Pyrophosphorylation via selective phosphoprotein derivatization

An important step in elucidating the function of protein post-translational modifications (PTMs) is gaining access to site-specifically modified, homogeneous samples for biochemical characterization. Protein pyrophosphorylation is a poorly characterized PTM, and here a chemical approach to obtain pyrophosphoproteins is reported. Photo-labile phosphorimidazolide reagents were developed for selective pyrophosphorylation, affinity-capture, and release of pyrophosphoproteins. Kinetic analysis of the reaction revealed rate constants between 9.2 × 10-3 to 0.58 M-1 s-1, as well as a striking proclivity of the phosphorimidazolides to preferentially react with phosphate monoesters over other nucleophilic side chains. Besides enabling the characterization of pyrophosphorylation on protein function, this work highlights the utility of phosphoryl groups as handles for selective protein modification for a variety of applications, such as phosphoprotein bioconjugation and enrichment.

Agonist-induced Ca2+ sensitization in smooth muscle: redundancy of Rho guanine nucleotide exchange factors (RhoGEFs) and response kinetics, a caged compound study

Many agonists, acting through G-protein-coupled receptors and Gα subunits of the heterotrimeric G-proteins, induce contraction of smooth muscle through an increase of [Ca(2+)]i as well as activation of the RhoA/RhoA-activated kinase pathway that amplifies the contractile force, a phenomenon known as Ca(2+) sensitization. Gα12/13 subunits are known to activate the regulator of G-protein signaling-like family of guanine nucleotide exchange factors (RhoGEFs), which includes PDZ-RhoGEF (PRG) and leukemia-associated RhoGEF (LARG). However, their contributions to Ca(2+)-sensitized force are not well understood. Using permeabilized blood vessels from PRG(-/-) mice and a new method to silence LARG in organ-cultured blood vessels, we show that both RhoGEFs are activated by the physiologically and pathophysiologically important thromboxane A2 and endothelin-1 receptors. The co-activation is the result of direct and independent activation of both RhoGEFs as well as their co-recruitment due to heterodimerization. The isolated recombinant C-terminal domain of PRG, which is responsible for heterodimerization with LARG, strongly inhibited Ca(2+)-sensitized force. We used photolysis of caged phenylephrine, caged guanosine 5'-O-(thiotriphosphate) (GTPγS) in solution, and caged GTPγS or caged GTP loaded on the RhoA·RhoGDI complex to show that the recruitment and activation of RhoGEFs is the cause of a significant time lag between the initial Ca(2+) transient and phasic force components and the onset of Ca(2+)-sensitized force.

Characterizing caged molecules through flash photolysis and transient absorption spectroscopy

Caged molecules are photosensitive molecules with latent biological activity. Upon exposure to light, they are rapidly transformed into bioactive molecules such as neurotransmitters or second messengers. They are thus valuable tools for using light to manipulate biology with exceptional spatial and temporal resolution. Since the temporal performance of the caged molecule depends critically on the rate at which bioactive molecules are generated by light, it is important to characterize the kinetics of the photorelease process. This is accomplished by initiating the photoreaction with a very brief but intense pulse of light (i.e., flash photolysis) and monitoring the course of the ensuing reactions through various means, the most common of which is absorption spectroscopy. Practical guidelines for performing flash photolysis and transient absorption spectroscopy are described in this chapter.

Direct structural analysis of modified RNA by fluorescent in-line probing

Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5′-terminal ³²P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels–Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as ‘duplexing’ allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure.

Improved nucleotide selectivity and termination of 3'-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates

We describe a novel 3′-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2′-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous bacteriophages and lower eukaryotes. A series of 5-(2-nitrobenzyloxy)methyl-dUTP analogs (dU.I–dU.V) were synthesized based on our previous work with photochemically cleavable terminators. These 2-nitrobenzyl alkylated HOMedUTP analogs were characterized with respect to incorporation, single-base termination, nucleotide selectivity and photochemical cleavage properties. Substitution at the α-methylene carbon of 2-nitrobenzyl with alkyl groups of increasing size was discovered as a key structural feature that provided for the molecular tuning of enzymatic properties such as single-base termination and improved nucleotide selectivity over that of natural nucleotides. 5-[(S)-α-tert-Butyl-2-nitrobenzyloxy]methyl-dUTP (dU.V) was identified as an efficient reversible terminator, whereby, sequencing feasibility was demonstrated in a cyclic reversible termination (CRT) experiment using a homopolymer repeat of ten complementary template bases without detectable UV damage during photochemical cleavage steps. These results validate our overall strategy of creating 3′-OH unblocked reversible terminator reagents that, upon photochemical cleavage, transform back into a natural state. Modified nucleotides based on 5-hydroxymethyl-pyrimidines and 7-deaza-7-hydroxymethyl-purines lay the foundation for development of a complete set of four reversible terminators for application in NGS technologies.

Photochemically induced RNA and DNA abasic sites

Two phosphoramidite building blocks were synthesized that can easily be deprotected by UV light to reveal natural abasic sites in oligoribonucleotides as well as in oligodeoxyribonucleotides. Another building block which releases a 2'-O-methylated abasic site upon UV radiation is also described.

DMACM-caged adenosine nucleotides: ultrafast phototriggers for ATP, ADP, and AMP activated by long-wavelength irradiation

The development of new photocleavable adenosine nucleotides based on the photochemistry of [7-(dimethylamino)coumarin-4-yl]methyl (DMACM) esters is described. The phototriggers liberate adenosine triphosphate (ATP), diphosphate, and monophosphate upon UV/Vis irradiation between 334 and 405 nm. The efficiency of photocleavage at long wavelengths is high as a result of a combination of appropriate quantum yields and intensive absorptivities. By using time-resolved fluorescence spectroscopy, we determined a lower limit of 1.6 x 10(9) s(-1) for the rate constant of the release of ATP from DMACM-caged ATP. The favorable properties of DMACM-caged ATP were confirmed in physiological studies by confocal laser scanning microscopy. We were able to uncage DMACM-caged ATP in cultures of mouse astrocytes and in brain tissue slices from mice and were also able to measure the effect of photoreleased ATP on the cellular response of astrocytes, namely the ability of the ATP to evoke Ca(2+) ion waves.

Characterization of a new caged proton capable of inducing large pH jumps

A new caged proton, 1-(2-nitrophenyl)ethyl sulfate (caged sulfate), is characterized by infrared spectroscopy and compared with a known caged, proton 2-hydroxyphenyl 1-(2-nitrophenyl)ethyl phosphate (caged HPP). In contrast to caged HPP, caged sulfate can induce large pH jumps and protonate groups that have pK values as low as 2.2. The photolysis mechanism of caged sulfate is analogous to that of P(3)-[1-(2-nitrophenyl)ethyl] ATP (caged ATP), and the photolysis efficiency is similar. The utility of this new caged compound for biological studies was demonstrated by its ability to drive the acid-induced conformational change of metmyoglobin. This transition from the native conformation to a partially unfolded form takes place near pH 4 and was monitored by near-UV absorption spectroscopy.

Microbial transformation of 2-hydroxy and 2-acetoxy ketones with Geotrichum sp

Biotransformation of a series of o-, m- and p-substituted alpha-hydroxy- and alpha-acetoxyphenylethanones 1a-h and 9a-g with Geotrichum sp. led to the corresponding 1,2-diols 2 and/or monoacetates 10 in moderate to excellent enantiomeric excesses. Alpha-hydroxy- and alpha-acetoxyphenylethanones and their m- and p-derivatives gave preponderantly the S-configuration products while in the case of the o-derivatives R-alcohol was provided as the major enantiomer. The results of stereoselectivity were discussed.

Pinane-Type Tridentate Reagents for Enantioselective Reactions: Reduction of Ketones and Addition of Diethylzinc to Aldehydes

The reduction of aryl and alkenyl methyl ketones using lithium aluminum hydride modified with (1R,2S,3S,5R)-(+)-10-anilino-3-ethoxy-2-hydroxypinane (10b) afforded chiral secondary alcohols in 83-96% chemical yields and 50-91% ee with dominance of R enantiomers. The reduction of acetophenone in the presence of lithium iodide gave the alcohol product with higher ee. On the other hand, the addition reaction of diethylzinc to benzaldehyde using the pinane-based diols 5-9 as promoters gave 1-phenylpropanol in favor of the S enantiomer up to 88% ee. Using the pinane-based alcohols 10a-e as promoters, the R enantiomer was obtained as the major product. The addition reactions of diethylzinc to various substituted benzaldehydes, employing the diol ligands 5c and 8e, afforded predominantly the corresponding (S)-alcohols. The chiral modifiers 5-10 were prepared from (1R)-(-)-myrtenol and were readily recovered (>90%) after the asymmetric reactions. In this study, LAH reduction and Et(2)Zn addition are complementary methods for the preparation of optically active secondary alcohols. The ligand 10-butylanilino-2,3-dihydroxypinane 5c promoted the Et(2)Zn additions effectively, whereas the modifier 10-anilino-3-ethoxy-2-hydroxypinane 10binduced the LAH reductions in a highly enantioselective manner.

Synthesis and evaluation of a photolyzable derivative of sphingosine 1-phosphate--caged SPP

The synthesis of a photolyzable sphingosine 1-phosphate derivative is reported via the reaction of N-(tert-butoxycarbonyl)-2-N,3-O- isopropylidenesphingosine 7 and bis(alpha-methyl-o-nitrobenzyl) N,N-diisopropyl-phosphoramidite. Stimulation of DNA synthesis upon illumination of caged SPP-loaded cells is also described.

Time-resolved crystallography on H-ras p21

We describe here the results obtained to date on a project aimed at characterizing the changes occurring in the protein product (p21) of the H-ras proto-oncogene during and as a result of hydrolysis of GTP at its active site. The approach used involves crystallization of p21 with a photosensitive precursor of GTP (caged GTP) at the active site followed by generation of GTP by photolysis and collection of X-ray diffraction data using the Laue method at a synchrotron source. The structure of p21 complexed with a single diastereomer of caged GTP is presented here. In contrast to crystals obtained with mixed diastereomers, the nucleotide appears to bind in a manner which is very similar to that of other guanine nucleotides (GDP, GTP, GppNHp). The current state of time resolved structural experiments using these crystals is presented.

The development and application of photosensitive caged compounds to aid time-resolved structure determination of macromolecules

Rapid photochemical release of biologically active molecules, typically enzyme substrates or effectors of proteins, within crystals is likely to play an important role in time-resolved macromolecular crystallography. Photosensitive or ‘caged’ compounds in which functional groups are protected by the l-(2-nitrophenyl)ethyl group are potentially useful because many such compounds are efficiently and fairly rapidly photolysed (product quantum yield ca. 0.5 and photolysis rate ca. 100 s -1 for esters of weakly acidic phosphates) and have proved effective probes of physiological mechanisms. However, their availability and successful application are unlikely to be universal, and in some cases limitations may arise because of low quantum yield, a photolysis rate that is slow compared with the mechanism being studied or the toxicity of the by-product, 2-nitrosoacetophenone. 3,5-Dinitrophenyl and 3,5'- dimethoxybenzoin esters are two other potentially useful photosensitive classes of compound (Kirby & Varvoglis, J. chem. Soc. chem. Commun. 406 (1967); Sheehan et al. , J. Am. chem. Soc . 93, 7222-7228 (1971); Baldwin et al., Tetrahedron 46, 6879-6884 (1990)). 3,5-Dinitrophenyl phosphate has a product quantum yield of 0.67 and releases P A at greater than 104 s_1. However the dinitrophenyl group is not generally photosensitive: for example the P 3-3,5-dinitrophenyl ester of ATP photolyses very inefficiently at pH 7. The S'A'-dimethoxybenzoin group is a promising photosensitive group for phosphate esters and the P 3 -3/,5'-dimethoxybenzoin ester of ATP photolyses at greater than 10 5 s -1 at neutral pH and 20 °C though with only about 4% photolysis on 347 nm pulse irradiation.

Inhibition of unloaded shortening velocity in permeabilized muscle fibres by caged ATP compounds

The effects of both the P3-1-(2-nitrophenyl)ethyl ester of adenosine 5'-triphosphate (NPE-caged ATP) and its separate diastereoisomers, and the P3-3',5'-dimethoxybenzoin ester of ATP (DMB-caged ATP) were studied on the unloaded shortening velocity of glycerinated rabbit psoas muscle fibres. The unloaded shortening velocities of the active fibres were measured as a function of ATP concentration (0.1-5 mM) using the 'slack-test' with and without 2 mM caged ATP. Shortening velocity followed a Michaelis-Menten relationship with ATP concentration, the Km for ATP being 170 microM. The caged ATP compounds inhibited shortening velocity, in a manner consistent with competitive inhibition, with a Ki of 1-2 mM. The R- and S-diastereoisomers of NPE-caged ATP showed the same degree of competitive inhibition of the shortening velocity, as did DMB-caged ATP. These observations suggest that caged ATP compounds bind to the ATPase site of the actomyosin where they compete with the substrate, Mg2+ ATP.