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Mechanics of an atomic crank of 1,6 Linked Polysaccharides by AFM and SMD Calculations

Gwangrog Lee Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC, 27708. Mechanics of an atomic crank of 1,6 Linked Polysaccharides by AFM and SMD Calculations. Please look at slide notes. Adhesive interactions.

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Mechanics of an atomic crank of 1,6 Linked Polysaccharides by AFM and SMD Calculations

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  1. Gwangrog Lee Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC, 27708 Mechanics of an atomic crank of 1,6 Linked Polysaccharides by AFM and SMD Calculations Please look at slide notes

  2. Adhesive interactions

  3. Polysaccharides: Pustulan (1→6-linked β-D-glucose). Single Molecule Force Spectroscopy by AFM. 1-5 Steered Molecular Dynamics simulations: NAMD and CHARMM (CSFF).6-7 Materials and Methods

  4. AFM experiment A B AFM Head D = x= L - L F k z split f i c c laser photodiode Cantilever, spring constant, k c Micro- D z manipulator c L i L f cantilever sample 1 Strain gauge piezo Piezo D z p 2 L PC interface

  5. SMD Simulation Force Sensor (cantilever) Potential being applied to the system:

  6. Demo of SMD simulation using NAMD

  7. 2000 1750 1500 1250 1000 750 500 250 Worm-like chain 0 200 0 50 100 150 p Lc F Freely jointed chain with segment elasticity x

  8. O1 1 t2 O5 O6 2 5 t3 6 3 t1 4 Pustulan b-1,6 O6-O1: Glycosidic linkage C1-O1: Glycosidic bond Atomic lever O6-C6: Aglycone bond Atomic crank t1: Dihedral angle of rotamer t2, t3 : Dihedral angle for monitoring chair-boat transition AFM recordings obtained on individual pustulan molecules of various lengths.

  9. Table 1.Ab initio calculations of the O6-O1 distance in the rotamers of β-D-glucose using the B3LYP/6-311++G** method.

  10. gt: w=+60 C6 O6 C5 O5 O1 gg: w=-60 tg: w=180 Pustulan ( black line ) Cellulose ( blue line ) Force-spectrograms of 20 different pustulan molecules are normalized at the common force (1400 pN) and superimposed. Definition of rotamer gt, gg, and tg rotamer of β-D- glucopyranose

  11. 5ns water-simulation and normalized force-spectrograms with a scale of monomer. gt +56° tg +167° 4.97 Å 6.27 Å 4C1gt 4C1tg Normalized Extension per Ring/Å

  12. A comparison of pulling speeds Green: 5ns Simulation Blue: 200ns Simulation Red: 1micros Simulation Normalized Extension per Ring/Å

  13. B Ring 5 Dihedral Angles/º C Ring 4 A comparison between force-extension curves of pustulan obtained by AFM and by SMD simulations of 10 rings for 1 micro seconds. A gt +69° tg +166° R5 4.94 6.06 gg -75° tg -174° R4 5.42 6.12 Normalized Extension per Ring/Å

  14. A Dihedral angles B O1-O6/Å Time/ns C 5.30 Å 5.94 Å 158° -70° 368.52 ns 368.53 ns Analysis of the one microsecond SMD trajectory of ring #4 reveals thermally driven and force driven conformational transitions between gg, gt, and tg states.

  15. 6.29Å 4.93Å F=0 F=2900 pN Cellulose ( blue line ) Pustulan ( red line ) A comparison of the works undergone under stretching condition of each polymer. Insert The initial and final structures of pyranose ring in pustulan 5.7 kcal/mol

  16. The hookean elasticity of pustulan is generated by forced gt→tg and gg→tg rotations about the C5-C6 bond. The work to rotate the atomic crank (O6-C6) about the C6-C5 bond is 5.7 kcal/mol (Wrot= Wpust- Wcell). Conclusion

  17. Rief, M., Oesterhelt, F., Heymann, B., and Gaub, H. E. (1997). Science 275, 1295-1297. Marszalek, P. E., Oberhauser, A. F., Pang, Y.-P., and Fernandez, J. M. (1998). Nature396, 661-664. Marszalek, P. E., Pang, Y. P., Li, H., Yazal, J. E., Oberhauser, A. F., and Fernandez, J. M. (1999). PNAS96, 7894-7898. Marszalek, P.E., Li, H. & Fernandez, J.M. (2001). Fingerprinting polysaccharides with single molecule AFM. Nat. Biotech.19, 258-262. Marszalek, P.E., Li, H., Oberhauser, A.F. & Fernandez, J.M. (2002). PNAS99, 4278-4283 Kuttel, M., Brady, J.W. & Naidoo, K.J. (2002) J. Comput. Chem. 23, 1236-1243. Humphrey, W., Dalke, A., & Schulten, K. J. Mol. Graphics, 14, 33-38 (1996). Kirschner, N. Karl & Woods, R.J. (2001) PNAS98, 10541-10545. Reference

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