週次 |
日期 |
單元主題 |
第1週 |
2/18 |
Course introduction
Protein structure (Chap 2): introduce amino acids, protein secondary structure
Build up secondary structures using amino acid models (Practice, homework)
授課老師:陳佩燁 |
第2週 |
2/25 |
Use molecular modeling software to display your protein (SwissPDBviewer) (Practice, homework)
Topology and motif
Protein folding theory, protein structural stability, protein folding kinetics
* bring laptop for in-class practices
授課老師:陳佩燁 |
第3週 |
3/04 |
Chaperone
Protein misfolding, amyloid, misfolding-related diseases
授課老師:陳佩燁 |
第4週 |
3/11 |
Understanding cell biology from structural biology aspect (Chap 11)
Importance of visualization
Seeing molecular mechanism in cell signaling
How protein kinases work
授課老師:何孟樵 |
第5週 |
3/18 |
Protein expression
Basic concept of protein biogenesis
Practical consideration of recombinant protein production
What can you do if you doesn’t get your protein
授課老師:何孟樵 |
第6週 |
3/25 |
Protein crystallography
The importance of resolution
General concept of protein crystallography
What protein crystallography can and cannot do
How to visualize/evaluate the result
授課老師:何孟樵 |
第7週 |
4/01 |
期中考 |
第8週 |
4/08 |
Protein sequence and structure
Bioinformatic analysis of sequence
Structural modeling
Intrinsically disordered protein
授課老師:吳昆峯 |
第9週 |
4/15 |
Molecular viewer introduction, PyMOL tutorial and practices
* bring laptop for in-class practices
** Homework will be assigned.
授課老師:吳昆峯 |
第10週 |
4/22 |
Protein misfolded and amyloid fibrils
Introduction of amyloid fibrils
Practical analysis of amyloid fibrils using ChimeraX and PyMOL
* bring laptop for in-class practices
** Homework will be assigned
授課老師:吳昆峯 |
第11週 |
4/29 |
Cryogenic electron microscopy
Theory and practical aspects
Biological application
Data visualization and analysis using ChimeraX
* bring laptop for in-class practices
** Homework will be assigned.
授課老師:吳昆峯 |
第12週 |
5/06 |
Principles of biomolecular NMR spectroscopy
Basic NMR experiments for protein structure determination and interactions
Advanced NMR tools for studying challenging biological systems
*Hands on exercise: visualization of membrane protein structures by PyMol
授課老師:徐尚德 |
第13週 |
5/13 |
Practical aspects of biomolecular NMR spectroscopy
Chemical shift assignments
Protein dynamics and interactions
NMR titration analysis
Protein dynamics
**Hands on exercise: deriving free energy of unfolding for individual residues by HDX data
授課老師:徐尚德 |
第14週 |
5/20 |
Structural mapping of NMR observables by PyMol
Defining binding sites by chemical shift perturbations
Describing protein dynamics by relaxation dynamics parameters – T1/T2/hetNOE and HDX
*Homework will be assigned to analyze NMR-derived information in 3D protein structures
授課老師:徐尚德 |
第15週 |
5/27 |
期末考 |