Projects
Name
A Quantum Mechanical and Molecular Mechanical and Molecular Dynamics Simulation for plant profilins involved in allergic reactions.
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
English, Spanish, Portuguese, French
Duration
4 weeks
Availability
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
yes yes yes yes yes No yes yes yes yes No yes
Type of Research Project
- Basic science
What is the background of the project?
Allergies are a considerable health problem. Allergy originated in the upper airways is one of the most important at epidemiological level. There is a wide variety of natural sources from which allergens come, specifically allergens that cause respiratory diseases are called aeroallergens, because they are suspended in the atmosphere. One of the most important are profilins, proteins present in eukaryotic cells involved in the rearrangement of the cytoskeleton. In this project, we pretend obtain relevant information about the interaction between profilin with receptors present in the human body, which detonate allergic rhinitis. A molecular dynamics simulation will be done between plant profilins and their human receptors to do this we will use quantum mechanics approximations through the Density Functional Theory and Molecular Mechanics with time dependent simulations in a canonical ensemble , all in conjunction of Parr-Pearson theory of chemical reactivity.
What is the aim of the project?
In this project, we pretend obtain relevant information about the interaction between profilin with receptors present in the human body, which detonate allergic rhinitis.
What techniques and methods are used?
A molecular dynamics simulation will be done between plant profilins and their human receptors to do this we will use quantum mechanics approximations through the Density Functional Theory and Molecular Mechanics with time dependent simulations in a canonical ensemble , all in conjunction of Parr-Pearson theory of chemical reactivity.
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
- If the project includes “lab work”
- the student will take active part in the practical aspect of the project
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
Articles
- DOI: 10.1186/1710-1492-6-1
- DOI: 10.1159/000321178
- DOI: 10.1016/S0091-6749(95)70178-8
- DOI: 10.1111/all.12509