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Proteins and beyond
 

Proteins and beyond

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    Proteins and beyond Proteins and beyond Presentation Transcript

    • From Drug Design toSelf-assembling Materials Ivan Coluzza
    • ProteinsA protein is made of a list of~20 different types of aminoacidsProteins fold tothermodynamically stablestructures at finitetemperature called NativeStatesDesign is the process offinding all sequences thatcan fold to a givenconfiguration http://xray.bmc.uu.se/~kurs/BiostrukfunkX2/practicals/practical_1/figs/peptide_bond.jpg
    • Folding vs Design E= Cij Sij ijFolding Design E= ¯ Cij Sij E= ¯ Cij Sij ij ij ADSVGCA...... EN = ¯ ¯ Cij Sij ij
    • Examples of caterpillar design - refoldingNuclear RNA C-Terminal domainexport factor Lipoprotein of the Ribosomal Protein G (1PGB) (1OAI) (2K57) Protein (1CTF) Coluzza I., Plos ONE 10.1371/journal.pone.0020853 (2011)
    • GroEL/GroES Chaperonin Hydrophilic Cage Equatorial Region~164 Å Hydrophobic Trap
    • Chaperonin reaction pathway Hydrophobic Hydrophilic 4a Non-Native Native State 2 1 4b Trans refolding path 3b Cis refolding path 3a Shuttling ! !Coluzza I., van der Vies S. M., Frenkel D. Biophysical Journal 90 (10): 3375-3381 (2006)
    • Artificial ProteinHydrogen Bonds C Patchy-Particles 1 2 C o 2.0 A 2.0 A o Hard Core Patch C 2 1 C Bond Bianchi et al. Phys. Rev. Lett. (2006) vol. 97 (16) pp. 4
    • Patchy-Polymer structure space1 Patch 2 Patches a Increasing interaction b range c
    • Understand protein Patchy polymers folding and designStructure Macroscopic Drug DesignPrediction FoldingAggregation(Alzheimer) Chaperonin & Direct conversion Folding under of simulations confinement results to Protein experiments Evolution Create a material design framework
    • ! 86"9/2)0:%)-,(6$ ! ;66(0</=%2 Acknowledgements 12/$"(-"%0>"6%2,6$% ! ! ?6"9((0@($)2A-"%%Christoph Dellago ! :6%2*6%01/B26$Cristos LikosBarbara Capone Marie Curie PrograPeter van Oostrum ! Grants FP6 !Ronald ZirbsErik ReimhultMark MillerMichele VendruscoloDaan FrenkelAngelo CacciutoAngel OrteMaria Jose RuedasSaskia van der ViesFrancesco Sciortino