14] Nuclear magnetic resonance of membrane-associated peptides and proteins

Abstract

Structural biology is based on the premise that the fundamental understanding of biological functions lies in the three-dimensional structures of proteins and other biopolymers. The two well-established experimental methods for determining the structures of proteins work very well for globular proteins: witness the explosive growth of the Protein Data Bank (PDB). However, approximately 30% of all expressed polypeptides are membrane-associated, and neither X-ray crystallography nor solution nuclear magnetic resonance (NMR) spectroscopy is very effective for these proteins. The lipids required for the structural integrity and functionality of membrane proteins impede crystallization as well as the rate of overall reorientation in solution. NMR of Proteins NMR spectroscopy can be applied to wide variety of samples, ranging from isotropic solutions to crystalline powders, including those with slowly reorienting or immobile macromolecules, such as membrane proteins in lipid environments. NMR is capable of resolving signals from all atomic sites in proteins, and each site has several well-characterized nuclear spin interactions that can be used as sources of information about molecular structure and dynamics, as well as chemical interactions. The spin interactions can be probed through radio frequency (rf) irradiations and sample manipulations that lead to complementary strategies for NMR spectroscopy of membrane proteins reconstituted in lipid micelles or bilayers. Comparisons between the results obtained with solution NMR experiments on lipid micelle samples, and solid-state NMR experiments on lipid bilayer samples, are especially valuable for membrane proteins with predominantly helical secondary structure. Multidimensional solution NMR methods can be successfully applied to relatively small membrane proteins in micelles; however, the size limitation is substantially more severe than for globular proteins because the many lipid molecules associated with each polypeptide slow its overall reorientation rate. In particular, using currently available instruments and methods, it is difficult to resolve, assign, and measure the “long-range” nuclear overhauser effects (NOEs) between hydrogens on hydrophobic side-chains that are needed to determine tertiary structures based on distance constraints. However, the ability to weakly align membrane proteins in micelles enables the measurement of residual dipolar couplings, and improves the feasibility of determining the structures of membrane proteins using solution NMR methods. Nonetheless, it is highly desirable to determine the structures of membrane proteins in the definitive environment of phospholipid bilayers, where solution NMR methods fail completely for all classes of membrane proteins. Fortunately, solid-state NMR spectroscopy is well suited for peptides and proteins immobilized in phospholipid bilayers. Both oriented sample and magic angle spinning methods provide approaches to measuring orientational and distance parameters for structure determination.