Unveiling the Structure of the HIV Capsid

An HIV capsid (4.2 million atoms, 1300+ proteins) produced via a simulation method that integrates data from multiple laboratory experiments is shown. The capsid contains 186 hexamers (blue) and 12 pentamers (green), with the arrangement of the pentamers determining the morphology of the capsid. The complete simulation contains 64 million atoms, and is among the largest biological structure simulation published. Generating the movie required petascale simulation, using 2000-3500 GPU-accelerated compute nodes. NVIDIA Tesla K20X GPUs provided four times greater speed, and VMD GPU ray tracing provided 6.5 times greater speed, than than traditional CPU-only nodes. The simulation enables study of HIV-1 dynamics in atomic detail.

Related website:

Related paper:
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Gongpu Zhao* , Juan R. Perilla*, Ernest L. Yufenyuy*, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang. Nature, 497:643-646, 2013.

Collaborators:

Klaus Schulten, Juan Perilla
U. Illinois Dept. of Physics

Peijun Zhang, Angela Gronenborn
U. Pittsburgh School of Medicine

Christoper Aiken
Vanderbilt U. School of Medicine

Video production by:
John Stone, Barry Isralewitz, Juan R. Perilla
Theoretical and Computational Biophysics Group