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Inicio

Hola!

Esta es la página de inicio de la parte Teórica del curso.

Consultas y canales de comunicación

  • Por email a la dirección del profesor titular.
  • mensajes en Discord con consultas en distintos canales
  • en el canal de YouTube van a estar subidos los videos de las clases teóricas

Bibliografía Adicional

Libros

  • Biochemistry, 5th Ed. Lubert Stryer, Jeremy M. Berg & John L. Tymoczo. W.H. Freeman & Co.

  • Introduction to Protein Structure, 2nd Ed. Carl Branden & John Tooze. Garland Publishing. Structure and Function of Intrinsically Disordered Proteins. P. Tompa Ed. Chapman & Hall/CRC Press.

Publicaciones científicas

Estructura y función de proteínas, clasificación de dominios y Modelado por homología:

  • Das S, Dawson NL, Orengo CA. Diversity in protein domain superfamilies. Curr. Op. Genet. Dev. 2015 35:40-9. PMID: 26451979.

  • Todd A.E., Orengo C.A., Thornton, J.M. Evolution of Function in protein superfamilies, from a structural perspective. J. Mol. Biol. 2001 307(4):1113-43. PMID: 11286560

  • Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V. A Completely

  • Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. J Mol Biol. 2018 Jul 20. S0022-2836(17)30587-9. PMID: 29258817

  • Gabler F, Nam SZ, Till S, Mirdita M, Steinegger M, Söding J, Lupas AN, Alva V. (2020). Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. Curr Protoc Bioinformatics. Dec;72(1):e108. doi: 10.1002/cpbi.108. PMID: 33315308

  • Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M. (2021). ColabFold - Making protein folding accessible to all. bioRxiv. doi: 10.1101/2021.08.15.456425

  • Jumper et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature 596(7873):583-589. doi: 10.1038/s41586-021-03819-2. PMID: 34265844

  • Baek M. et. al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373(6557):871-876. PMID: 34282049

  • Abramson, J., Adler, J., Dunger, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024). https://doi.org/10.1038/s41586-024-07487-w. PMID: 38718835

Dominios de señalización, proteínas modulares y “scaffolds”

  • Scott, J.D. & Pawson, T. (2009). Cell signaling in space and time: where proteins come together and when they're apart. Science. Nov 27;326(5957):1220-4. PMID: 19965465

  • Langeberg, L.K., Scott, J.D. (2015). Signalling scaffolds and local organization of cellular behaviour. Nat Rev Mol Cell Biol. Apr;16(4):232-44. PMID: 25785716

Desorden proteico

  • Wright PE, Dyson HJ. (1999). Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol. 293(2):321-331. doi:10.1006/jmbi.1999.3110. PMID: 10550212

  • Uversky V.N, Gillespie, J.R., Fink, A.L. (2000). Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 41:415–427. PMID: 11025552

  • Dyson, H.J. & Wright, P.E. (2005). Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol. Mar;6(3):197-208. PMID: 15738986

  • Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z and Uversky VN. The unfoldomics decade: an update on intrinsically disordered proteins. PMID: 18831774

  • Tompa, P. (2012). Intrinsically disordered proteins: a 10-year recap. Trends Biochem Sci. Dec;37(12):509-16. PMID: 22989858

  • Oldfield, C.J. & Dunker, A.K. (2014). Intrinsically disordered proteins and intrinsically disordered protein regions. Annu Rev Biochem. 83:553-84. PMID: 24606139

  • van der Lee R, Buljan M, Lang B, et al. (2014). Classification of intrinsically disordered regions and proteins. Chem Rev. 114(13):6589-6631. doi:10.1021/cr400525m. PMID: 24773235

  • Propiedades de secuencia de regiones flexibles Marsh JA, Forman-Kay JD. (2010). Sequence determinants of compaction in intrinsically disordered proteins. Biophys J. 98(10):2383-2390. doi:10.1016/j.bpj.2010.02.006. PMID: 20483348.

  • Das RK, Pappu R V. (2013). Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. Proc Natl Acad Sci U S A; 110(33):13392-13397. doi:10.1073/pnas.1304749110. PMID: 23901099.

  • Das RK, Ruff KM, Pappu R V. (2015). Relating sequence encoded information to form and function of intrinsically disordered proteins. Curr Opin Struct Biol. 32:102-112. doi:10.1016/j.sbi.2015.03.008. PMID: 25863585

  • Mier P. et. al. (2020). Disentangling the complexity of low complexity proteins. Brief. Bioinform. 21(2):458-472. PMID: 30698641

  • Lupas, A.N., Bassler, J. (2017). Coiled Coils- A model system for the 21st century. Trends Biochem Sci. 42(2):130-140. PMID: 27884598

Motivos Lineales

  • Tompa, P., Davey, N.E., Gibson, T.J., and Babu, M.M. (2014). A million peptide motifs for the molecular biologist. Mol Cell. Jul 17;55(2):161-9. PMID: 25038412

  • Davey, N.E., et al. (2012). Attributes of short linear motifs. Mol Biosyst. Jan;8(1):268-81. PMID: 21909575.

  • Via, A., et al. (2015) How pathogens use linear motifs to perturb host cell networks. Trends Biochem Sci. Jan;40(1):36-48. PMID: 25475989

  • Davey, N.E., Travé, G., Gibson, T.J. (2010). How viruses hijack cell regulation. Trends Biochem Sci. Mar;36(3):159-69. PMID: 21146412

Métodos experimentales para el estudio de la función de proteínas

  • Gibson, T.J. et al., Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. Cell Commun Signal. Nov 18;13:42. PMID: 26581338

  • Gibson, T.J., Seiler, M., Veitia, R.A. (2013) The transience of transient overexpression Nat Methods. Aug;10(8):715-21. PMID: 23900254

  • Greenspan N.S. (2011). Attributing functions to genes and gene products. Trends Biochem Sci. 2011 Jun;36(6):293-7. PMID: 21269834

  • Passaro S, Corso G, Wohlwend J et al. Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction. bioRxiv (Preprint). 2025 Jun 18:2025.06.14.659707. doi: 10.1101/2025.06.14.659707. PMID: 40667369.

Diseño de Proteínas

  • Watson, J.L., Juergens, D., Bennett, N.R. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023). https://doi.org/10.1038/s41586-023-06415-8. PMID: 37433327

  • Dauparas J, Anishchenko I, Bennett N, et al. Robust deep learning-based protein sequence design using ProteinMPNN. Science. 2022 Oct 7;378(6615):49-56. doi: 10.1126/science.add2187. Epub 2022 Sep 15. PMID: 36108050.