Structural characterization and biological function of bivalent binding of CD2AP to intrinsically disordered domain of chikungunya virus nsP3 protein

Virology. 2019 Nov:537:130-142. doi: 10.1016/j.virol.2019.08.022. Epub 2019 Aug 22.


Alphavirus nsP3 proteins contain long, intrinsically disordered, hypervariable domains, HVD, which serve as hubs for interaction with many cellular proteins. Here, we have deciphered the mechanism and function of HVD interaction with host factors in alphavirus replication. Using NMR spectroscopy, we show that CHIKV HVD contains two SH3 domain-binding sites. Using an innovative chemical shift perturbation signature approach, we demonstrate that CD2AP interaction with HVD is mediated by its SH3-A and SH3-C domains, and this leaves the SH3-B domain available for interaction with other cellular factor(s). This cooperative interaction with two SH3 domains increases binding affinity to CD2AP and possibly induces long-range allosteric effects in HVD. Our data demonstrate that BIN1, CD2AP and SH3KBP1 play redundant roles in initiation of CHIKV replication. Point mutations in both CHIKV HVD binding sites abolish its interaction with all three proteins, CD2AP, BIN1 and SH3KBP1. This results in strong inhibition of viral replication initiation.

Keywords: Alphaviruses; BIN1; CD2AP; Chikungunya virus; Intrinsically disordered proteins; NMR; SH3 domain-containing proteins; SH3KBP1; Viral replication; nsP3.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / metabolism*
  • Binding Sites
  • Cells, Cultured
  • Chikungunya virus / physiology*
  • Cytoskeletal Proteins / metabolism*
  • Fibroblasts / virology
  • Host-Pathogen Interactions*
  • Humans
  • Magnetic Resonance Spectroscopy
  • Nuclear Proteins / metabolism
  • Protein Binding
  • Protein Interaction Mapping
  • Tumor Suppressor Proteins / metabolism
  • Viral Nonstructural Proteins / metabolism*
  • Virus Replication*


  • Adaptor Proteins, Signal Transducing
  • BIN1 protein, human
  • CD2-associated protein
  • Cytoskeletal Proteins
  • Nuclear Proteins
  • SH3KBP1 protein, human
  • Tumor Suppressor Proteins
  • Viral Nonstructural Proteins
  • nsp3 protein, alphavirus