Design of a Protein Kinase-Inducible Domain

Luminescent lanthanide metallopeptides for biomolecule sensing and cellular imaging

Lanthanide ions display unique luminescent properties that make them particularly attractive for the development of bioprobes, including long-lived excited states that allow the implementation of time-gated experiments and the elimination of background fluorescence associated with biological media, as well as narrow emission bands in comparison with typical organic fluorophores, which allow ratiometric and multiplex assays. These luminescent complexes can be combined with peptide ligands to endow them with additional targeting, responsiveness, and selectivity, thus multiplying the opportunities for creative probe design. In this feature article we will present some of the main strategies that researchers have used to develop lanthanide metallopeptide probes for the detection of proteins and nucleic acids, as well as for monitoring enzymatic activity and cellular imaging.

Recent Progress in Fluorescent Chemosensors for Protein Kinases

Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.

De novo design of tyrosine and serine kinase-driven protein switches

Kinases play central roles in signaling cascades, relaying information from the outside to the inside of mammalian cells. De novo designed protein switches capable of interfacing with tyrosine kinase signaling pathways would open new avenues for controlling cellular behavior, but, so far, no such systems have been described. Here we describe the de novo design of two classes of protein switch that link phosphorylation by tyrosine and serine kinases to protein-protein association. In the first class, protein-protein association is required for phosphorylation by the kinase, while in the second class, kinase activity drives protein-protein association. We design systems that couple protein binding to kinase activity on the immunoreceptor tyrosine-based activation motif central to T-cell signaling, and kinase activity to reconstitution of green fluorescent protein fluorescence from fragments and the inhibition of the protease calpain. The designed switches are reversible and function in vitro and in cells with up to 40-fold activation of switching by phosphorylation.

Design of Tunable Protein Interfaces Controlled by Post-Translational Modifications

The design of protein interaction interfaces is a cornerstone of synthetic biology, where they can be used to promote the association of protein subunits into active molecular complexes or into protein nanostructures. In nature, protein interactions can be modulated by post-translational modifications (PTMs) that modify the protein interfaces with the addition and removal of various chemical groups. PTMs thus represent a means to gain control over protein interactions, yet they have seldom been considered in the design of synthetic proteins. Here, we explore the potential of a reversible PTM, serine phosphorylation, to modulate the interactions between peptides. We designed a series of interacting peptide pairs, including heterodimeric coiled coils, that contained one or more protein kinase A (PKA) recognition motifs. Our set of peptide pairs comprised interactions ranging from nanomolar to micromolar affinities. Mass spectrometry analyses showed that all peptides were excellent phosphorylation substrates of PKA, and subsequent phosphate removal could be catalyzed by lambda protein phosphatase. Binding kinetics measurements performed before and after treatment of the peptides with PKA revealed that phosphorylation of the target serines affected both the association and dissociation rates of the interacting peptides. We observed both the strengthening of interactions (up to an 11-fold decrease in K_d) and the weakening of interactions (up to a 180-fold increase in K_d). De novo-designed PTM-modulated interfaces will be useful to control the association of proteins in biological systems using protein-modifying enzymes, expanding the paradigm of self-assembly to encompass controlled assembly of engineerable protein complexes.

Cysteine oxidation to the sulfinic acid induces oxoform-specific lanthanide binding and fluorescence in a designed peptide

Cysteine sulfinic acid (Cys-SO₂^-) is a protein post-translational modification that is formed reversibly under oxidative conditions. A short, encodable peptide was developed whose metal binding and terbium luminescence are dependent on cysteine (Cys) oxidation to the sulfinic acid. The protein design is based on the modification of a key metal-binding aspartate (Asp) in a canonical EF-Hand motif (DKDADGWISPAEAK) to Cys. In this design, Cys in the thiol oxidation state does not mimic the native Asp, and thus the peptide binds terbium(III) (Tb³⁺) poorly and exhibits weak terbium luminescence (fluorescence). In contrast, when Cys is oxidized to the Cys sulfinic acid oxoform, the Cys sulfinate effectively mimics Asp, resulting in a significant increase in terbium affinity and luminescence. Asp residues at positions 1, 3, and 5 of the EF-Hand motif were examined as potential sites for Cys oxidation-responsive metal binding. The peptide with Cys at residue 1 exhibited the highest Tb³⁺ affinity in both oxidation states. The peptide with Cys at residue 3 exhibited a 4.2-fold distinction in affinity between the oxidation states. Most significantly, the peptide with Cys at residue 5 had only modest Tb³⁺ affinity as the Cys thiol, but exhibited a 30-fold increase in Tb³⁺ affinity and an 18-fold increase in Tb³⁺ luminescence on Cys oxidation to the sulfinic acid. This peptide (Ac-DKDACGWISPAEAK-NH₂) exhibited selective Tb³⁺ binding via Cys-SO₂^- over the thiol, S-glutathionyl, S-nitrosyl, and sulfonic acid oxoforms, indicating substantially greater Lewis basicity of the sulfinate than the sulfonate. NMR spectroscopy and quantum homology modeling indicated that the designed peptide binds metal with an overall geometry similar to that of an EF-Hand motif, with the Cys sulfinate effectively replacing Asp as a metal-binding ligand. This peptide was applied to detect Cys oxidation to the sulfinic acid by fluorescence spectroscopy, suggesting its broader application in understanding Cys sulfinic acid biology.

Design of a Protein Motif Responsive to Tyrosine Nitration and an Encoded Turn-Off Sensor of Tyrosine Nitration

Tyrosine nitration is a protein post-translational modification that is predominantly non-enzymatic and is observed to be increased under conditions of nitrosative stress and in numerous disease states. A small protein motif (14-18 amino acids) responsive to tyrosine nitration has been developed. In this design, nitrotyrosine replaced the conserved Glu12 of an EF-hand metal-binding motif. Thus, the non-nitrated peptide bound terbium weakly. In contrast, tyrosine nitration resulted in a 45-fold increase in terbium affinity. Nuclear magnetic resonance spectroscopy indicated direct binding of nitrotyrosine to the metal and EF-hand-like metal contacts in this designed peptide. Nitrotyrosine is an efficient quencher of fluorescence. To develop a sensor of tyrosine nitration, the initial design was modified to incorporate Glu residues at EF-hand positions 9 and 16 as additional metal-binding residues, to increase the terbium affinity of the peptide with unmodified tyrosine. This peptide with a tyrosine at residue 12 bound terbium and effectively sensitized terbium luminescence. Tyrosine nitration resulted in a 180-fold increase in terbium affinity ( Kd = 1.6 μM) and quenching of terbium luminescence. This sequence was incorporated as an encoded protein tag and applied as a turn-off fluorescent protein sensor of tyrosine nitration. The sensor was responsive to nitration by peroxynitrite, with fluorescence quenched upon nitration. The greater terbium affinity upon tyrosine nitration resulted in a large dynamic range and sensitivity to substoichiometric nitration. An improved approach for the synthesis of peptides containing nitrotyrosine was also developed, via the in situ silyl protection of nitrotyrosine. This work represents the first designed, encodable protein motif that is responsive to tyrosine nitration.

Phosphorylation-dependent protein design: design of a minimal protein kinase-inducible domain

Protein kinases and phosphatases modulate protein structure and function, which in turn regulate cellular activities. The development of novel proteins and protein motifs that are responsive to protein phosphorylation provides new ways to probe the functions of individual protein kinases and the intracellular effects of their activation and downregulation. Herein we develop a minimal motif that is responsive to protein phosphorylation, termed a minimal protein kinase-inducible domain. The encodable protein motif comprises a 7- or 8-residue sequence (DKDADXW or DKDADXXW), derived from EF-Hand calcium-binding domains, that is necessary but not sufficient for binding terbium, combined with a protein phosphorylation site (Ser or Thr at residue 9) that, upon phosphorylation, completes the metal-binding motif. Thus, the motif binds metal poorly and exhibits weak terbium luminescence when not phosphorylated. Upon phosphorylation, the peptide binds metal with significantly higher affinity and exhibits robust terbium luminescence. Phosphorylation results in up to a 23× increase in terbium luminescence. Minimal phosphorylation-dependent motifs as small as 9 residues (DKDADGWIS) were developed. NMR spectroscopy on this lanthanum(iii)·phosphopeptide complex confirmed that binding occurs in a manner similar to that in an EF-Hand, despite the absence of the conserved Glu12 typically present in an EF-Hand. By combining molecular design with known protein kinase recognition sequences, minimal protein kinase-inducible domains were developed that were responsive to phosphorylation by Protein Kinase A (PKA: DKDADRRW(S/pS)IIAK), Protein Kinase C (PKC: DKDADGWI(T/pT)FRRKA), and Casein Kinase 1 (CK1: DKDADDWA(S/pS)I). Phosphorylation by PKA was quantified in HeLa cell extracts, with a 4.4× increase in fluorescence (terbium luminescence) observed at 544 nm. The optimized minimal motif includes alternating aspartate residues at positions 1, 3, and 5, plus binding through the main-chain carbonyl at position 7; a lysine at position 2 to provide electrostatic balance and reduce binding in the absence of phosphorylation; an alanine at residue 4 to promote the αL conformation observed at that position of the EF Hand; a tryptophan at residue 7 or 8 to sensitize terbium luminescence; and a phosphorylation site with serine or threonine at residue 9. Residues at positions 6; 7 or 8; and 10 or later may be changed to provide kinase specificity. In the CK1-responsive peptide, the acidic residues in the proto-terbium-binding motif are employed as part of the kinase recognition sequence. This work thus presents fundamental rules for the design of compact phosphorylation-responsive terbium-binding motifs, with potential further application to motifs responsive to other protein post-translational modifications.

Redox-Responsive Protein Design: Design of a Small Protein Motif Dependent on Glutathionylation

Cysteine S-glutathionylation is a protein post-translational modification that promotes cellular responses to changes in oxidative conditions. The design of protein motifs that directly depend on defined changes to protein side chains provides new methods for probing diverse protein post-translational modifications. A canonical, 12-residue EF-hand motif was redesigned to be responsive to cysteine glutathionylation. The key design principle was the replacement of the metal-binding Glu12 carboxylate of an EF-hand with a motif capable of metal binding via a free carboxylate in the glutathione-conjugated peptide. In the optimized peptide (DKDADGWCG), metal binding and terbium luminescence were dependent on glutathionylation, with weaker metal binding in the presence of reduced cysteine but increased metal affinity and a 3.5-fold increase in terbium luminescence at 544 nm when cysteine was glutathionylated. Nuclear magnetic resonance spectroscopy indicated that the structure at all residues of the glutathionylated peptide changed in the presence of metal, with chemical shift changes consistent with the adoption of an EF-hand-like structure in the metal-bound glutathionylated peptide. This small protein motif consists of canonical amino acids and is thus genetically encodable, for its potential use as a localized tag to probe protein glutathionylation.

Application of lanthanide luminescence in probing enzyme activity

Enzymes play critical roles in the regulation of cellular function and are implicated in numerous disease conditions. Reliable and practicable assays are required to study enzyme activity, to facilitate the discovery of inhibitors and activators of enzymes related to disease. In recent years, a variety of enzyme assays have been devised that utilise luminescent lanthanide(iii) complexes, taking advantage of their high detection sensitivities, long luminescence lifetimes, and line-like emission spectra that permit ratiometric and time-resolved analyses. In this Feature article, we focus on recent progress in the development of enzyme activity assays based on lanthanide(iii) luminescence, covering a variety of strategies including Ln(iii)-labelled antibodies and proteins, Ln(iii) ion encapsulation within defined peptide sequences, reactivity-based Ln(iii) probes, and discrete Ln(iii) complexes. Emerging approaches for monitoring enzyme activity are discussed, including the use of anion responsive lanthanide(iii) complexes, capable of molecular recognition and luminescence signalling of polyphosphate anions.

Modular, Antibody-free Time-Resolved LRET Kinase Assay Enabled by Quantum Dots and Tb(3+)-sensitizing Peptides

Fluorescent drug screening assays are essential for tyrosine kinase inhibitor discovery. Here we demonstrate a flexible, antibody-free TR-LRET kinase assay strategy that is enabled by the combination of streptavidin-coated quantum dot (QD) acceptors and biotinylated, Tb(3+) sensitizing peptide donors. By exploiting the spectral features of Tb(3+) and QD, and the high binding affinity of the streptavidin-biotin interaction, we achieved multiplexed detection of kinase activity in a modular fashion without requiring additional covalent labeling of each peptide substrate. This strategy is compatible with high-throughput screening, and should be adaptable to the rapidly changing workflows and targets involved in kinase inhibitor discovery.

Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(III) and Eu(III) ions for specific sensing of a viral RNA

Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.

Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases

Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.

Design and evaluation of a real-time activity probe for focal adhesion kinase

Focal adhesion kinase (FAK) has been identified as a potential therapeutic target for the treatment of metastatic cancers. Herein we describe the design, synthesis and optimization of a direct activity sensor for FAK and its application to screening FAK inhibitors. We find that the position of the sensing moiety, a phosphorylation-sensitive sulfonamido-oxine fluorophore, can dramatically influence the performance of peptide sensors for FAK. Real-time fluorescence activity assays using an optimized sensor construct, termed FAKtide-S2, are highly reproducible (Z' = 0.91) and are capable of detecting as little as 1 nM recombinant FAK. Utilizing this robust assay format, we define conditions for the screening of FAK inhibitors and demonstrate the utility of this platform using a set of well-characterized small molecule kinase inhibitors. Additionally, we provide the selectivity profile of FAKtide-S2 among a panel of closely related enzymes, identifying conditions for selectively monitoring FAK activity in the presence of off-target enzymes. In the long term, the chemosensor platform described in this work can be used to identify novel FAK inhibitor scaffolds and potentially assess the efficacy of FAK inhibitors in disease models.

A real-time, fluorescence-based assay for Rho-associated protein kinase activity

Inhibitors of Rho-associated protein kinase (ROCK) enzymatic activity have been shown to reduce the invasive phenotype observed in metastatic hepatocellular carcinoma (HCC). We describe the design, synthesis, and evaluation of a direct probe for ROCK activity utilizing a phosphorylation-sensitive sulfonamido-oxine fluorophore, termed Sox. The Sox fluorophore undergoes an increase in fluorescence upon phosphorylation of a proximal amino acid via chelation-enhanced fluorescence (CHEF, ex. = 360 nm and em. = 485 nm), allowing for the direct visualization of the rate of phosphate addition to a peptide substrate over time. Our optimal probe design, ROCK-S1, is capable of sensitively reporting ROCK activity with a limit of detection of 10 pM and a high degree of reproducibility (Z'-factor = 0.6 at 100 pM ROCK2). As a proof-of-principle for high-throughput screening (HTS) we demonstrate the ability to rapidly assess the efficacy of a 78 member, small molecule library against ROCK2 using a robotics platform. We identify two previously unreported ROCK2 inhibitor scaffolds, PHA665752 and IKK16, with IC50 values of 3.6 μM and 247 nM respectively. Lastly, we define conditions for selectively monitoring ROCK activity in the presence of potential off-target enzymes (PKCα, PKA, and PAK) with similar substrate specificities.

Towards the computational design of protein post-translational regulation

Protein post-translational modifications (PTMs) are a fast and versatility mechanism used by the cell to regulate the function of proteins in response to changing conditions. PTMs can alter the activity of proteins by allosteric regulation or by controlling protein interactions, localization and abundance. Recent advances in proteomics have revealed the extent of regulation by PTMs and the different mechanisms used in nature to exert control over protein function via PTMs. These developments can serve as the foundation for the rational design of protein regulation. Here we review the advances in methods to determine the function of PTMs, protein allosteric control and examples of rational design of PTM regulation. These advances create an opportunity to move synthetic biology forward by making use of a level of regulation that is of yet unexplored.

KINATEST-ID: a pipeline to develop phosphorylation-dependent terbium sensitizing kinase assays

Nonreceptor protein tyrosine kinases (NRTKs) are essential for cellular homeostasis and thus are a major focus of current drug discovery efforts. Peptide substrates that can enhance lanthanide ion luminescence upon tyrosine phosphorylation enable rapid, sensitive screening of kinase activity, however design of suitable substrates that can distinguish between tyrosine kinase families is a huge challenge. Despite their different substrate preferences, many NRTKs are structurally similar even between families. Furthermore, the development of lanthanide-based kinase assays is hampered by incomplete understanding of how to integrate sequence selectivity with metal ion binding, necessitating laborious iterative substrate optimization. We used curated proteomic data from endogenous kinase substrates and known Tb(3+)-binding sequences to build a generalizable in silico pipeline with tools to generate, screen, align, and select potential phosphorylation-dependent Tb(3+)-sensitizing substrates that are most likely to be kinase specific. We demonstrated the approach by developing several substrates that are selective within kinase families and amenable to high-throughput screening (HTS) applications. Overall, this strategy represents a pipeline for developing efficient and specific assays for virtually any tyrosine kinase that use HTS-compatible lanthanide-based detection. The tools provided in the pipeline also have the potential to be adapted to identify peptides for other purposes, including other enzyme assays or protein-binding ligands.

A time-resolved luminescence biosensor assay for anaplastic lymphoma kinase (ALK) activity

A novel time-resolved luminescence biosensor assay for anaplastic lymphoma kinase (ALK) was developed. We used a straightforward strategy to modify a known ALK substrate into a peptide biosensor that can accommodate terbium luminescence sensitization upon its phosphorylation by ALK. Since this strategy is generalizable, this high-throughput screening compatible assay serves as an example for development of other kinase assays that employ terbium luminescence as a read-out.

Formation of complexes between PAMAM-NH2 G4 dendrimer and L-α-tryptophan and L-α-tyrosine in water

Interactions between electromagnetic radiation and the side substituents of aromatic amino acids are widely used in the biochemical studies on proteins and their interactions with ligand molecules. That is why the aim of our study was to characterize the formation of complexes between PAMAM-NH2 G4 dendrimer and L-α-tryptophan and L-α-tyrosine in water. The number of L-α-tryptophan and L-α-tyrosine molecules attached to the macromolecule of PAMAM-NH2 G4 dendrimer and the formation constants of the supramolecular complexes formed have been determined. The macromolecule of PAMAM-NH2 G4 can reversibly attach about 25 L-α-tryptophan molecules with equilibrium constant K equal to 130±30 and 24±6 L-α-tyrosine molecules. This characterization was deduced on the basis of the solubility measurements of the amino acids in aqueous dendrimer solutions, the (1)H NMR and 2D-NOESY measurements of the dendrimer solutions with the amino acids, the equilibrium dialysis and the circular dichroism measurements of the dendrimer aqueous solutions with L-α-tryptophan. Our date confirmed the interactions of L-α-tryptophan and L-α-tyrosine with the dendrimer in aqueous solution and indicated a reversible character of the formed complexes.

OGlcNAcylation and phosphorylation have similar structural effects in α-helices: post-translational modifications as inducible start and stop signals in α-helices, with greater structural effects on threonine modification

OGlcNAcylation and phosphorylation are the major competing intracellular post-translational modifications of serine and threonine residues. The structural effects of both post-translational modifications on serine and threonine were examined within Baldwin model α-helical peptides (Ac-AKAAAAKAAAAKAAGY-NH₂ or Ac-YGAKAAAAKAAAAKAA-NH₂). At the N-terminus of an α-helix, both phosphorylation and OGlcNAcylation stabilized the α-helix relative to the free hydroxyls, with a larger induced structure for phosphorylation than for OGlcNAcylation, for the dianionic phosphate than for the monoanionic phosphate, and for modifications on threonine than for modifications on serine. Both phosphoserine and phosphothreonine resulted in peptides more α-helical than alanine at the N-terminus, with dianionic phosphothreonine the most α-helix-stabilizing residue here. In contrast, in the interior of the α-helix, both post-translational modifications were destabilizing with respect to the α-helix, with the greatest destabilization seen for threonine OGlcNAcylation at residue 5 and threonine phosphorylation at residue 10, with peptides containing either post-translational modification existing as random coils. At the C-terminus, both OGlcNAcylation and phosphorylation were destabilizing with respect to the α-helix, though the induced structural changes were less than in the interior of the α-helix. In general, the structural effects of modifications on threonine were greater than the effects on serine, because of both the lower α-helical propensity of Thr and the more defined induced structures upon modification of threonine than serine, suggesting threonine residues are particularly important loci for structural effects of post-translational modifications. The effects of serine and threonine post-translational modifications are analogous to the effects of proline on α-helices, with the effects of phosphothreonine being greater than those of proline throughout the α-helix. These results provide a basis for understanding the context-dependent structural effects of these competing protein post-translational modifications.

OGlcNAcylation and phosphorylation have opposing structural effects in tau: phosphothreonine induces particular conformational order

Phosphorylation and OGlcNAcylation are dynamic intracellular protein post-translational modifications that frequently are alternatively observed on the same serine and threonine residues. Phosphorylation and OGlcNAcylation commonly occur in natively disordered regions of proteins, and often have opposing functional effects. In the microtubule-associated protein tau, hyperphosphorylation is associated with protein misfolding and aggregation as the neurofibrillary tangles of Alzheimer's disease, whereas OGlcNAcylation stabilizes the soluble form of tau. A series of peptides derived from the proline-rich domain (residues 174-251) of tau was synthesized, with free Ser/Thr hydroxyls, phosphorylated Ser/Thr (pSer/pThr), OGlcNAcylated Ser/Thr, and diethylphosphorylated Ser/Thr. Phosphorylation and OGlcNAcylation were found by CD and NMR to have opposing structural effects on polyproline helix (PPII) formation, with phosphorylation favoring PPII, OGlcNAcylation opposing PPII, and the free hydroxyls intermediate in structure, and with phosphorylation structural effects greater than OGlcNAcylation. For tau196-209, phosphorylation and OGlcNAcylation had similar structural effects, opposing a nascent α-helix. Phosphomimic Glu exhibited PPII-favoring structural effects. Structural changes due to Thr phosphorylation were greater than those of Ser phosphorylation or Glu, with particular conformational restriction as the dianion, with mean (3)JαN = 3.5 Hz (pThr) versus 5.4 Hz (pSer), compared to 7.2, 6.8, and 6.2 Hz for Thr, Ser, and Glu, respectively, values that correlate with the backbone torsion angle ϕ. Dianionic phosphothreonine induced strong phosphothreonine amide protection and downfield amide chemical shifts (δmean = 9.63 ppm), consistent with formation of a stable phosphate-amide hydrogen bond. These data suggest potentially greater structural importance of threonine phosphorylation than serine phosphorylation due to larger induced structural effects.

Proline editing: a general and practical approach to the synthesis of functionally and structurally diverse peptides. Analysis of steric versus stereoelectronic effects of 4-substituted prolines on conformation within peptides

Functionalized proline residues have diverse applications. Herein we describe a practical approach, proline editing, for the synthesis of peptides with stereospecifically modified proline residues. Peptides are synthesized by standard solid-phase peptide synthesis to incorporate Fmoc-hydroxyproline (4R-Hyp). In an automated manner, the Hyp hydroxyl is protected and the remainder of the peptide synthesized. After peptide synthesis, the Hyp protecting group is orthogonally removed and Hyp selectively modified to generate substituted proline amino acids, with the peptide main chain functioning to "protect" the proline amino and carboxyl groups. In a model tetrapeptide (Ac-TYPN-NH2), 4R-Hyp was stereospecifically converted to 122 different 4-substituted prolyl amino acids, with 4R or 4S stereochemistry, via Mitsunobu, oxidation, reduction, acylation, and substitution reactions. 4-Substituted prolines synthesized via proline editing include incorporated structured amino acid mimetics (Cys, Asp/Glu, Phe, Lys, Arg, pSer/pThr), recognition motifs (biotin, RGD), electron-withdrawing groups to induce stereoelectronic effects (fluoro, nitrobenzoate), handles for heteronuclear NMR ((19)F:fluoro; pentafluorophenyl or perfluoro-tert-butyl ether; 4,4-difluoro; (77)SePh) and other spectroscopies (fluorescence, IR: cyanophenyl ether), leaving groups (sulfonate, halide, NHS, bromoacetate), and other reactive handles (amine, thiol, thioester, ketone, hydroxylamine, maleimide, acrylate, azide, alkene, alkyne, aryl halide, tetrazine, 1,2-aminothiol). Proline editing provides access to these proline derivatives with no solution-phase synthesis. All peptides were analyzed by NMR to identify stereoelectronic and steric effects on conformation. Proline derivatives were synthesized to permit bioorthogonal conjugation reactions, including azide-alkyne, tetrazine-trans-cyclooctene, oxime, reductive amination, native chemical ligation, Suzuki, Sonogashira, cross-metathesis, and Diels-Alder reactions. These proline derivatives allowed three parallel bioorthogonal reactions to be conducted in one solution.

Time-resolved luminescence detection of spleen tyrosine kinase activity through terbium sensitization

Disruption of regulatory protein phosphorylation can lead to disease and is particularly prevalent in cancers. Inhibitors that target deregulated kinases are therefore a major focus of chemotherapeutic development. Achieving sensitivity and specificity in high-throughput compatible kinase assays is key to successful inhibitor development. Here, we describe the application of time-resolved luminescence detection to the direct sensing of spleen tyrosine kinase (Syk) activity and inhibition using a novel peptide substrate. Chelation and luminescence sensitization of Tb(3+) allowed the direct detection of peptide phosphorylation without any antibodies or other labeling reagents. Characterizing the Tb(3+) coordination properties of the phosphorylated vs unphosphorylated form of the peptide revealed that an inner-sphere water was displaced upon phosphorylation, which likely was responsible for both enhancing the luminescence intensity and also extending the lifetime, which enabled gating of the luminescence signal to improve the dynamic range. Furthermore, a shift in the optimal absorbance maximum for excitation was observed, from 275 nm (for the unphosphorylated tyrosine peptide) to 266 nm (for the phosphorylated tyrosine peptide). Accordingly, time-resolved measurements with excitation at 266 nm via a monochromator enabled a 16-fold improvement in base signal-to-noise for distinguishing phosphopeptide from unphosphorylated peptide. This led to a high degree of sensitivity and quantitative reproducibility, demonstrating the amenability of this method to both research laboratory and high-throughput applications.

Detection of phosphorylation states by intermolecular sensitization of lanthanide-peptide conjugates

The luminescence of a designed peptide equipped with a coordinatively-unsaturated lanthanide complex is modulated by the phosphorylation state of a serine residue in the sequence. While the phosphorylated state is weakly emissive, even in the presence of an external antenna, removal of the phosphate allows coordination of the sensitizer to the metal, yielding a highly emissive supramolecular complex.

Electrochemical investigations into Tau protein phosphorylations

Hyperphosphorylation of Tau, a protein that stabilizes microtubules, leads to the breakdown of the microtubular structure and ultimately to the formation of neurofibrillar tangles within neurons. Here, we report monitoring of Tau phosphorylations electrochemically, using Tau protein films chemically linked to gold surfaces and 5'-γ-ferrocenyl (Fc) adenosine triphosphate (Fc-ATP) as a co-substrate. Fc-phosphorylation reactions of Tau are explored using the three protein kinases, glycogen synthase kinase (GSK-3β), sarcoma (Src)-related kinase, and protein kinase A (PKA), which catalyze Fc-phosphorylation of different residues and regions within Tau. The kinetic parameters of the biochemical process (K(M) and V(max)) were determined.

Probing the role of the linker in ferrocene-ATP conjugates: monitoring protein kinase catalyzed phosphorylations electrochemically

The synthesis and electrochemical properties of ferrocene conjugates are presented for the purpose of investigating adenosine 5'-[γ-ferrocenoylalkyl] triphosphate (1 a-4 a, ferrocene (Fc)-ATP) as co-substrates for phosphorylation reactions. Compounds 1 a-4 a were synthesized, purified by HPLC, and characterized by NMR spectroscopy and mass spectrometry. In solution, all Fc-ATP bioconjugates exhibit a reversible one-electron redox process with a half-wave potential (E(1/2)) in the 390-430 mV range, peak separations (ΔE(p)) in the 40-70 mV range, and the peak current ratio (i(pa)/i(pc)) near unity. The peptide-modified surface Glu-Gly-Ile-Tyr-Asp-Val-Pro was used to study the sarcoma-related protein (Src) kinase activity by employing the Fc-ATP bioconjugates as co-substrates. Subsequent kinase-catalyzed transfer of the γ-Fc-phosphate group to the tyrosine residues of the surface-bound peptides was characterized by a formal potential (E°) ≈390 mV (vs. Ag/AgCl). The Fc-coverage, estimated by time-of-flight secondary-ion mass spectrometry (TOF-SIMS) and cyclic voltammetry (CV), suggested validity of Fc-ATP conjugates as kinase co-substrates. Depending on the length of the alkyl spacer of the Fc-ATP conjugate, different current densities were obtained, pointing to a direct correlation between the two. Molecular modeling revealed that the structural constraint imposed by the short alkyl spacer (1 a) causes a steric congestion and negatively affects the outcome of phosphorylation reaction. An optimal analytical response was obtained with the Fc-ATP conjugates with linker lengths longer than six CH(2) groups.

Identification of regions responsible for the open conformation of S100A10 using chimaeric S100A11-S100A10 proteins

S100A11 is a dimeric EF-hand calcium-binding protein. Calcium binding to S100A11 results in a large conformational change that uncovers a broad hydrophobic surface used to interact with phospholipid-binding proteins (annexins A1 and A2) and facilitate membrane vesiculation events. In contrast with other S100 proteins, S100A10 is unable to bind calcium due to deletion and substitution of calcium-ligating residues. Despite this, calcium-free S100A10 assumes an 'open' conformation that is very similar to S100A11 in its calcium-bound state. To understand how S100A10 is able to adopt an open conformation in the absence of calcium, seven chimaeric proteins were constructed where regions from calcium-binding sites I and II, and helices II-IV in S100A11 were replaced with the corresponding regions of S100A10. The chimaeric proteins having substitutions in calcium-binding site II displayed increased hydrophobic surface exposure as assessed by bis-ANS (4,4'-dianilino-1,1'-binaphthyl-5,5'disulfonic acid, dipotassium salt) fluorescence and phenyl-Sepharose binding in the absence of calcium. This response is similar to that observed for Ca2+-S100A11 and calcium-free S100A10. Further, this substitution resulted in calcium-insensitive binding to annexin A2 for one chimaeric protein. The results indicate that residues within site II are important in stabilizing the open conformation of S100A10 and presentation of its target binding site. In contrast, S100A11 chimaeric proteins with helical substitutions displayed poorer hydrophobic surface exposure and, consequently, unobservable annexin A2 binding. The present study represents a first attempt to systematically understand the molecular basis for the calcium-insensitive open conformation of S100A10.

Design of lanthanide fingers: compact lanthanide-binding metalloproteins

Lanthanides have interesting chemical properties; these include luminescent, magnetic, and catalytic functions. Toward the development of proteins incorporating novel functions, we have designed a new lanthanide-binding motif, lanthanide fingers. These were designed based on the Zif268 zinc finger, which exhibits a beta beta alpha structural motif. Lanthanide fingers utilize an Asp(2)Glu(2) metal-coordination environment to bind lanthanides through a tetracarboxylate peptide ligand. The iterative design of a general lanthanide-binding peptide incorporated the following key elements: 1) residues with high alpha-helix and beta-sheet propensities in the respective secondary structures; 2) an optimized big box alpha-helix N-cap; 3) a Schellman alpha-helix C-cap motif; and 4) an optional D-Pro-Ser type II' beta-turn in the beta-hairpin. The peptides were characterized for lanthanide binding by circular dichroism (CD), NMR, and fluorescence spectroscopy. In all instances, stabilization of the peptide secondary structures resulted in an increase in metal affinity. The optimized protein design was a 25-residue peptide that was a general lanthanide-binding motif; this binds all lanthanides examined in a competitive aqueous environment, with a dissociation constant of 9.3 microM for binding Er(3+). CD spectra of the peptide-lanthanide complexes are similar to those of zinc fingers and other beta beta alpha proteins. Metal binding involves residues from the N-terminal beta-hairpin and the C terminal alpha-helical segments of the peptide. NMR data indicated that metal binding induced a global change in the peptide structure. The D-Pro-Ser type II' beta-turn motif could be replaced by Thr-Ile to generate genetically encodable lanthanide fingers. Replacement of the central Phe with Trp generated genetically encodable lanthanide fingers that exhibited terbium luminescence greater than that of an EF-hand peptide.

Dueling post-translational modifications trigger folding and unfolding of a beta-hairpin peptide

Protein post-translational modifications (PTMs) are used in nature as a means of turning on or off a myriad of biological events. Methylation of lysine and phosphorylation of serine are important PTMs in the histone code found to modulate chromatin packing, which in turn affects gene expression. The design of peptides that fold into secondary structures can help to further our understanding of complex protein interactions. Here we report the design of the Trpswitch peptide sequence that folds into a moderately stable beta-hairpin structure in aqueous solution and show that the stability of the structure can be tuned by incorporation of dimethyllysine or phosphoserine. Dimethylated Trpswitch results in an increase in beta-hairpin stability, while phosphorylated Trpswitch is unstructured at neutral pH. When both modifications are incorporated into Trpswitch, a less stable beta-hairpin structure is observed. This system provides a model to demonstrate how multiple PTMs may work in concert or against each other to influence structure.

Design of an encodable tyrosine kinase-inducible domain: detection of tyrosine kinase activity by terbium luminescence

Tyrosine kinases are critical mediators of intracellular signaling and of intracellular responses to extracellular signaling. Changes in tyrosine kinase activity are implicated in numerous human diseases, including cancers, diabetes, and pathogen infectivity. To address questions in tyrosine phosphorylation, we have designed a protein tyrosine kinase-inducible domain, a small, genetically encodable protein motif whose structure is dependent on its tyrosine phosphorylation state. Tyrosine kinase-inducible domain peptides are based on EF-hand loops in which a structurally critical Glu12 residue is replaced by tyrosine at residue 11 or at residue 15 of the protein. Tyrosine kinase-inducible domain peptides bind terbium(III) in a phosphorylation-dependent manner, showing strong terbium luminescence when phosphorylated but weak terbium luminescence when not phosphorylated. Lanthanide binding was confirmed by NMR. A tyrosine kinase-inducible domain peptide, pKID-Abl, was designed to incorporate a recognition sequence of the Abl kinase. Incubation of pKID-Abl with Abl kinase resulted in a large increase in terbium luminescence. This increase in luminescence was abolished when pKID-Abl and Abl kinase were incubated with the Abl kinase inhibitor Gleevec. In addition, incubation of phosphorylated pKID-Abl with the tyrosine phosphatase YOP resulted in a large reduction in terbium luminescence. pKID-Abl was employed as a fluorescent sensor of Abl tyrosine kinase activity in HeLa cell extracts, exhibiting low luminescence with extracts from serum-starved cells and increased luminescence using extracts from EGF-treated cells. These results indicate that tyrosine kinase-inducible domains may be used as sensors of tyrosine kinase and tyrosine phosphatase activity and in the detection of tyrosine kinase inhibitors.

Controlling peptide folding with repulsive interactions between phosphorylated amino acids and tryptophan

Phosphorylated amino acids were incorporated into a designed beta-hairpin peptide to study the effect on beta-hairpin structure when the phosphate group is positioned to interact with a tryptophan residue on the neighboring strand. The three commonly phosphorylated residues in biological systems, serine, threonine, and tyrosine, were studied in the same beta-hairpin system. It was found that phosphorylation destabilizes the hairpin structure by approximately 1.0 kcal/mol, regardless of the type of phosphorylated residue. In contrast, destabilization due to glutamic acid was about 0.3 kcal/mol. Double mutant cycles and pH studies are consistent with a repulsive interaction as the source of destabilization. These findings demonstrate a novel mechanism by which phosphorylation may influence protein structure and function.

Understanding and exploiting substrate recognition by protein kinases

Protein kinases play a virtually universal role in cellular regulation and are emerging as an important class of new drug targets, yet the cellular functions of most human kinases largely remain obscure. Aspects of substrate recognition common to all kinases in the ATP nucleotide binding site have been exploited in the generation of analog-specific mutants for exploring kinase function and discovering novel protein substrates. Likewise, understanding interactions with the protein substrate, which differ substantially between kinases, can also help to identify substrates and to produce tools for studying kinase pathways, including fluorescent biosensors. Principles of kinase substrate recognition are particularly valuable in guiding bioinformatics and phosphoproteomics approaches that impact our understanding of signaling pathways and networks on a global scale.

Design of a Hybrid Biosensor for Enhanced Phosphopeptide Recognition Based on a Phosphoprotein Binding Domain Coupled with a Fluorescent Chemosensor

Protein-based fluorescent biosensors with sufficient sensing specificity are useful analytical tools for detection of biologically important substances in complicated biological systems. Here, we present the design of a hybrid biosensor, specific for a bis-phosphorylated peptide, based on a natural phosphoprotein binding domain coupled with an artificial fluorescent chemosensor. The hybrid biosensor consists of a phosphoprotein binding domain, the WW domain, into which has been introduced a fluorescent stilbazole having Zn(II)-dipicolylamine (Dpa) as a phosphate binding motif. It showed strong binding affinity and high sensing selectivity toward a specific bis-phosphorylated peptide in the presence of various phosphate species such as the monophosphorylated peptide, ATP, and others. Detailed fluorescence titration experiments clearly indicate that the binding-induced fluorescence enhancement and the sensing selectivity were achieved by the cooperative action of both binding sites of the hybrid biosensor, i.e., the WW domain and the Zn(II)-Dpa chemosensor unit. Thus, it is clear that the tethered Zn(II)-Dpa-stilbazole unit operated not only as a fluorescence signal transducer, but also as a sub-binding site in the hybrid biosensor. Taking advantage of its selective sensing property, the hybrid biosensor was successfully applied to real-time and label-free fluorescence monitoring of a protein kinase-catalyzed phosphorylation.

Hydroxyapatite surface-induced peptide folding

Herein, we describe the design and surface-binding characterization of a de novo designed peptide, JAK1, which undergoes surface-induced folding at the hydroxyapatite (HA)-solution interface. JAK1 is designed to be unstructured in buffered saline solution, yet undergo HA-induced folding that is largely governed by the periodic positioning of gamma-carboxyglutamic acid (Gla) residues within the primary sequence of the peptide. Circular dichroism (CD) spectroscopy and analytical ultracentrifugation indicate that the peptide remains unfolded and monomeric in solution under normal physiological conditions; however, CD spectroscopy indicates that in the presence of hydroxyapatite, the peptide avidly binds to the mineral surface adopting a helical structure. Adsorption isotherms indicate nearly quantitative surface coverage and Kd = 310 nM for the peptide-surface binding event. X-ray photoelectron spectroscopy (XPS) coupled with the adsorption isotherm data suggests that JAK1 binds to HA, forming a self-limiting monolayer. This study demonstrates the feasibility of using HA surfaces to trigger the intramolecular folding of designed peptides and represents the initial stages of defining the design rules that allow HA-induced peptide folding.

A Cl? anion-responsive luminescent Eu3+ complex with a chiral tripod: ligand substituent effects on ternary complex stoichiometry and anion sensing selectivity

A new series of N3,O-mixed donor tripods was prepared for luminescent Eu3+ complexes, in which the soft quinoline nitrogen, tertiary amine nitrogen, and hard amide oxygen donors were cooperatively involved. The mixed donor tripods formed more stable 1 : 1 complexes with Eu(NO3)3, La(NO3)3 and Tb(NO3)3 than the corresponding N4 donor tripods, and their Eu3+ complexes particularly exhibited anion-responsive luminescence properties. NMR, UV, and luminescence spectroscopic characterizations revealed that -CH3 substitution on the tripod skeleton remarkably altered the preferred stoichiometry of the "tripod-Eu3+-anion" ternary complex and gave anion-dependent europium luminescence. Although the disubstituted tripod preferred to form non-luminescent 2 : 1 (tripod : Eu3+) complexes with Eu(NO3)3 and other salts, it formed a luminescent 1 : 1 complex with EuCl3. Thus, this type of tripod offered Cl- anion-selective luminescence enhancement that was easily observed by the naked eye.

Phosphorylation-dependent metal binding by alpha-synuclein peptide fragments

Alpha-synuclein (alpha-syn) is the major protein component of the insoluble fibrils that make up Lewy bodies, the hallmark lesions of Parkinson's disease. Its C-terminal region contains motifs of charged amino acids that potentially bind metal ions, as well as several identified phosphorylation sites. We have investigated the metal-binding properties of synthetic model peptides and phosphopeptides that correspond to residues 119-132 of the C-terminal, polyacidic stretch of human alpha-syn, with the sequence Ac-Asp-Pro-Asp-Asn-Glu-Ala-Tyr-Glu-Met-Pro-Ser-Glu-Glu-Gly (alpha-syn119-132). The peptide pY125 replaces tyrosine with phosphotyrosine, whereas pS129 replaces serine with phosphoserine. By using Tb(3+) as a luminescent probe of metal binding, we find a marked selectivity of pY125 for Tb(3+) compared with pS129 and alpha-syn119-132, a result confirmed by isothermal titration calorimetry. Truncated or alanine-substituted peptides show that the phosphoester group on tyrosine provides a metal-binding anchor that is supplemented by carboxylic acid groups at positions 119, 121, and 126 to establish a multidentate ligand, while two glutamic acid residues at positions 130 and 131 contribute to binding additional Tb(3+) ions. The interaction of other metal ions was investigated by electrospray ionization mass spectrometry, which confirmed that pY125 is selective for trivalent metal ions over divalent metal ions, and revealed that Fe(3+) and Al(3+) induce peptide dimerization through metal ion cross-links. Circular dichroism showed that Fe(3+) can induce a partially folded structure for pY125, whereas no change was observed for pS129 or the unphosphorylated analog. The results of this study show that the type and location of a phosphorylated amino acid influence a peptide's metal-binding specificity and affinity as well as its overall conformation.