Structural model of the tubular assembly of the Rous sarcoma virus capsid protein

Bo Chen, Ph.D.
University of Central Florida
PSB 160/161, 1:30-2:30pm

Jaekyun Jeon1, Xin Qiao1, Ivan Hung2, Alok K. Mitra5, Ambroise Desfosses5, Daniel Huang1, Peter L. Gor’kov2, Rebecca C. Craven4, Richard L. Kingston5, Zhehong Gan2, Fangqiang Zhu3, and Bo Chen1*

1Department of Physics, University of Central Florida, Orlando, FL 32816, USA
2National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
3Department of Physics, Indiana University – Purdue University Indianapolis, IN 46202, USA
4Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA 17033, USA
5School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand

The Rous Sarcoma Virus (RSV) is the ideal platform to study retrovirus. The RSV capsid enclosing the viral genome materials is assembled from ~ 1500 copies of the 237-residue RSV capsid protein (CA). In vitro, tubular assembly can be obtained with the CA with similar underlying structural properties as the authentic RSV capsid. Due to strong polymorphism, RSV CA assemblies are challenging for structural characterization by techniques such as X-ray diffraction or cryo Electron Microscopy (cryo-EM). We introduced a novel method to exploit well-resolved NCACX spectra of the RSV CA tubular assembly to assist the resonance assignment of NCOCX spectra. We achieved a nearly complete assignment: 234 residues out of the 237 residues were sequentially assigned. Based on this, site-specific dynamics and secondary structural information were determined. Combining with constraints from cryo-EM, we established an atomic resolution model of the tubular assembly by molecular dynamics flexible fitting. Our model shows that significant structural rearrangements take place at flexible loops and the 310 helix regions, while the rest of the protein retains its structure upon assembly. The analyses of our model suggests the assembly polymorphism is attributed to the disorder of the trimer interface between C-terminal domains. In addition, the different contact angles between helices at assembly interfaces of tubular and planar assemblies for HIV and RSV CA, which suggests the two system undergo different assembly pathways.