Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban

Purified, reconstituted cardiac Ca2+-ATPase is regulated by phospholamban but not by direct phosphorylation with Ca2+/calmodulin-dependent protein kinase

Regulation of calcium transport by sarcoplasmic reticulum provides increased cardiac contractility in response to beta-adrenergic stimulation. This is due to phosphorylation of phospholamban by cAMP-dependent protein kinase or by calcium/calmodulin-dependent protein kinase, which activates the calcium pump (Ca2+-ATPase). Recently, direct phosphorylation of Ca2+-ATPase by calcium/calmodulin-dependent protein kinase has been proposed to provide additional regulation. To investigate these effects in detail, we have purified Ca2+-ATPase from cardiac sarcoplasmic reticulum using affinity chromatography and reconstituted it with purified, recombinant phospholamban. The resulting proteoliposomes had high rates of calcium transport, which was tightly coupled to ATP hydrolysis (approximately 1.7 calcium ions transported per ATP molecule hydrolyzed). Co-reconstitution with phospholamban suppressed both calcium uptake and ATPase activities by approximately 50%, and this suppression was fully relieved by a phospholamban monoclonal antibody or by phosphorylation either with cAMP-dependent protein kinase or with calcium/calmodulin-dependent protein kinase. These effects were consistent with a change in the apparent calcium affinity of Ca2+-ATPase and not with a change in Vmax. Neither the purified, reconstituted cardiac Ca2+-ATPase nor the Ca2+-ATPase in longitudinal cardiac sarcoplasmic reticulum vesicles was a substrate for calcium/calmodulin-dependent protein kinase, and accordingly, we found no effect of calcium/calmodulin-dependent protein kinase phosphorylation on Vmax for calcium transport.

Molecular dynamics simulations of water within models of ion channels

The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.

Fourier transform infrared spectroscopy and site-directed isotope labeling as a probe of local secondary structure in the transmembrane domain of phospholamban

Phospholamban is a 52-amino acid residue membrane protein that regulates Ca(2+)-ATPase activity in the sarcoplasmic reticulum of cardiac muscle cells. The hydrophobic C-terminal 28 amino acid fragment of phospholamban (hPLB) anchors the protein in the membrane and may form part of a Ca(2+)-selective ion channel. We have used polarized attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy along with site-directed isotope labeling to probe the local structure of hPLB. The frequency and dichroism of the amide I and II bands appearing at 1658 cm-1 and 1544 cm-1, respectively, show that dehydrated and hydrated hPLB reconstituted into dimyristoylphosphatidycholine bilayer membranes is predominantly alpha-helical and has a net transmembrane orientation. Specific local secondary structure of hPLB was probed by incorporating 13C at two positions in the protein backbone. A small band seen near 1614 cm-1 is assigned to the amide I mode of the 13C-labeled amide carbonyl group(s). The frequency and dichroism of this band indicate that residues 39 and 46 are alpha-helical, with an axial orientation that is approximately 30 degrees relative to the membrane normal. Upon exposure to 2H2O (D2O), 30% of the peptide amide groups in hPLB undergo a slow deuterium/hydrogen exchange. The remainder of the protein, including the peptide groups of Leu-39 and Leu-42, appear inaccessible to exchange, indicating that most of the hPLB fragment is embedded in the lipid bilayer. By extending spectroscopic characterization of PLB to include hydrated, deuterated as well as site-directed isotope-labeled hPLB films, our results strongly support models of PLB that predict the existence of an alpha-helical hydrophobic region spanning the membrane domain.

Mapping the lipid-exposed surfaces of membrane proteins

Phospholamban forms a stable complex of five long transmembrane helices. We show that the relative rotational orientation of the helices in the pentameric complex can be distinguished by S-H to S-D exchange of cysteine sulphydryl groups located in the transmembrane segment of the protein and exposed to the lipid environment. Of the three cysteine residues in phospholamban, two residues (Cys 36 and Cys 46) are oriented towards the helix interface and protected from exchange, while the third cysteine (Cys 41) is oriented towards the lipid interface and undergoes exchange with water diffused into the bilayer. Distinguishing the external and internal faces of a membrane protein by sulphydryl exchange provides a general approach for determining the three-dimensional fold of membrane proteins and enhances model building efforts to generate high-resolution structures.

Modeling of a five-stranded coiled coil structure for the assembly domain of the cartilage oligomeric matrix protein

The three-dimensional structure of the assembly domain of the cartilage oligomeric matrix protein (COMP) has been modeled. The model demonstrates a parallel five-stranded coiled coil and fits well with a large amount of experimental data that describe the oligomerization state, the alpha-helical conformation, the helix directionality and the properties of the (abcdefg)n repeat sequence containing apolar residues at (a) and (d) positions. Comparison of the pentamer model with the known dimer, trimer, and tetramer coiled coils revealed interactions that could mediate the switch to the formation of the pentamer coiled coil. The most distinctive feature of the pentamer model involves ion pair interactions. Charged side chains of the pentamer can form (f-g), (f-b'), and (e-c') interhelical ion pairs, which are neither experimentally observed nor modeled in the di-, tri-, and tetramers. A polar glutamine residue could be adopted at an interior (d) position of the modeled structure due to the formation of a symmetrical network of buried hydrogen bonds between five such glutamines. The pentamer model contains an axial cavity that can accept water molecules. Conformational analysis was carried out in an attempt to determine the three-dimensional structure of the disulfide bonded C-terminal region of the pentamer. Recent data on crystallization of the COMP assembly domain (Efimov et al., Proteins 24:259-262, 1996) indicate that the prediction can be tested experimentally in the near future.

Molecular mimicry in channel-protein structure

The approach to probing the sequence-structure relationship of ion-channel proteins using small peptides stems from the abundance of sequence information and the virtual absence of structures at atomic resolution. It is anticipated that model peptides may fold predictably into stable structures and reproduce functional properties of specific proteins. Model peptides are well suited to the application of NMR methods to determine protein structure in a membrane environment or to high-resolution X-ray diffraction analysis. It is timely to ask what we have learned through this strategy and where it may lead in our quest to understand the sequence-structure determinism.

Engineering membrane proteins

Much of the research on integral membrane proteins mirrors that on soluble proteins; however, membrane protein engineering also has its own ends and means, many of which take advantage of the peculiar situation of membrane proteins, whose chains are distributed between one lipidic and two aqueous phases. Extramembrane loops have been shortened, cut, or elongated with segments forming proteolytic cleavage sites, foreign epitopes, extra transmembrane segments, or even whole proteins, with the aim of facilitating purification, biochemical/biophysical studies, or crystallogenesis. Transmembrane alpha-helices have been deleted, duplicated, exchanged, transported into a foreign context or replaced with synthetic peptides, in order to both understand their integration into, and assembly in, the membrane and unravel their functional role. Insertion of cysteine residues has been the basis for a great diversity of experiments, ranging from the exploration of secondary, tertiary and quaternary structures of the transmembrane region to the creation of anchoring points for reporter molecules. Chemical engineering--the synthesis of protein fragments or even of whole proteins--offers particularly exciting new prospects, given the small size of folding domains in alpha-helical membrane proteins. Membrane protein engineering is rapidly developing its own agenda of questions and tool chest of techniques.