Relocating the active-site lysine in rhodopsin and implications for evolution of retinylidene proteins

Type I and type II rhodopsins share several structural features including a G protein-coupled receptor fold and a highly conserved active-site Lys residue in the seventh transmembrane segment of the protein. However, the two families lack significant sequence similarity that would indicate common ancestry. Consequently, the rhodopsin fold and conserved Lys are widely thought to have arisen from functional constraints during convergent evolution. To test for the existence of such a constraint, we asked whether it were possible to relocate the highly conserved Lys296 in the visual pigment bovine rhodopsin. We show here that the Lys can be moved to three other locations in the protein while maintaining the ability to form a pigment with 11-cis-retinal and activate the G protein transducin in a light-dependent manner. These results contradict the convergent hypothesis and support the homology of type I and type II rhodopsins by divergent evolution from a common ancestral protein.The retinylidene proteins are integral membrane proteins that covalently bind a retinal chromophore. Amino acid sequence comparison divides these proteins into two families known as type I and type II rhodopsins (1). Type I rhodopsins, such as bacteriorhodopsin from the archaeon Halobacterium salinarum, function as light-driven ion transporters, channels, and phototaxis receptors. Type II rhodopsins, best known for the visual pigment of mammalian rod photoreceptor cells, function primarily as photosensitive receptor proteins in metazoan eyes and in certain extraocular tissues. Henceforth, we will use the term “rhodopsin” to refer to the visual pigment of bovine rod photoreceptor cells and “bacteriorhodopsin” to refer to the light-driven proton pump of H. salinarum.Rhodopsin is a prototypical member of the large family of G protein-coupled receptors (GPCRs; specifically class A GPCRs) (2). It is composed of an apoprotein (called “opsin”) and an 11-cis-retinal chromophore, resulting in a pigment with λ_max = 500 nm. The GPCR fold comprises seven transmembrane α-helices oriented in a particular spatial arrangement with a specific connectivity (SCOP classification scop.b.g.c.A; ref. 3). In rhodopsin, the N terminus resides in the intradiscal (i.e., extracellular) space and the C terminus in the cytoplasm. The 11-cis-retinal chromophore is covalently attached to the protein by means of a protonated Schiff base to the ε-amino group of Lys296 in the seventh helix. The GPCR fold and active-site Lys are absolutely conserved among all visual pigments of higher eukaryotes.Upon absorption of light, the 11-cis-retinal isomerizes to the all-trans form. The protein responds with a conformational change leading to an enzymatic cascade that begins with activation of the G protein transducin and ends with closure of cation channels in the plasma membrane and hyperpolarization of the rod cell (4). A key intermediate in the photoactivation of rhodopsin is the species metarhodopsin II (MII) (5). MII is the only intermediate capable of activating transducin and is characterized by an absorption maximum in the near UV (λ_max = 380 nm), resulting from deprotonation of the Schiff base.Like rhodopsin, bacteriorhodopsin adopts the GPCR fold (1, 3, 6). Bacteriorhodopsin is oriented with the N terminus in the extracellular space and the C terminus in the cytoplasm. The retinal chromophore is attached to the protein covalently by means of a protonated Schiff base to the ε-amino group of a Lys residue, Lys216, in the seventh transmembrane α-helix. Upon absorption of light, a key intermediate, M, in the proton pumping cycle forms in which the Schiff base nitrogen is no longer protonated. With the exception of a few fungal proteins of unknown function, the GPCR fold and the active-site Lys are also conserved among all type I rhodopsin homologs.Despite the striking structural and functional similarities of the type I and type II rhodopsins, there is no significant sequence identity between these two families that would suggest a common ancestral origin (1). It is widely believed that the common fold and active-site Lys are products of convergent evolution resulting from functional constraints on the proteins (1, 7–12). To test this hypothesis, we have focused on the visual pigment rhodopsin and asked whether it is possible to move the active-site Lys296 to a different location in the protein. We attempted to move the Lys to five different locations: two positions in transmembrane helix (TM) 2, one in TM3, one to a different location in TM7, and one in the β-hairpin loop connecting TM4 and TM5 that forms part of the retinal binding pocket. Surprisingly, four of the five mutants combine with 11-cis-retinal to form pigments with near wild-type spectral properties, and three of these four activate transducin in a light-dependent manner with specific activities approaching that of wild-type rhodopsin. These results demonstrate that an absolutely conserved, common structural feature—the Schiff base Lys in helix seven—is not required for rhodopsin’s photosensitive function, contradicting a key prediction of convergent evolution resulting from functional constraint.     

Unusual 1H NMR chemical shifts support (His) C(epsilon) 1...O==C H-bond: proposal for reaction-driven ring flip mechanism in serine protease catalysis

13C-selective NMR, combined with inhibitor perturbation experiments, shows that the C(epsilon)(1)H proton of the catalytic histidine in resting alpha-lytic protease and subtilisin BPN' resonates, when protonated, at 9.22 ppm and 9.18 ppm, respectively, which is outside the normal range for such protons and approximately 0.6 to 0.8 ppm further downfield than previously reported. They also show that the previous alpha-lytic protease assignments [Markley, J. L., Neves, D. E., Westler, W. M., Ibanez, I. B., Porubcan, M. A. & Baillargeon, M. W. (1980) Front. Protein Chem. 10, 31-61] were to signals from inactive or denatured protein. Simulations of linewidth vs. pH demonstrate that the true signal is more difficult to detect than corresponding signals from inactive derivatives, owing to higher imidazole pK(a) values and larger chemical shift differences between protonated and neutral forms. A compilation and analysis of available NMR data indicates that the true C(epsilon)(1)H signals from other serine proteases are similarly displaced downfield, with past assignments to more upfield signals probably in error. The downfield displacement of these proton resonances is shown to be consistent with an H-bond involving the histidine C(epsilon)(1)H as donor, confirming the original hypothesis of Derewenda et al. [Derewenda, Z. S., Derewenda, U. & Kobos, P. M. (1994) J. Mol. Biol. 241, 83-93], which was based on an analysis of literature x-ray crystal structures of serine hydrolases. The invariability of this H-bond among enzymes containing Asp-His-Ser triads indicates functional importance. Here, we propose that it enables a reaction-driven imidazole ring flip mechanism, overcoming a major dilemma inherent in all previous mechanisms, namely how these enzymes catalyze both the formation and productive breakdown of tetrahedral intermediates.     

Light-induced chromophore activity and signal transduction in phytochromes observed by 13C and 15N magic-angle spinning NMR

Both thermally stable states of phytochrome, Pr and Pfr, have been studied by (13)C and (15)N cross-polarization (CP) magic-angle spinning (MAS) NMR using cyanobacterial (Cph1) and plant (phyA) phytochrome sensory modules containing uniformly (13)C- and (15)N-labeled bilin chromophores. Two-dimensional homo- and heteronuclear experiments allowed most of the (13)C chemical shifts to be assigned in both states. Chemical shift differences reflect changes of the electronic structure of the cofactor at the atomic level as well as its interactions with the chromophore-binding pocket. The chromophore in cyanobacterial and plant phytochromes shows very similar features in the respective Pr and Pfr states. The data are interpreted in terms of a strengthened hydrogen bond at the ring D carbonyl. The red shift in the Pfr state is explained by the increasing length of the conjugation network beyond ring C including the entire ring D. Enhanced conjugation within the pi-system stabilizes the more tensed chromophore in the Pfr state. Concomitant changes at the ring C propionate carboxylate and the ring D carbonyl are explained by a loss of hydrogen bonding to Cph1-His-290 and transmittance of conformational changes to the ring C propionate via a water network. These and other conformational changes may lead to modified surface interactions, e.g., along the tongue region contacting the bilin chromophore.     

Combined quantitative (1)H and (13)C nuclear magnetic resonance spectroscopy for characterization of heparin preparations.

The sulfation patterns of pig and bovine mucosal commercial heparin preparations can be characterized and distinguished from each other easily by analysis of their monodimensional proton and carbon nuclear magnetic resonance ((1)H and (13)C-NMR) spectra. NMR spectroscopy can detect and quantify signals associated with major sequences as well as with minor residues such as the typical ones associated with the antithrombin (AT) binding sequence and the "linkage region." Contaminants arising from industrial preparation processes are also detectable.     

No evidence for bradykinin hydrolysis in human erythrocyte suspensions: 1H NMR studies

In view of their permeability to small peptides, it has been postulated that human erythrocytes may play a role in terminating the action of some circulating peptide hormones. Work using classical paper chromatographic techniques for detecting free amino acids indicated that the octapeptide, des-(Arg9)-bradykinin, enters these cells and its amino-terminal arginine residue is released by cytosolic aminopeptidase-P. We have used 1H NMR to monitor directly the release of arginine from bradykinin. The hydrolytic reaction rate in hemolysates, with an initial peptide concentration of 13.0 mmol l-1 was 6.5 mmol (1 packed red cell)-1 h-1. But no reaction was evident after a 4.5-h incubation with intact cells, thus contradicting the earlier suggestion that erythrocytes are involved in the primary inactivation of this hormone. This is consistent with our previous findings that the pentapeptide leu-enkephalin fails to enter human erythrocytes but that its lower-order degradation products may do so.     

The role of the retinylidene Schiff base counterion in rhodopsin in determining wavelength absorbance and Schiff base pKa.

Glu-113 serves as the retinylidene Schiff base counterion in bovine rhodopsin. Purified mutant rhodopsin pigments were prepared in which Glu-113 was replaced individually by Gln (E113Q), Asp (E113D), Asn (E113N), or Ala (E113A). E113Q, E113N, and E113A existed as pH-dependent equilibrium mixtures of unprotonated and protonated Schiff base (PSB) forms. The Schiff base pKa values determined by spectrophotometric titration were 6.00 (E113Q), 6.71 (E113N), and 5.70 (E113A). Thus, mutation of Glu-113 markedly reduced the Schiff base pKa. The addition of NaCl promoted the formation of a PSB in E113Q and E113A. An exogenously supplied solute anion replaced Glu-113 to compensate for the positive charge of the PSB in these mutants. The lambda max values of the PSB forms of the mutants in NaCl were 496 nm (E113Q), 506 nm (E113A), 510 nm (E113D), and 520 nm (E113N). To evaluate the effect of different types of solute anions on lambda max values, mutants were prepared in sodium salts of halides, perchlorate, and a series of carboxylic acids of various sizes and acidity. The lambda max values of E113Q and E113A depended on the solute anion present and ranged from 488 nm to 522 nm for E113Q and from 486 nm to 528 nm for E113A. The solute anion affected the lambda max values of E113N and E113D to lesser degrees. The reactivities of the mutants to hydroxylamine were also studied. Whereas rhodopsin was stable to hydroxylamine in the dark, E113N reacted slowly and E113Q reacted rapidly under these conditions, indicating structural differences in the Schiff base environments. The lambda max values and solute anion dependencies of the Glu-113 mutants indicate that interactions between Schiff base and its counterion play a significant role in determining the lambda max of rhodopsin.     

Conformational characterization of a single-site mutant of murine epidermal growth factor (EGF) by 1H NMR provides evidence that leucine-47 is involved in the interactions with the EGF receptor.

Epidermal growth factor (EGF) is a small protein containing 53 amino acids and three disulfide bonds. There is significant current interest in structure-function relationships in EGF and EGF-like proteins, including the homologous type-alpha transforming growth factors. The Leu-47 residue of murine EGF (mEGF) is one of several that are strongly conserved among the EGF-like growth factors, suggesting that it may contribute to the active site of mEGF. In several different binding assays, the activity of the mutant analog in which Leu-47 is replaced by Ser [( Ser47]mEGF) ranges from 8 to 18 times weaker than that of wild-type mEGF. The NMR data summarized in this paper demonstrate that the significant differences in the binding activities of wild-type and [Ser47]mEGF cannot be attributed to structural changes remote from the three-dimensional site of mutation. The only minor conformational changes that are indicated by these data involve side chains of residues proximal to Leu-47 in the three-dimensional structure. Therefore, Leu-47 and/or residues spatially adjacent to Leu-47 constitute part of the active site of mEGF.     

NMR spectroscopy in studies of light-induced structural changes in mammalian rhodopsin: applicability of solution (19)F NMR

We report high resolution solution (19)F NMR spectra of fluorine-labeled rhodopsin mutants in detergent micelles. Single cysteine substitution mutants in the cytoplasmic face of rhodopsin were labeled by attachment of the trifluoroethylthio (TET), CF(3)-CH(2)-S, group through a disulfide linkage. TET-labeled cysteine mutants at amino acid positions 67, 140, 245, 248, 311, and 316 in rhodopsin were thus prepared. Purified mutant rhodopsins (6-10 mg), in dodecylmaltoside, were analyzed at 20 degrees C by solution (19)F NMR spectroscopy. The spectra recorded in the dark showed the following chemical shifts relative to trifluoroacetate: Cys-67, 9.8 ppm; Cys-140, 10.6 ppm; Cys-245, 9.9 ppm; Cys-248, 9.5 ppm; Cys-311, 9.9 ppm; and Cys-316, 10.0 ppm. Thus, all mutants showed chemical shifts downfield that of free TET (6.5 ppm). On illumination to form metarhodopsin II, upfield changes in chemical shift were observed for (19)F labels at positions 67 (-0.2 ppm) and 140 (-0.4 ppm) and downfield changes for positions 248 (+0.1 ppm) and 316 (+0.1 ppm) whereas little or no change was observed at positions 311 and 245. On decay of metarhodopsin II, the chemical shifts reverted largely to those originally observed in the dark. The results demonstrate the applicability of solution (19)F NMR spectroscopy to studies of the tertiary structures in the cytoplasmic face of intact rhodopsin in the dark and on light activation.     

1H-[13C] NMR measurements of [4-13C]glutamate turnover in human brain.

A limitation of previous methods for studying human brain glucose metabolism, such as positron emission tomography, is that metabolic steps beyond glucose uptake cannot be studied. Nuclear magnetic resonance (NMR) has the advantage of allowing the nondestructive measurement of 13C distribution in specific carbon positions of metabolites. In this study 1H-[13C] NMR spectroscopy in conjunction with volume localization was used to measure the rate of incorporation of 13C isotope from infused enriched [1-13C]glucose to human brain [4-13C]glutamate. In three studies C4 glutamate turnover time constants of 25, 20, and 17 min were measured in a 21-cm3 volume centered in the region of the visual cortex. Based on an analysis of spectrometer sensitivity the spatial resolution of the method can be improved to < 4 cm3. In conjunction with metabolic modeling and other NMR measurements this method can provide a measure of regional rates of the brain tricarboxylic acid cycle and other metabolic pathways.     

Increased tricarboxylic acid cycle flux in rat brain during forepaw stimulation detected with 1H[13C]NMR.

NMR spectroscopy was used to test recent proposals that the additional energy required for brain activation is provided through nonoxidative glycolysis. Using localized NMR spectroscopic methods, the rate of C4-glutamate isotopic turnover from infused [1-(13)C]glucose was measured in the somatosensory cortex of rat brain both at rest and during forepaw stimulation. Analysis of the glutamate turnover data using a mathematical model of cerebral glucose metabolism showed that the tricarboxylic acid cycle flux [(V(TCA)] increased from 0.49 +/- 0.03 at rest to 1.48 +/- 0.82 micromol/g/min during stimulation (P < 0.01). The minimum fraction of C4-glutamate derived from C1-glucose was approximately 75%, and this fraction was found in both the resting and stimulated rats. Hence, the percentage increase in oxidative cerebral metabolic rate of glucose use (CMRglc) equals the percentage increases in V(TCA) and cerebral metabolic rate of oxygen consumption (CMRO2). Comparison with previous work for the same rat model, which measured total CMRglc [Ueki, M., Linn, F. & Hossman, K. A. (1988) J. Cereb. Blood Flow Metab. 8, 486-4941, indicates that oxidative CMRglc supplies the majority of energy during sustained brain activation.     

Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation

A recently determined set of 20 NMR-derived conformations of a 48-residue all-alpha-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed (13)C(alpha) chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed (13)C(alpha) chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed (13)C(alpha) chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed (13)C(alpha) chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-A resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed (13)C(alpha) chemical shifts in solution than the 3BHP crystal structure. In addition, the (13)C(alpha)-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures.     

New view of lipid bilayer dynamics from 2H and 13C NMR relaxation time measurements.

Natural abundance 13C spin-lattice (T1) relaxation time measurements are reported for unilamellar vesicles of 1,2-dipalmitoylphosphatidylcholine (1,2-dipalmitoyl-sn-glycero-3-phosphocholine), in the liquid crystalline phase, at magnetic field strengths of 1.40, 1.87, 2.35, 4.23, 7.05, 8.45, and 11.7 tesla (resonance frequencies of 15.0, 20.0, 25.1, 45.3, 75.5, 90.5, and 126 MHz, respectively), and the results are compared to previous 2H T1 studies of multilamellar dispersions. For both the 13C and 2H T1 studies, a dramatic frequency dependence of the relaxation was observed. At superconducting magnetic field strengths (4.23-11.7 tesla), plots of the 13C T1(-1) relaxation rates as a function of acyl chain segment position clearly reveal the characteristic "plateau" signature of the liquid crystalline phase, as found previously from 2H NMR studies. The dependence of T1(1) on ordering, determined previously from 2H NMR, and the T1(-1) dependence on frequency, determined from both 13C and 2H NMR studies, suggest that a unified picture of the bilayer molecular dynamics can be provided by a simple relaxation law of the form T1(-1) approximately equal to A tau f + BS2C-H omega -1/2(0). In the above expression, A and B are constants, SC-H (= SC-D) is the bond segmental order parameter, and omega 0 is the nuclear Larmor frequency. The first (A) term includes contributions from fast, local segmental motions characterized by the effective correlation time tau f, whereas the second (B) term describes slower, collective fluctuations in the local ordering. The value of tau f approximately equal to 10(-11) sec, obtained by extrapolating T1(-1) to infinite frequency, suggests that the segmental microviscosity of the bilayer hydrocarbon region does not differ appreciably from that of the equivalent n-paraffinic liquids of similar chain length.     

Molecular Dynamics of Poly(Ethylene Glycol) Intercalated in Clay,Studied Using 13C Solid-State NMR

In this study, Cross-Polarization Magic-angle Spinning CP/MAS, 2D Exchange, Centerband-Only Detection of Exchange (CODEX), and Separated-Local-Field (SLF) NMR experiments were used to study the molecular dynamics of poly(ethylene glycol) (PEG) inside Hectorite/PEG intercalation compounds in both single- and double-layer configurations. The results revealed that the overall amplitude of the motions of the PEG chain in the single-layer configuration is considerably smaller than that observed for the double-layer intercalation compound. This result indicates that the effect of having the polymer chain interacting with both clay platelets is to produce a substantial decrease in the motional amplitudes of those chains. The presence of these dynamically restricted segments might be explained by the presence of anchoring points between the clay platelets and the PEG oxygen atoms, which was induced by the Na⁺ cations. By comparing the PEG motional amplitudes of the double-layered nanocomposites composed of polymers with different molecular weights, a decrease in the motional amplitude for the smaller PEG chain was observed, which might also be understood using the presence of anchoring points.     

Preliminary analysis of 1H and 13C spectral and relaxation behavior in methionine-enkephalin.

Nuclear magnetic resonance studies on the conformational dynamics of the pentapeptide H-Tyr-Gly-Gly-Phe-Met-OH are reported. This peptide, for which the generic trivial name "methionine-enkephalin" has been suggested, is pharmacologically active as a ligand for the mammalian opiate receptor(s). The studies reported are parallel investigations in two solvents (dimethylsulfoxide and water) of: 1H and 13C high resolution spectral assignments; 1H and 13C spin-lattice relaxation times, temperature dependence of amide proton chemical shifts, and half-times for chemical exchange or amide protons. From these data we conclude that the tyrosine side chain of methionine-enkephalin exhibits restricted motion with respect to the main peptide backbone of the molecule. On the other hand both the phenylalanyl and methionyl side chains are undergoing intramolecular reorientation with relatively high frequency.     

13C NMR isotopomer analysis reveals a connection between pyruvate cycling and glucose-stimulated insulin secretion (GSIS)

Cellular metabolism of glucose is required for stimulation of insulin secretion from pancreatic beta cells, but the precise metabolic coupling factors involved in this process are not known. In an effort to better understand mechanisms of fuel-mediated insulin secretion, we have adapted 13C NMR and isotopomer methods to measure influx of metabolic fuels into the tricarboxylic acid (TCA) cycle in insulinoma cells. Mitochondrial metabolism of [U-13C3]pyruvate, derived from [U-13C6]glucose, was compared in four clonal rat insulinoma cell 1-derived cell lines with varying degrees of glucose responsiveness. A 13C isotopomer analysis of glutamate isolated from these cells showed that the fraction of acetyl-CoA derived from [U-13C6]glucose was the same in all four cell lines (44 +/- 5%, 70 +/- 3%, and 84 +/- 4% with 3, 6, or 12 mM glucose, respectively). The 13C NMR spectra also demonstrated the existence of two compartmental pools of pyruvate, one that exchanges with TCA cycle intermediates and a second pool derived from [U-13C6]glucose that feeds acetyl-CoA into the TCA cycle. The 13C NMR spectra were consistent with a metabolic model where the two pyruvate pools do not randomly mix. Flux between the mitochondrial intermediates and the first pool of pyruvate (pyruvate cycling) varied in proportion to glucose responsiveness in the four cell lines. Furthermore, stimulation of pyruvate cycling with dimethylmalate or its inhibition with phenylacetic acid led to proportional changes in insulin secretion. These findings indicate that exchange of pyruvate with TCA cycle intermediates, rather than oxidation of pyruvate via acetyl-CoA, correlates with glucose-stimulated insulin secretion.     

Toward solving the folding pathway of barnase: the complete backbone 13C, 15N, and 1H NMR assignments of its pH-denatured state.

The structures of the major folding intermediate, the transition state for folding, and the folded state of barnase have been previously characterized. We now add a further step toward a complete picture of the folding of barnase by reporting the backbone 15N, 13C, and 1H NMR assignments for barnase unfolded at pH 1.8 and 30 degrees C. These assignments, which were obtained from a combination of heteronuclear magnetization transfer and backbone triple-resonance NMR experiments, constitute the first stage in the structural characterization of this denatured state by NMR. Interresidue nuclear Overhauser effect contacts and deviations from 1H random-coil chemical shifts provide evidence for stable residual structure. The structured regions span residues in the native protein that contain its major alpha-helix and central strands of the beta-sheet. Earlier experiments have shown that these regions are predominantly intact in the major folding intermediate and that their docking is partly rate determining in folding.     

Immunological evidence for the in vivo occurrence of a crosslinked complex of poly(ADP-ribosylated) histone H1.

The poly(ADP-ribosylation) of histones, which occurs within a limited and functionally specific domain of chromatin, is a novel post-translational modification. However, in the past it has been difficult to study this process in living cells because the substrate of the reaction (NAD) does not permeate the plasma membrane. In the current study, antibodies specific for histone H1 and poly(ADP-ribose) were used to study the occurrence of poly(ADP-ribose)+ species of H1 in vivo. Perchloric acid-extracted proteins from synchronously growing HeLa cells were fractionated by electrophoresis and transferred to nitrocellulose, and the transferred moieties were allowed to react with the specific antibodies and then with 125I-labeled protein A. The results conclusively demonstrate the natural occurrence of poly(ADP-ribose)-crosslinked complexes of histone H1 (i.e., H1 dimer), at the S/G2 phase transition of the cell cycle.