Indole Side Chain Of Tryptophan Research Articles

Dithiolated peptides incorporating bis(tryptophan)s for cooperative mercury(II) binding

The indole side chain of tryptophan is a versatile π-donor that can participate in various types of cation-π interactions. An understanding of how it may contribute as an auxiliary binding group in mercury(II) complexes can provide valuable insights toward the design of effective chelators for optimal mercury immobilization. In this study, we investigate how the incorporation of two tryptophan residues in model dicysteinyl peptides might participate in peptide-mercury(II) complex stabilization. Two pentapeptides consisting of a Cys-Trp-Cys sequence motif containing a second tryptophan residue at the N-terminal (BT1) or C-terminal (BT2) were designed. An analogous cyclohexapeptide (BT3) was included to evaluate how tryptophan residues, restricted in constrained peptidic turn motifs, might take part in mercury(II) complexation. Their interactions with mercury(II) were investigated by spectroscopic methods and computational modeling. UV–vis studies indicate the formation of 1:1 dithiolated mercury(II) complex, which is corroborated by ESI-MS analysis. Spectroscopic studies reveal that the tryptophan indole group(s) in BT1 and BT3 can participate in mercury(II) cation-π interactions. Optimized 1:1 mercury(II)-BT3 structures indicate that both indole rings are very close to the mercury(II) coordination site and could stabilize it by shielding it from ligand exchange. These findings provide some useful insights toward use of aromatic donor groups as hydrophobic shields in designing more effective metal chelating agents.

Copper‐Promoted N‐Arylation of the Indole Side Chain of Tryptophan Using Triarylbismuthines

A simple protocol for the regioselective N‐arylation of the indole side chain of tryptophan using triarylbismuth reagents as the arylating agent is reported. The reaction is catalyzed by copper(II) acetate, and operates in the presence of triethylamine or pyridine under air at 50 °C. This reaction allows the transfer of aryl groups bearing electron neutral, donating or withdrawing substituents at any position of the ring, shows high functional group tolerance, and retains the integrity of the stereogenic center. The protocol was utilized to N‐arylate tryptophan‐containing di‐ and tripeptides.

TEAD–YAP Interaction Inhibitors and MDM2 Binders from DNA‐Encoded Indole‐Focused Ugi Peptidomimetics

AbstractDNA‐encoded combinatorial synthesis provides efficient and dense coverage of chemical space around privileged molecular structures. The indole side chain of tryptophan plays a prominent role in key, or “hot spot”, regions of protein–protein interactions. A DNA‐encoded combinatorial peptoid library was designed based on the Ugi four‐component reaction by employing tryptophan‐mimetic indole side chains to probe the surface of target proteins. Several peptoids were synthesized on a chemically stable hexathymidine adapter oligonucleotide “hexT”, encoded by DNA sequences, and substituted by azide‐alkyne cycloaddition to yield a library of 8112 molecules. Selection experiments for the tumor‐relevant proteins MDM2 and TEAD4 yielded MDM2 binders and a novel class of TEAD‐YAP interaction inhibitors that perturbed the expression of a gene under the control of these Hippo pathway effectors.

TEAD-YAP Interaction Inhibitors and MDM2 Binders from DNA-Encoded Indole-Focused Ugi Peptidomimetics.

DNA‐encoded combinatorial synthesis provides efficient and dense coverage of chemical space around privileged molecular structures. The indole side chain of tryptophan plays a prominent role in key, or “hot spot”, regions of protein–protein interactions. A DNA‐encoded combinatorial peptoid library was designed based on the Ugi four‐component reaction by employing tryptophan‐mimetic indole side chains to probe the surface of target proteins. Several peptoids were synthesized on a chemically stable hexathymidine adapter oligonucleotide “hexT”, encoded by DNA sequences, and substituted by azide‐alkyne cycloaddition to yield a library of 8112 molecules. Selection experiments for the tumor‐relevant proteins MDM2 and TEAD4 yielded MDM2 binders and a novel class of TEAD‐YAP interaction inhibitors that perturbed the expression of a gene under the control of these Hippo pathway effectors.

Oxidative Modification of Tryptophan-Containing Peptides.

We herein present a broadly useful method for the chemoselective modification of a wide range of tryptophan-containing peptides. Exposing a tryptophan-containing peptide to 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) resulted in a selective cyclodehydration between the peptide backbone and the indole side chain of tryptophan to form a fully conjugated indolyl-oxazole moiety. The modified peptides show a characteristic and significant emission maximum at 425 nm, thus making the method a useful strategy for fluorescence labeling.

Water-Tryptophan Interactions: Lone-pair⋅⋅⋅π or O-H⋅⋅⋅π? Molecular Dynamics Simulations of β-Galactosidase Suggest that Both Modes Can Co-exist.

In proteins, the indole side chain of tryptophan can interact with water molecules either in-plane, forming hydrogen bonds, or out-of-plane, with the water molecule contacting the aromatic π face. The latter interaction can be either of the lone pair⋅⋅⋅π (lp⋅⋅⋅π) type or corresponds to the O-H⋅⋅⋅π binding mode, an ambiguity that X-ray structures usually do not resolve. Here, we report molecular dynamics (MD) simulations of a solvated β-galactosidase monomer, which illustrate how a water molecule located at the π face of an indole side chain of tryptophan can adapt to the position of proximate residues and "select" its binding mode. In one such site, the water molecule is predicted to rapidly oscillate between the O-H⋅⋅⋅π and lp⋅⋅⋅π binding modes, thus gaining entropic advantage. Our MD simulations provide support for the role of lp⋅⋅⋅π interactions in the stabilization of protein structures.

Biological matching of chemical reactivity: pairing indole nucleophilicity with electrophilic isoprenoids.

The indole side chain of tryptophan has latent nucleophilic reactivity at both N1 and all six (nonbridgehead) carbons, which is not generally manifested in post-translational reactions of proteins. On the other hand, all seven positions can be prenylated by the primary metabolite Δ(2)-isopentenyl diphosphate by dimethyallyl transferase (DMATs) family members as initial steps in biosynthetic pathways to bioactive fungal alkaloids including ergots and tremorgens. These are formulated as regioselective capture of isopentenyl allylic cationic transition states by the indole side chain as a nucleophile. The balance of regiospecificity and promiscuity among these indole prenyltransferases continues to raise questions about possible Cope and azaCope rearrangements of nascent products. In addition to these two electron reaction manifolds, there is evidence for one electron reaction manifolds in indole ring biosynthetic functionalization.

Excited state photoreaction between the indole side chain of tryptophan and halocompounds generates new fluorophores and unique modifications.

Photoreaction of indole containing compounds with chloroform and other trichlorocompounds generates products with redshifted fluorescence. In proteins, this reaction can be used for the fluorescent detection of proteins. Little characterization of products generated through the photochemical reaction of indoles with halocompounds has been done, yet is fundamental for the development of other fluorophores, protein labeling agents, and bioactive indole derivatives. Here, we have characterized which isomers form in the photoreaction between tryptophan and chloroform using (1)H-NMR of tryptophan and methylated derivatives to reveal that the two major products that are formed result from modification at the 4- and 6-carbon positions of the indole ring. Reaction at position 6 generates 6-formyl tryptophan and the reaction at position 4 generates an imine because the formyl derivative that is initially formed reacts further with the tryptophan amine group. The spectroscopic properties and product molecular weights of photoproducts formed from photoreaction of tryptophan with other trihalo and monohalocompounds are also determined. The indole ring of tryptophan can be modified with various additions from halocompounds, including the addition of labels to the indole ring via methylene groups. This opens possibilities for generating novel tryptophan based fluorophores and protein labeling strategies using this photochemistry.

Specificity of Ion−Protein Interactions: Complementary and Competitive Effects of Tetrapropylammonium, Guanidinium, Sulfate, and Chloride Ions

The interactions of ions with a model peptide (a single melittin alpha-helix) in solutions of tetrapropylammonium sulfate or guanidinium chloride were examined by molecular dynamics simulations. The tetrapropylammonium cation shares the geometrical property of essentially flat faces with the previously examined guanidinium cation, and it was found that that this geometry leads to a strong preference for tetrapropylammonium to interact in a similar stacking-type fashion with flat nonpolar groups such as the indole side chain of tryptophan. In contrast to guanidinium, however, tetrapropylammonium does not exhibit strong ion pairing or clustering with sulfate counterions in the solution. Sulfate was found to interact almost exclusively and strongly with the cationic groups of the peptide, such that, already in a 0.1 m solution of tetrapropylammonium sulfate, the 6+ charge of the peptide is effectively locally neutralized. In combination with previous simulations, neutron scattering studies, and experiments on the conformational stability of model peptides, the present results suggest that the Hofmeister series can be explained in higher detail by splitting ions according to the effect they have on hydrogen bonding, salt bridges, and hydrophobic interactions in the protein and how these effects are altered by the counterion.

The indole side chain of tryptophan as a versatile pi-donor.

Single-armed, 15- and 18-membered lariat ether receptor systems having indolylethyl side arms bind Na+ and K+ in the ring. The indole residue serves as a pi-donor to the ring-bound cation. Whether the five- or six-membered ring interacts most directly with Na+ or K+ depends on whether the sidearm is attached to indole's 3- or 5-position. This suggests that structural as well as electronic factors are important in pi-complexation of alkali metal cations.

Tryptophan-containing mutant of human (group IIa) secreted phospholipase A2 has a dramatically increased ability to hydrolyze phosphatidylcholine vesicles and cell membranes.

Human nonpancreatic (group IIa) secreted phospholipase A2 (human sPLA2) is associated with a number of inflammatory disorders in which the extracellular concentrations of this enzyme can become highly elevated. It is probable that the enzyme normally acts as an acute-phase protein whose function is to facilitate the removal of infectious organisms or damaged host cells as part of the normal inflammatory response. The enzyme shows negligible activity with phosphatidylcholine (PC) vesicles and cell membranes, presumably reflecting the enzyme's lack of ability to bind productively to such condensed neutral interfaces. Mammalian pancreatic enzymes show modest activity with such interfaces and contain a unique tryptophan at position 3, which is part of the presumptive interfacial binding surface of these enzymes. Human sPLA2 does not contain tryptophan. The amphiphilic indole side chain of tryptophan is noted for its ability to penetrate the lipid interface of membranes, and tryptophan residues appear to be associated with the ability of lipases and phospholipases A2 to bind to and hydrolyze such interfaces. We have investigated in detail the properties of a V3W mutant of human sPLA2, which has a unique tryptophan on the interfacial binding surface of this enzyme. Although this enzyme shows a modest ( approximately 50%) reduction in activity when anionic substrates are used under standard assay conditions, the activity of the enzyme on phosphatidylcholine vesicles and cell membranes is dramatically increased compared with human sPLA2. This is particularly the case with small unilamellar vesicles of PC, where activity is enhanced over 250-fold compared to the almost zero activity expressed by human sPLA2. This enhanced activity is best explained by increased interfacial binding and activation of the V3W mutant and is not due to enhanced active-site binding and hydrolysis. The results highlight the important role that tryptophan residues can play in interfacial binding, particularly to condensed zwitterionic interfaces. The interfacial characteristics of the mutant human enzyme now resemble more closely the mammalian pancreatic enzymes that already have a tryptophan at position 3.

Assignment of the spectra of protein radicals in cytochrome c peroxidase

In oxidized cytochrome c peroxidase a peak at 570 nm has been attributed to an intermediate tryptophan free radical of indeterminate protonation state. Ab initio calculations of the spectra of the neutral and cationic free radicals of the indole side chain of tryptophan are used to assign the absorption spectra to the neutral radical. Earlier assignment attempts were confused by the large blue shift in water of the in vacuo transition. The relevant calculated transitions of both the neutral and cationic indole radicals, in fact, shift substantially to the blue in aqueous solution

ChemInform Abstract: SELECTIVE REMOVAL OF THE O‐NITROPHENYLSULFENYL PROTECTING GROUP IN PEPTIDE SYNTHESIS

AbstractDas Mercaptopyridin (I) ist ein geeignetes spezifisches Reagenz zur Entfernung der o‐Nitrophenylsulfenyl‐Schutzgruppe bei konventionellen wie auch nach der Festphasenmethode durchgeführten Peptidsynthesen.

The kinetics of complex formation of hen egg lysozyme with chloranil

1. 1. The rate of complex formation of hen egg-white lysozyme with chloranil in dimethyl-sulfoxide at different molar ratios was investigated. 2. 2. The reaction rates were studied by the “stopped-flow” method. The complex forming reactions follow kinetics of first order. A linear dependence of K obs (sec −1) with donor concentration was obtained. The formation of lysozyme-chloranil complex is similar to that for the free tryptophanchloranil complex. The complex formation reaction between lysozyme and chloranil in dimethyl-sulfoxide inactivates the enzyme activity. 3. 3. The absorption and fluorescence spectra showed that the indole side chain of tryptophan can act as an electron donor in the complex formation reaction with chloranil. 4. 4. The kinetic study with excess of chloranil, suggests that chloranil reacts first with tryptophyl residues in active site than other amino acid residues. The inhibition curve course confirmed this assumption.