Atomistic MD Simulations of CBM3a Interacting with Cellulose.

MH Markus Hackl
EC Edward V. Contrada
JA Jonathan E. Ash
AK Atharv Kulkarni
JY Jinho Yoon
HC Hyeon-Yeol Cho
KL Ki-Bum Lee
JY John M. Yarbrough
CL Cesar A. López
SG Sandrasegaram Gnanakaran
SC Shishir P. S. Chundawat
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Initial coordinates of cellulose I were built using a cellulose builder script (79). The fiber was constructed to generate a parallelepiped geometry with crystalline parameters 4 4 5. Initial coordinates of CBM3a were downloaded from the Protein Data Bank (PDB) (ID: 4JO5), and missing sidechains were reconstructed using the Chimera molecular viewer with the most populated rotameric configurations based on the Dunbrack database (80). All simulations were carried with the Amber16 molecular dynamics package (81), and spatial coordinates were collected every 100 ps for analysis. A detailed description of the system setup as well as MD protocol is provided in SI Appendix. Initial and final MD simulation configurations of WT and Y67A mutant interactions with the cellulose surface are provided in rtf format as SI Appendix.

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