Photoaffinity labeling as an approach to study supramolecular nucleoprotein complexes

Structural and Molecular Kinetic Features of Activities of DNA Polymerases

DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.

Continuous flow reactor for the production of stable amyloid protein oligomers

The predominant working hypothesis of Alzheimer's disease is that the proximate pathologic agents are oligomers of the amyloid β-protein (Aβ). "Oligomer" is an ill-defined term. Many different types of oligomers have been reported, and they often exist in rapid equilibrium with monomers and higher-order assemblies. This has made formal structure-activity determinations difficult. Recently, Ono et al. [Ono, K., et al. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 14745-14750] used rapid, zero-length, in situ chemical cross-linking to stabilize the oligomer state, allowing the isolation and study of pure populations of oligomers of a specific order (number of Aβ monomers per assembly). This approach was successful but highly laborious and time-consuming, precluding general application of the method. To overcome these difficulties, we developed a "continuous flow reactor" with the ability to produce theoretically unlimited quantities of chemically stabilized Aβ oligomers. We show, in addition to its utility for Aβ, that this method can be applied to a wide range of other amyloid-forming proteins.

Facile synthesis of 8-azido-6-benzylaminopurine

Bromination of 6-benzylaminopurine (1) with Br(2) in AcOH in the presence of AcONa afforded 6-benzylamino-8-bromopurine (2) in 59% yield. The position of bromination was confirmed by direct transformation of bromide 2 by reaction with NaN(3) in dimethyl sulfoxide to 8-azido-6-benzylaminopurine (3) in a yield of 70% and comparison of its properties with the known compound 2-azido-6-benzylaminopurine (11). Compounds 3 and 11 were checked for their biological activity in specific biotests based on the primary cytokinin effects in living plants. Both synthesized compounds displayed effects similar to the typical cytokinin 6-benzylaminopurine (1).

Why do p-nitro-substituted aryl azides provide unintended dark reactions with proteins?

Aryl azide-mediated photo cross-linking has been widely used to obtain structural features in biological systems, even though the reactive species generated upon photolysis in aqueous solution have not been well characterized. We have established a mechanistic framework for the formation of adducts between photoactivated 5-azido-2-nitrobenzoyl reagents and protein functional groups. Photolysis of the aryl azide tethered to biotin via an amide linkage yields a cross-link with streptavidin. The ability of the pre-irradiated reagent to form a similar cross-link indicates that it is the long-lived reactive intermediate that contributes to the cross-link formation. The reactive intermediate forms an adduct with tryptophan. The sequence of the labeled peptide is found to be GlyTrp(*)ThrValAlaTrp(*)LysAsn, corresponding to residues 74-81 of the streptavidin sequence, where Trp(*) designates the modified Trp-75 and Trp-79. A peak at m/z 1455.1 corresponding to the calculated [M(peptide)+aryl nitrene+2O](+) molecular ion value has been observed for the labeled peptide. Product structure identification experiments support the assignment that the long-lived reactive intermediate is a p-nitro-N-arylhydroxylamine, which undergoes a number of transformations in aqueous solution leading to nitroso derivatives. A plausible mechanism of the interaction between tryptophan and nitroso compound is discussed.

Trapping of DNA topoisomerase I on nick-containing DNA in cell free extracts of Saccharomyces cerevisiae

The aim of the present study was to identify proteins that bind nicked DNA intermediates formed in the course of base excision repair (BER) in cell free extracts of Saccharomyces cerevisiae. In mammalian cells, nicks in DNA are targets of proteins such as PARP-1 or XRCC1 that have no homologues in yeast. One of the most promising methodologies to trap proteins that interact with damaged DNA lies in using a photocrosslinking technique with photoactivable dNTP analogues such as exo-N-{2-[N-(4-azido-2,5-difluoro-3-chloropyridine-6-yl)-3-aminopropionyl]-aminoethyl}-2'-deoxycytidine-5'-triphosphate (FAP-dCTP) for enzymatic synthesis of DNA probes with a photoreactive dNMP residue at the 3'-margin of a nick. Using this approach, we identified a major covalent DNA-protein adduct between a nick-containing 34-mer DNA duplex and a protein of a molecular mass of around 100-kDa. Unexpectedly, the formation of the 100-kDa adduct did not require the incorporation of the photoreactive dNMP residue at the 3'-margin of the nick nor exposure to near UV-light. However, the formation of the 100-kDa adduct strictly required a nick or a short gap in the DNA probe. Furthermore, the 100-kDa adduct was not detected in yeast extracts lacking DNA topoisomerase I (Top1). To further establish the nature of crosslinked protein, yeast Top1 was tagged with a Myc-epitope. In this case, the mobility of the Top1-DNA adduct increased by 7- kDa. Therefore, our data speak in favor of Top1 trapping by nicked DNA. In support of this hypothesis, purified yeast Top1 was also crosslinked to nicked DNA structures. Undamaged, uracil- and abasic (AP) site-containing DNAs were unable to trap Top1 under the same assay conditions. Since nicked DNA structures are frequently formed in the course of BER, their covalent linkage to Top1 has the potential to interfere with BER in vivo.

Phenylalanine 90 and 93 Are Localized within the Phenol Binding Site of Human UDP-Glucuronosyltransferase 1A10 as Determined by Photoaffinity Labeling, Mass Spectrometry, and Site-Directed Mutagenesis

4-Azido-2-hydroxybenzoic acid (4-AzHBA), a novel photoactive benzoic acid derivative, has been synthesized and used as a photoprobe to identify the phenol binding site of UDP-glucuronosyltransferases (UGTs). Analysis of recombinant His-tag UGTs from the 1A family for their ability to glucuronidate p-nitrophenol (pNP) and 4-methylumbelliferone (4-MU) revealed that UGT1A10 shows high activity toward phenols and phenol derivatives. Purified UGT1A10 was photolabeled with 4-AzHBA, digested with trypsin, and analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-mass spectrometry. A single modified peak corresponding to amino acid residues 89-98 (EFMVFHAQWK) of UGT1A10 was identified. The attachment site of the 4-AzHBA probe was localized to the quadruplet Phe(90)-Met(91)-Val(92)-Phe(93) using ESI LC-MS/MS. Sequence alignment revealed that the Phe(90) and Phe(93) are conserved in UGT1A7-10. Site-directed mutagenesis of these two amino acids was then followed by kinetic analysis of the mutants with two phenolic substrates, pNP and 4-MU, containing one and two planar rings, respectively. Using the combination of photoaffinity labeling, enzymatic digestion, MALDI-TOF and LC-MS mass spectrometry, and site-directed mutagenesis, we have determined for the first time that Phe(90) and Phe(93) are directly involved in the catalytic activity of UGT1A10 toward 4-MU and pNP.

Structural study of metastable amyloidogenic protein oligomers by photo-induced cross-linking of unmodified proteins

Oligomers of amyloidogenic proteins are believed to be key effectors of cytotoxicity and cause a variety of amyloid-related diseases. Dissociation or inhibition of formation of the toxic oligomers is thus an attractive strategy for the prevention and treatment of these diseases. In order to develop reagents capable of inhibiting protein oligomerization, the structures and mechanisms of oligomer formation must be understood. However, structural studies of oligomers are difficult because of the metastable nature of the oligomers and their existence in mixtures with monomers and other assemblies. A useful method for characterization of oligomer size distributions in vitro is photo-induced cross-linking of unmodified proteins (PICUP) (Fancy and Kodadek, 1999). By providing "snapshots" of dynamic oligomer mixtures, PICUP enables quantitative analysis of the relations between primary and quaternary structures, offering insights into the molecular organization of the oligomers. This chapter discusses the photochemical mechanism; reviews the scope, usefulness, and limitations of PICUP for characterizing metastable protein assemblies; and provides detailed experimental instructions for performing PICUP experiments.

Photoanalogues of the initiation substrates of the RNA polymerase II, 5-azido-2-nitrobenzoyl derivatives of the ATP gamma-amidophosphate: the possible photoinduced degradation of the functional group to an N-arylhydroxylamine

Photoanlogues of the initiation substrates of the RNA polymerase II, N3ArNH(CH2)(n)NHpppA where N3Ar is 5-azido-2-nitrobenzoyl group (n = 2 or 4) were synthesized, allowing the preparation of photoreactive oligonucleotides in situ by RNA polymerase II for application as photolabels. Photolysis of p-nitro-substituted aromatic azide in aqueous medium was investigated. Using the azoxy-coupling reaction it was possible to determine whether a nitrene or p-nitrophenyl hydroxylamine azoxy compound is the trappable intermediate that is generated at ambient temperature in aqueous solution.

Analyzing the handoff of DNA from UvrA to UvrB utilizing DNA-protein photoaffinity labeling

To better define the molecular architecture of nucleotide excision repair intermediates it is necessary to identify the specific domains of UvrA, UvrB, and UvrC that are in close proximity to DNA damage during the repair process. One key step of nucleotide excision repair that is poorly understood is the transfer of damaged DNA from UvrA to UvrB, prior to incision by UvrC. To study this transfer, we have utilized two types of arylazido-modified photoaffinity reagents that probe residues in the Uvr proteins that are closest to either the damaged or non-damaged strands. The damaged strand probes consisted of dNTP analogs linked to a terminal arylazido moiety. These analogs were incorporated into double-stranded DNA using DNA polymerase beta and functioned as both the damage site and the cross-linking reagent. The non-damaged strand probe contained an arylazido moiety coupled to a phosphorothioate-modified backbone of an oligonucleotide opposite the damaged strand, which contained an internal fluorescein adduct. Six site-directed mutants of Bacillus caldotenax UvrB located in different domains within the protein (Y96A, E99A, R123A, R183E, F249A, and D510A), and two domain deletions (Delta2 and Deltabeta-hairpin), were assayed. Data gleaned from these mutants suggest that the handoff of damaged DNA from UvrA to UvrB proceeds in a three-step process: 1) UvrA and UvrB bind to the damaged site, with UvrA in direct contact; 2) a transfer reaction with UvrB contacting mostly the non-damaged DNA strand; 3) lesion engagement by the damage recognition pocket of UvrB with concomitant release of UvrA.

Rapid photochemical cross-linking--a new tool for studies of metastable, amyloidogenic protein assemblies

Amyloidoses comprise a class of diseases characterized pathologically by the presence of deposits of fibrillar, aberrantly folded proteins, known as amyloids. Historically, these deposits were considered the key factors causing disease. However, recent evidence suggests that soluble protein oligomers, which are precursors for amyloid fibrils, are the primary toxic effectors responsible for the disease process. Understanding the mechanism by which these oligomers exert their toxicity requires knowledge of the structure, kinetics, and thermodynamics of their formation and conversion into larger assemblies. Such studies have been difficult due to the metastable nature of the oligomers. For the amyloid beta-protein (Abeta), a consensus about the size and relative abundance of small oligomers has not been achieved. We describe here the application of the method Photoinduced Cross-Linking of Unmodified Proteins (PICUP) to the study of Abeta oligomerization. This approach distinguishes oligomerization patterns of amyloidogenic and nonamyloidogenic proteins, allows quantification of each component in oligomer mixtures, and provides a means of correlating primary structure modifications with assembly characteristics. PICUP thus is a powerful tool for the investigation of small, metastable protein oligomers. The method provides essential insights into the factors that control the assembly of pathogenic protein oligomers, facilitating efforts toward the development of therapeutic agents.

Photoaffinity labeling of proteins in bovine testis nuclear extract

A binary system of photoaffinity reagents for selective affinity labeling of DNA polymerases has been developed. The photoreactive probe was formed in nuclear extract, using an end-labeled oligonucleotide containing a synthetic abasic site. This site was incised by apurinic/apyrimidinic endonuclease and then dNMPs carrying a photoreactive adduct were added to the 3(') hydroxyl using base-substituted arylazido derivatives of dUTP or dCTP. This results in the synthesis of photoreactive base excision repair (BER) intermediates. The photoreactive group was then activated, either directly (UV light exposure 320nm) or in the presence of the sensitizer of dTTP analog containing a pyrene group (Pyr-dUTP) under UV light 365nm. DNA polymerase beta was the main target crosslinked by photoreactive BER intermediates in this nuclear extract. In contrast, several proteins were labeled under the conditions of direct activation of arylazido group.

Binary system for selective photoaffinity labeling of base excision repair DNA polymerases

A system of photoaffinity reagents for selective labeling of DNA polymerases in extracts has been examined. To create the photoreactive DNA probe in situ, DNA substrates containing a synthetic abasic site are incubated in mouse embryonic fibroblast (MEF) cellular extract in the presence of base-substituted arylazido derivatives of dNTPs. This results in synthesis of a photoreactive long patch base excision repair (BER) intermediate. The arylazido photoreactive group is then activated through energy transfer from the pyrene group of a dNTP analog (Pyr-dUTP), following 365 nm UV light exposure. Pyr-dUTP binds to the active site of DNA polymerases, and the pyrene group, when excited by 365 nm UV light, activates the nearby photoreactive group in the BER intermediate resulting in crosslinking of DNA-bound DNA polymerases. Under these conditions, various DNA binding proteins that are unable to bind Pyr-dUTP are not crosslinked to DNA. DNA polymerase beta is the predominant crosslinked protein observed in the MEF extract. In contrast, several other DNA binding proteins are labeled under conditions of direct UV light activation of the photoreactive group at 312 nm. This study illustrates use of a new method of selective labeling of DNA polymerases in a crude cellular extract.

p-Azidophenyl phosphate is a photoactivatable phosphorylating reagent and p-benzoquinone monoimine precursor

p-Azidophenyl phosphate (I) has been exposed to ultraviolet light (lambda=313 nm) in aqueous solution with or without Lys. Analysis of the photoproducts by means of UV-VIS, IR, (1)H, (13)C and (31)P NMR spectroscopy has revealed that under irradiation of I inorganic phosphate (P(i)) is released, and p-benzoquinone monoimine (II) and p-benzoquinone (III) have appeared. The electrophilic nature of the intermediate results in a high tendency to react with lysine molecules, whereas the reaction with water is less favourable when I is irradiated in the presence of Lys. The product formed in this case is a phosphoramidate whose structure has been tentatively supported by (31)P NMR spectroscopy. These results imply that a p-azidophenyl phosphate is a highly potent aryl nitrene-precursor, which can be transformed easily into p-benzoquinone monoimine and is able to phosphorylate nucleophilic groups of amino acids. This finding is of great importance for the discussions about the chemical nature of protein photomodification products when p-azidophenyl phosphate derivatives are used as modifying reagents.

A binary system of photoreagents for high-efficiency labeling of DNA polymerases

To increase the efficiency of photoaffinity labeling of DNA polymerases, a binary system of photoaffinity reagents was applied. Photoreactive radioactive primers were synthesized by DNA polymerases beta (pol beta) or DNA polymerase from Thermus thermophilus (pol Tte) using a template-primer duplex in the presence of a dTTP analogue containing 4-azidotetrafluorobenzoyl group linked via spacers of varying length to 5-position of uridine ring- 5-[N-(2,3,5,6-tetrafluoro-4-azidobenzoyl)-amino-trans-propenyl-1]-2'-deoxyuridine-5'-triphosphate (FAB-4-dUTP) or 5-[N-[[(2,3,5,6-tetrafluoro-4-azidobenzoyl)-butanoyl]-amino]-trans-3-aminopropenyl-1]-2'-deoxyuridine-5'-triphosphate (FAB-9-dUTP). The reaction mixtures were UV irradiated (lambda = 365-450 nm) in the absence or presence of a dTTP analog, containing a pyrene moiety-5-[N-(4-(1-pyrenyl)-butylcarbonyl)-amino-trans-propenyl-1]-2'-deoxyuridine-5'-triphosphate (Pyr- 8-dUTP) or 5-[N-(4-(1-pyrenyl)-ethylcarbonyl)-amino-trans-propenyl-1]-2'-deoxyuridine-5'-triphosphate (Pyr-6-dUTP). The most efficient crosslinking of both DNA polymerases was observed in the case of photoreactive DNA primer, carrying the FAB-4-dUMP moiety at the 3'-end, and Pyr-6-dUTP as a sensitizer. The binary system of photoaffinity reagents allows increasing photoaffinity labeling of the both DNA polymerases in comparison to the primer crosslinking without photosensitizer.

8-N(3)-3'-biotinyl-ATP, a novel monofunctional reagent: differences in the F(1)- and V(1)-ATPases by means of the ATP analogue

A novel photoaffinity label, 8-N(3)-3'-biotinyl-ATP, has been synthesized. The introduction of an additional biotin residue is advantageous for easy detection of labeled proteins. This could be first tested by reaction with the F(1)-ATPase from the thermophilic bacterium PS3 (TF(1)). UV irradiation of TF(1) in the presence of 8-N(3)-3'-biotinyl-ATP results in a nucleotide-dependent binding of the analogue in the noncatalytic alpha and the catalytic beta subunits of TF(1), demonstrating the suitability of this analogue as a potential photoaffinity label. Reaction with the V(1)-ATPase, however, led to labeling of subunit E, which has been suggested as a structural and functional homologue of the gamma subunit of the F-ATPases. MALDI-TOF mass spectrometry has been used to map the regions of subunit E involved in the binding of 8-N(3)-3'-biotinyl-ATP.

Long-lived reactive intermediate photogenerated from N-(5-azido-2-nitrobenzoyl)-N'-(D-biotinyl)-1,2-diaminoethane as an affinity reagent to streptavidin

Irradiation of a complex between N-(5-azido-2-nitrobenzoyl)-N'-(D-biotinyl)-1,2-diaminoethane (I) and streptavidin with light of 313 nm led to the covalent attachment of the photobiotin analogue I to the protein. Streptavidin could also be labelled in the dark with prephotolyzed I. These results indicate that a long-lived reactive intermediate was formed upon irradiation. Moreover, after cleavage of labelled streptavidin with proteinase K this intermediate appears to be covalently attached to the same peptide as the one obtained by direct photoaffinity labelling. An iminosulfurane II derived from the reaction of biotin sulfur atom with aryl nitrene is responsible for the dark-labelling reaction. The photoproduct II converts in an aqueous solution almost completely into N-(5-amino-2-nitrobenzoyl)-N'-(D-(S-oxo)biotinyl)-1,2-diaminoethane (the half-life of II is 10 days).

Ligand-integrin alpha v beta 3 interaction determined by photoaffinity cross-linking: a challenge to the prevailing model

Integrin alpha(V)beta(3) plays a crucial role in angiogenesis, apoptosis, and bone remodeling, mainly by interacting with matrix proteins through recognition of an Arg-Gly-Asp (RGD) motif. Recently, a small cyclic RGD-containing alpha(V)beta(3)-ligand possessing a C-terminal photoreactive group was photo-cross-linked within beta(3)[99-118], in the N-terminus of the beta(3) chain [Bitan G et al. (1999) Biochemistry 38, 3414-3420]. In this paper, a photoreactive group at the N-terminus of the RGD-ligand is shown to interact within beta(3)[167-171], approximately 60 residues C-terminal to the previously identified domain. On the basis of these findings, a model of the putative I-like domain of the beta(3) subunit, homologous to alpha(M)-, alpha(L)-, and alpha(2)-I-domains, reveals that the beta(3)[99-118] and beta(3)[167-171] contact sites are close to each other and are on the opposite side relative to the metal ion-dependent adhesion site (MIDAS) motif. These observations contradict the prevailing model that proposes proximity between metal- and RGD-binding sites on the I-like domain. Our data suggest that either the I-like domain structure predicted for beta(3) is incorrect, or there is no spatial proximity between the RGD-binding site and the MIDAS motif in the I-like domain. Our results indicate that the current models for ligand-receptor interaction should be revisited.

Study of the chemical structures of the photo-cross-linking products between Tyr and the 5-azido-2-nitrobenzoyl residue

Irradiation of N-(tyrosyl)-N'-(5-azido-2-nitrobenzoyl)-1,2-diaminoethane (I) initiates chemical reactions that lead to different products depending on the experimental conditions. All of these products are attributed to the reactions of triplet 4-nitrobenzoyl nitrene (4NBN). The reactions of triplet 4NBN with the tyrosyl residue result in the formation of two distinct products: compound II, which is unstable in aqueous solution, and the stable compound cyclo-[1-(4'-nitro-3'-benzoyl)-2-(aminotyrosyl)-N,N'-ethylenediami ne] (III). The formation of II is detected only in aerobic conditions. The unstable photoproduct II converts almost completely into compound III when its solution is concentrated. The photoproducts II and III have absorption spectra that are close to those of the photolabelled peptides. This finding is important for speculating about the chemical nature of the photomodification products of protein tyrosyl residues by the arylazide group.