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Analysis of the Lymn-Taylor Cycle and Structural Dynamics of Myosin via PCA and Involvement Coefficient

This study explores the Lymn-Taylor cycle, examining the binding and hydrolysis of ATP by myosin during muscle contraction. We apply Principal Component Analysis (PCA) to reduce complex motion data into key components while preserving essential information. The Individual Involvement Coefficient is calculated to assess the contribution of significant structural elements during conformational changes in myosin. We summarize our findings and propose directions for future research in improving our understanding of molecular dynamics in muscle proteins.

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Analysis of the Lymn-Taylor Cycle and Structural Dynamics of Myosin via PCA and Involvement Coefficient

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Presentation Transcript

  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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