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Advanced Courses IV

Code 15045
Year 1
Semester S2
ECTS Credits 5
Workload TP(40H)
Scientific area Biomedicina/Medicina/Bioquímica
Entry requirements Without entry requirements
Learning outcomes Upon successfully finishing the curricular unit of Advanced Courses IV – Medical Structural Biology, the student must be able to:

1- State the main computational biochemistry techniques for molecular simulation in protein systems.
2- Use the methods of analyzing protein-protein and protein-ligand interactions to validate kinetic and thermodynamic parameters of biomolecules in solution.
3– Analyze nucleic acid-ligand interactions via laboratory techniques for selecting target molecules and structural studies.
4- Identify the characteristics of a preparative and structurally harmless technique in the separation of a complex mixture of proteins in liquid chromatography.
5- Describe the methods for determining the three-dimensional structure of biomolecules with therapeutic relevance: 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: Energy of bond angles; Torsional energy; Parameter deduction; Force fields; C) Molecular Dynamics Simulations: Equations of Motion; Long Range Forces; Soothing 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 the stability of DNA and RNA and determine the affinity and kinetics of the reaction between biomolecule-ligand by SPR in order to select the ligands. 3- Structural Biology Module – A) Strategies for separating proteins by liquid chromatography; B) Co-crystallization and Soaking; SAXS; Cryo-EM - Fundamentals, image formation 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.
Teaching Methodologies and Assessment Criteria The activities carried out in the Advanced Course IV are primarily based on the active participation of students in: tutorials for guided information research, discussion and resolution of case studies proposed by teachers; seminars/workshops carried out by researchers/teachers from research centers of excellence (national and international) and with curricular experience in the different areas under analysis and emphasizing simulations and discussions in the design of new molecules based on the structure of biomolecules deposited on the bases of international data.
Language Portuguese. Tutorial support is available in English.
Last updated on: 2024-05-14

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