Glycine Subunits Research Articles

Peptide Modifications: Versatile Tools in Peptide and Natural Product Syntheses

Peptide modifications via C–C bond formation have emerged as valuable tools for the preparation and alteration of non-proteinogenic amino acids and the corresponding peptides. Modification of glycine subunits in peptides allows for the incorporation of unusual side chains, often in a highly stereoselective manner, orchestrated by the chiral peptide backbone. Moreover, modifications of peptides are not limited to the peptidic backbone. Many side-chain modifications, not only by variation of existing functional groups, but also by C–H functionalization, have been developed over the past decade. This account highlights the synthetic contributions made by our group and others to the field of peptide modifications and their application in natural product syntheses.1 Introduction2 Peptide Backbone Modifications via Peptide Enolates2.1 Chelate Enolate Claisen Rearrangements2.2 Allylic Alkylations2.3 Miscellaneous Modifications3 Side-Chain Modifications3.1 C–H Activation3.1.1 Functionalization via Csp3–H Bond Activation3.2.2 Functionalization via Csp2–H Bond Activation3.2 On Peptide Tryptophan Syntheses4 Conclusion

A prelude to building mathematical models for polypeptide folding: analysis on the conformational potential energy hypersurface cross-sections of N-acetyl-glycyl-glycine-N′-methylamide

Finding a relationship on how a three-dimensional protein folds from its linear amino acid chain gets more complex with increasing chain length, so working on a smaller peptide conformational problem can provide initial ideas on what are the main molecular forces and how these influence the folding process. Following the study of conformations of amino acid units entering the proteins to understand the secondary structure of small peptides, this paper proposes mathematical models for the several two-rotor cross-sections of the five-dimensional N-acetyl-glycyl-glycine-N′-methylamide potential energy hypersurface (PEHS). These cross-sections are extracted along the first glycine subunit, with its coordinates fixed at the five energy minima of the glycine diamide. The resulting mathematical models yield an average RMSE of 1.36 kJ mol−1 and an average R2 of 0.9923 with respect to energy values obtained from DFT calculations. The minima geometries obtained from these models are also in good agreement with DFT-optimized energy minima conformers. An important aspect of this study also tackles the relationship between the PEHS of the glycyl-glycine diamide and its glycine subunits. It has been observed that there are deviations up to 28.35 kJ mol−1 and 29.52 kJ mol−1 between the PEHS cross-sections along γL and γD conformations, respectively, in the first glycine subunit. This may suggest that there are significant backbone–backbone intermolecular forces acting on the dipeptide. The abovementioned findings can help in developing more complex mathematical models for polypeptide folding from amino acid subunits.

Total syntheses and biological evaluation of miuraenamides.

The miuraenamides, relatively simple representatives of a class of cyclodepsipeptides with high antitumor activity, can be easily and flexibly obtained by the concept of peptide modification. A reaction sequence consisting of an aldol reaction, oxidation, and methylation of the glycine subunit of the cyclodepsipeptides allows the incorporation of the unusual α,β-unsaturated dehydroamino acid in one of the last steps of the synthesis.

Selective peptide modifications via ruthenium-catalyzed allylic alkylations.

Ruthenium-catalyzed allylic alkylations are an interesting alternative to palladium-catalyzed processes, since they can provide products which are not accessible under Pd-catalysis. Chiral terminal allylic substrates can be reacted with perfect stereo- and regioretention, and also (Z)-configured allylic substrates can be converted isomerization-free. This allows highly stereoselective modifications of peptides at glycine subunits. The configuration at the α-position of the new generated α-amino acid can be controlled by the chiral peptide chain, and at the β-position by using chiral allylic substrates.

Ligand-induced protein mobility in complexes of carbonic anhydrase II and benzenesulfonamides with oligoglycine chains.

This paper describes a biophysical investigation of residual mobility in complexes of bovine carbonic anhydrase II (BCA) and para-substituted benzenesulfonamide ligands with chains of 1–5 glycine subunits, and explains the previously observed increase in entropy of binding with chain length. The reported results represent the first experimental demonstration that BCA is not the rigid, static globulin that has been typically assumed, but experiences structural fluctuations upon binding ligands. NMR studies with 15N-labeled ligands demonstrated that the first glycine subunit of the chain binds without stabilization or destabilization by the more distal subunits, and suggested that the other glycine subunits of the chain behave similarly. These data suggest that a model based on ligand mobility in the complex cannot explain the thermodynamic data. Hydrogen/deuterium exchange studies provided a global estimate of protein mobility and revealed that the number of exchanged hydrogens of BCA was higher when the protein was bound to a ligand with five glycine subunits than when bound to a ligand with only one subunit, and suggested a trend of increasing number of exchanged hydrogens with increasing chain length of the BCA-bound ligand, across the series. These data support the idea that the glycine chain destabilizes the structure of BCA in a length-dependent manner, causing an increase in BCA mobility. This study highlights the need to consider ligand-induced mobility of even “static” proteins in studies of protein-ligand binding, including rational ligand design approaches.

Receptor targets of amacrine cells

Amacrine cells are a morphologically and functionally diverse group of inhibitory interneurons. Morphologically, they have been divided into approximately 30 types. Although this diversity is probably important to the fine structure and function of the retinal circuit, the amacrine cells have been more generally divided into two subclasses. Glycinergic narrow-field amacrine cells have dendrites that ramify close to their somas, cross the sublaminae of the inner plexiform layer, and create cross talk between its parallel ON and OFF pathways. GABAergic wide-field amacrine cells have dendrites that stretch long distances from their soma but ramify narrowly within an inner plexiform layer sublamina. These wide-field cells are thought to mediate inhibition within a sublamina and thus within the ON or OFF pathway. The postsynaptic targets of all amacrine cell types include bipolar, ganglion, and other amacrine cells. Almost all amacrine cells use GABA or glycine as their primary neurotransmitter, and their postsynaptic receptor targets include the most common GABA(A), GABA(C), and glycine subunit receptor configurations. This review addresses the diversity of amacrine cells, the postsynaptic receptors on their target cells in the inner plexiform layer of the retina, and some of the inhibitory mechanisms that arise as a result. When possible, the effects of GABAergic and glycinergic inputs on the visually evoked responses of their postsynaptic targets are discussed.

Sulfur Deficiency Changes Mycosporine‐like Amino Acid (MAA) Composition of Anabaena variabilis PCC 7937: A Possible Role of Sulfur in MAA Bioconversion

In the present investigation we show for the first time that bioconversion of a primary mycosporine-like amino acid (MAA) into a secondary MAA is regulated by sulfur deficiency in the cyanobacterium Anabaena variabilis PCC 7937. This cyanobacterium synthesizes the primary MAA shinorine (RT = 2.2 min, lambda(max) = 334 nm) under normal conditions (PAR + UV-A + UV-B); however, under sulfur deficiency, a secondary MAA palythine-serine (RT = 3.9 min, lambda(max) = 320 nm) appears. Addition of methionine to sulfur-deficient cultures resulted in the disappearance of palythine-serine, suggesting the role of primary MAAs under sulfur deficiency in recycling of methionine by donating the methyl group from the glycine subunit of shinorine to tetrahydrofolate to regenerate the methionine from homocysteine. This is also the first report for the synthesis of palythine-serine by cyanobacteria which has so far been reported only from corals. Addition of methionine also affected the conversion of mycosporine-glycine into shinorine, consequently, resulted in the appearance of mycosporine-glycine (RT = 3.6 min, lambda(max) = 310 nm). Our results also suggest that palythine-serine is synthesized from shinorine. Based on these results we propose that glycine decarboxylase is the potential enzyme that catalyzes the bioconversion of shinorine to palythine-serine by decarboxylation and demethylation of the glycine unit of shinorine.

A glycine site‐specific NMDA receptor antagonist protects retina ganglion cells from ischemic injury by modulating apoptotic cascades

Glutamate neurotoxicity is one of the causative factors leading to neural degeneration including retina. Inhibition of NMDA receptors has been shown neuroprotective effects. However, specifically inhibition of glycine subunit in NMDA receptors and its effects on retina neural protection has not been tested. In this study, using a glycine site-specific NMDA receptor antagonist, we investigated its neuroprotective effects on rat retinal ganglion cells (RGCs) from a transient ischemic injury and its possible underlying mechanisms. Following an ischemia/reperfusion injury the structural damages of rat retinas were assessed by an immunofluorescence method and the apoptosis of retinal neural cells was evaluated by using a terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) method. The survived RGCs were labeled by retrograde manner and counted on whole-mounted retinas. In the presence of glycine site-specific NMDA receptor antagonist, the thickness of retina was sustained, especially in the inner nuclear layers compared with mock controls. While a significantly higher numbers of TUNEL-positive apoptotic cells and fewer of RGCs were observed in the retina without the glycine antagonist, indicating its strong protective roles. Some apoptotic factors such as Bax, Bcl-2, CAMK II, COX1, COX4, Caspase-3, and GRIN1 gene have been tested from retinal samples with or without the glycine antagonist. A significantly lower of expressions of Bax, CAMK II, COX1, COX4, Caspase-3, and GRIN1 have been shown in the retinas with the antagonist. Bcl-2/Bax ratio was significantly higher with the antagonist, suggested that the glycine site-specific NMDA receptor antagonist protecting RGC death might through inhibition of apoptotic signaling.

Ion channel alterations and epilepsy in mice and man

Physiological CNS function relies on a balance of impulses mediated by voltage and ligand gated ion channels. Various forms of epilepsy correlate with mutations of genes coding for voltage dependent sodium (e.g., benign familial neonatal seizures), potassium (e.g., benign familial neonatal convulsions), and calcium (e.g., juvenile myoclonic epilepsy) channels. Mice carrying mutations in the orthologous ion channel genes serve as models of corresponding human disorders. From these studies, it has become apparent that ion conducting as well as accessory subunits of these channel types may be affected. The mouse mutant entla develops an absence epilepsy characterized by 2 and 4Hz EEG patterns, in addition to ataxia and paroxysmal dyskinesia. The underlying mutation on mouse Chr 9 was identified as an allele of the Cacna2d2 gene. This gene encodes the accessory α2δ-2 subunit of P/Q type calcium channels, a target of the antiepileptic drug gabapentin. The entla allele harbors an exon duplication that interferes with posttranslational processing, i.e. the formation of a disulfide linkage. This results in a dramatic reduction of both, calcium currents and [3H]gabapentin binding. The entla mouse thus represents a model of genetically alteratered protein processing producing a complex absence epilepsy syndrome. At the postsynaptic face, the neurotransmitter signal is converted to excitatory or inhibitory currents by binding to ligand gated ion channels. Mutations of the nicotinic receptor α4 subunit gene (CHNRA4) cause autosomal dominant nocturnal frontal lobe epilepsy. In contrast, mutations of the glycine subunit genes α1 (GLRA1) and β (GLRB) result in hyperekplexia (startle disease, stiff baby syndrome), a non-epileptic neurological condition. Upon recombinant expression, mutant acetylcholine and glycine receptor subunits frequently display altered transmitter binding and ion conductance.

A straightforward approach towards cyclic peptides via ring-closing metathesis—scope and limitations

N- and C-terminal diallylated peptides are obtained by several approaches, such as peptide Claisen rearrangement, N- and O- allylation, and the Ugi reaction of allyl-protected components. These diallylated peptides are suitable substrates for ring-closing metathesis and the success of this cyclisation was investigated with respect to the ring size, the position of the allyl moieties and the reaction parameters. In general, excellent yields are obtained for cyclisation of allyl glycine subunits and N-allylated amides, while allyl esters and allyl carbamates often presented serious problems. However, yields of up to 73% were obtained under optimised conditions, and the new generated double bond is formed with excellent trans-selectivity.

Selective antagonism of rat inhibitory glycine receptor subunits.

Retinal ganglion cells exhibit fast and slow inhibitory synaptic glycine currents that can be selectively inhibited by strychnine and 5,7-dichlorokynurenic acid (DCKA), respectively. In this study we examined whether strychnine and DCKA selectivity correlated with the subunit composition of the glycine receptor. Homomeric alpha1, alpha2 or alpha2* glycine subunits were in vitro expressed in human embryonic kidney cells (HEK 293). In cells expressing the alpha1 subunit, responses to 200 microm glycine were blocked by 1 microm strychnine but not by 500 microm DCKA. In cells expressing the alpha2 subunit, both 1 microm strychnine and 500 microm DCKA were effective antagonists of 200 microm glycine. In cells expressing alpha2* subunits, which are much less glycine-sensitive, 10 mm glycine was inhibited by 500 microm DCKA but not by 1 microm strychnine. A single amino acid mutation in the alpha1 subunit (R196G), converted this subunit from DCKA-insensitive to DCKA-sensitive. In conclusion, the comparative effectiveness of strychnine and DCKA can be used to distinguish between the alpha1, alpha2 and alpha2* receptor responses. Furthermore, a single amino acid near the glycine receptor's putative agonist binding site may account for differences in DCKA sensitivity amongst the alpha subunits.

Molecular Determinants of Proton Modulation of Glycine Receptors

Extracellular pH regulates glycine receptors through an unknown mechanism. Here we demonstrate that acidic pH remarkably inhibited glycine-activated whole-cell currents in recombinant glycine alpha1 and alpha1beta receptors transiently expressed in human embryonic kidney 293 cells. The proton effect was voltage-independent and pharmacologically competed with glycine receptor agonist glycine and antagonist strychnine. Using site-directed mutagenesis, we have identified an N-terminal domain that is essential for proton-induced inhibition of glycine current. In alpha1 homomers, removal of the hydroxyl group by mutation of residue Thr-112 to Ala or Phe abolished inhibition of glycine currents by acidification. In contrast, mutation of Thr-112 to another hydroxylated residue (Tyr) produced receptors that retained partial proton sensitivity. In alpha1beta heteromers, a single mutation of the beta subunit T135A, which is homologous to alpha1 Thr-112, reduced proton sensitivity, whereas the double mutation alpha1(T112A)beta(T135A) almost completely eliminated the proton sensitivity. In addition, the mutation alpha1 H109A greatly reduced sensitivity to protons in homomeric alpha1 receptors. The results demonstrate that extracellular pH can regulate the function of glycine alpha1 and alpha1beta receptors. An extracellular domain consisting of Thr-112 and His-109 at the alpha1 subunit and Thr-135 at the beta subunit plays a critical role in determining proton modulation of glycine receptor function.

Self-assembly of novel [3]- and [2]rotaxanes with two different ring components: donor-acceptor and hydrogen bonding interactions and molecular-shuttling behavior.

Three of the first kind of hetero[3]rotaxanes, which comprise one linear component and one neutral and one tetracationic ring component, have been assembled by using the intermolecular hydrogen bonding and donor-acceptor interactions. Three neutral [2]rotaxanes and three tetracationic [2]rotaxanes have also been synthesized as intermediate products or for the sake of property comparison. The linear molecules are incorporated with two glycine subunits, for templating the formation of the neutral tetraamide cyclophane, and one or two hydroquinone subunits, for inducing the formation of the tetracationic cyclophane. Variable-temperature (1)H NMR investigation reveals that the shuttling behavior of the tetracationic ring component along the linear component is substantially influenced by the existence of the neutral ring component. The spatial repelling interaction of the neutral ring on the electron-deficient tetracationic ring simultaneously weakens the latter's "positioning" tendency at both electron-rich hydroquinone sites of the linear component. As a result, the activation energy associated with the shuttling process of the tetracationic ring between the two hydroquinone sites is remarkably reduced in comparison to that of the shuttling process of the corresponding neutral ring-free [2]rotaxanes. For the first time, the rotation of the dipyridinium subunit around the axis formed by the two methylene groups connecting them within the tetracationic cyclophane has been investigated by variable-temperature (1)H NMR spectroscopy and the associated kinetic data have also been successfully obtained. Furthermore, the UV-vis and fluorescent properties of the new [2]- and [3]rotaxanes have been studied. The results demonstrate that [3]rotaxanes with different ring components possess unique kinetic features that are not available in [3]rotaxanes with identical ring components.

The glycine site modulates NMDA-mediated changes of intracellular free calcium in cultures of hippocampal neurons

Recent evidence indicates that the N- methyl- d-aspartate (NMDA) receptor-channel complex contains a glycine subunit whose activation may be necessary for channel operation. It has been previously shown that stimulation of the NMDA receptor leads to an increase in intracellular ionic Ca 2+ ([Ca 2+] i); therefore, we examined the role of the NMDA receptor-associated glycine site in modulating [Ca 2+] i using the fluorescent dye Fura II in hippocampal neuron cultures. A 3-s pulse of 200 μM NMDA resulted in a mean [Ca 2+] i increase of 363 nM above the average resting concentration of 122 nM. Perfusion of the glycine site antagonist 7-chlorokynurenate (Cl-Kyn) essentially eliminated the NMDA-induced alteration in [Ca 2+] i. Either 40 μM glycine or 50 μM d-serine completely reversed the effect of Cl-Kyn, indicating that the drug was acting at the glycine site. The NMDA receptor antagonists 2-amino-5-phosphonovalerate (AP5) and ketamine, which bind to the glutamate recognition site and the ion channel, respectively, also blocked the NMDA-mediated [Ca 2+] i response; however, glycine or d-serine did not reverse this effect. These data show that the glycine binding site coupled to the NMDA receptor modulates the NMDA-mediated increase in [Ca 2+] i. Antagonists of the glycine site provide a new tool to investigate and possibly control neuroplasticity and neurotoxicity related to the NMDA receptor complex.