Breakthroughs in (non)structural characterization of macromolecules 1400-22BSCoM-en
1. Standard and non-standard protein amino acids and non-protein amino acids. First-, second-, third- and fourth-order structure of proteins; domains and motifs.
2. The life of a protein from translation to degradation. Protein folding and chaperones. Protein quality control and degradation pathways; lysosomes, proteasomes and their structure.
3. From 22 amino acids to huge proteomes. Post-translational modifications. Differences in codon distribution between organisms. Naturally occurring and artificially programmed recoding; orthogonal translation and modified ribosomes.
4. The beginnings of protein structural studies - X-ray crystallography. Nobel Prizes for hemoglobin and DNA structures. Protein Data Bank and other structural databases. How to read and understand structural data?
5. Other canonical methods of protein structure research – CryoEM and NMR. Nobel Prizes, the revolution in resolution and its consequences. Protein Data Bank and lesser-known structural
databases cd.
6. How RoseTTA and AlphaFold have influenced the development of structural biology and how can a non-structural biologist use them? Visualization of models and verification of their reliability.
7. Non-standard methods of protein structure research – MicroED, time-resolved crystallography.
How do different methods complement each other? Integrative structural biology. Structures of ribosome, spliceosome, and integrator complexes.
8. (Non-)structural biology of dynamic systems – how do we study intrinsically unstructured proteins and regions (IDPs, IDRs)? Why do classical methods of structural biology fail? Diffraction methods, XL- MS, AFM, NMR and electron microscopy.
9. The phenomenon of liquid-liquid phase separation. Membraneless compartments in the cell: stress granules, p-bodies, photobodies. Well-known and newly discovered roles of LLPS in the cell. Methods for studying LLPS.
10. Overview of the methods used for studying protein-protein interactions: in vivo, in vitro, and in silico. How can interactions be inferred from structural data, how can interaction studies supplement structural data, and what mistakes should be avoided?
11. Large-scale genomic studies (NGS, microarrays) as support for protein structural studies. Identification of genes encoding new proteins with unknown structures, identification of splicing
events and mutations affecting protein structure and activity.
12. Mass spectrometry in support for protein structural studies.
13-14. More than proteins – from small histones through nucleosomes to chromatin structure.
Koordynatorzy przedmiotu
Efekty kształcenia
Knowledge: the graduate knows and understands
K_W03 the current state of knowledge in the main areas of biotechnology; has knowledge of: scientific terminology, the latest research, discoveries and their applications in biotechnology (...)
K_W05 in depth the principles of research planning, modern data collection techniques and the use of various research tools
K_W12 specialist vocabulary in the field of natural sciences in a selected modern language (English) Skills: the graduate is able to
K_U02 use a modern language (English) at B2+ level to a degree that enables them to use scientific literature and communicate with foreigners
K_U03 critically analyze and select information, especially from electronic sources
K_U07 draw conclusions and formulate judgments based on data from various sources Social competences: the graduate is prepared to
K_K04 use objective sources of scientific information and apply the principles of critical reasoning when solving practical problems
Kryteria oceniania
To pass the course, students must obtain a minimum of 55% points from short „exit tests” held at the end of each lecture. Exit tests will contain test questions and/or open questions. Each test will be graded on a scale of 0–10 points. The final grade for the course will be the average of the results obtained, after discarding the two extreme values. The distribution of final grades will be adjusted to the results of the entire group (so-called Gaussian curve). Two absences from lectures are allowed.
Literatura
Rupp, B. Biomolecular Crystallography
1) Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). https://doi.org/10.1038/s41586-021-03819-2
2) Su, Qi et al. Liquid-liquid phase separation: Orchestrating cell signaling through time and space Molecular Cell, Volume 81, Issue 20, 4137 – 4146
3) Nannenga, B.L., Gonen, T. Publisher Correction: The cryo-EM method microcrystal electron diffraction (MicroED). Nat Methods 18, 574 (2021). https://doi.org/10.1038/s41592-021-
01114-6
4) Chin, J. Expanding and reprogramming the genetic code. Nature 550, 53–60 (2017). https://doi.org/10.1038/nature24031
5) Sun, Jing-Liang et al. Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives Molecular Plant, Volume 14, Issue 1, 95 - 114
Więcej informacji
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