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Advanced Courses IV

Advanced Courses IV

Code	16867
Year	1
Semester	S2
ECTS Credits	5
Workload	TP(40H)
Scientific area	Biomedicina/Medicina/Bioquímica
Entry requirements	Without requirements.
Learning outcomes	Upon successful completion of the Advanced Course IV – Medical Structural Biology course, students should be able to: 1. List the main computational biochemistry techniques for molecular simulation in protein systems. 2. Use methods for analyzing protein-protein and protein-ligand interactions to validate the kinetic and thermodynamic parameters of biomolecules in solution. 3. Analyze nucleic acid-ligand interactions using laboratory techniques for target molecule selection and structural studies. 4. Identify, in liquid chromatography, characteristics of a preparative and structurally innocuous technique for separating a complex protein mixture. 5. Describe methods for determining the three-dimensional structure of therapeutically relevant biomolecules: nucleic acids and proteins. 6. Research and critically analyze scientific articles related to the topics taught in the course.
Syllabus	1- Computational Biochemistry Module - A) Methodologies; B) Molecular Mechanics: Bond Angle Energy; Torsion Energy; Parameter Deduction; Force Fields; C) Molecular Dynamics Simulations: Equations of Motion; Long-Range Forces; Smoothing Functions; Properties (Density; Rotational Dynamics; Atomic Fluctuations; Molecular Orientation). 2- Biophysics Module in Biomolecular Recognition - A) Protein-protein and protein-ligand interactions by: Microcalorimetry and SPR using an optical biosensor; B) Nucleic Acid-Ligand Interactions: Circular Dichroism Spectroscopy to analyze DNA and RNA stability and determination of the affinity and kinetics of the biomolecule-ligand reaction by SPR to select ligands. 3- Structural Biology Module - A) Strategies for protein separation by liquid chromatography; B) Co-crystallization and Soaking; SAXS; Cryo-EM - Fundamentals, imaging methods, sample preparation, resolution limits.
Main Bibliography	1- Huynh K. and Partch C.L., “Analysis of protein stability and ligand interactions by thermal shift assay”, Current Protocols in Protein Science, 2015, 2:79. https://doi.org/10.1002/0471140864.ps2809s79; 2- Hu T., Sprague E.R., Fodor M., Stams T., Clark K.L. Cowan-Jacob S.W., "The impact of structural biology in medicine illustrated with four case studies", Journal of Molecular Medicine, 2018, 96:9–19. https://doi.org/10.1007/s00109-017-1565-x; 3- “Advances Methods in Structural Biology: part of the Methods in Molecular Biology”, 2023, Springer Protocols, Human Press, ISBN 978-1-0716-3146-1; 4- Gomes D., Correia M.A.S., Romão M.J., Passarinha L.A., Sousa A. “Integrated approaches for the separation and purification of recombinant HPV16 E6 protein from Escherichia coli crude extracts” Separation and Purification Technology, 2023, 315: 123647. https://doi.org/10.1016/j.seppur.2023.123647.
Language	Portuguese. Tutorial support is available in English.