Protein structure determination and prediction
This page is organized as follows:
Keywords are terms that you need to understand to follow the lecture. To test your knowledge, try to define and explain these keywords (in a few sentences). If you cannot think of anything to say about a keyword, read up on that topic.
Under Sources you find literature we suggest (textbooks, web pages, articles) that will help you to understand the topic. You can use this as a resource to complete your knowledge of the keywords and to help you answer the questions and solve the tasks. You are not required to read and study any of these, but they provide more detailed knowledge on the topic and are a good complement to the lecture. Of course you can feel free to use any other source you like.
In the section Exercise we provide Questions and Hands-on tasks that allow you to test and further your knowledge of the given topic. During the exercise session you can ask questions pertaining to the topic (keywords and exercises).
Keywords
- Biological database: PDB
- X-ray, NMR, cryo-EM
- Structure comparison: Structural alinment, superposition, RMSD
- RMSD
- Structure comparisons: CATH, SCOP, TopSearch
- Protein domains: CATH, SCOP, TopSearch, Pfam
- HSSP-curve
- Homology modeling
- Visualisation tools
Sources
- Protein structure determination
- Protein structure determination: Short section in wikipedia
- Electron density map: Look at the second figure, especially at the yellow grid.
- Introduction to proteins: Section "What do proteins look like?" (scroll down to find the section)
- Looking at protein structures: Short introduction to molecular visualization
- Proteopedia has nice sections on protein structure in general and especially on Ramachandran Plots
- RMSD: Wikiomics
- RMSD: Wikipedia
- Structural alignment
- SCOP: Database Structural Classification of Proteins
- CATH: Database Protein Structure Classification
- HSSP-curve: In particular Figures 3 and 4
- Homology modeling
- SWISS-MODEL
Excercise
Questions
- What is the basic principle behind X-ray crystallization and NMR? Describe in 1-3 sentences/bullet points each.
- What are the main steps in X-ray crystallization?
- Which of the three methods (X-ray crystallization, NMR, cryo-EM) is the oldest one? Which one is responsible for the majority of the structures in the PDB?
- What is an electron density map?
- What is the downside of crystallizing proteins for X-ray diffraction?
- How do SCOP and CATH classify protein structures?
- What is the difference between structural and sequence alignment?
- The RMSD can measure the quality of a structural alignment. How is it calculated? What are the limitations of the RMSD?
- Is it possible to predict a protein structure from its sequence?
- What are the main steps in homology modeling?
- What are possible limitations in homology modeling?
Hands on tasks
- Generate a structural alignment using e.g. the Dali (here is the Dali pairwise comparison, on the results page check 3D superimposition) or TopMatch server
- Align: PDB IDs 3TRX and 1XWC; 1A6Z and 1BII; 1HBG and 1GDI
- For each of the protein structure pairs, find out protein name, organism of origin and function. Check e.g. PDB and UniProt
- Check the RMSD for the complete proteins and for certain regions
- Generate a homology model of ... using SWISS-MODEL
