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An analysis of the simplified normal modes of Ecotin

An analysis of the simplified normal modes of Ecotin. Hugh Shanahan University College London October 2001. and here am i patiently squeezing four dimensional ideas onto a two dimensional stage e e cummings. Outline. Ecotin and panspecificity

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An analysis of the simplified normal modes of Ecotin

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  1. An analysis of the simplified normal modes of Ecotin Hugh Shanahan University College London October 2001 and here am i patiently squeezing four dimensional ideas onto a two dimensional stage e e cummings

  2. Outline • Ecotin and panspecificity • Model of interaction (Eggers et al.) • Dynamics and normal mode analysis • A simplified model • Results • Temperature factors • Motions • Conclusions

  3. Ecotin

  4. Simulation • Molecular Dynamics (or Monte Carlo) is very very expensive • Considers all (or at least many) possible degrees of freedom • Never Clear when enough time steps (or configurations) is enough • In this case we are not concerned with local atomic displacements • Want large collective displacements

  5. And now for some scary Math…………..

  6. Difficulty with NMA • The potential used is semi-empirical • The original structure does not necessarily lie at a minimum for the “full” potential • One has to minimise the energy of the structure before performing NMA • May also have to deal with local minima

  7. Alright, but what exactly are you doing ?? Basically, take one of these…….

  8. And just think about the C ’s…... a

  9. Now put springs between them……. And that’s it !!!

  10. Results • Can compute the temperature factors (the RMS variation of the atoms..) • In test cases, the agreement is quite good...

  11. Ecotin Temperature Factors • But in the case of Ecotin, the agreement is not so good….

  12. The possible range of structures from this ensemble do not give the bound structure…….

  13. Conclusions • Motions are dominated by the two lowest eigenvalues, which are anti-symmetric. • Motion between bound and unbound state is, on the other hand, symmetric. • What is going wrong ? • NMA tends to over amplify regions where Temperature factors have a peak, some correlation with accessibility. • Model is in vacuum. Can include effect of water by introducing viscosity.

  14. Acknowledgements • Advice and direction… • David Jones • Janet Thornton • Suggestions on the technical implementation… • Graham Smith (ICRF) • Mark Williams

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