Related Experiment Video

Updated: Jul 19, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

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

Olga K Baryshnikova1, Brian D Sykes

  • 1Department of Biochemistry and Protein Engineering Network of Centres of Excellence, University of Alberta, Edmonton, Alberta T6G 2S2, Canada.

Protein Science : a Publication of the Protein Society
|November 1, 2006
PubMed

Insights

Chemokine SDF-1alpha (CXCL12) dynamics reveal monomer-dimer equilibrium crucial for its function. NMR relaxation data show SDF-1alpha is rigid with flexible ends, highlighting its oligomerization importance.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Chemical Physics

Background:

  • Stromal cell-derived factor-1alpha (SDF-1alpha), a chemokine, interacts with CXCR4, mediating cancer metastasis and HIV-1 pathogenesis.
  • Contrasting NMR (monomeric) and X-ray (dimeric) structures suggest oligomerization influences SDF-1alpha function.
  • Biochemical and in vivo data support the functional importance of chemokine dimerization.

Purpose of the Study:

  • To investigate the dynamics of SDF-1alpha using Nuclear Magnetic Resonance (NMR) relaxation measurements.
  • To determine the monomer-dimer equilibrium constant for SDF-1alpha.
  • To analyze the flexibility and motion of monomeric SDF-1alpha.

Main Methods:

  • Measurement of main chain (15)N NMR relaxation data at various SDF-1alpha concentrations.
  • Determination of the dimerization constant (Kd) from concentration-dependent relaxation data.
  • Application of the model-free approach to analyze NMR relaxation data for monomeric and dimeric states.

Main Results:

  • A monomer-dimer equilibrium constant of approximately 5 mM was determined for SDF-1alpha.
  • Extrapolation of relaxation data allowed analysis of monomeric SDF-1alpha dynamics.
  • Model-free analysis revealed SDF-1alpha is rigid on the ns-ps timescale with flexible termini, and dimeric interfaces exhibit slow ms timescale motions.

Conclusions:

  • NMR relaxation measurements effectively characterize oligomerization processes like SDF-1alpha dimerization.
  • The study elucidates the dynamics of SDF-1alpha, linking its structural flexibility to its functional monomer-dimer equilibrium.
  • Understanding SDF-1alpha dynamics provides insights into its role in cancer and viral pathogenesis.

More Related Videos

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling10:27

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.