Backbone dynamics of SDF-1alpha determined by NMR: interpretation in the presence of monomer-dimer equilibrium

Protein Sci. 2006 Nov;15(11):2568-78. doi: 10.1110/ps.062255806.

Abstract

SDF-1alpha is a member of the chemokine family implicated in various reactions in the immune system. The interaction of SDF-1alpha with its receptor, CXCR4, is responsible for metastasis of a variety of cancers. SDF-1alpha is also known to play a role in HIV-1 pathogenesis. The structures of SDF-1alpha determined by NMR spectroscopy have been shown to be monomeric while X-ray structures are dimeric. Biochemical data and in vivo studies suggest that dimerization is likely to be important for the function of chemokines. We report here the dynamics of SDF-1alpha determined through measurement of main chain (15)N NMR relaxation data. The data were obtained at several concentrations of SDF-1alpha and used to determine a dimerization constant of approximately 5 mM for a monomer-dimer equilibrium. The dimerization constant was subsequently used to extrapolate values for the relaxation data corresponding to monomeric SDF-1alpha. The experimental relaxation data and the extrapolated data for monomeric SDF-1alpha were analyzed using the model free approach. The model free analysis indicated that SDF-1alpha is rigid on the nano- to picosecond timescale with flexible termini. Several residues involved in the dimer interface display slow micro- to millisecond timescale motions attributable to chemical exchange such as monomer-dimer equilibrium. NMR relaxation measurements are shown to be applicable for studying oligomerization processes such as the dimerization of SDF-1alpha.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Chemokine CXCL12
  • Chemokines / chemistry
  • Chemokines, CXC / chemistry*
  • Dimerization
  • Humans
  • Models, Molecular
  • Models, Theoretical
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Osmolar Concentration
  • Protein Binding

Substances

  • CXCL12 protein, human
  • Chemokine CXCL12
  • Chemokines
  • Chemokines, CXC