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Can we learn anything new from hydrogen bonds?

Can we learn anything new from hydrogen bonds?. Marta Enciso Universidad Complutense de Madrid. Proteins and hydrogen bonds. Protein structure Protein design Folding Aggregation. Wylie, JACS, 2009. Chen, PNAS, 2009. Kannan, Int. J. Mol. Sci., 2009.

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Can we learn anything new from hydrogen bonds?

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  1. Can we learn anything new from hydrogen bonds? Marta Enciso Universidad Complutense de Madrid

  2. Proteins and hydrogenbonds • Protein structure • Protein design • Folding • Aggregation Wylie, JACS, 2009 Chen, PNAS, 2009 Kannan, Int. J. Mol. Sci., 2009 Dobson, Annu. Rev. Biochem., 2006 BIFI 2011 - Marta Enciso

  3. Ourcoarsegrainedapproach Distance • System description • Potential definition • Geometrical restrictions • Energy calculation • Simulation technique Angle ME & A. Rey, J. Chem. Phys., 2010 BIFI 2011 - Marta Enciso

  4. Anhomopeptidestudy A C Meaningful region Frozen region B D ME & A. Rey, J. Chem. Phys., 2010 BIFI 2011 - Marta Enciso

  5. Proteinstudies I:Identification of hydrogenbonds Domain B of protein A flavodoxin domain B protein A α-spectrin T4 lysozyme fibronectin PDZ domain PyMOL Ours STRIDE DSSP BIFI 2011 - Marta Enciso

  6. Proteinstudies II:Proteinfolding and interproteininteractions ProteinFolding Topology-basedmodels ProteinFolding + Hydrogen bonds Hydrophobics L. Prieto, D. de Sancho & A. Rey, J. Chem. Phys., 2005 BIFI 2011 - Marta Enciso

  7. Proteinstudies II: folding Fibronectin type III domain Peakwidth *J. Clarke, JMB, 1997 BIFI 2011 - Marta Enciso

  8. Proteinstudies II: interproteininteractions Fibronectintype III domain Twochains BIFI 2011 - Marta Enciso

  9. A correctdescription of hydrogenbondsisnecessaryforunderstandingproteinfolding and aggregation • Wehavedesigned a coarse-grainedhydrogen bond model • Wehaveproveditsvalidityforobtainingsecondarystructureelements and detectingreal hydrogenbonds • It can besuccessfullyappliedtothestudy of proteinfolding and interproteininteractions Conclusions BIFI 2011 - Marta Enciso

  10. Acknowledgements Grupo de Simulación de Proteínas Departamento de Química Física I Universidad Complutense de Madrid Antonio Rey Ramiro Perezzan David de Sancho (U. Cambridge) Lidia Prieto (CUNY) María Larriva (U. Navarra)

  11. Can we learn anything new from hydrogen bonds? Marta Enciso Universidad Complutense de Madrid

  12. Simulatinghydrogenbonds • First principles – Quantum Mechanics • Empiric potentials • Atomic resolution • Coarse-grained models • Others • Our approach BIFI 2011 - Marta Enciso

  13. Modelgeometricalconstrains • R1 is a spatial restriction that designates the distance between the two carbons of the hydrogen bonded residues R1 = rij = rj− ri • R2 is an orientational restrain which computes the cosine of the angle associated to the relative orientation between the auxiliary vectors of both residues • R2 = cos(hi, hj) • R3 is also an orientational quantity that computes the cosine of the angle between the direction of the tentative hydrogen bond in the model and each of the auxiliary vectors; thus, R3 is independently calculated for both i and j beads R3i and R3j • R3 = cos(hi, rij)

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