1 / 18

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

totie
Télécharger la présentation

An analysis of the simplified normal modes of Ecotin

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related