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, Please look at slide notes

Adhesive interactions

Materials and Methods 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

AFM experiment

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

Demo of SMD simulation using NAMD

Freely jointed chain with segment elasticity x p F LcLc Worm-like chain

AFM recordings obtained on individual pustulan molecules of various lengths. Pustulan  -1, O6O6 O5O5 t1t1 t3t3 t2t2 O1O1 O 6 -O 1 : Glycosidic linkage C 1 -O 1 : Glycosidic bond Atomic lever O 6 -C 6 : Aglycone bond Atomic crank t 1 : Dihedral angle of rotamer t 2, t 3 : Dihedral angle for monitoring chair-boat transition

Table 1. Ab initio calculations of the O 6 -O 1 distance in the rotamers of β-D-glucose using the B3LYP/ G** method. Rotamerβ- D- Glucose ω/ω/ O 1 O 6 /Ǻ 4 C 1 gt C 1 gg C 1 tg

Force-spectrograms of 20 different pustulan molecules are normalized at the common force (1400 pN) and superimposed. O6O6 C6C6 C5C5 O5O5 tg:  gg:  gt:  O1O1 Definition of rotamer gt, gg, and tg rotamer of β-D- glucopyranose Cellulose ( blue line ) Pustulan ( black line )

5ns water-simulation and normalized force- spectrograms with a scale of monomer. tg +167° gt +56° 4.97 Å6.27 Å 4 C 1gt 4 C 1tg Normalized Extension per Ring/Å

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

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

ns ns -70° 158° 5.30 Å 5.94 Å Time/ns O 1 -O 6 /Å C A B Dihedral angles Analysis of the one microsecond SMD trajectory of ring #4 reveals thermally driven and force driven conformational transitions between gg, gt, and tg states.

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

Conclusion The hookean elasticity of pustulan is generated by forced gt→tg and gg→tg rotations about the C 5 -C 6 bond. The work to rotate the atomic crank (O 6 -C 6 ) about the C 6 -C 5 bond is 5.7 kcal/mol (W rot = W pust - W cell ).

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