Molecular dynamics simulations of enhanced green fluorescent proteins: effects of F64L,S65T and T203Y mutations on the ground-state proton equilibria

Molecular dynamics simulations with the Amber force field are carried out to study two mutants of the green fluorescent protein (GFP), namely EGFP (F64L/S65T) and T203Y-EGFP (E(2)GFP). Those variants display an opposite equilibrium between the structural A and B states, associated with neutral and anionic protonation forms of the chromophore. Configurations of those two states are simulated for each variant and the energetics of their equilibrium in the two mutants is studied by evaluating the change in the relative free energy of A and B states (DeltaG(AB)) upon T203Y mutation. The resulting DeltaDeltaG(AB) agrees with the value inferred from absorption measurements. A comparison of the hydrogen bond network around the chromophore rationalizes the different population of state A and B in EGFP and E(2)GFP. On the basis of structural and energetic considerations, a mechanism for destabilization of the neutral chromophore in S65T mutants is proposed. Simulations of the B state of the S65T variant and of WT GFP are also performed for comparison and to test the force field parameters of the chromophore derived for the present calculations. Possible paths of proton transfer leading to nonfluorescent states of the chromophore are discussed in light of the photodynamical behavior of GFP, as revealed by fluorescence correlation spectroscopy and single-molecule experiments.     

Novel 2-aminothiazonaphthalimides as visible light activatable photonucleases: effects of intercalation, heterocyclic-fused area and side chains

A new family of 2-aminothiazonaphthalimides with different side chains as novel intercalative and visible light activatable photonucleases, was designed, synthesized and quantitatively evaluated. The order of their photocleaving abilities was parallel to that of their intercalative properties. The compound with linear heterocyclic-fused chromophore could intercalate into and photocleave DNA more efficiently than the one with angular heterocyclic-fused chromophore. B(2), the most efficient compound, caused obvious DNA damage at 1 microM. Mechanism experiment showed that superoxide anion was involved.     

Analysis of N-glycosylation of phospholipase A2 from venom of individual bees by microbore high-performance liquid chromatography-electrospray mass spectrometry using an ion trap mass spectrometer

The N-linked oligosaccharides were released from the phospholipase A2 (PLA) with glycopeptidases and reductively aminated with the chromophore, p-aminobenzoic acid ethyl ester (ABEE). The ABEE-labeled oligosaccharides were separated by microbore high-performance liquid chromatography (micro-HPLC) using a reversed-phase column and analyzed by electrospray mass spectrometry. Differentiation between alpha-1,3 and alpha-1,6 core-fucosylated glycans was achieved by comparison the glycans released by glycopeptidases peptide-N-glycanase A (PNase A) and peptide-N-glycanase F (PNase F). All N-linked oligosaccharides except 3B and 3C could be identified in this approach. The analysis of PLA oligosaccharides from the venom of individual bees indicated that glycosylation patterns between the younger and the older bees were similar.     

Synthesis and study of a gramicidin B mutant possessing a ditryptophan crosslink.

Recent studies of peptide dimers linked by Trp-Trp (ditryptophan) crosslinks suggest that the crosslinks can reinforce antiparallel beta-structure. Depending on environment, gramicidins A, B and C form either helical ion channels with parallel beta-structure or non-functional pores with antiparallel beta-structure. In the channel conformation of the gramicidins Trp9 and Trp15 are close in space, but in the pore conformation Trp9 and Trp15 are far apart. We hypothesized that a ditryptophan crosslink between Trp9 and Trp15 could pre-organize gramicidin in an active conformation. To test the potential for preorganization, an intramolecular ditryptophan crosslink was formed between Trp9 and Trp15 in a W13F mutant of gramicidin B. Photooxidative conditions were shown to generate ditryptophan crosslinks in low yields. While not preparatively useful, photooxidative tryptophan crosslinking may have implications for protein aging processes like cataract formation. The ditryptophan crosslink in the gramicidin B mutant substantially lowered the antibiotic activity of the gramicidin B mutant, unlike the ditryptophan crosslink in the antibiotic X-indolicidin. The biaryl chromophore generated diagnostic Cotton effects in the CD spectrum that revealed the absolute stereochemistry of the biaryl chromophore, but the biaryl chromophore obscured diagnostic features below 220 nm. However, changes in peptide conformation were reflected in changes in the biaryl region of the CD spectrum above 240 nm.     

The structures of the phytochrome chromophore in both photoreversible forms.

Spectral measurements of phytochrome are performed after unfolding of the peptide chain. By comparison with bile pigments of known structure, structure 1a, containing a hydrogenated ring A, is deduced for the PR chromophore. Its spectral properties indicate that the chromophore of the physiologically active PFR form has lost the double bond of the bridge joining rings A and B.     

Refined three-dimensional structures of two cyanobacterial C-phycocyanins at 2.1 and 2.5 A resolution. A common principle of phycobilin-protein interaction

The crystal structure of the light-harvesting protein-pigment complex C-phycocyanin (C-PC) from Mastigocladus laminosus (at 2.1 A resolution (1 A = 0.1 nm] has been refined by energy-restrained least-squares methods to a conventional R-factor of 21.7%. In the same way, the crystal structure of C-PC from Agmenellum quadruplicatum has been refined further (2.5 A, R = 18.4%); pyrrole rings C and D of the chromophore at position A84 have been corrected with respect to the previously reported structure. The two C-PC structures are very similar, 213 C alpha positions have a root-mean-square deviation of 0.49 A. Polar and ionic side-chain interactions are discussed in detail and the two subunits of C-PC from M. laminosus are compared to each other. All three chromophores are completely defined and their tetrapyrroles exhibit very similar geometry. The structure of a C-PC chromophore resembles a cleaved porphyrin which has been twisted roughly 180 degrees around the C-5-C-6 and C-14-C-15 bonds. Accordingly, the configuration/conformation of the chromophores is Z-anti, Z-syn, Z-anti (with the exception of the "configuration" of C-15 of chromophore B155, which is almost midway between Z and E). The three chromophores interact similarly with the protein. They arch around aspartate residues (A87, B87 and B39), and the nitrogens of pyrroles B and C are within hydrogen-bonding distance of one of the carboxylate oxygens. Most of the propionic side-chains of the chromophores form salt bridges with arginine and lysine residues. The updated relative chromophore distances and orientations confirm our conclusion that hexameric aggregates are probably the basic functional units, and that inter-hexameric energy transfer takes place preferentially via the central B84 chromophores.     

Quantitative calculations of fluorescence polarization and absorption anisotropy kinetics of double- and triple-chromophore complexes with energy transfer.

A new method is presented for calculation of the fluorescence depolarization and kinetics of absorption anisotropy for molecular complexes with a limited number of chromophores. The method considers absorption and emission of light by both chromophores, and also energy transfer between them, with regard to their mutual orientations. The chromophores in each individual complex are rigidly positioned. The complexes are randomly distributed and oriented in space, and there is no energy transfer between them. The new "practical" formula for absorption anisotropy and fluorescence depolarization kinetics, P(t) = [3B(t) - 1 + 2A(t)]/[3 + B(t) + 4A(t)], is derived both for double- and triple-chromophore complexes with delta-pulse excitation. The parameter B(t) is given by (a) B(t) = cos2(theta) for double-chromophore complexes, and (b) B(t) = q12(t)cos2(theta 12) + q13(t)-cos2(theta 13) + q23(t)cos2(theta 23) for triple-chromophore complexes, where q12(t) + q13(t) + q23(t) = 1. Here theta ij are the angles between the chromophore transition dipole moments in the individual molecular complex. The parameters qij(t) and A(t) are dependent on chromophore spectroscopic features and on the rates of energy transfer.     

Kinetics and mechanism of inactivation of the RTEM-2 beta-lactamase by phenylpropynal. Identification of the characteristic chromophore

beta-Lactamases of all three classes, A, B, and C, are inactivated by phenylpropynal and p-nitrophenylpropynal. The inactivation of RTEM-2 beta-lactamase and of Bacillus cereus beta-lactamase I is accelerated in the presence of A type substrates such as dicloxacillin, quinacillin, and cefoxitin, which are thought to expand or loosen the conformation of these enzymes. In the presence and absence of cefoxitin the inactivation of the RTEM-2 beta-lactamase is first and second order, respectively, in phenylpropynal concentration. The additional phenylpropynal molecule in the latter case may serve the same function as cefoxitin, viz. catalyze access to sensitive functional groups. Correlation of the loss of activity of the RTEM-2 enzyme with the extent of modification suggests that the modification of any one of about four kinetically equivalent groups leads to inactivation. Modification of all of the above mentioned enzymes leads to formation of a characteristic chromophore of unusual stability to nucleophiles, which absorbs maximally between 315 and 320 nm. A consideration of the properties of model compounds demonstrated that the protein-bound chromophore is that of a 1-phenyl-3-imino-1-propen-1-ammonium ion (Formula: see text), formed by reaction of phenylpropynal with two enzymic amine groups, and thus cross-linking the enzyme intramolecularly. Phenylpropynal may be a convenient general reagent for rapid and stable intramolecular cross-linking of proteins through lysine.     

Bacterial siderophores: structures of pyoverdins Pt, siderophores of Pseudomonas tolaasii NCPPB 2192, and pyoverdins Pf, siderophores of Pseudomonas fluorescens CCM 2798. Identification of an unusual natural amino acid

Pyoverdins were isolated and characterized respectively from the cultures of Pseudomonas tolaasii NCPPB 2192 (pyoverdins Pt, Pt A, and Pt B) and Pseudomonas fluorescens CCM 2798 (Pyoverdins Pf/1, Pf/2, Pf, Pf/3/1, and Pf/3/2) each grown in iron-deficient conditions. Their structures were established by using FAB-MS, NMR, and CD techniques. These siderophores are chromopeptides, and all but one (pyoverdin Pf/3/3) possess at the N-terminal end of their peptide chain the same chromophore that has been reported in pyoverdin Pa from Pseudomonas aeruginosa ATCC 15692 [Wendenbaum, S., Demange, P., Dell, A., Meyer, J. M., & Abdallah, M. A. (1983) Tetrahedron Lett. 24, 4877-4880] and pseudobactin B 10 from Pseudomonas B10 [Teintze, M., Hossain, M. B., Barnes, C. L., Leong, J., & Van der Helm, D. (1981) Biochemistry 20, 6446-6457] which is derived from 2,3-diamino-6,7-dihydroxyquinoline. In pyoverdins Pt this chromophore is bound to a linear peptide chain D-Ser-L-Lys-L-Ser-D-Ser-L-Thr-D-Ser-L-OHOrn-L-Thr-D-Ser-D-OHOrn (cyclic) which has its C-terminal end blocked by cyclic D-N delta-hydroxyornithine. In pyoverdins Pf, the peptide chain is also linear, SerCTHPMD-Gly-L-Ser-D-threo-OHAsp-L-Ala-Gly-D-Ala-Gly-L-O HOrn(cyclic), and contains an unusual natural amino acid which is the result of the condensation of 1 mol of serine and 1 mol of 2,4-diaminobutyric acid, forming a cyclic amidine. The pyoverdins Pt differ only in substituent bound to the nitrogen on C-3 of the chromophore, which is succinic acid in pyoverdin Pt A, succinamide in pyoverdin Pt, and alpha-ketoglutaric acid bound to the chromophore by its C-5 carbon atom in pyoverdin Pt B. Similarly, pyoverdin Pf/1, pyoverdin Pf/2, pyoverdin Pf (the major compound), and pyoverdin Pf/3/2 are substituted respectively by L-malic acid, succinic acid, L-malic amide, and succinamide. Pyoverdin Pf/3/3 has the same chromophore as azotobactin, the peptidic siderophore of Azotobacter vinelandii. These pyoverdins are very similar to pseudobactin B 10, the siderophore of Pseudomonas B10: they are linear peptides containing three bidentate groups strongly chelating Fe(III) and blocked at their N-terminal end by the catecholic chromophore and at their C-terminal end by cyclic N delta-hydroxyornithine. They differ therefore from other pyoverdins such as those from P. aeruginosa ATCC 15692 which contain a partly cyclic peptide [Briskot, G., Taraz, K., & Budzikiewicz, H. (1989) Liebigs Ann. Chem., 375-384].     

Circular dichroism of 1,3-dioxane-type (2'-naphthyl)methylene acetals of glycosides

The CD spectra are reported for a series of 1,3-dioxane-type 4,6-O-(2'-naphthyl)methylene acetals of carbohydrates with and without interacting aromatic protective groups on the C-1, C-2, and C-3 hydroxy groups. In the absence of interacting chromophores, the signs of the (1)B transitions are not sensitive to the configuration of C-4, while the signs of the weak (1)L(a) bands are opposite in the galacto and gluco derivatives. The equatorial parallel conformation is found to be the preferred conformation of the 2-naphthyl group in the solid state by X-ray diffraction. The intense (1)B(a) and (1)B(b) transitions of the naphthalene chromophore allowed a safe configurational assignment by exciton coupled interaction with the aromatic protective groups in para-methoxyphenyl-beta-D-glycosides. The origin of the observed CEs were deduced and the additivity of the interactions was studied. The direction of the hydrogenolytic cleavage of 4,6-O-(2'-naphthyl)methylene acetal of carbohydrates could also be detected by the (1)B(b) transition of the 2-naphthyl chromophore.     

The protein-chromophore bond in B phycoerythrin from Porphyridium cruentum. Radiosulfur labeling experiments

Red algae of the species Porphyridium cruentum were grown in a minimum sulfate medium containing 35SO42-. 35S-labeled phycoerythrin was extracted. B Phycoerythrin, b phycoerythrin and R phycocyanin could be separated from other proteins by using a carrier-free electrophoresis on columns. The final ratio A545/A280 of B phycoerythrin thus obtained was greater than or equal to 5. 35S-labeled B phycoerythrin was digested proteolytically with trypsin and pepsin. The resulting 35S-containing bilipeptides were separated by isoelectric focusing. Zones of enhanced chromophore concentration always showed an enhanced radioactivity. Peptide fractions with a low molar ratio sulfur/chromophore (1.1-1.8) were purified to remove sucrose and the carrier ampholyte. A modified, optimized Edman degradation followed. A butylacetate-soluble, red Edman product was obtained that contained most of the chromophore and the bulk of the radioactivity. This product was purified by two-dimensional thin-layer chromatography. The main spot of the chromatogram was subjected to acidic hydrolysis. The major part of the radioactivity in the hydrolysate cochromatographed with cysteine. That proves cysteine to be the binding amino acid in all cases investigated.     

Naphthoquinone-lactones and extended quinones from Ventilago calyculata

New quinones have been isolated from the root bark of Ventilago calyculata. Ventilatones A and B are benzisochromanquinones, related to the ventiloquinones, which have an additional fused lactone ring while ventileins A and B are benzisochroman dimers having a dihydroxy-peri-xanthenoxanthenequinone chromophore.     

The suicide inactivation of ox liver short-chain acyl-CoA dehydrogenase by propionyl-CoA. Formation of an FAD adduct.

R-Phycoerythrin contains two covalently bound bilin prosthetic groups, phycoerythrobilin and phycourobilin. The two chromophore types were separated as their peptide-bound derivatives by subjecting tryptic digests of R-phycoerythrin to adsorption chromatography on Sephadex G-25. The structure and apoprotein linkages of the bound phycoerythrobilin were found to be identical with those previously reported for this phycobilin [Killilea, O'Carra & Murphy (1980) Biochem. J. 187, 311-320]. Phycourobilin is a tetrapyrrole, containing no oxo bridges and has the same order of side chains as IX alpha bilins. The chromophore is linked to the peptide through two and possibly three of its pyrrole rings. One linkage possibly consists of an ester bond between the hydroxy group of a serine residue and the propionic acid side chain of one of the inner rings. The second linkage is a labile thioether bond between a cysteine residue and the C2 side chain of pyrrole ring A. The third linkage is a stable thioether bond between a cysteine residue and the alpha-carbon atom of the C2 side chain of pyrrole ring D. Ring D is unsaturated and is attached to ring C through a saturated carbon bridge. Rings B and C have a conjugated system of five bonds, as found in other urobilinoid pigments. Ring A is attached to ring B via a saturated carbon bridge. Both of the alpha-positions of ring A are in the reduced state, but the ring does contain an unsaturated centre (probably a double bond between the beta-carbon and the ring nitrogen atom). The presence of this double bond and its isomerization into the bridge position between rings A and B would explain the extension of the conjugated system of phycourobilin to that of a phycoerythrobilinoid/rhodenoid pigment in acid or alkali.     

Green fluorescent protein variants as ratiometric dual emission pH sensors. 2. Excited-state dynamics

In the preceding paper [Hanson, G. T., McAnaney, T. B., Park, E. S., Rendell, M. E. P., Yarbrough, D. K., Chu, S., Xi, L., Boxer, S. G., Montrose, M. H., and Remington, S. J. (2002) Biochemistry 41, 15477-15488], novel mutants of the green fluorescent protein (GFP) that exhibit dual steady-state emission properties were characterized structurally and discussed as potential intracellular pH probes. In this work, the excited-state dynamics of one of these new dual emission GFP variants, deGFP4 (C48S/S65T/H148C/T203C), is studied by ultrafast fluorescence upconversion spectroscopy. Following excitation of the high-energy absorption band centered at 398 nm and assigned to the neutral form of the chromophore, time-resolved emission was monitored from the excited state of both the neutral and intermediate anionic chromophores at both high and low pH and upon deuteration of exchangeable protons. The time-resolved emission dynamics and isotope effect appear to be very different from those of wild-type GFP [Chattoraj, M., King, B. A., Bublitz, G. U., and Boxer, S. G. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 8362-8367]; however, due to overlapping emission bands, the apparent difference can be analyzed quantitatively within the same framework used to describe GFP excited-state dynamics. The results indicate that the pH-sensitive steady-state emission characteristics of deGFP4 are a result of a pH-dependent modulation of the rate of excited-state proton transfer. At high pH, a rapid interconversion from the excited state of the higher energy neutral chromophore to the lower energy intermediate anionic chromophore is achieved by proton transfer. At low pH, excited-state proton transfer is slowed to the point where it is no longer rate limiting.     

Spectroscopic characterization of the photocycle intermediates of photoactive yellow protein.

The absorption spectra of photocycle intermediates of photoactive yellow protein mutants were compared with those of the corresponding intermediates of wild type to probe which amino acid residues interact with the chromophore in the intermediate states. B and H intermediates were produced by irradiation and trapped at 80 K, and L intermediates at 193 K. The absorption spectra of these intermediates produced from R52Q were identical to those from wild type, whereas those from E46Q and T50V were 7-15 nm red-shifted as those in the dark states. The absorption spectra of M intermediates were measured by flash photolysis at room temperature. Those of Y42F, T50V, and R52Q were identical to that of wild type, whereas that of E46Q was 11 nm red-shifted. Assuming that the intermediates of mutants have a structure comparable to that of wild type, these findings suggest the following: Glu46 interacts with the chromophore throughout the photocycle, interaction between the chromophore and Thr50 as well as Tyr42 is lost upon the formation of M intermediate, and Arg52 never interacts with the chromophore directly. The hydrogen-bonding network around the phenolic oxygen of the chromophore would be thus maintained until L intermediate decays, and the global conformational change would take place by the loss of the hydrogen bond between the chromophore and Tyr42. This model conflicts with some of the results of previous crystallographic studies, suggesting that the reaction mechanism in the crystal may be different from that in solution.     

Mutational analysis of Deinococcus radiodurans bacteriophytochrome reveals key amino acids necessary for the photochromicity and proton exchange cycle of phytochromes

The ability of phytochromes (Phy) to act as photointerconvertible light switches in plants and microorganisms depends on key interactions between the bilin chromophore and the apoprotein that promote bilin attachment and photointerconversion between the spectrally distinct red light-absorbing Pr conformer and far red light-absorbing Pfr conformer. Using structurally guided site-directed mutagenesis combined with several spectroscopic methods, we examined the roles of conserved amino acids within the bilin-binding domain of Deinococcus radiodurans bacteriophytochrome with respect to chromophore ligation and Pr/Pfr photoconversion. Incorporation of biliverdin IXalpha (BV), its structure in the Pr state, and its ability to photoisomerize to the first photocycle intermediate are insensitive to most single mutations, implying that these properties are robust with respect to small structural/electrostatic alterations in the binding pocket. In contrast, photoconversion to Pfr is highly sensitive to the chromophore environment. Many of the variants form spectrally bleached Meta-type intermediates in red light that do not relax to Pfr. Particularly important are Asp-207 and His-260, which are invariant within the Phy superfamily and participate in a unique hydrogen bond matrix involving the A, B, and C pyrrole ring nitrogens of BV and their associated pyrrole water. Resonance Raman spectroscopy demonstrates that substitutions of these residues disrupt the Pr to Pfr protonation cycle of BV with the chromophore locked in a deprotonated Meta-R(c)-like photoconversion intermediate after red light irradiation. Collectively, the data show that a number of contacts contribute to the unique photochromicity of Phy-type photoreceptors. These include residues that fix the bilin in the pocket, coordinate the pyrrole water, and possibly promote the proton exchange cycle during photoconversion.     

Efficiency enhancement of long-range energy transfer by sequential multistep FRET using fluorescence labeled DNA.

The efficiency of long-range (ca. 80 A) fluorescence energy transfer was enhanced about 1.5 times by a third chromophore located midway between two chromophores. A third chromophore should act like a relay station in sequential multistep energy transfer.     

The role of phospholipid headgroups in mediating bilayer organization. Perturbations induced by the presence of a tethered chromophore

We report on the dynamics of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-lissamine rhodamine B sulfonyl ammonium salt (Rhodamine-PE), incorporated into unilamellar vesicles composed of 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC). A key question in the investigation of any bilayer system using tethered fluorescent probes is the role that the chromophore itself plays in determining the organization of phospholipid bilayers. In this work, we investigate the role of headgroup-bound chromophores by measuring the steady state and time-resolved fluorescence response of the tethered rhodamine chromophore as a function of concentration in the bilayer. We find that both the steady state and dynamical properties of the chromophores change with concentration, in a manner consistent with the introduction of disorganization to the bilayers. Steady state fluorescence spectra show a clear perturbation of the rhodamine emission spectrum at a chromophore concentration of 0.25 mol%, which is not seen for lower concentrations, and fluorescence anisotropy data show that both the motional freedom and confining volume experienced by the chromophore increase with concentration. Taken collectively, our data point to the importance of using low concentrations of optical probes in the interrogation of bilayer structures.     

Unusual Spectral Properties of Bacteriophytochrome Agp2 Result from a Deprotonation of the Chromophore in the Red-absorbing Form Pr

Phytochromes are widely distributed photoreceptors with a bilin chromophore that undergo a typical reversible photoconversion between the two spectrally different forms, Pr and Pfr. The phytochrome Agp2 from Agrobacterium tumefaciens belongs to the group of bathy phytochromes that have a Pfr ground state as a result of the Pr to Pfr dark conversion. Agp2 has untypical spectral properties in the Pr form reminiscent of a deprotonated chromophore as confirmed by resonance Raman spectroscopy. UV/visible absorption spectroscopy showed that the pK_a is >11 in the Pfr form and ∼7.6 in the Pr form. Unlike other phytochromes, photoconversion thus results in a pK_a shift of more than 3 units. The Pr/Pfr ratio after saturating irradiation with monochromatic light is strongly pH-dependent. This is partially due to a back-reaction of the deprotonated Pr chromophore at pH 9 after photoexcitation as found by flash photolysis. The chromophore protonation and dark conversion were affected by domain swapping and site-directed mutagenesis. A replacement of the PAS or GAF domain by the respective domain of the prototypical phytochrome Agp1 resulted in a protonated Pr chromophore; the GAF domain replacement afforded an inversion of the dark conversion. A reversion was also obtained with the triple mutant N12S/Q190L/H248Q, whereas each single point mutant is characterized by decelerated Pr to Pfr dark conversion.