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Outline: The Lymn-Taylor cycle PCA method (theory & applications)

Outline: The Lymn-Taylor cycle PCA method (theory & applications) Individual involvement coefficient (theory & applications) Summary Future work. http://www.sciencemag.org/feature/data/1049155s1.mov. The Lymn-Taylor cycle. Myosin is bound to actin

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Outline: The Lymn-Taylor cycle PCA method (theory & applications)

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  1. Outline: • The Lymn-Taylor cycle • PCA method (theory & applications) • Individual involvement coefficient (theory & applications) • Summary • Future work

  2. http://www.sciencemag.org/feature/data/1049155s1.mov

  3. The Lymn-Taylor cycle • Myosin is bound to actin • (2) ATP binds to myosin and then myosin dissociates from actin • (3) Hydrolysis of ATP to ADP and Pi leads to a change in conformation for myosin • (4) Myosin rebinds to actin and actin is “rowed” past myosin with the release of the hydrolyzed products (ADP and Pi) Power-Stroke Recovery-Stroke Geeves & Holmes : Annu. Rev. Biochem. 1999. 68:687–728

  4. (3) CLOSED OPEN (2)

  5. PC2 PC1 Principal Component Analysis • we want to simplify the problem by reducing the dimension of the system • we want to preserve as much as possible of the original information content % - the contribution to the total variance of the data a – number of the first principal components b – the total number of the principal components

  6. 15 eigenvectors 80% Good projection of data MD of S1-Myosin head in OPEN conformation

  7. Total nr. of eigenvectors = more than 2200 (only Cα atoms) MD of S1-Myosin head in CLOSED conformation ATP ADP+Pi

  8. PC2 P R d2 d1 PC1 PC2 PC1 Are we choosing the right eigenvectors?!

  9. PC2=L2 PC1=L1 P R Ik - individual involvement coefficient (X1-X2) – displacement vector Ck – the cumulative involvement coefficient I1 displacement vector I2 Li & Cui : Biophysical Journal 2004. 743-763 Individual involvement coefficient

  10. „Important modes“ ???? Individual involvement coefficient for different MD trajectories

  11. “Important” elements of S1-Myosin head in CLOSED conformation (ATP)

  12. “Important” elements: P-Loop: red Converter Domain: green Relay-helix : cyan • calculate the % from the total variance (PCA) • calculate the individual involvement coefficients • for some of them visualize the first mode (VMD) Lever Arm : yellow SH1-Helix : pink Switch2: blue Switch2-Loop: white

  13. All “Important” elements

  14. „Important“ element: Relay-helix

  15. „Important“ element: Converter-domain + lever-arm

  16. „Important“ element: Switch2

  17. „Important“ element : Switch1

  18. „Important“ element : Ploop

  19. Summary: • a good projection of the data is obtained with PCA • the mode with the largest contribution  functionally relevant motion • to analyze the conformational change Individual Involvement Coefficient • the conformational change was decomposed into the motion of some structural elements.

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