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
Slide 2

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.
Slide 3

The Molecular Modeling Toolbox
Molecular Mechanics Methods Quantum Mechanical Methods
Molecules modeled as spheres (atoms) connected by springs (bonds)
Molecules represented using electron structure (Schrödinger equation)
• Fast, >10 6 atoms
• Computationally expensive , <10-100 atoms, depending on method
• Limited flexibility due to lack of electron treatment
• Highly flexible – any property can in principle be calculated
Typical applications
 Simulating biomolecules in explicit solvent/membrane
 Chemical reactions
 Spectra
 Geometry optimization
 Conformational search
 Accurate (gas phase) structures, energies
Slide 4

The insulin project at the NP3 centre*
• Synthesis: Engineered insulin with a novel metalion bindingsite
• 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)
Slide 5
*http://www.np3.life.ku.dk/

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

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
Slide 7
Image source: http://en.wikipedia.org/wiki/Circular_dichroism

Engineered insulin as a building block 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
Slide 8
Insulin chain figure from : http://www.abpischools.org.uk/page/modules/diabetes_16plus/diabetes5.cfm?coSiteNavigation_allTopic=1

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

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
E rel
(QM) = 0.0kJ/mol
 -fac
E rel
(QM) = 0.0 kJ/mol
B29 B29 A1 A1
 -mer
E rel
(QM) = 2.1 kJ/mol
 -mer
E rel
(QM) = 2.1 kJ/mol
Slide 10

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
Slide 11

Conformational search on a truncated B29 trimer
Conformational search: [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
Slide 12

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

Slide 14
Clustering: Building a larger calculator

Henrik K. Munch b , Søren Thiis Heide a , Thomas Hoeg-Jensen c , Peter
Waaben Thulstrup a and Knud J. Jensen b 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)
Slide 15