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Conformational Dynamics of the HIV-Vif Protein Complex.

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Area of Science:

  • Structural biology
  • Virology
  • Biochemistry

Background:

  • Human immunodeficiency virus-1 viral infectivity factor (Vif) targets APOBEC3 antiviral proteins for ubiquitination.
  • The Vif-containing Elongin-B, Elongin-C, Vif, and CBF-β (VCBC) complex, along with Cullin5 (CUL5), forms a key ubiquitination machinery.
  • The dynamics of the VCBC-CUL5 complex are not well understood.

Purpose of the Study:

  • To characterize the dynamics of the VCBC complex with and without CUL5 and an APOBEC3 protein.
  • To investigate the conformational flexibility of the VCBC complex in different binding states.

Main Methods:

  • Molecular dynamics (MD) simulations were employed to analyze complex dynamics.
  • Methyl-transverse relaxation-optimized spectroscopy (13C-methyl-TROSY) NMR was used to assess conformational dynamics.

Main Results:

  • MD simulations revealed global dynamics (twisting, clamshell opening) in the VCBC complex.
  • The VCBC-CUL5 complex exhibited a more static conformation, consistent with crystal structures.
  • NMR data confirmed VCBC complex dynamics on the μs-ms timescale and showed increased rigidity upon APOBEC3F binding.

Conclusions:

  • The VCBC complex displays significant conformational flexibility, which is reduced upon binding to CUL5 or APOBEC3F.
  • The flexible linker region in Vif contributes to the complex's global dynamics.
  • The VCBC complex's conformational plasticity presents a potential therapeutic target for inhibiting ubiquitination complex assembly.