| Academic Unit: |
Computational Sciences and Engineering |
| Mode of Delivery: |
Face to face |
| Prerequisites: |
None |
| Language of Instruction: |
English |
| Level of Course Unit: |
Doctorate |
| Course Coordinator: |
Ebru Demet AKDOĞAN |
| Course Lecturer(s): |
Ebru Demet AKDOĞAN |
| Course Objectives: |
This course aims to introduce the dynamic properties of proteins. In addition, it describes the protein folding, binding, and aggregation equilibria and kinetics. It introduces the allostery in proteins which is a fundamental feature for regulating protein functions. Also, it emphasizes principles and models, as well as computational methods for simulating protein actions. |
| Course Contents: |
The lecture starts by giving a survey of some fascinating actions and mechanisms of proteins. Next, protein folding equilibria and the forces that drive folding and other actions are introduced. Some of the best-known cooperative conformational transitions such as helix-coil transformation and amyloid aggregation will be discussed. Furthermore, one of protein’s most important dynamic feature which is allostery will be introduced. In the second part, the basic principles and applications of computational modeling and simulations will be presented. Finally, the collective motions involved in protein actions will be discussed via elastic network models. |
| Learning Outcomes of the Course Unit (LO): |
- 1- Basic knowledge about protein actions and mechanisms
- 2- Basic understanding about protein folding, equilibria and the forces driving folding
- 3- Basic understanding about cooperative conformational transitions
- 4- Basic understanding about allostery in proteins
- 5- Basic understanding about computer simulation methods and conformational sampling
- 6- Able to perform Molecular Dynamics simulations
- 7- Basic understanding about collective motions and elastic network models
|
| Planned Learning Activities and Teaching Methods: |
One term project, two midterm exams, one final exam |
| Week | Subjects | Related Preperation |
LO |
| 1 |
An Introduction to Protein Actions and Mechanisms |
Reading the related chapter from textbook |
1 |
| 2 |
Project Discussion |
Installing necessary software tools |
1 |
| 3 |
Protein Folding, Equilibria and Driving Forces |
Reading the related chapter from textbook |
2 |
| 4 |
Cooperative conformational transitions |
Reading the related chapter from textbook |
3 |
| 5 |
Allostery in Proteins |
Reading the related chapter from textbook |
4 |
| 6 |
Project Discussion |
Work on project |
5 |
| 7 |
Computer Simulation Methods |
Reading the related chapter from textbook |
5,6 |
| 8 |
Midterm I |
Study of the related chapters covered in the first seven weeks |
1-5 |
| 9 |
Conformational Sampling |
Reading the related chapter from textbook |
6 |
| 10 |
Project Discussion |
Work on project |
1 - 6 |
| 11 |
Collective Motions |
Reading the related chapter from textbook |
7 |
| 12 |
Elastic Network Models |
Reading the related chapter from textbook |
7 |
| 13 |
Project Discussion |
Work on project |
1-7 |
| 14 |
Midterm II |
Study of the related chapters covered in the last five weeks |
1-7 |
At Kadir Has University, a Semester is 14 weeks; The weeks 15 and 16 are reserved for final exams.
THE RELATIONSHIP BETWEEN COURSE LEARNING OUTCOMES (LO) AND PROGRAM QUALIFICATIONS (PQ)
| # |
PQ1 |
PQ2 |
PQ3 |
PQ4 |
PQ5 |
PQ6 |
PQ7 |
PQ8 |
PQ9 |
PQ10 |
| LO1 |
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| LO2 |
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| LO3 |
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| LO4 |
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| LO5 |
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| LO6 |
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| LO7 |
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Contribution: 1 Low, 2 Average, 3 High
