The family of Retroviruses are characterized by their ability to incorporate viral DNA into a host cell's genome. Most retroviruses infect cells during mitosis, when the chromatin is exposed to the cytoplasm. Conversely, the genus of Lentiviruses, like the human immunodeficiency virus (HIV), have evolved in order to infect non-dividing cells. Since the host cell's chromatin is protected by the nucleus, the HIV infection process requires coordination between reverse transcription of viral RNA and nuclear import. Viral RNA is encased in a shell of the capsid protein CA. Originally thought to play a trivial role in the infection process, it is now well established that the viral capsid fulfills several essential functions. In particular, capsid involvement in the prevention of innate sensor triggering, regulation of reverse transcription, and regulation of the nuclear import pathway is of central importance to the successful infection of a host cell.

HIV-1 Helical Assembly MDFF


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.

Additional resources


PDB structures

We published two representative structures of the HIV-1 capsid structure. To load these structures into VMD please use the following script:

For 3J3Y:

foreach i {1VUU 1VUV 1VUW 1VUX 1VUY 1VUZ 1VV0 1VV1 1VV2 1VV3 1VV4 1VV5 1VV6 1VV7 1VV8 1VV9 1VVA 1VVB 1VVF 1VVG 1VVH 1VVI } { mol new $i }

Molecular dynamics trajectory of capsid structure 3J3Y.

In (Nature, 497:643-646, 2013) we report a 64 million atom molecular dynamics simulation of structure 3J3Y that revealed stability as seen in a 100 ns trajectory. This claim is corroborated here through snapshots of the trajectory at 50 ns, 60 ns, ... 100 ns to which we add for the sake of comparison the pdb entry 3J3Y. The snapshots can be viewed through VMD.

To open the trajectory simply use VMD to open the PSF file (File -> New Molecule -> HIVcapsid.pdf), and then add the dcd file (File -> Load Data Into Molecule -> HIVcapsid.dcd).

The reader can inspect that the simulated structure indeed remains stable and close to the structure reported in the protein data base. Further details of the trajectory will be reported in a forthcoming publication.

In releasing the trajectory data we follow the example of David Shaw Research who likewise released trajectory data for protein folding, except that we do not require registration and signing of a license. The latter generosity is simply dictated by our lack of legal support, but we expect that the use of the trajectories is properly acknowledged through explicit reference of use of the trajectories and of Nature, 497:643-646, 2013.

Readers who wish to carry out their own molecular dynamics simulations are referred to the VMD website, in particular to the mini-tutorial for solvating large structures, as well as to the NAMD web site, in particular to instructions to run NAMD for very large structures. The program NAMD is described here and its application in a simulation of a very large (100 Million atom) system based on NAMD 2.8 is described here.

For 3J3Q :

foreach i { 1VU4 1VU5 1VU6 1VU7 1VU8 1VU9 1VUA 1VUC 1VUD 1VUE 1VUF 1VUG 1VUH 1VUI 1VUJ 1VUK 1VUL 1VUM 1VUN 1VUO 1VUP 1VUQ 1VUR 1VUS 1VUT } { mol new $i }


Page created and maintained by Juan R. Perilla.