Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

4-POS Board 4 Conformational Ensembles of the HIV Vif Complex K. Aurelia Ball 1 , Lieza Chan 1 , Eliese Tierney 1 , David Stanley 3 , Matthew Jacobson 2 , John Gross 2 . 1 Skidmore College, Saratoga Springs, NY, USA, 2 University of California San Francisco, San Francisco, CA, USA, 3 University Of California Berkeley, Berkeley, CA, USA. Like many viruses, HIV hijacks the host cell's apparatus for normal protein ubiquitination and degradation, using it to eliminate antiviral proteins. Understanding how a virus recruits and targets the ubqiuitination complex is critical for developing therapeutics to prevent it. One HIV protein responsible for this hijacking is Virion infectivity factor (Vif). Vif is intrinsically disordered but loses flexibility as it binds more host proteins, a process that may be crucial for function. We are investigating the complex formed with Vif and the host proteins Elongin B (EloB), Elongin C (EloC), and Core-Binding Factor subunit beta (CBF-beta) to determine what remaining conformational flexibility Vif retains as part of this large complex with folded proteins. Using molecular dynamics simulations, we have found that this Vif-host protein complex exhibits large-scale conformational changes and occupies alternate conformational states. These conformational dynamics are altered when additional proteins such as Cullin 5, part of the ubiquitination complex, or APOBEC3F, an antiviral protein targeted by Vif for ubiquitination, are bound to the complex. We observe a reduction in large scale motions of the complex and a reduction in the sampling of the conformational landscape when an additional protein is bound. Additionally, we find that the partially disordered C-terminus of EloB is important for the structural stability of the complex. These computational results are supported by methyl-labeled NMR spectroscopy. The alternate conformations sampled in our simulations are important for better understanding the function of the complex in ubiquitinating APOBEC, as well as how a disordered protein like Vif can affect the dynamics of a larger complex of folded proteins.

37