Magnetic resonance in the solid state: applications to protein folding, amyloid fibrils and membrane proteins

Cu(II) binding to various forms of amyloid-β peptides. Are they friends or foes?

In the present micro-review, we describe the Cu(II) binding to several forms of amyloid-β peptides, the peptides involved in Alzheimer's disease. It has indeed been shown that in addition to the "full-length" peptide originating from the precursor protein after cleavage at position 1, several other shorter peptides do exist in large proportion and may be involved in the disease as well. Cu(II) binding to amyloid-β peptides is one of the key interactions that impact both the aggregating properties of the amyloid peptides and the Reactive Oxygen Species (ROS) production, two events linked to the etiology of the disease. Binding sites and affinity are described in correlation with Cu(II) induced ROS formation and Cu(II) altered aggregation, for amyloid peptides starting at position 1, 3, 4, 11 and for the corresponding pyroglutamate forms when they could be obtained (i.e. for peptides cleaved at positions 3 and 11). It appears that the current paradigm which points out a toxic role of the Cu(II) - amyloid-β interaction might well be shifted towards a possible protective role when the peptides considered are the N-terminally truncated ones.

Study of Amyloids Using Yeast

We detail some of the genetic, biochemical, and physical methods useful in studying amyloids in yeast, particularly the yeast prions. These methods include cytoduction (cytoplasmic mixing), infection of cells with prion amyloids, use of green fluorescent protein fusions with amyloid-forming proteins for cytology, protein purification and amyloid formation, and electron microscopy of filaments.

Secondary structural analysis of proteins based on (13)C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database

Magic-angle-spinning solid-state (13)C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-(13)C,(15)N labeled samples. To overcome this problem, we present a method for assigning (13)C chemical shifts and secondary structures from unresolved two-dimensional (13)C-(13)C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to (13)C(α), (13)C(β), and (13)C' chemical shifts and cross-peak intensities. The experimental (13)C-(13)C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific C(α), C(β), and C' chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50-200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved (13)C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.

Study of amyloids using yeast

We detail some of the genetic, biochemical, and physical methods useful in studying amyloids in yeast, particularly the yeast prions. These methods include cytoduction (cytoplasmic mixing), infection of cells with prion amyloids, use of green fluorescent protein fusions with amyloid-forming proteins for cytology, protein purification and amyloid formation, and electron microscopy of filaments.

Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method

Phospholamban (PLN) is a type II membrane protein that inhibits the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA), thereby regulating calcium homeostasis in cardiac muscle. In membranes, PLN forms pentamers that have been proposed to function either as a storage for active monomers or as ion channels. Here, we report the T-state structure of pentameric PLN solved by a hybrid solution and solid-state NMR method. In lipid bilayers, PLN adopts a pinwheel topology with a narrow hydrophobic pore, which excludes ion transport. In the T state, the cytoplasmic amphipathic helices (domains Ia) are absorbed into the lipid bilayer with the transmembrane domains arranged in a left-handed coiled-coil configuration, crossing the bilayer with a tilt angle of approximately 11° with respect to the membrane normal. The tilt angle difference between the monomer and pentamer is approximately 13°, showing that intramembrane helix-helix association forces dominate over the hydrophobic mismatch, driving the overall topology of the transmembrane assembly. Our data reveal that both topology and function of PLN are shaped by the interactions with lipids, which fine-tune the regulation of SERCA.

A reconstitution protocol for the in vitro folded human G protein-coupled Y2 receptor into lipid environment

Although highly resolved crystal structures of G protein-coupled receptors have become available within the last decade, the need for studying these molecules in their natural membrane environment, where the molecules are rather dynamic, has been widely appreciated. Solid-state NMR spectroscopy is an excellent method to study structure and dynamics of membrane proteins in their native lipid environment. We developed a reconstitution protocol for the uniformly (15)N labeled Y(2) receptor into a bicelle-like lipid structure with high yields suitable for NMR studies. Milligram quantities of target protein were expressed in Escherichia coli using an optimized fermentation process in defined medium yielding in over 10mg/L medium of purified Y(2) receptor solubilized in SDS micelles. The structural integrity of the receptor molecules was strongly increased through refolding and subsequent reconstitution into phospholipid membranes. Specific ligand binding to the integrated receptor was determined using radioligand affinity assay. Further, by NMR measurement a dispersion of the (15)N signals comparable to native rhodopsin was shown. The efficiency of the reconstitution could also be inferred from the fact that reasonable (13)C NMR spectra at natural abundance could be acquired.

Targeted 13C-13C distance measurements in a microcrystalline protein via J-decoupled rotational resonance width measurements

Rotational resonance width (R(2)W) magic-angle spinning (MAS) NMR experiments are performed to measure (13)C-(13)C distances in the hydrophobic core of the microcrystalline model protein G(Beta1). Such inter-residue distances are of particular value in NMR structure determinations. The experiments are done at a Larmor frequency of 750 MHz (1)H where the contribution of (13)C chemical shift anisotropy (CSA) to the R(2) transfer mechanism is significant. To minimize line broadening in the 2D spectra, we employ a combination of even/odd isotopic labeling with [1,3-(13)C] glycerol, and J-decoupling in the indirect dimension. This results in high-precision distance measurements between aromatic side chains of three tyrosine residues and distant methyl groups in the hydrophobic core of the protein. Even in the absence of information on the relative orientation of the shift tensors, we obtain relatively high precision data, which can be further improved by additional constraints on the tensor orientations.

Tilt and azimuthal angles of a transmembrane peptide: a comparison between molecular dynamics calculations and solid-state NMR data of sarcolipin in lipid membranes

We report molecular dynamics simulations in the explicit membrane environment of a small membrane-embedded protein, sarcolipin, which regulates the sarcoplasmic reticulum Ca-ATPase activity in both cardiac and skeletal muscle. In its monomeric form, we found that sarcolipin adopts a helical conformation, with a computed average tilt angle of 28 +/- 6 degrees and azymuthal angles of 66 +/- 22 degrees, in reasonable accord with angles determined experimentally (23 +/- 2 degrees and 50 +/- 4 degrees, respectively) using solid-state NMR with separated-local-field experiments. The effects of time and spatial averaging on both (15)N chemical shift anisotropy and (1)H/(15)N dipolar couplings have been analyzed using short-time averages of fast amide out-of-plane motions and following principal component dynamic trajectories. We found that it is possible to reproduce the regular oscillatory patterns observed for the anisotropic NMR parameters (i.e., PISA wheels) employing average amide vectors. This work highlights the role of molecular dynamics simulations as a tool for the analysis and interpretation of solid-state NMR data.