Photoreactive Probe Research Articles

A Conserved Acidic Motif Is Crucial for Enzymatic Activity of Protein O-Mannosyltransferases

Protein O-mannosylation is an essential modification in fungi and mammals. It is initiated at the endoplasmic reticulum by a conserved family of dolichyl phosphate mannose-dependent protein O-mannosyltransferases (PMTs). PMTs are integral membrane proteins with two hydrophilic loops (loops 1 and 5) facing the endoplasmic reticulum lumen. Formation of dimeric PMT complexes is crucial for mannosyltransferase activity, but the direct cause is not known to date. In bakers' yeast, O-mannosylation is catalyzed largely by heterodimeric Pmt1p-Pmt2p and homodimeric Pmt4p complexes. To further characterize Pmt1p-Pmt2p complexes, we developed a photoaffinity probe based on the artificial mannosyl acceptor substrate Tyr-Ala-Thr-Ala-Val. The photoreactive probe was preferentially cross-linked to Pmt1p, and deletion of the loop 1 (but not loop 5) region abolished this interaction. Analysis of Pmt1p loop 1 mutants revealed that especially Glu-78 is crucial for binding of the photoreactive probe. Glu-78 belongs to an Asp-Glu motif that is highly conserved among PMTs. We further demonstrate that single amino acid substitutions in this motif completely abolish activity of Pmt4p complexes. In contrast, both acidic residues need to be exchanged to eliminate activity of Pmt1p-Pmt2p complexes. On the basis of our data, we propose that the loop 1 regions of dimeric complexes form part of the catalytic site.

Labeling and enrichment of Arabidopsis thaliana matrix metalloproteases using an active-site directed, marimastat-based photoreactive probe

Matrix metalloproteases (MMPs) are secreted or membrane-bound zinc-containing proteases that play diverse roles in development and immunity in plants and in tissue remodeling in animals. We developed a photoreactive probe based on the MMP inhibitor marimastat, conjugated to a 4-azidotetrafluorobenzoyl moiety as photoreactive group and biotin as detection or sorting function. The probe labels At2-MMP, At4-MMP, At5-MMP, and likely other plant MMPs in leaf extracts, as shown by transient At-MMP expression in Nicotiana benthamiana, protein blot, and LC–MS/MS analysis. This MMP probe is a valuable tool to study the post-translational status of MMPs during plant immunity and other MMP-regulated processes.

Anti‐apoptotic Bcl‐2 uses not only the BH1‐3 groove but also the BH4 region to bind and inhibit pro‐apoptotic Bax oligomerization

Bcl‐2 family proteins regulate permeabilization of mitochondrial outer membrane, the commitment step of apoptosis which is often impaired in tumor cells. In particular, pro‐apoptotic Bax form oligomeric pores in the membrane to initiate apoptosis, whereas anti‐apoptotic Bcl‐2 or Bcl‐XL inhibits Bax oligomerization. Complex structures of Bcl‐2 family proteins determined in solution suggest that a groove on Bcl‐2 formed by the Bcl‐2 homology region 1–3 (BH1‐3) binds to the BH3 region of Bax. However, the structure of Bcl‐2‐Bax hetero‐complex in the membrane is elusive. We used site‐specific photocross‐linking to capture Bax‐Bcl‐2 or Bax‐Bcl‐XL hetero‐complex formed in membrane surrogate (detergent micelles) or real membrane, respectively. Many of the resulting photo‐adducts were formed by the photo‐reactive probes located in the BH3 region of Bax and the BH1‐3 groove of Bcl‐2, supporting that complex model proposed by the structural studies. However, Bax‐Bcl‐2 dimer‐specific photo‐adducts were also detected from probes located in other regions including the helix 6 of Bax and the BH4 region of Bcl‐2, suggesting an additional interface in the hetero‐dimer. Surprisingly mutations in the BH3:BH1‐3 groove interface inhibited the interactions in the helix 6:BH4 interface, and vice versa. The mutation also abolished the Bcl‐2 inhibition of Bax oligomerization. Therefore, Bcl‐2 binds to Bax through two interdependent interfaces to inhibit Bax oligomerization in the membrane surrogate. Preliminary studies of Bcl‐XL‐Bax dimer formed in liposomes indicate that the same mechanism may be used for the hetero‐complex formed in real membranes. Further studies are under way to test this hypothesis. (The project is supported by the NIH grant GM062964 to J.L.)

A photoreactive probe that differentiates the binding sites of noncompetitive GABA receptor antagonists

γ-Aminobutyric acid (GABA) receptors are postsynaptic membrane protein complexes that are important not only in the regulation of the nervous system but also as targets of drugs and insecticides. We synthesized a photoreactive straight-chain noncompetitive antagonist (NCA), 2-nitro-4-[3-(trifluoromethyl)-3H-diazirin-3-yl]phenyl 4-(4-methoxycarbonyl-1-butynyl)benzoate (NMB), to probe the NCA binding site. Our data show that this probe labels the NCA site and demonstrate that the NCA insecticide fipronil binds at a site distinct from that of other NCAs, such as picrotoxinin and 4'-ethynyl-4-n-propylbicycloorthobenzoate. The unique molecule NMB will be useful in identifying the cross-linking site of straight-chain NCAs in GABA receptors and mapping allosteric binding sites. Such studies should provide invaluable information in designing novel NCAs.

Bax Forms an Oligomer via Separate, Yet Interdependent, Surfaces

Interactions of Bcl-2 family proteins regulate permeability of the mitochondrial outer membrane and apoptosis. In particular, Bax forms an oligomer that permeabilizes the membrane. To map the interface of the Bax oligomer we used Triton X-100 as a membrane surrogate and performed site-specific photocross-linking. Bax-specific adducts were formed through photo-reactive probes at multiple sites that can be grouped into two surfaces. The first surface overlaps with the BH1-3 groove formed by Bcl-2 Homology motif 1, 2, and 3; the second surface is a rear pocket located on the opposite side of the protein from the BH1-3 groove. Further cross-linking experiments using Bax BH3 peptides and mutants demonstrated that the two surfaces interact with their counterparts in neighboring proteins to form two separated interfaces and that interaction at the BH1-3 groove primes the rear pocket for further interaction. Therefore, Bax oligomerization proceeds through a series of interactions that occur at separate, yet allosterically, coupled interfaces.

Inhomogeneous Distribution of Solid State Photochromic Reaction of Diarylethene Derivatives

Free volume in polymer matrices has been revealed with a photo-reactive probe technique by using various photochromic compounds and polymer matrices. The effect of photoreactions of diarylethene derivatives in methyl methacrylate polymer was determined in terms of inhomogeneous distribution of solid state photochromic reaction. The quantum yield of the photoisomerization from open-ring isomer to close-ring one, and the backward reaction were determined by the change in absorption during isomerization. The forward reaction is inhomogeneous due to conformational distribution of diarylethene.

Pen2 and Presenilin-1 Modulate the Dynamic Equilibrium of Presenilin-1 and Presenilin-2 γ-Secretase Complexes

gamma-Secretase is known to play a pivotal role in the pathogenesis of Alzheimer disease through production of amyloidogenic Abeta42 peptides. Early onset familial Alzheimer disease mutations in presenilin (PS), the catalytic core of gamma-secretase, invariably increase the Abeta42:Abeta40 ratio. However, the mechanism by which these mutations affect gamma-secretase complex formation and cleavage specificity is poorly understood. We show that our in vitro assay system recapitulates the effect of PS1 mutations on the Abeta42:Abeta40 ratio observed in cell and animal models. We have developed a series of small molecule affinity probes that allow us to characterize active gamma-secretase complexes. Furthermore we reveal that the equilibrium of PS1- and PS2-containing active complexes is dynamic and altered by overexpression of Pen2 or PS1 mutants and that formation of PS2 complexes is positively correlated with increased Abeta42:Abeta40 ratios. These data suggest that perturbations to gamma-secretase complex equilibrium can have a profound effect on enzyme activity and that increased PS2 complexes along with mutated PS1 complexes contribute to an increased Abeta42:Abeta40 ratio.

Synthesis and evaluation of photoreactive probes to elucidate iodide efflux in thyrocytes

Four photoreactive analogues of 3-biphenyl-4′-yl-5,6-dihydroimidazo[2,1- b]thiazole were prepared and evaluated as iodide sequestering agents in sodium iodide symporter-expressing cells. One of these new photoactivatable compounds retained biological activity and was further radiolabeled with tritium. This compound may provide a useful tool for labeling, purification, and identification of target protein responsible for iodide efflux in thyrocytes.

Probing the Structure of the Affinity-Purified and Lipid-Reconstituted Torpedo Nicotinic Acetylcholine Receptor

The Torpedo nicotinic acetylcholine receptor (nAChR) is the only member of the Cys-loop superfamily of ligand-gated ion channels (LGICs) that is available in high abundance in a native membrane preparation. To study the structure of the other LGICs using biochemical and biophysical techniques, detergent solubilization, purification, and lipid reconstitution are usually required. To assess the effects of purification on receptor structure, we used the hydrophobic photoreactive probe 3-trifluoromethyl-3-(m-[(125)I]iodophenyl)diazirine ([(125)I]TID) to compare the state-dependent photolabeling of the Torpedo nAChR before and after purification and reincorporation into lipid. For the purified nAChR, the agonist-sensitive photolabeling within the M2 ion channel domain of positions M2-6, M2-9, and M2-13, the agonist-enhanced labeling of deltaThr274 (deltaM2-18) within the delta subunit helix bundle, and the labeling at the lipid-protein interface (alphaMu4) were the same as for the nAChR in native membranes. However, addition of agonist did not enhance [(125)I]TID photolabeling of deltaIle288 within the deltaM2-M3 loop. These results indicate that after purification and reconstitution of the Torpedo nAChR, the difference in structure between the resting and desensitized states within the M2 ion channel domain was preserved, but not the agonist-dependent change of structure of the deltaM2-M3 loop. To further characterize the pharmacology of [(125)I]TID binding sites in the nAChR in the desensitized state, we examined the effect of phencyclidine (PCP) on [(125)I]TID photolabeling. PCP inhibited [(125)I]TID labeling of amino acids at the cytoplasmic end of the ion channel (M2-2 and M2-6) while potentiating labeling at M2-9 and M2-13 and allosterically modulating the labeling of amino acids within the delta subunit helix bundle.

The N-Terminal Parts of VIP and Antagonist PG97–269 Physically Interact with Different Regions of the Human VPAC1 Receptor

Vasoactive intestinal peptide (VIP) is a widespread neuropeptide, which exerts many biological functions through interaction with the VPAC1 receptor, a class II G protein-coupled receptor. Photoaffinity labeling studies combined with 3D molecular modeling demonstrated that the central and C-terminal parts of VIP (segment 6-28) have physical contacts with the N-terminal ectodomain (N-Ted) of VPAC1 receptor. However, the domain of the hVPAC1 receptor interacting with the N-terminus of VIP (1-5) is still unknown. We have synthesized a photoreactive probe Bpa0-VIP. After photolabeling and receptor cleavage, Nu-PAGE analysis revealed a 5-kDa labeled fragment corresponding to the 130-137 sequence of hVPAC1 receptor, indicating that the N-terminus of VIP also interacts with the N-ted. A photoreactive probe, Bpa0-PG97-269, was also synthesized with the specific peptide antagonist PG97-269. After photoaffinity labeling, a glycosylated 15-kDa fragment is identified by cyanogen bromide (CNBr) cleavage and corresponds to the 43-66 sequence of the hVPAC1 receptor N-ted. These results indicate that: (1) the N-terminal part of VIP physically interacts with the N-ted in the continuity of 6-28 VIP sequence; (2) the N-terminal part of VIP and the selective peptide antagonist (PG97-269) have different sites of interaction with the VPAC1 receptor N-ted.

Optimization of Activity-Based Probes for Proteomic Profiling of Histone Deacetylase Complexes

Histone deacetylases (HDACs) are key enzymatic regulators of the epigenome and serve as promising targets for anticancer therapeutics. Recently, we developed a photoreactive "clickable" probe, SAHA-BPyne, to report on HDAC activity and complex formation in native biological systems. Here, we investigate the selectivity, sensitivity, and inhibitory properties of SAHA-BPyne and related potential activity-based probes for HDACs. While we identified several probes that are potent HDAC inhibitors and label HDAC complex components in native proteomic preparations, SAHA-BPyne was markedly superior for profiling HDAC activities in live cells. Interestingly, the enhanced performance of SAHA-BPyne as an in situ activity-based probe could not be solely ascribed to potency in HDAC binding, implying that other features of the molecule were key to efficient active site-directed labeling in living systems. Finally, we demonstrate the value of in situ profiling of HDACs by comparing the activity and expression of HDAC1 in cancer cells treated with the cytotoxic agent parthenolide. These results underscore the utility of activity-based protein profiling for studying HDAC function and may provide insight for the future development of click chemistry-based photoreactive probes for the in situ analysis of additional enzyme activities.

Crosslinking of the NER damage recognition proteins XPC-HR23B, XPA and RPA to photoreactive probes that mimic DNA damages

A new assay to probe the mechanism of mammalian nucleotide excision repair (NER) was developed. Photoreactive arylazido analogues of dNMP in DNA were shown to be substrates for the human NER system. Oligonucleotides carrying photoreactive “damages” were prepared using the multi-stage protocol including one-nucleotide gap filling by DNA polymerase β using photoreactive dCTP or dUTP analogues followed by ligation of the resulting nick. Photoreactive 60-mers were annealed with single-stranded pBluescript II SK (+) and subsequently primer extension reactions were performed. Incubation of HeLa extracts with the plasmids containing photoreactive moieties resulted in an excision pattern typical of NER. DNA duplexes containing photoreactive analogues were used to analyze the interaction of XPC-HR23B, RPA, and XPA with damaged DNA using the photocrosslinking assay. Crosslinking of the XPC-HR23B complex with photoreactive 60-mers resulted in modification of its XPC subunit. RPA crosslinked to ssDNA or mismatched dsDNA more efficiently than to dsDNA, whereas XPA did not show a preference for any of the DNA species. XPC and XPA photocrosslinking to DNA decreased in the presence of Mg 2+ whereas RPA crosslinking to DNA was not sensitive to this cofactor. Our data establish a photocrosslinking assay for the investigation of the damage recognition step in human nucleotide excision repair.

Free Volume Distribution and Local Environment of a Polymer with Photo-reactive Probe Technique

Free volume distribution of poly (methyl methacrylate) was determined with a photo-reactive probe technique. Fairly large part of the free volume in PMMA has been found to be the more reactive than the reaction in solution using azobenzene as the photochromic probe, while there is some free volume fraction where quantum yield of photoreaction is restricted to zero. Information on the bulk region is clearly observed using a novel photochromic probe, which is obtained by connecting azobenzene to PMMA polymer chain. Effect of polymer relaxation on the quantum yield distribution shows contrast between azobenzene and polymer-connected azobenzene, which reflects the information on vacant or bulk region, respectively. Information on the free volume where the space is crowed by the probe molecule is also obtained by using azobenzene dimer as the photo reactive probe, showing the decrease in the photoreactivity and homogenous quantum yield distribution.

Photoaffinity labeling and its application in structural biology

This review contains a brief consideration of some theoretical aspects of photoaffinity (photoreactive) labeling (PAL), and the most widely used photoreactive groups, such as arylazide, benzophenone, and 3-(trifluoromethyl)-3-phenyldiazirine, are characterized in comparison. Experimental methodology is described, including modern approaches of mass spectrometry for analysis of cross-linking products between the photoreactive probes and biomolecules. Examples of PAL application in diverse fields of structural biology during the last five-ten years are presented. Potential drug targets, transport processes, stereochemistry of interaction of G-protein-coupled receptors with ligands, as well as structural changes in nicotinic acetylcholine receptor are considered. Applications of photoaffinity ganglioside and phospholipid probes for studying biological membranes and of nucleotide probes in investigations of replicative and transcriptional complexes, as well as photoaffinity glycoconjugates for detecting carbohydrate-binding proteins are covered. In combination with modern techniques of instrumental analysis and computer-aided modeling, PAL remains the most important approach in studies on the organization of biological systems.

Azido ruthenium: a new photoreactive probe for calcium-binding proteins

Ca2+, involved in almost all processes of cell life, mediates its activity through reversible interaction with specific binding sites in proteins. Although several Ca2+-dependent activities are known, many of the proteins responsible remain unidentified. Here we describe the synthesis, purification, characterization and potential uses of a new Ca2+-like reagent, azido ruthenium (AzRu), which can be photoactivated. AzRu strongly inhibits Ca2+-dependent activities. AzRu can be used to probe proteins in solution or embedded in membranes. AzRu has no effect on Ca2+-independent or Mg2+-dependent activity. After exposure to ultraviolet irradiation, AzRu binds covalently and specifically to Ca2+-binding proteins, thus providing a new approach for identifying and purifying Ca2+-binding proteins, for characterizing their Ca2+-binding sites and for exploring previously unknown Ca2+-dependent processes. In this protocol we also include a description of the preparation of [103Ru]AzRu, which can be used for labeling Ca2+-binding sites in proteins and identifying previously unknown Ca2+-binding proteins. The preparation of AzRu takes approximately 2-3 days.

Membrane Integrity during the Co‐translational Integration of Multi‐spanning Membrane Proteins

Maintaining the permeability barrier of the membrane of the endoplasmic reticulum (ER) is particularly problematic when multi-spanning membrane proteins are integrated into the bilayer at sites termed translocons. Previous work has demonstrated that ion passage through the aqueous pore in the translocon is regulated by a complex choreography of interactions that involve primarily a ribosome in the cytosol, a translocon in the ER membrane, and BiP, an Hsp70 homolog located in the ER lumen. To identify the mechanisms involved in maintaining membrane integrity, we have used fluorescence spectroscopy, fluorescence resonance energy transfer, and photocrosslinking to examine various aspects of integration intermediates with different numbers of transmembrane segments (TMSs) from the point of view of the nascent chain. Specifically, we have now characterized how sequential TMSs in the nascent chain regulate the closing and opening of opposite ends of the translocon pore by incorporating a fluorescent or photoreactive probe into the nascent chain using chemically-modified aminoacyl-tRNA derivatives, an experimental approach that we originated. (Supported by NIH grant GM 26494 and the Robert A. Welch Foundation.)

Photochemical Fishing Approaches for Identifying Target Proteins and Elucidating the Structure of a Ligand-binding Region Using Carbene-generating Photoreactive Probes

Photoaffinity labeling enables the direct probing of a target protein through a covalent bond between a ligand and its binding protein, and even a complex formed by weak interactions can be isolated by the method. The photochemical fishing approach accelerates the throughput, isolating crosslinked complexes and analyzing the structure of the ligand binding site within the protein. We used carbene-generating phenyldiazirine for this approach because practical examinations had shown that the phenyldiazirine functioned as the powerful barb on the hook. Improving the synthetic pathways of the photoprobes and using chemoselective-integrated photoreactive units makes possible the easy and rapid preparation of carbene-generating photoreactive probes including the derivatives in peptides, proteins, DNAs, and carbohydrates. This review also shows several recent impacts of photoaffinity labeling, including the in vivo preparation of photoreactive proteins in living cells.

Diffusion Coefficient and the Secondary Structure of Poly-l-glutamic Acid in Aqueous Solution

The diffusion coefficients (D) of poly-L-glutamic acid (PLG) at various pHs are investigated by the laser-induced transient-grating method with a new photoreactive probe molecule. The pH dependence of D is compared with that of the helical content of PLG measured by circular dichroism. It is found that the pH dependences of both quantities are very similar. Since the frictions of the translational diffusion of charged and protonated carboxyl groups are found to be similar each other, it is concluded that the conformation of the main polymer chain is the main factor in determining the diffusion process; in other words, the alpha-helix conformation makes the molecular diffusion faster. This result indicates that the conformational change of a protein can be detected by monitoring the diffusion coefficient.

Double-spanning Plant Viral Movement Protein Integration into theEndoplasmic Reticulum Membrane Is Signal Recognition Particle-dependent,Translocon-mediated, andConcerted

The current model for cell-to-cell movement of plant viruses holds that transport requires virus-encoded movement proteins that intimately associate with endoplasmic reticulum membranes. We have examined the early stages of the integration into endoplasmic reticulum membranes of a double-spanning viral movement protein using photocross-linking. We have discovered that this process is cotranslational and proceeds in a signal recognition particle-dependent manner. In addition, nascent chain photocross-linking to Sec61alpha and translocating chain-associated membrane protein reveal that viral membrane protein insertion takes place via the translocon, as with most eukaryotic membrane proteins, but that the two transmembrane segments of the viral protein leave the translocon and enter the lipid bilayer together.

The Cotranslational Contacts between Ribosome-bound Nascent Polypeptides and the Subunits of the Hetero-oligomeric Chaperonin TRiC Probed by Photocross-linking

The hetero-oligomeric eukaryotic chaperonin TRiC (TCP-1-ring complex, also called CCT) interacts cotranslationally with a diverse subset of newly synthesized proteins, including actin, tubulin, and luciferase, and facilitates their correct folding. A photocross-linking approach has been used to map the contacts between individual chaperonin subunits and ribosome-bound nascent chains of increasing length. Whereas a cryo-EM study suggests that chemically denatured actin interacts with only two TRiC subunits (delta and either beta or epsilon), actin and luciferase chains photocross-link to at least six TRiC subunits (alpha, beta, delta, epsilon, xi, and theta) at different stages of translation. Furthermore, the photocross-linking of actin, but not luciferase, nascent chains to TRiC subunits zeta and theta was length-dependent. In addition, a single photoreactive probe incorporated at a unique site in actin nascent chains of different lengths reacted covalently with multiple TRiC subunits, thereby indicating that the nascent chain samples the polypeptide binding sites of different subunits. We conclude that elongating actin and luciferase nascent chains contact multiple TRiC subunits upon emerging from the ribosome, and that the TRiC subunits contacted by nascent actin change as it elongates and starts to fold.