one of their about general aspects of the research topic (2nd week) and another about his/her work (last week). The student will also be participant of the others group meeting and journal club. If the student will be coming July’s last week, he/she can attend freely the 2nd Latin American Congress on Computational Physics, Chemistry and Biology.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a poster
- The student will prepare a presentation
- The student will prepare an abstract
- The student’s name will be mentioned in a future publication
- The student will have the opportunity to present the results together with the supervisor at a conference
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
The student must have previous basic knowledge in: Molecular biology, Chemistry, Cellular Biology, Genetics.
Are there any legal limitations in the student’s involvement
No
Hours
6
Type of students accepted
This project accepts:
- Medical students
- Graduated students (less than 6 months)
- Pre-Medical students from the American-British system
- Students in biomedical fields
Articles
- DOI: 10.3389/fphys.2012.00363
- DOI: 10.1016/j.plefa.2014.08.003
- DOI: 10.1080/07391102.2012.698246