Introduction of fundamental methods and techniques currently used to design protein molecules for use in biotechnology. Introduction to computational protein design and programming environments related to protein structure visualization and modification. Discussion of selected scientific papers for their fundamental relevance covering the aspects of protein design.
Prerequisite(s)
Course Code Course Name…
Corequisite(s)
Course Code Course Name…
Special Requisite(s)
The minimum qualifications that are expected from the students who want to attend the course.(Examples: Foreign language level, attendance, known theoretical pre-qualifications, etc.)
-Stefan Lutz and Uwe T. Bornscheuer (ed),Protein Engineering Handbook, Wiley, 2009.
-Carl Branden and John Tooze, Introduction to Protein Structure, Garland Publishing, 1999.
Recommended reading will be selected chapters from textbook
-Additional readings & homeworks & scientific papers will be posted online.
Other Sources
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Course Schedules
Week
Contents
Learning Methods
1. Week
Introduction. Amino acids found in proteins.
Classroom presentation
2. Week
Motifs of Protein structure. Computational protein design. Vector NTI Program
Classroom presentation. Laboratory
3. Week
Protein structure modeling: Swiss Model and Pymol
Classroom presentation. Laboratory
4. Week
Protein folding. Protein purification. Proteins as Products
Classroom presentation
5. Week
Enzyme catalysis and kinetics
Classroom presentation
6. Week
Prediction, Engineering, and Design of Protein Structures. Midterm Examination
Project
7. Week
Mutagenesis and Protein Engineering: Directed Evolution, DNA shuffling and Error Prone PCR
Classroom presentation
8. Week
Library construction methods for directed evolution. Methods of protein modification: Review Research Papers
Oral presentation
9. Week
Homology Independent in vitro Recombination Methods: Review Research Papers.
Oral presentation
10. Week
Methods of protein modification continue: Review Research Papers. Rational Protein Design: Site Directed and Saturation Mutagenesis. Review Research Papers
Oral presentation
11. Week
AutoDock Program
Laboratory
12. Week
Finding substrate channels in protein structure (CAVER)
Laboratory
13. Week
Rational Protein Design: Reshaping protein specificity, reengineering catalytic mechanisms, engineering by molecular assembling, Review Research Papers
Classroom presentation. Oral presentation
14. Week
Open for contingencies, quizzes, review, and student evaluations.
Classroom presentation
15. Week
Final Exams Week
16. Week
Final Exams Week
17. Week
Final Exams Week
Assessments
Evaluation tools
Quantity
Weight(%)
Midterm(s)
1
30
Quizzes
2
15
Homework / Term Projects / Presentations
1
25
Final Exam
1
30
Program Outcomes
PO-1
To apply all knowledge about basic sciences such as mathematics, physics, chemistry and biology to all problems in molecular biology and genetics
PO-2
To be able to identify, model and produce solutions against to problems related to molecular biology and genetics
PO-3
To start a procedure, proceed and finalize about determined problem by using analytical techniques
PO-4
To be able to understand all knowledge about living organisms which is main subject of molecular biology and genetics
PO-5
To contribute scientific research and development and add further information
PO-6
To be able to analyze data, design an experiment and proceed and annoate the results
PO-7
To be able to use current techniques and analysis methods in molecular biology and genetics
PO-8
To be able to be a part of a team in disciplinary or multidisciplinary, national or international public problems focused projects and use at least one foreign language for vocational purposes
PO-9
To be able to behave individually, take initiative and creativity skills
PO-10
To communicate briefly and clear using oral or written presentation skills to present individual working performance and independent decisions
PO-11
To carry responsibility to vocational and ethical issues
PO-12
To be aware about quality assessment
PO-13
To adopt in principle the importance of life-learning subject and graduate self-development by following new literature about field and apply current knowledge
Learning Outcomes
LO-1
Can apply computational tools to predict and analyze three dimensional structures of proteins.
LO-2
Understands the fundamental principles of protein design and methods of protein modification.
LO-3
Has the ability to objectively discuss the problem and the merits of possible solutions.
LO-4
Can organize content of a presentation or document according to the informational needs and technical background of the audience.
LO-5
Submits written work without errors in spelling, grammar, punctuation, and usage.
LO-6
Develops independence in researching current literature, patents, and design standards.
LO-7
Understands the social, cultural, political, and environmental impacts of engineering activities.
LO-8
Recognizes the structure and basic functions of DNA, RNA, and protein.
LO-9
Understand the fundamental concepts of protein structure and can apply this knowledge in designing proteins for bioengineering purposes.
LO-10
Can identify how protein structure relates to protein activity
