Theoretical and practical course in protein biochemistry, biophysics and structural biology
Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos
Faculdade de Medicina de Ribeirão Preto, 20 to 31 March 2023
This practical course was made possible thanks to generous support from the Brazilian Federal Foundation for Support and Evaluation of Graduate Education (CAPES 88887.717453/2022-00) and the Royal Society (ICA\R1\201019).
All of the course material is distrubuted under a CC BY 4.0 license. You are welcome to share and adapt them so long as you acknowledge the source. If you would like the original powerpoint copies of the talks please contact Stephen.
In case you're interested in how the course was received, you can download a summary of feedback from our anonymous exit survey. Pleasingly, all the students would strongly recommend the course to their colleagues.
Photos
Photos from the course can be found here.
Course material
- Course Practical Handbook and biochemical calculations answer sheet
- Computer Lab Handbook and 3ogo phases (for COOT tutorial)
- Seminar #1: Protein expression systems
- Seminar #2: Bioinformatics for protein expression
- Seminar #3: Protein purification 1: Lysis and affinity capture
- Seminar #4: Protein purification 2: Size exclusion and other chromatography
- Seminar #5: Protein purification 3: Quality control
- Seminar #6: Biochemistry of protein interactions
- Seminar #7: Biophysics of protein interactions
- Workshop: SPR (Biacore) analysis
- Seminar #8: Visualising protein structures
- Seminar #9: Protein structure determination
- Seminar #10: Protein structure prediction
Useful software links
- ProtParam: https://web.expasy.org/protparam/
- ApE plasmid editor: https://jorgensen.biology.utah.edu/wayned/ape/
- UniProt knowledgebase: https://www.uniprot.org/
- NCBI BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi
- ChimeraX: https://www.cgl.ucsf.edu/chimerax
- COOT (main site): https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
- COOT (WinCOOT download): http://bernhardcl.github.io/coot/wincoot-download.html
- COOT (MacOS instructions): https://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot
- AlphaFold: https://github.com/deepmind/alphafold
- ColabFold: https://github.com/sokrypton/ColabFold
Size exclusion chromatography (SEC) traces
| EGFP | csv | |
| mTurquoise2 | csv | |
| mVenus | csv | |
| mCherry | csv | |
| anti-GFP nanobody | csv |
SPR sensorgrams
- Sensorgram #1: Ligand capture (FC1 = 12.2 ng/mL GST, FC2 = 13.5 ng/mL antiGFPnano-GST)
- Sensorgram #2: Ligand capture (repeat, FC1 = 12.3 ng/mL GST)
- Sensorgram #3: Regeneration scouting 1 (10 nM GFP; 10 mM Gly pH 2.2, 2.1, 2.0 for 20 s, 100 mM Gly for 5 s or 15 s)
- Sensorgram #4: Regeneration scouting 2 (10 nM GFP; 100, 200 and 500 mM Gly pH 2.0 for 2×5 s)
- Sensorgram #5: Kinetic binding (2 nM to 15.6 pM EGFP, mVenus, mTurquoise2 and mCherry)
- Analysis: Kinetic analysis
Vector maps
If you would like an aliquot of these vectors please contact Luis (Latin America) or Stephen (rest of world).| His6-EGFP | His6-mTurquoise2 | His6-mVenus | His6-mCherry | antiGFPnanobody-GST | GST-3Cprotease |
Other
- AKTA Start cheat sheet
- List of equipment and consumables required to host the course