The conformation of membrane-bound and detergent-solubilised bovine rhodopsin. A comparative hydrogen-isotope exchange study

Functional Studies on Membrane Proteins by Means of H/D Exchange in Infrared: Structural Changes in Na+ NQR from V. cholerae in the Presence of Lipids

H/D exchange kinetics at the level of the amide proton in the mid infrared (1700-1500 cm^-1) make it possible to study the conformational flexibility of membrane proteins, independent of size or the presence of detergent or lipids. Slow, medium, and fast exchanging domains are distinguished, which reveal a different accessibility to the solvent. Whereas amide hydrogens undergo rapid exchange with solvent in an open structure, hydrogens experience much slower exchange when involved in H-bonded structures or when sterically inaccessible to the solvent. Here, we describe the protocol that was used to study the effect of phospholipids on the overall structure of the Na⁺ NQR from V. cholerae, a sodium pumping membrane protein.

Mass spectrometry techniques for detection of ligand-dependent changes in the conformational flexibility of cellular retinol-binding protein type I localized by hydrogen/deuterium exchange

Hydrogen/deuterium exchange, measured by electrospray ionization with orthogonal quadrupole time-of-flight mass spectrometry (ESI-Q-TOFMS) and by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), was used as a means to probe and map differences in conformational flexibility between the ligand-free and ligand-bound forms of cellular retinol-binding protein type I. Labelled fragments were obtained by digestion of the protein with pepsin. The differences in space-resolved time courses of deuterium incorporation identified regions that exhibit a remarkably higher degree of flexibility in the apo-protein than in the holo-protein. These segments encompass residues that are thought, on the basis of structural homology of the retinol carrier with other members of the intracellular lipid-binding proteins family, to belong to the dynamic portal through which all-trans retinol can access its high-affinity, solvent-shielded, binding site.

Photoactivation of rhodopsin causes an increased hydrogen-deuterium exchange of buried peptide groups

A key step in visual transduction is the light-induced conformational changes of rhodopsin that lead to binding and activation of the G-protein transducin. In order to explore the nature of these conformational changes, time-resolved Fourier transform infrared spectroscopy was used to measure the kinetics of hydrogen/deuterium exchange in rhodopsin upon photoexcitation. The extent of hydrogen/deuterium exchange of backbone peptide groups can be monitored by measuring the integrated intensity of the amide II and amide II' bands. When rhodopsin films are exposed to D2O in the dark for long periods, the amide II band retains at least 60% of its integrated intensity, reflecting a core of backbone peptide groups that are resistant to H/D exchange. Upon photoactivation, rhodopsin in the presence of D2O exhibits a new phase of H/D exchange which at 10 degrees C consists of fast (time constant approximately 30 min) and slow (approximately 11 h) components. These results indicate that photoactivation causes buried portions of the rhodopsin backbone structure to become more accessible.

A biophysical study of integral membrane protein folding

In order to characterize the thermodynamic constraints on the process of integral membrane protein folding and assembly, we have conducted a biophysical dissection of the structure of bacteriorhodopsin (BR), a prototypical alpha-helical integral membrane protein. Seven polypeptides were synthesized, corresponding to each of the seven transmembrane alpha-helices in BR, and the structure of each individual polypeptide was characterized in reconstituted phospholipid vesicles. Five of the seven polypeptides form stable transmembrane alpha-helices in isolation from the remainder of the tertiary structure of BR. However, using our reconstitution protocols, the polypeptide corresponding to the F helix in BR does not form any stable secondary structure in reconstituted vesicles, and the polypeptide corresponding to the G helix forms a hyperstable beta-sheet structure with its strands oriented perpendicular to the plane of the membrane. [The polypeptide corresponding to the C helix spontaneously equilibrates in a pH-dependent manner between a transmembrane alpha-helical conformation, a peripherally bound nonhelical conformation, and a fully water soluble conformation; the conformational properties of this polypeptide are the subject of the accompanying paper: Hunt et al. (1997) Biochemistry 36, 15177-15192.] Our observations suggest that the folding of alpha-helical integral membrane proteins may proceed spontaneously. However, the preference for a non-native conformation exhibited by two of the polypeptides suggests that the formation of some transmembrane substructures could require external constraints such as the links between the helices, interactions with the rest of the protein, or the involvement of cellular chaperones or translocases. Our results also suggest a strategy for improving the thermodynamic stability of alpha-helical integral membrane proteins, a goal that could facilitate attempts to overexpress and/or refold them.

Fourier transform infrared study of the rod outer segment disk and plasma membranes of vertebrate retina

Phospholipid composition and structure of disk and plasma membranes purified from bovine rod outer segments (ROS) are examined using Fourier transform infrared spectroscopy. Vibrational data indicate that both disk and plasma membranes lack sphingophospholipids, in contrast to the lens membranes. The hydrocarbon chains of the disk lipids are unsaturated by a factor of 5 over the acyl chains of the plasma lipids. The plasma lipids with 3-fold higher cholesterol and 5-fold higher saturation melt at a higher temperature (26 degrees C) than the disk lipids which melt at 16 degrees C. The transition temperature decreases by more than 20 degrees C in going from disk lipids to disk membrane, indicating a large drop in the enthalpy of the ROS membrane-matrix, presumably due to enhanced rhodopsin-lipid interaction. The lipid composition predisposes the disk and plasma membranes to be fluid and structurally disordered (about 84%) around physiological temperature. The fluid phospholipid environment of the disk membrane (i.e., just a few degrees above subzero temperatures) is considered to be vital for the ROS photoreceptor function. The amide I band profile of rhodopsin indicates an extensive alpha-helical (53%) peptide chain, with little beta-sheet (21%) and beta-turns (18%) in ROS membranes. This structure and/or conformation is conserved between 0-60 degrees C even though disk and plasma lipids undergo a phase change. The H-D exchange data indicate that as much as 84% of the peptide residues of ROS membranes in partially bleached retinas is accessible to D2O solvent after 1 h.(ABSTRACT TRUNCATED AT 250 WORDS)

Rhodopsin-detergent micelles aggregate upon activation of cyclic guanosine monophosphate phosphodiesterase

In the presence of G protein and phosphodiesterase, GTP induces aggregation of phospholipid-free rhodopsin-detergent micelles or rhodopsin reconstituted in phospholipid vesicles. The net electrical charge of the vesicle is not critical to the aggregation process since this phenomenon is not altered by reconstitution with phospholipids with different charge. The aggregation process is observed by monitoring changes in the light-scattering properties of the detergent micelles or vesicle suspension and by phase-contrast microscopy. The lowest light intensity which triggers the aggregation process and concomitant light-scattering changes in a rhodopsin-detergent micellar suspension bleaches 6% rhodopsin. Under these conditions, the signal saturates at 30% rhodopsin bleaching. The aggregation process appears likely to depend on the protein-protein interaction, and the presence of a disk membrane is not necessary for this process.

Binding stoichiometry of a fluorescent cGMP analogue to membranes of retinal rod outer segments

The high-affinity binding of the cGMP analogue 8-(5-thioacetamidofluorescein)-cGMP to rod outer segment membranes depleted of peripherally bound proteins has been defined by equilibrium dialysis (mean +/- SD): membranes contain about one cGMP binding site per 130 rhodopsin molecules; the concentration of free ligand for half saturation is 2.0 +/- 0.6 microM; the apparent Hill coefficient of the bound versus free ligand relationship is 1.7 +/- 0.5; half saturation of the binding sites is sufficient for 85% activation of calcium permeability. A gating mechanism is proposed.

Hydrogen exchange and the dynamic structure of proteins

In native proteins, buried, labile protons undergo isotope exchange with solvent hydrogens, but the kinetics of exchange are markedly slower than in unfolded polypeptides. This indicates that, whereas buried protein atoms are shielded from solvent, the protein fluctuates around the time average structure and occasionally exposes buried sites to solvent. Generally, hydrogen exchange studies are designed to characterize the nature of the fluctuations between conformational substates, to monitor the shift in conformational equilibria among protein substates due to ligand binding or other factors, or to monitor the major cooperative denaturation transition. In this article, we review the recent reports of hydrogen exchange in proteins, focusing on recent advances in methodology, especially with regard to the implications of the results for the mechanism of hydrogen exchange in folded proteins.

Molecular dynamics of two homologous neurotoxins revealed by 1H-2H exchange: an infrared spectrometry study

Temperature effects on the hydrogen exchange kinetics and the infrared spectra of two homologous snake neurotoxins (Laticauda semifasciata erabutoxin b and Naja nigricollis toxin alpha) were investigated between 10 and 40 degrees C, at their isoionic pH. (1) Erabutoxin b is more accessible to the solvent than toxin alpha. (2) With increasing temperature, both toxin molecules undergo a global transition affecting the most accessible as well as the most buried hydrogens: the overall accessibility changes are more important for erabutoxin b than for toxin alpha. The different conformational stabilities of the toxins are also qualitatively supported by the temperature-induced shifts which affect the infrared amide I band of toxin alpha only. The existence of two conformer families could be responsible for the different conformational stability of these proteins.

Fourier transform infrared study of photoreceptor membrane. I. Group assignments based on rhodopsin delipidation and reconstitution

Fourier transform infrared spectroscopy has been used to study the structure of bovine photoreceptor membrane. Rhodopsin appears to contain an extensive alpha-helical structure which is arranged predominantly perpendicular to the membrane plane. Spectra of delipidated rhodopsin and rhodopsin membranes reconstituted from dioleyl-phosphatidylcholine were compared with native photoreceptor membrane from rod outer segments in order to facilitate peak assgnments. It is concluded that spectroscopic peaks characteristic of several protein and lipid groups can be assigned. We also find delipidation leads to alteration of the rhodopsin structure which is resorted upon reconstitution. Membranes both suspended in 2H2O and dehydrated were compared in order to detect possible conformational differences. Dehydration does not appear to grossly alter rhodopsin structure, although it may affect delipidated rhodopsin.