This dataset contains input structures and parameters for coarse-grained molecular dynamics simulation of SAS-6 protein oligomers as well as post-processing files and analysis scripts. Abstract of related publication: Discovering mechanisms governing organelle assembly is a fundamental pursuit in the life sciences. The centriole is an evolutionarily conserved organelle with a signature 9-fold symmetrical chiral arrangement of microtubules imparted onto the cilium it templates. The first structure in nascent centrioles is a cartwheel, which comprises stacked 9-fold symmetrical SAS-6 ring polymers and emerging orthogonal to a surface surrounding resident centrioles. The mechanisms through which SAS-6 polymerization ensures centriole organelle architecture remain elusive. We deployed photothermally-actuated off-resonance tapping high-speed atomic force microscopy (PORT-HS-AFM) to decipher surface SAS-6 self-assembly mechanisms. We discovered that the surface shifts the reaction equilibrium by ~104 compared to solution. Moreover, coarse-grained molecular dynamics simulations and PORT-HS-AFM revealed that the surface converts the inherently helical propensity of SAS-6 polymers into 9-fold rings with residual asymmetry, which may guide ring stacking and impart chiral features to centrioles and cilia. Overall, our work reveals fundamental design principles governing centriole assembly.

Gromacs, 2018.5

UCSF Chimera, 1.12

martinize.py, 2.6

VMD, 1.9.3