Dipolar Waves in helical proteins

Dipole-dipole couplings are a major source of structural information. The strength of this moment varies as a function of distance apart between two objects and the angle with respect to a reference axis. In structural biology of proteins, these moments are routinely measured using the state-of-the-art nuclear magnetic resonance (NMR) spectroscopy in the form of residual dipolar couplings (RDCs) and dipolar couplings (DCs) in weakly, partially and strongly oriented samples.

A new method called rotationally aligned solid state NMR (RA-SSNMR) has recently been developed to measure DCs from proteins embeded in biological membrane mimetics. The method relies on naturally occuring rotationally diffusion around the bilayer normal. It is a well known fact that membrane proteins undergo fast rotational motion in phospholipid bilayers under physiological conditions of temperature, pH and hydration (For references, please check my 2015 publication in Biophysica Biochimica Acta). RA-SSNMR is a powerful technique to measure both 1H-13C and 1H-15N DCs from unformly isotope labeled proteins.

The above figure demonstrates the simulation of an ideal helix and experimental measurement of DCs from three different membrane proteins, when plotted as a function of residue numbers yield a sinusoidal type wave pattern popularly known as dipolar waves (DWs). The amplitude and periodicity of these waves are strongly related to the topology and helicity in the proteins. For example the simulated pattern for an ideal helix is shown for tilt angles of 0, 10 and 20 degrees with respect the vertical axis for demonstration only. The right side figures are from a single transmembrane helix (1TM) of viral protein u from human immunodeficiency virus 1 (HIV-1) [1], two tranmenrane helices (2TM) of mercury transporter protein (MerF) [2] and seven transmembrane helices (7TM) of CXC chemokine receptor 1, a human G protein-coupled receptor (GPCR) [3]. The amplitude of the dipolar wave for 1TM helix is measured for a tilt angle of 28 degree. DWs are extremely informative helping the computational biologists to identify the start and end residues of a secondary structure, helical break, periodicity, and kinks in helical conformations. This is clearly evident from the 2TM and 7TM DWs.

References:

1. Das BB, Zhang H and Opella SJ, Dipolar Assisted Assignment Protocol for Rotationally Aligned Membrane Proteins in Phospholipid Bilayer, J. Magn. Reson. 242, 224-232.

2. Das BB, Nothnagel HJ, Lu GJ, Son WS, Tian Y, Marassi FM, Opella SJ. Structure determination of a membrane protein in proteoliposomes. J Am Chem Soc., 134(4), 2047-56.

3. Park SH, Das BB, Casagrande F, Tian Y, Nothnagel HJ, Chu M, Kiefer H, Maier K, De Angelis A, Marassi FM and Opella SJ, Structure of the Chemokine Receptor CXCR1 in Phospholipid Bilayers, Nature, 491, 779–783.