Tyrosine Side Chains Research Articles

19F‐NMR shows that active site aromatic residues in CYP121 of Mycobacterial tuberculosisplay a dual role in substrate interaction and protein structure

CYP121 is an essential cytochrome P450 enzyme (CYP) from Mycobacterium tuberculosis.CYP121 mediates an atypical phenol‐coupling reaction that converts cyclodityrosine (cYY) into mycocylosin. Our lab has previously employed a 19F nuclear magnetic resonance (NMR) label, 3‐bromo‐1,1,1‐trifluoroacetone (BTFA), to study dynamics of the FG‐loop, a region connecting the F and G‐helices. In other CYPs, the FG‐loop region has been implicated in active site access and substrate recognition. The 19F‐NMR spectrum for the FG‐loop in CYP121 is heterogeneous, suggesting that in solution there are multiple conformations. Upon titration of cYY, the signal converges to a single peak representing a bound state. Interestingly, this labeling site exists approximately 20 angstroms away from the active site heme, where ligand binding is typically measured in CYPs by UV‐visible spectroscopy. Crystal structures show an invariable protein structure with ligands clustered near the FG‐helices, away from the heme.Here we investigate the specificity of this interaction site by expanding our use of 19F labeling. Supplementing cells with 5‐fluoroindole (5‐FI) during recombinant protein expression, 19F was incorporated into each tryptophan residue of CYP121. This method of labeling allowed for four tryptophan residues to be monitored, which span the entire protein structure. Notably, two residues, Trp‐182 and Trp‐380, are located adjacent to the CYP121 homodimer interface. The 19F‐NMR spectrum contains three distinct signals, two of which are equal in intensity, and a third which has been determined to be two overlapping resonances. Addition of cYY causes a shift of equilibrium in the spectra, with the overlapped resonances resolving and resulting in four peaks of roughly equal area and intensity. These results suggest that only the active site residue Trp‐182 is affected by the addition of cYY. Using this labeling scheme, we also tested alanine substitutions of Trp‐182 and another active site aromatic residue, Phe‐168. 19F‐NMR spectra from these mutants indicate a general perturbation of the structure, with only one Trp residue left unaffected. Since Trp‐182 extends into a hydrophobic pocket of CYP121 (suggesting a structural role), additional substitutions were made using tyrosine and leucine side chains. The conservative W182Y mutant yielded similar disorder as seen when replaced with alanine, while W182L results a partially restored spectrum. Interestingly, both mutants bind substrate in a similar manner as wild‐type when measured by UV‐visible spectroscopy, although with weakened affinity.These findings indicate that while Phe‐168 and Trp‐182 are involved in substrate interaction, they also play a role in the fold of the protein, with mutagenesis causing long range changes in structure.

Direct Intracellular Delivery of Benzene Diazonium Ions As Observed by Increased Tyrosine Phosphorylation.

A challenge within the field of bioconjugation is developing probes to uncover novel information on proteins and other biomolecules. Intracellular delivery of these probes offers the promise of giving relevant context to this information, and these probes can serve as hypothesis-generating tools within complex systems. Leveraging the utility of triazabutadiene chemistry, herein, we discuss the development of a probe that undergoes reduction-mediated deprotection to rapidly deliver a benzene diazonium ion (BDI) into cells. The intracellular BDI resulted in an increase in global tyrosine phosphorylation levels. Seeing phosphatase dysregulation as a potential source of this increase, a tyrosine phosphatase (PTP1B) was tested and shown to be both inhibited and covalently modified by the BDI. In addition to the expected azobenzene formation at tyrosine side chains, key reactive histidine residues were also modified.

Visualizing protein breathing motions associated with aromatic ring flipping

Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips—that is, 180° rotations—despite their role in maintaining the protein fold1–3. It was suggested that large-scale ‘breathing’ motions of the surrounding protein environment would be necessary to accommodate these ring flipping events1. However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa.

Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems.

The flexibility of β hairpin structure known as the flap plays a key role in catalytic activity and substrate intake in pepsin-like aspartic proteases. Most of these enzymes share structural and sequential similarity. In this study, we have used apo Plm-II and BACE-1 as model systems. In the apo form of the proteases, a conserved tyrosine residue in the flap region remains in a dynamic equilibrium between the normal and flipped states through rotation of the χ1 and χ2 angles. Independent MD simulations of Plm-II and BACE-1 remained stuck either in the normal or flipped state. Metadynamics simulations using side-chain torsion angles (χ1 and χ2 of tyrosine) as collective variables sampled the transition between the normal and flipped states. Qualitatively, the two states were predicted to be equally populated. The normal and flipped states were stabilized by H-bond interactions to a tryptophan residue and to the catalytic aspartate, respectively. Further, mutation of tyrosine to an amino-acid with smaller side-chain, such as alanine, reduced the flexibility of the flap and resulted in a flap collapse (flap loses flexibility and remains stuck in a particular state). This is in accordance with previous experimental studies, which showed that mutation to alanine resulted in loss of activity in pepsin-like aspartic proteases. Our results suggest that the ring flipping associated with the tyrosine side-chain is the key order parameter that governs flap dynamics and opening of the binding pocket in most pepsin-like aspartic proteases.

Identification of an electrostatic toolkit for encoding fluorinated phenylalanine residues within proteins expressed in prokaryotic and mammalian cells

The aromatic side-chains of phenylalanine, tyrosine, and tryptophan engage in a variety of chemically expedient bonding modes. These interactions may range from purely hydrophobic/steric contributions to bona fide electrostatic bonds owing to the quadruple moment on the face of the aromatic. Explicitly testing the functional role for a given aromatic side chain is difficult using conventional mutagenesis, since mutation to a non-aromatic natural amino acid causes concomitant changes in amino acid shape, while obliterating the electrostatic component in an all-or-none manner.

Direct Evidence for Aligned Binding of Cellulase Enzymes to Cellulose Surfaces.

The conversion of biomass into green fuels and chemicals is of great societal interest. Engineers have been designing new cellulase enzymes for the breakdown of otherwise insoluble cellulose materials. A barrier to the rational design of new enzymes has been our lack of a molecular picture of how cellulase binding occurs. A critical factor is the attachment via the enzyme's carbohydrate binding module (CBM). To elucidate the structural and mechanistic details of cellulase adsorption, we have combined experimental data from sum frequency generation spectroscopy with molecular dynamics simulations to probe the equilibrium structure and surface alignment of a 14-residue peptide mimicking the CBM. The data show that binding is driven by hydrogen bonding and that tyrosine side chains within the CBM align the cellulase with the registry of the cellulose surface. Such an alignment is favorable for the translocation and effective cellulose breakdown and is therefore likely an important parameter for the design of novel enzymes.

Enzymatic crosslinking and food allergenicity: A comprehensive review.

Food allergy has become a major global public health concern. In the past decades, enzymatic crosslinking technique has been employed to mitigate the immunoreactivity of food allergens. It is an emerging non-thermal technique that can serve as a great alternative to conventional food processing approaches in developing hypoallergenic food products, owing to their benefits of high specificity and selectivity. Enzymatic crosslinking via tyrosinase (TYR), laccase (LAC), peroxidase (PO), and transglutaminase (TG) modifies the structural and biochemical properties of food allergens that subsequently cause denaturation and masking of the antigenic epitopes. LAC, TYR, and PO catalyze the oxidation of tyrosine side chains to initiate protein crosslinking, while TG initiates isopeptide bonding between lysine and glutamine residues. Enzymatic treatment produces a high molecular weight crosslinked polymer with reduced immunoreactivity and IgE-binding potential. Crosslinked allergens further inhibit mast cell degranulation due to the lower immunostimulatory potential that assists in the equilibration of T-helper (Th)1/Th2 immunobalance. This review provides an updated overview of the studies carried out in the last decade on the potential application of enzymatic crosslinking for mitigating food allergenicity that can be of importance in the context of developing hypoallergenic/non-allergenic food products.

Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy.

Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515cm-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.

Photo-induced fragmentation of tyrosine side chains in IgG4-Fc: Effect of protein sequence, conformation and glycan structure

This account summarizes recent work on photo-induced side chain cleavage reactions of Tyr in IgG4-Fc. These processes are initiated via photo-ionization of Trp to a Trp radical cation, followed by one-electron oxidation of Tyr to a Tyr radical cation, where fragmentation of the Cα-Cβ bond leads to an intermediary glycyl radical. The latter converts into Gly via hydrogen atom transfer, or into various backbone cleavage products subsequent to the addition of oxygen. Site-directed mutation of Trp381 to Phe381 significantly reduces the yields of Tyr side chain cleavage products, underlining a critical role of Trp for these reactions. Likewise, conformational changes of IgG4-Fc induced by increasing contents of 1-propanol in the solution diminishes the yields of Tyr side chain cleavage products. Variations of the glycan structure at Asn297 had an effect on Tyr side chain cleavage, where larger glycan structures led to lower yields. This result is in interesting contrast to Trp side chain cleavage in IgG1-Fc, where larger glycan structures led to higher yields. The opposite trends for Trp and Tyr side chain cleavage as a function of glycan structure are consistent with a connection between the precursors for both reactions, radical cations of Trp and Tyr, related by electron transfer. The potential significance of these reactions for protein integrity in formulations of pharmaceutical proteins will be discussed.

Novel Roles of SH2 and SH3 Domains in Lipid Binding.

Signal transduction, the ability of cells to perceive information from the surroundings and alter behavior in response, is an essential property of life. Studies on tyrosine kinase action fundamentally changed our concept of cellular regulation. The induced assembly of subcellular hubs via the recognition of local protein or lipid modifications by modular protein interactions is now a central paradigm in signaling. Such molecular interactions are mediated by specific protein interaction domains. The first such domain identified was the SH2 domain, which was postulated to be a reader capable of finding and binding protein partners displaying phosphorylated tyrosine side chains. The SH3 domain was found to be involved in the formation of stable protein sub-complexes by constitutively attaching to proline-rich surfaces on its binding partners. The SH2 and SH3 domains have thus served as the prototypes for a diverse collection of interaction domains that recognize not only proteins but also lipids, nucleic acids, and small molecules. It has also been found that particular SH2 and SH3 domains themselves might also bind to and rely on lipids to modulate complex assembly. Some lipid-binding properties of SH2 and SH3 domains are reviewed here.

Elucidation of the structure of supramolecular polymorphs in peptide nanofibres using Raman spectroscopy

AbstractPeptide fibre formation via molecular self‐assembly is a key step in a range of cellular processes and increasingly considered as an approach to produce supramolecular biomaterials. We previously demonstrated the self‐assembly of the tripeptide lysine‐dityrosine (KYY) as a substrate for the formation of proton‐conducting melanin‐like materials. Point based Raman scattering is one of several techniques which were used to characterise the secondary structure of the KYY nanofibre but as is often the case with this type of fibre, the spectra are rather complex and in addition there were variations in intensity between samples making interpretation difficult. Using Raman mapping we show that, as a drop of KYY in solution dries, it self‐assembles into two different fibre forms and the simpler spectra obtained for each are easier to interpret. The tyrosine amide marker bands, 852 and 828 cm−1, are present in both forms with similar intensities indicating the formation of a similar secondary structure in both forms with some stacking of the tyrosine rings. However, the tyrosine marker bands at 1614 and 1661 cm−1 vary considerably in intensity between the two forms. It is concluded that both forms consist of stacked polypeptide units joined by hydrogen bonds to form structures similar to β‐sheet structures in longer peptides. There are other clear differences such the large intensity difference in the lysine side chain band at 1330 cm−1 and the relative intensities of the bands at 982 and 1034 cm−1. These differences are attributed to changes in the conformation of tyrosine side chains causing different electron withdrawing effects on the ring.

Molecular Simulations Reveal the Dynamics of the T-Cell Receptor in a T-Cell Model Membrane

The T-cell antigen receptor (TCR) initiates immune responses by recognising a wide variety of foreign peptides presented by Major Histocompatibility Complex (MHC) proteins. The TCR consists of non-covalently associated TCRαβ, CD3εγ, CD3εδ and ζζ dimers. The CD3 and ζζ subunits have long intracellular tails that regulate TCR signalling. Despite significant knowledge of the TCR structure and topology, lack of information on the arrangement of its cytoplasmic tails limits our understanding of the molecular mechanism of intracellular signal propagation in a T-cell. In this study, we used molecular modelling to model the entire TCR structure and performed multi-scale molecular dynamics simulations of the TCR embedded in a complex lipid bilayer which mimics the T-cell membrane. Our simulations revealed conformational changes within the transmembrane region of the resting TCR, and also showed that the intracellular signalling tails of CD3 and ζζ subunits fold into an intertwined conformation forming contacts with each other. Additionally, the tails strongly interacted with the inner leaflet of the membrane via cationic stretches, whilst intracellular tyrosine side-chains transiently penetrated into the hydrophobic region of the membrane. Phosphatidyl inositol phosphate (PIP) lipids and cholesterol formed preferential protein-lipid interactions creating a unique local lipid environment around the TCR. Our study provides insights into the TCR's complete structure and dynamics in a membrane in atomic resolution. Further, this potentially forms the basis to study the molecular mechanism of initiation of TCR signalling.

Copper‐Promoted O‐Arylation of the Phenol Side Chain of Tyrosine Using Triarylbismuthines

A general method for the O‐arylation of the side chain of tyrosine using triarylbismuth reagents is reported. The reaction is mediated by copper diacetate, operates at 50 °C under oxygen in dichloromethane in the presence of pyridine, shows excellent functional group compatibility, and retains the integrity of the stereogenic center. The protocol was used to arylate the tyrosine residue of dipeptides and tripeptides.

Supramolecular Gelatin Networks Based on Inclusion Complexes

Hydrogel forming physical networks based on gelatin are an attractive approach toward multifunctional biomaterials with the option of reshaping, self-healing, and stimuli-sensitivity. However, it is challenging to design such gelatin-based hydrogels to be stable at body temperature. Here, gelatin functionalized with desaminotyrosine (DAT) or desaminotyrosyl tyrosine (DATT) side chains is crosslinked with cyclodextrin (CD) dimers under formation of inclusions complexes. The supramolecular networks displayed at room temperature decreased water uptake (200-600 wt% for DAT-based systems, 200 wt% for DATT based systems), and increased storage moduli up to 25.6kPa determined by rheology compared to DAT(T) gelatin. The gel-sol transition temperature increased from 33 up to 42°C. The presented system that is completely based on natural building blocks may form the basis for materials that may potentially respond by dissolution or changes of properties to changes in environmental conditions or to the presence of CD guest molecules.

Protein quantification by bicinchoninic acid (BCA) assay follows complex kinetics and can be performed at short incubation times

Amongst the available methodologies for protein determination, the bicinchoninic acid (BCA) assay highlights for its simplicity, sensitivity, repeatability and reproducibility. Nevertheless, in spite that the general principle behind this methodology is known, there are still unanswered questions regarding the chemistry behind the assay and the experimental conditions commonly employed. The present work explored the kinetics, and the analytical response of the assay to free amino acids, peptides (containing tryptophan and tyrosine), and proteins. Results revealed kinetic profiles characterized by the absence of plateaus, with behaviors depending on the type of the sample. The latter, along with contribution to the BCA index elicited by oxidation products generated at the side chain of tryptophan and tyrosine, as well as pre-oxidized β-casein, evidenced the presence of complex reaction mechanisms. In spite of such complexity, our results showed that the BCA index is not modulated by the incubation time. This applies for responses producing absorbance intensities (at 562 nm) higher than 0.1. Therefore, we propose that the assay can be applied at shorter incubation times (15 min) than those indicated in manufactures specifications, and usually used by researches and industry (30 min at 37 °C).

Advancesin enrichment and detection methods for N-phosphorylated proteins

Protein phosphorylation plays an important role in various life processes, such as signaling, metabolism, and growth. In addition to the well-known O-phosphorylation, which occurs on serine, threonine and tyrosine side chains, N-phosphorylation, occurring on histidine, arginine and lysine side chains, has attracted much attention. However, due to the chemical instability of N-phosphorylation, the studies on it are still in the nascent stage. In this review, enrichment and detection methods for protein N-phosphorylation are reviewed, and future research in this field is prospected.

STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding.

The use of fragments to biophysically characterize a protein binding pocket and determine the strengths of certain interactions is a computationally and experimentally commonly applied approach. Almost all drug like molecules contain at least one aromatic moiety forming stacking interactions in the binding pocket. In computational drug design, the strength of stacking and the resulting optimization of the aromatic core or moiety is usually calculated using high level quantum mechanical approaches. However, as these calculations are performed in a vacuum, solvation properties are neglected. We close this gap by using Grid Inhomogeneous Solvation Theory (GIST) to describe the properties of individual heteroaromatics and complexes and thereby estimate the desolvation penalty. In our study, we investigated the solvation free energies of heteroaromatics frequently occurring in drug design projects in complex with truncated side chains of phenylalanine, tyrosine, and tryptophan. Furthermore, we investigated the properties of drug-fragments crystallized in a fragment-based lead optimization approach investigating PDE-10-A. We do not only find good correlation for the estimated desolvation penalty and the experimental binding free energy, but our calculations also allow us to predict prominent interaction sites. We highlight the importance of including the desolvation penalty of the respective heteroaromatics in stacked complexes to explain the gain or loss in affinity of potential lead compounds.

NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups.

Hydrogen bonds between protein side-chain hydroxyl (OH) and phosphate groups are one of the most common types of intermolecular hydrogen bonds in protein-DNA/RNA complexes. Using NMR spectroscopy, we identified and characterized the hydrogen bonds between tyrosine side-chain OH and DNA phosphate groups in a protein-DNA complex. These OH groups exhibited relatively slow hydrogen-exchange rates and sizable scalar couplings between hydroxyl 1H and DNA phosphate 31P nuclei across the hydrogen bonds. Information about intermolecular hydrogen bonds facilitates investigations of the DNA/RNA recognition by the protein.

ROS and MAPK Cascades in the Post-harvest Senescence of Horticultural Products

Plants are naturally sessile and cannot move away from adverse environmental conditions. Environmental stress may induce loss of membrane integrity, which is a seminal feature of premature senescence. Therefore, plants must respond in other ways to protect themselves from abiotic and biotic stresses that involve protein kinases, which are crucial to signal transduction pathways. Protein kinases are involved in the phosphorylation of serine/threonine and tyrosine side chains of proteins. Among these protein kinases, mitogen-activated protein kinase (MAPK) cascade genes are key components of signal transduction pathways that help transduce extracellular signals to intracellular responses in animals, plants, and fungi. Interestingly, reactive oxygen species (ROS) are important and common messengers that are produced in various biotic and abiotic stresses; ROS are known to activate many of the MAPKs. In this review, we highlight the mechanisms of crosstalk between ROS and MAPK cascades in the post-harvest senescence of horticultural products and summarize recent findings about MAPK regulation and functioning in various cellular processes.

Electron Paramagnetic Resonance Spectroscopic Identification of the Fe-S Clusters in the SPASM Domain-Containing Radical SAM Enzyme PqqE.

Pyrroloquinoline quinone (PQQ) is an important redox active quinocofactor produced by a wide variety of bacteria. A key step in PQQ biosynthesis is a carbon-carbon cross-link reaction between glutamate and tyrosine side chains within the ribosomally synthesized peptide substrate PqqA. This reaction is catalyzed by the radical SAM enzyme PqqE. Previous X-ray crystallographic and spectroscopic studies suggested that PqqE, like the other members of the SPASM domain family, contains two auxiliary Fe-S clusters (AuxI and AuxII) in addition to the radical SAM [4Fe-4S] cluster. However, a clear assignment of the electron paramagnetic resonance (EPR) signal of each Fe-S cluster was hindered by the isolation of a His6-tagged PqqE variant with an altered AuxI cluster. In this work, we are able to isolate soluble PqqE variants by using a less disruptive strep-tactin chromatographic approach. We have unambiguously identified the EPR signatures for four forms of Fe-S clusters present in PqqE through the use of multifrequency EPR spectroscopy: the RS [4Fe-4S] cluster, the AuxII [4Fe-4S] cluster, and two different clusters ([4Fe-4S] and [2Fe-2S]) bound in the AuxI site. The RS [4Fe-4S] cluster, the AuxII [4Fe-4S] cluster, and the [2Fe-2S] cluster form in the AuxI site can all be reduced by sodium dithionite, with g tensors of their reduced form determined as [2.040, 1.927, 1.897], [2.059, 1.940, 1.903], and [2.004, 1.958, 1.904], respectively. The AuxI [4Fe-4S] cluster that is determined on the basis of its relaxation profile can be reduced only by using low-potential reductants such as Ti(III) citrate or Eu(II)-DTPA to give rise to a g1 = 2.104 signal. Identification of the EPR signature for each cluster paves the way for further investigations of SPASM domain radical SAM enzymes.