The analysis of the structure of proteins and other macromolecules is essential to understand biochemical processes at the molecular level. Likewise, characterizing the interactions of proteins with different macromolecules (interactome) allows us to rationalize their involvement in different biological processes.

This subject provides an integrated and updated view of the knowledge of proteins at a structural and chemical level. The student will become familiar with proteomics approaches, the concepts derived from the structural analysis of proteins, and the latest advances in engineering applied to them.

Proteomics Introduction. Descriptive proteomics, expression proteomics and functional proteomics. Analysis of subproteomes and protein complexes. Analysis of cellular signaling pathways. Analysis of interactions between proteins. Mass spectrometry applied to proteins. MALDI, and ESI ionization methods. Fragmentation methods. Identification of proteins by mass spectrometry. Fingerprint of peptide masses and fingerprint of peptide fragments. Mass spectral data processing. Quantitative proteomics. Quantification based on 2DE, DIGE. Quantification based on mass spectrometry. Absolute quantification: internal standard, semiquantitative methods. Relative quantification: labeling-free methods, labeling methods (SILAC, iTRAQ). Directed quantification: SRM.

Protein structure Amino acids: Properties and classification. Hydrophobicity scale. Ionization. Functional groups. Peptides: Peptide bond. Primary structure. Secondary structure. Conformational constraints of polypeptides. Types of secondary structure: helices, sheets, turns and loops. Tertiary and quaternary structure of proteins: Motifs and structural domains. Classification of globular proteins. Membrane proteins. Fibrous proteins. Oligomeric proteins.

Protein engineering "De novo" design of protein structure. Rational design. Modular design. Minimization of designed structures. Ability to design alpha, beta and turn structures. Applications of protein design: stabilization of protein structures. Directed evolution of proteins.

Theoretical classes, student seminars based on research articles representative of the subject taught and computational approaches and practices.

• Final Assessment System
• Tools and qualification percentages:
  • Written test to be taken (%): 40
  • Multiple-Choice Test (%): 40
  • Realization of Practical Work (exercises, cases or problems) (%): 10
  • Individual works (%): 10

The exams (written and/or test) will count 75-80% of the final grade. Internships and jobs the remaining 20-25%. It will be enough to not take the final test to be rated as "not presented".

This subject is governed by the “Protocol on academic ethics and prevention of dishonest or fraudulent practices in evaluation tests and academic work at the UPV/EHU”, with the consequences provided for in section 5 of said protocol.

If the subject is not passed in the ordinary call, the partial grades of the passed sections will be saved for the extraordinary call of the current year.

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Basic bibliography

- Proteins and Proteomics: A laboratory manual. R.J. Simpson. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. 2003.



- Introduction to protein structure. Branden, C. y Tooze, J. 2nd Edition. Garland Publishing, 1999.

In-depth bibliography

- Proteomics for Biological Discovery. Veenstra T.D. and Yates III J.R. Wiley, New Jersey, 2006.

- Estructura de proteínas. Gómez-Moreno, C y Sancho J. (coords.) Ariel Ciencia, 2003

Journals

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Web addresses

http://www.rcsb.org/pdb/ Protein Data Bank (PDB): banco de datos que contiene listados de coordenadas atómicas para las proteínas y ácidos nucleicos cuya estructura tridimensional ha sido resuelta.
http://www.ebi.ac.uk/ Sitio del European Bioinformatics Institute. Bases de datos y programas para análisis de secuencias y estructuras.