Development of Gadolinium(III) Spin Labels to Study Architecture and Dynamics of Membrane Proteins

Figure 1: Spin labeling.  SDSL is accomplished by introducing an EPR-active side chain at selected locations in proteins. For example, by attaching a Gd3+ based spin label on residues of interest in proteorhodhopsin.

 

Figure 2: PR hexamer.  Putative model of PR hexamer, with distances measured using a Gd3+ based spin label.

Membrane proteins control the flow of matter, energy, and information between the interior and exterior of a cell and are of fundamental importance to a wide range of cellular processes. Despite their prevalence, membrane proteins remain poorly understood due to their notorious resistance to standard NMR and X-ray crystallography techniques. An emerging technique, electron paramagnetic resonance (EPR) in conjunction with site-directed spin labeling (SDSL) facilitates elucidation of protein structure by allowing measurement of distances between selectively labeled sites on a protein or protein complex. This technique has several advantages over conventional NMR, including sensitivity of absolute number of spins, spatial resolution for spin-spin distance measurements, and time resolution of dynamical structure change.

The goal of this project is to develop a new class of spin labels based on the spin-7/2 Gd3+ ion to enable structural studies under a variety of biologically important conditions that are difficult or impossible with conventional nitroxide spin labels. The paramagnetic core of the Gd3+ ion is well shielded by outer electrons, making it much less sensitive to the local chemical environment and will survive for days in vivo. Unlike nitroxides, Gd3+ spectra are relatively insensitive to nearby protons, allowing for EPR in environments that are not deuterated. Distance measurements can be performed on samples less than 1/10th the volume of samples using nitroxides, enabling study of proteins that are difficult to express in large quantities. Additionally, with continuous wave EPR using Gd3+ based spin labels we are able to achieve superior sensitivity for making distance measurements at biologically relevant temperatures. The paramagnetic attributes of the Gd3+ ion are particularly favorable at high magnetic fields and frequencies, one of the frontiers of EPR.

Currently, we are particularly interested in study structure and conformational changes in proteorhodhopsin (PR), a recently discovered light-activated proton pump found in marine bacterioplanktons. PR belongs to the large class of the heptahelical trans-membrane (7TM) proteins, which make up 40% of all drug targets.

We are also interested in studying the phenomenon of chemotaxis in bacteria using high-field EPR with SDSL. Bacteria are able to sense rapid changes concentration gradients of certain chemicals and alter their behavioral responses accordingly. This environmental adaptation is associated with transmembrane receptors that transmit information from outside the membrane to the cytoplasm. In combination with NMR and other methods, we hope to understand the structures, dynamics, and interactions of the proteins involved in this signaling system.

UCSB Researchers

PIs: Prof.  Mark Sherwin (Physics), Prof. Songi Han (Chemistry and Biochemistry)

Graduate Students: Devin Edwards (Physics), Jessica Clayton (Physics)

Undergraduates: Andrew Pierce (Physics), Mary-Lou Bailey (Physics and Biology).

Collaborators

Prof. Daniella Goldfarb (Weizmann Institute of Science)

Prof. Adelheid Godt and Mian Qi (Bielefeld University)

Prof. Rick Dahlquist (UCSB)

Publications

  1. D. Edwards, S. Takahashi, M. S. Sherwin, S. Han, Distance measurements across randomly distributed nitroxide probes from the temperature-dependence of the electron spin phase memory time at 240 GHz.  Journal of Magnetic Resonance 223, 198-206 (2012) [doi.org/10.1016/j.jmr.2012.07.004]
  2. D.T. Edwards, Z. Ma, T.J. Meade, D. Goldfarb, S. Han & M.S. Sherwin, Extending the distance range accessed with continuous wave EPR with Gd3+ spin probes at high magnetic fields. Submitted to PCCP (2012).