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Molecular Modeling : The Computer is the Lab

Molecular Modeling : The Computer is the Lab. Niels Johan Christensen IGM/Bioinorganic Chemistry/NP3 centre. Overview. Brief intro to molecular modeling Molecular modeling at the NP3 centre: Application to novel insulin complexes Clustering Acknowledgements Questions.

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Molecular Modeling : The Computer is the Lab

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  1. MolecularModeling: The Computer is the Lab Niels Johan Christensen IGM/Bioinorganic Chemistry/NP3 centre

  2. Overview • Brief intro to molecular modeling • Molecular modeling at the NP3 centre: Application to novel insulin complexes • Clustering • Acknowledgements • Questions

  3. What is Molecular Modeling? Wikipedia´(http://en.wikipedia.org/wiki/Molecular_modelling): Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies…. inevitably computers are required to perform molecular modelling of any reasonably sized system…. Andrew R. Leach, ”Molecular modelling, principles and applications”, second edition: …we shall not concern ourselves with semantics but rather shall consider any theoretical or computational technique that provides insight into the behaviour of molecular systems to be an example of molecular modelling.

  4. The Molecular Modeling Toolbox • Molecular Mechanics Methods • Molecules modeled as spheres (atoms) connected by springs (bonds) • Fast, >106 atoms • Limited flexibility due to lack of electron treatment • Quantum Mechanical Methods • Molecules represented using electron structure (Schrödinger equation) • Computationally expensive , <10-100 atoms, depending on method • Highly flexible – any property can in principle be calculated Typicalapplications • Simulating biomolecules in explicit solvent/membrane • Geometry optimization • Conformational search • Chemical reactions • Spectra • Accurate (gas phase) structures, energies

  5. The insulin project at the NP3 centre* • Synthesis: Engineered insulin with a novel metalion binding-site • Experimental data: CD, UV-vis • Goal: Elucidate the structure of a the novel insulin-complex in solution • Molecular modeling methodologies employed: • Molecular mechanics • Molecular dynamics • Quantum mechanics (Density functional theory) *http://www.np3.life.ku.dk/

  6. Prelude: Isomers of a (2,2’)-bipyridine Fe(II) complex   Facial (fac)  -fac -fac Meridional (mer) -mer  -mer

  7. Circular dichroism • Measures differential absorption of left and right circularly polarized light by chiral molecules • Only CD can establish the absolute configuration of molecules in solution Image source: http://en.wikipedia.org/wiki/Circular_dichroism

  8. Engineered insulin as a buildingblock in bionanotechnology Hexamer of native insulin. Zinc (grey sphere) coordinated by HisB10 (green licorice) Monomers of engineered insulin: Bipyridine has been introduced at position A1 (left) or B29 (right). HisB10 is also shown Insulin chain figure from : http://www.abpischools.org.uk/page/modules/diabetes_16plus/diabetes5.cfm?coSiteNavigation_allTopic=1

  9. [Fe( )3]2+ Three bipy-functionalized insulins form 4 distinct complexes with iron(II). Here, B29 functionalized insulin (similar for A1):  -fac -fac -mer -mer Which species dominate in solution?

  10. Circular Dichroism – calculated vs measured QM calculations on truncated systems (inset), measurements on B29 and A1 engineered insulin trimers in solution with Fe(II) -fac Erel(QM) = 0.0kJ/mol -fac Erel(QM) = 0.0 kJ/mol Calculated Calculated B29 B29 A1 A1 Measured Measured -mer Erel(QM) = 2.1 kJ/mol -mer Erel(QM) = 2.1 kJ/mol Calculated Calculated

  11. Circular Dichroism – calculated vs measured • Comparison of measured/calculated CD sign changes allows determination of enantiomer dominating in solution: A1 (), B29 () • Meridional (mer) and facial (fac) configuation cannot be firmly established from CD alone. • Energies from a conformational search on (truncated) systems may help in determining fac/mer preferences

  12. Conformational search on a truncated B29 trimer Conformationalsearch: [Fe(bipy)3]2+ core fixed, rotate remaining groups systematically to find lowest energy:  -fac 0.0 kJ/mol -fac 14.3 kJ/mol -mer 25.4 kJ/mol -mer 30.0 kJ/mol

  13. Molecular dynamics simulations can be used to elucidate the dynamics of biomolecules • Example: Rearrangement of an engineered insulin monomer

  14. Clustering: Building a larger calculator

  15. Acknowledgements Henrik K. Munchb, Søren Thiis Heidea, Thomas Hoeg-Jensenc, Peter Waaben Thulstrupa and Knud J. Jensenb a Bioinorganic Chemistry, Department of Basic Sciences and Environment, Faculty of Life Sciences, University of Copenhagen, Denmark b Bioorganic Chemistry, Department of Basic Sciences and Environment, Faculty of Life Sciences, University of Copenhagen, Denmark c Novo Nordisk , Maaloev, Denmark Det Strategiske Forskningsråds Programkomite for Nanovidenskab og -teknologi, Bioteknologi og IT (NABIIT)

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