Genetically Encoding Photocaged Quinone Methide to Multitarget Protein Residues Covalently in Vivo.

Genetically introducing covalent bonds into proteins in vivo with residue specificity is affording innovative ways for protein research and engineering, yet latent bioreactive unnatural amino acids (Uaas) genetically encoded to date react with one to few natural residues only, limiting the variety of proteins and the scope of applications amenable to this technology. Here we report the genetic encoding of (2 R)-2-amino-3-fluoro-3-(4-((2-nitrobenzyl)oxy) phenyl) propanoic acid (FnbY) in Escherichia coli and mammalian cells. Upon photoactivation, FnbY generated a reactive quinone methide (QM), which selectively reacted with nine natural amino acid residues placed in proximity in proteins directly in live cells. In addition to Cys, Lys, His, and Tyr, photoactivated FnbY also reacted with Trp, Met, Arg, Asn, and Gln, which are inaccessible with existing latent bioreactive Uaas. FnbY thus dramatically expanded the number of residues for covalent targeting in vivo. QM has longer half-life than the intermediates of conventional photo-cross-linking Uaas, and FnbY exhibited cross-linking efficiency higher than p-azido-phenylalanine. The photoactivatable and multitargeting reactivity of FnbY with selectivity toward nucleophilic residues will be valuable for addressing diverse proteins and broadening the scope of applications through exploiting covalent bonding in vivo for chemical biology, biotherapeutics, and protein engineering.

Photo-Cross-Linking of IKs Demonstrates State-Dependent Interactions between KCNE1 and KCNQ1.

The slow delayed rectifier potassium current (IKs) is a key repolarizing current during the cardiac action potential. It consists of four KCNQ1 α-subunits and up to four KCNE1 ß-subunits, which are thought to reside within external clefts of the channel. The interaction of KCNE1 with KCNQ1 dramatically delays opening of the channel but the mechanisms by which this occur are not yet fully understood. Here, we have used unnatural amino acid photo-cross-linking to investigate the dynamic interactions that occur between KCNQ1 and KCNE1 during activation gating. The unnatural amino acid p-Benzoylphenylalanine was successfully incorporated into two residues within the transmembrane domain of KCNE1: F56 and F57. UV-induced cross-linking suggested that F56Bpa interacts with KCNQ1 in the open state, whereas F57Bpa interacts predominantly in resting channel conformations. When UV was applied at progressively more depolarized preopen holding potentials, cross-linking of F57Bpa with KCNQ1 was slowed, which indicates that KCNE1 is displaced within the channel's cleft early during activation, or that conformational changes in KCNQ1 alter its interaction with KCNE1. In E1R/R4E KCNQ1, a mutant with constitutively activated voltage sensors, F56Bpa and F57Bpa KCNE1 were cross-linked in open and closed states, respectively, which suggests that their actions are mediated mainly by modulation of KCNQ1 pore function.

Tracking G-protein-coupled receptor activation using genetically encoded infrared probes.

Rhodopsin is a prototypical heptahelical family A G-protein-coupled receptor (GPCR) responsible for dim-light vision. Light isomerizes rhodopsin's retinal chromophore and triggers concerted movements of transmembrane helices, including an outward tilting of helix 6 (H6) and a smaller movement of H5, to create a site for G-protein binding and activation. However, the precise temporal sequence and mechanism underlying these helix rearrangements is unclear. We used site-directed non-natural amino acid mutagenesis to engineer rhodopsin with p-azido-l-phenylalanine residues incorporated at selected sites, and monitored the azido vibrational signatures using infrared spectroscopy as rhodopsin proceeded along its activation pathway. Here we report significant changes in electrostatic environments of the azido probes even in the inactive photoproduct Meta I, well before the active receptor state was formed. These early changes suggest a significant rotation of H6 and movement of the cytoplasmic part of H5 away from H3. Subsequently, a large outward tilt of H6 leads to opening of the cytoplasmic surface to form the active receptor photoproduct Meta II. Thus, our results reveal early conformational changes that precede larger rigid-body helix movements, and provide a basis to interpret recent GPCR crystal structures and to understand conformational sub-states observed during the activation of other GPCRs.

Photo-induced reversible structural transition of cationic diphenylalanine peptide self-assembly.

The photo-induced self-assembly of a cationic diphenylalanine peptide (CDP) is investigated using a photoswitchable sulfonic azobenzene as the manipulating unit. A reversible structural transition between a branched structure and a vesicle-like structure is observed by alternating between UV and visible light irradiation.

Identification of SUMO Binding Proteins Enriched after Covalent Photo-Cross-Linking.

Post-translational modification with the small ubiquitin-like modifier (SUMO) affects thousands of proteins in the human proteome and is implicated in numerous cellular processes. The main outcome of SUMO conjugation is a rewiring of protein-protein interactions through recognition of the modifier's surface by SUMO binding proteins. The SUMO-interacting motif (SIM) mediates binding to a groove on SUMO; however, the low affinity of this interaction and the poor conservation of SIM sequences complicates the isolation and identification of SIM proteins. To address these challenges, we have designed and biochemically characterized monomeric and multimeric SUMO-2 probes with a genetically encoded photo-cross-linker positioned next to the SIM binding groove. Following photoinduced covalent capture, even weak SUMO binders are not washed away during the enrichment procedure, and very stringent washing conditions can be applied to remove nonspecifically binding proteins. A total of 329 proteins were isolated from nuclear HeLa cell extracts and identified using mass spectrometry. We found the molecular design of our probes was corroborated by the presence of many established SUMO interacting proteins and the high percentage (>90%) of hits containing a potential SIM sequence, as predicted by bioinformatic analyses. Notably, 266 of the 329 proteins have not been previously reported as SUMO binders using traditional noncovalent enrichment procedures. We confirmed SUMO binding with purified proteins and mapped the position of the covalent cross-links for selected cases. We postulate a new SIM in MRE11, involved in DNA repair. The identified SUMO binding candidates will help to reveal the complex SUMO-mediated protein network.

Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine.

Azido-modified aromatic amino acids have been used as powerful infrared probes for the site-specific detection of proteins because of their large transition dipole strengths. However, their complex absorption profiles hinder their wider application. The complicated absorption profile of 4-azido-l-phenylalanine (pN3Phe) in isopropanol was identified and attributed to accidental Fermi resonances (FRs) by means of linear absorption and two-dimensional (2D) IR spectroscopies. The 2D IR results of pN3Phe in H2O and D2O further demonstrate that the FRs are distinctively influenced by the hydrogen-bonding environment. Under the influence of FRs, the 2D IR shape is distorted, indicating that pN3Phe is not a good candidate in spectral diffusion studies. A three-state model and first-principles calculations were used to analyze unperturbed energy levels, unveiling the FRs between the azide asymmetric stretching band and two combination bands. Furthermore, the anharmonic frequency calculations suggest that changing the substitution position of the azide group from para to meta can effectively modulate the FRs by reducing the coupling strength. This work provides a deep understanding of the FRs in azido-modified aromatic amino acids and sheds light on the modification of azido-modified amino acids for wider utilization as vibrational probes.

Microdosimetric Modeling of Biological Effectiveness for Boron Neutron Capture Therapy Considering Intra- and Intercellular Heterogeneity in 10B Distribution.

We here propose a new model for estimating the biological effectiveness for boron neutron capture therapy (BNCT) considering intra- and intercellular heterogeneity in 10B distribution. The new model was developed from our previously established stochastic microdosimetric kinetic model that determines the surviving fraction of cells irradiated with any radiations. In the model, the probability density of the absorbed doses in microscopic scales is the fundamental physical index for characterizing the radiation fields. A new computational method was established to determine the probability density for application to BNCT using the Particle and Heavy Ion Transport code System PHITS. The parameters used in the model were determined from the measured surviving fraction of tumor cells administrated with two kinds of 10B compounds. The model quantitatively highlighted the indispensable need to consider the synergetic effect and the dose dependence of the biological effectiveness in the estimate of the therapeutic effect of BNCT. The model can predict the biological effectiveness of newly developed 10B compounds based on their intra- and intercellular distributions, and thus, it can play important roles not only in treatment planning but also in drug discovery research for future BNCT.

Influence of near-infrared radiation on the pKa values of L-phenylalanine.

The effect of pH on L-phenylalanine (L-phe) before and after exposure to near-infrared (NIR) radiation (15 min, 700-2000 nm) was investigated by attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. Characteristic bands of L-phe were described and the pK(a) values were retrieved from IR spectra by using an intensity ratio method according to our recent paper (Olsztynska et al., Appl. Spectrosc. 55, 901 (2001)). It has been found that the irradiation process modifies pK(a) values of L-phe. The spectroscopic study clearly shows the shift of acid-base equilibrium after exposure to NIR radiation. The phenomenon is due to modification of the water structure. Intra- and intermolecular hydrogen bonds weaken, which could induce conformational changes of the phe molecule. Subsequently, hydrophobic interactions strongly increase. These processes favor aggregation of phe molecules, which leads to deprotonation of the -NH(3)(+) to -NH(2) group and protonation of the -COO(-) to -COOH group, changing the pK(a) values.

Boron neutron capture therapy of brain tumors: enhanced survival following intracarotid injection of either sodium borocaptate or boronophenylalanine with or without blood-brain barrier disruption.

The purpose of the present study was to determine whether the efficacy of boron neutron capture therapy could be enhanced by means of intracarotid (i.c.) injection of sodium borocaptate (BSH) or boronophenylalanine (BPA) with or without blood-brain barrier disruption (BBB-D). For biodistribution studies, F98 glioma-bearing rats were injected i.v. or i.c. with either BSH (30 mg of boron/kg of body weight) or BPA (24 mg of boron/kg of body weight) with or without mannitol-induced, hyperosmotic BBB-D and killed 2.5 h later. The highest tumor boron concentrations for BSH and BPA were attained following i.c. injection with BBB-D (48.6 and 94.0 microg/g, respectively) compared to i.c. (30.8 and 42.7 microg/g) and i.v. injection (12.9 and 20.8 microg). Using the same doses of BSH and BPA, therapy experiments were initiated 14 days after intracerebral implantation of F98 glioma cells. Animals were irradiated 2.5 h after i.v. or i.c. administration of the capture agent with or without BBB-D using a collimated beam of thermal neutrons at the Brookhaven Medical Research Reactor. The median survival times of rats given BSH or BPA i.c. were 52 and 69 days, respectively, for rats with BBB-D; 39 and 48 days for rats without BBB-D; 33 and 37 days for i.v. injected rats; 29 days for irradiated controls; and 24 days for untreated controls. i.c. injection of either BSH or BPA resulted in highly significant enhancement (P = 0.01 and P = 0.0002, respectively) of survival times compared to i.v. injection, and this was further augmented by BBB-D (P = 0.02 and P = 0.04, respectively) compared to i.c. injection. Normal brain tissue tolerance studies were carried out with non-tumor-bearing rats, which were treated in the same way as tumor-bearing animals. One year after irradiation, the brains of these animals showed only minimal radiation-induced changes in the choroid plexus, but no differences were discernible between irradiated controls and those that had BBB-D followed by i.c. injection of either BSH or BPA. Our data clearly show that the route of administration, as well as BBB-D, can enhance the uptake of BSH and BPA, and, subsequently, the efficacy of boron neutron capture therapy.

Dosimetry determines the initial OH radical concentration in fast photochemical oxidation of proteins (FPOP).

Fast photochemical oxidation of proteins (FPOP) employs laser photolysis of hydrogen peroxide to give OH radicals that label amino acid side-chains of proteins on the microsecond time scale. A method for quantitation of hydroxyl radicals after laser photolysis is of importance to FPOP because it establishes a means to adjust the yield of •OH, offers the opportunity of tunable modifications, and provides a basis for kinetic measurements. The initial concentration of OH radicals has yet to be measured experimentally. We report here an approach using isotope dilution gas chromatography/mass spectrometry (GC/MS) to determine quantitatively the initial •OH concentration (we found ~0.95 mM from 15 mM H2O2) from laser photolysis and to investigate the quenching efficiencies for various •OH scavengers.

Gamma-radiation-induced interactions between amino acids and glucagon.

The interaction of glucagon and phenylalanine mediated by the OH . radical causes formation of higher molecular weight products of glucagon and phenylalanine, loss of amino acid residues in glucagon, and formation of adducts of glucagon and phenylalanine. The relative yields of these products depend upon the molar ratio of phenylalanine to glucagon in solution. At low ratios, glucagon aggregation and loss of amino acid residues predominate; at high ratios, the formation of phenylalanine dimers (and possible trimers and tetramers) predominates. The formation of adducts reaches a maximum at a phenylalanine:glucagon molar ratio of 3-4, and then decreases gradually, as the molar ratio increases, but is still discernible even at high molar ratios. Mechanisms for the formation of adducts are suggested. The influence of the primary aqueous radical intermediates, OH., H., and e-aq, on adduct formation has been evaluated for several different amino acids by irradiating in the presence of specific radical scavengers. For the aromatic amino acids (phenylalanine, tryptophan, and tyrosine), OH. is considerably more effective than e-aq for mediating adduct formation, whereas for histidine and methionine, these primary radicals are equally effective.

Binding-site specificity of the radiolytically induced crosslinking of phenylalanine to glucagon.

The gamma-radiation-induced crosslinking of phenylalanine to glucagon, mediated by OH ., has been shown to involve a limited number of binding sites on the glucagon molecule. Glucagon-phenylalanine adducts were partially separated from other radiolysis products with Sephadex gel filtration; further isolation of adducts was achieved with reverse-phase high-performance liquid chromatography (HPLC). Amino acid analysis of the isolated adducts indicates that the aromatic residues (phenylalanine and tyrosine), basic residues (histidine and lysine), and sulfur-containing residue (methionine) of glucagon are predominantly involved in crosslinking; these are essentially the same residues implicated in glucagon-glucagon crosslinking. Acid hydrolysates and chymotryptic digests of glucagon-phenylalanine adducts were examined with HPLC. The number of amino acid-phenylalanine adducts and also chymotryptic peptides observed was much greater than would have been expected based on the amino acid analysis. This observation is best accounted for by the involvement in crosslinking of radicals formed on the glucagon with more than one possible phenylalanine-derived free radical.

Binding site specificity of gamma-radiation-induced crosslinking between phenylalanine and a phenylalanine-containing tetrapeptide.

The binding site specificity of crosslinking mediated by the hydroxyl radical has been investigated in a simple model system: a tetrapeptide, Gly-Gly-Phe-Leu, and 14C-labeled phenylalanine. Crosslinking leads to the tetrapeptide-phenylalanine adduct which has been isolated by gel filtration. The amino acid analysis of these adducts compared with those of gamma-radiation-induced dimers of the tetrapeptide and of the dipeptide, Gly-Phe, shows that only the phenylalanine residue is affected and that the same new peaks appear in each case. Spectrophotometric measurement indicates that the extinction coefficient at 260 nm of dimeric tetrapeptide is four times higher than that of monomeric, as is dimeric phenylalanine compared to monomeric. These observations suggest a common crosslinking mechanism in all three cases that involves the aromatic ring of phenylalanine. The appearance of several radioactive peaks in the gel filtration separation of the acid hydrolysate of the adduct suggests that the crosslinking involves more than one possible modification of the phenylalanine. Three distinct tetrapeptide-Phe species, corresponding to molecular weights of 555, 573, and 591, were observed by fast atom bombardment mass spectrometry. The partial release of radioactive phenylalanine from the tetrapeptide-phenylalanine adducts by acid hydrolysis indicates the liability of some phenylalanine-phenylalanine bonds.

Photolysis of desmosine and isodesmosine by ultraviolet light.

It is known that the pyridinium ring of a model compound such as N-methyl pyridinium chloride is cleaved by U.V. radiation at 254 nm. At acid pH the products obtained are methylamine and glutaconaldehyde. Under the same conditions desmosine and isodesmosine are degraded into lysine and probably into the homologous substituted ketone of glutaconaldehyde. At pH 6.0-7.0, a transient open-chain aminoaldehyde intermediate is observed which can either reform the original compound or be cleaved as at low pH. When intact elastin is photolysed for 20 minutes in water, approximately 75% of the (iso) desmosines are destroyed, accompanied by an increase of free lysine residues. No change in the concentration of the other amino acids, including tyrosine, are noted. It is therefore likely that the crosslinks engaged in peptide links are also cleaved photochemically.

Monitoring conformational changes in peroxisome proliferator-activated receptor α by a genetically encoded photoamino acid, cross-linking, and mass spectrometry.

Chemical cross-linking combined with an enzymatic digestion and mass spectrometric analysis of the reaction products has evolved into an alternative strategy to structurally resolve protein complexes. We investigated conformational changes in peroxisome proliferator-activated receptor α (PPARα) upon ligand binding. Using E. coli cells with a special tRNA/aminoacyl-tRNA synthetase pair, two PPARα variants were prepared in which Leu-258 or Phe-273 were site-specifically replaced by the genetically encoded photoreactive amino acid p-benzoylphenylalanine (Bpa). PPARα variants were subjected to UV-induced cross-linking, both in the absence and in the presence of ligands. After the photo-cross-linking reaction, reaction mixtures were enzymatically digested and peptides were analyzed by mass spectrometry. The inter-residue distances disclosed by the photochemical cross-links served to monitor conformational changes in PPARα upon agonist and antagonist binding. The data obtained with our strategy emphasize the potential of genetically encoded internal photo-cross-linkers in combination with mass spectrometry as an alternative method to monitor in-solution 3D-protein structures.

In vitro studies on stability of L-p-boronophenylalanine-fructose complex (BPA-F).

Boron neutron capture therapy (BNCT) is an experimental drug-targeted treatment combining tumour-seeking boronated drug(s) and subsequent ¹°B activation by neutrons. Synthetic amino acid, L-p-boronophenylalanine (BPA), administered as a fructose complex (BPA-F) is used in BNCT trials. We tested the in vitro biological and structural stability of the BPA-F as a function of time (11 days). The BPA-F samples were analyzed using biological bacterial endotoxin and sterility tests. Visual tests were clarity, degree of opalescence and coloration according to European Pharmacopoeia. The structural stability of the BPA-F was monitored via ¹H NMR signal intensity of the aromatic protons of the BPA-F samples. A slight change of BPA-F samples in coloration was observed during storage. BPA-fructose complex remained sterile and bacterial endotoxin tests were negative. In the end of study period, relative intensity of the (1)H NMR signals of the BPA-F sample was ≥ 90% of the initial relative intensity. The biological properties of the BPA-fructose complex and chemical structure of the complex remained the same during the test period. Visually the solutions stayed clear, but there was a slight change in colour. The tests indicate that the prepared batch of BPA-F complex can be used for the patient infusion at least for a week.