can we learn anything new from hydrogen bonds?

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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. - PowerPoint PPT Presentation

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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

BIFI 2011 - Marta Enciso

Wylie, JACS, 2009

Kannan, Int. J. Mol. Sci., 2009

Chen, PNAS, 2009Dobson, Annu. Rev. Biochem., 2006

Proteins and hydrogen bondsProtein structureProtein designFoldingAggregation2

BIFI 2011 - Marta Enciso

System descriptionPotential definitionGeometrical restrictionsEnergy calculationSimulation techniqueME & A. Rey, J. Chem. Phys., 2010Our coarse grained approach

DistanceAngle

BIFI 2011 - Marta Enciso

Frozen regionMeaningful region

ME & A. Rey, J. Chem. Phys., 2010An homopeptide study

C

D

B

A4BIFI 2011 - Marta Enciso

Protein studies I:Identification of hydrogen bondsDomain B ofprotein A

DSSPSTRIDEPyMOLOurs flavodoxindomain B protein A -spectrinT4 lysozyme fibronectin PDZ domain

BIFI 2011 - Marta Enciso

L. Prieto, D. de Sancho & A. Rey, J. Chem. Phys., 2005Protein studies II:Protein folding and interprotein interactions

Protein FoldingTopology-based modelsProtein FoldingHydrophobicsHydrogenbonds+

BIFI 2011 - Marta Enciso

Protein studies II: folding

*J. Clarke, JMB, 1997Experiment*4 KTopology-based8 KTopology+HB5 KPeak width

Fibronectin type III domain

BIFI 2011 - Marta Enciso

Protein studies II: interprotein interactions

Fibronectin type III domainTwo chains

ConclusionsBIFI 2011 - Marta Enciso A correct description of hydrogen bonds is necessary for understanding protein folding and aggregation

We have designed a coarse-grained hydrogen bond model

We have proved its validity for obtaining secondary structure elements and detecting real hydrogen bonds

It can be successfully applied to the study of protein folding and interprotein interactionsAcknowledgements

Grupo de Simulacin de ProtenasDepartamento de Qumica Fsica IUniversidad Complutense de Madrid

Antonio ReyRamiro PerezzanDavid de Sancho (U. Cambridge)Lidia Prieto (CUNY)Mara Larriva (U. Navarra)

Can we learn anything new from hydrogen bonds?

Marta Enciso Universidad Complutense de Madrid

BIFI 2011 - Marta Enciso

Simulating hydrogen bondsFirst principles Quantum Mechanics

Empiric potentialsAtomic resolutionCoarse-grained modelsOthersOur approach

12

R1 is a spatial restriction that designates the distance between the two carbons of the hydrogen bonded residuesR1 = 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 residuesR2 = 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 R3jR3 = cos(hi, rij)Model geometrical constrains

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