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While α-linked amino acids in the l-form are exclusively utilized in mammalian protein building, β-linked and d-form amino acids also have important biological roles. Unfortunately, the structural elucidation and separation of these different amino acid types in peptides has been analytically challenging to date due to the numerous isomers present, limiting our knowledge about their existence and biological roles. Here, we utilized an ultrahigh resolution ion mobility spectrometry platform coupled with mass spectrometry (IMS-MS) to separate amyloid β (Aβ) peptides containing l-aspartic acid, d-aspartic acid, l-isoaspartic acid, and d-isoaspartic acid residues which span α- and β-linked amino acids in both d- and l-forms. The results illustrate how IMS-MS could be used to better understand age-related diseases or protein folding disorders resulting from amino acid modifications.

A small library of peptidyl adenosine antibiotic analogs was synthesized, under the Pilot Scale Library Program of the NIH Roadmap initiative, from 2',3'-O-isoproylideneadenosine-5'-carboxylic acid 2 in excellent yield. The coupling of the amino terminus of L-2-aminophenylbutyric methyl ester to a free 5'-carboxylic acid moiety of 2 followed by sodium hydroxide treatment led to carboxylic acid analog 4. Hydrolysis of this latter gave unprotected nucleoside analog 5. Intermediate 4 served as the precursor for the preparation of novel peptidyl adenosine analogs 6-18 in good yields and high purity through peptide coupling reactions to diverse amine derivatives. No marked anticancer and antimalaria activity was noted on preliminary cellular testing; however these analogs should be useful candidates for other types of biological activity.

Proteins are large polymers of amino acids linked by peptide bonds (Figure 1). The amino acid subunits of proteins are organic molecules that include a carboxylic acid linked through a carbon atom to a primary (or secondary, in proline) amine with the chemical formula H 2 N-CHR-COOH, in which R is a side group that largely determines the chemical properties of the amino acid. The simplest amino acid is glycine, H 2 N-CH 2 -COOH, in which the R side group is a hydrogen atom. Although this chemical template can be modified into an infinite array of molecules based on variations in the R group, only approximately 20 amino acids occur in proteins. The R groups confer acidic, alkaline, polar, or nonpolar properties to the various amino acids.

Unnatural heavy metal-containing amino acid analogs have shown to be very important in the analysis of protein structure, using methods such as X-ray crystallography, mass spectroscopy, and NMR spectroscopy. Synthesis and incorporation of selenium-containing methionine analogs has already been shown in the literature however with some drawbacks due to toxicity to host organisms. Thus synthesis of heavy metal tryptophan analogs should prove to be more effective since the amino acid tryptophan is naturally less abundant in many proteins. For example, bioincorporation of β-seleno[3,2-b]pyrrolyl-L-alanine ([4,5]SeTrp) and β-selenolo[2,3-b]pyrrolyl-L-alanine ([6,7]SeTrp) has been shown in the following proteins without structural or catalytic perturbations: human annexin V, barstar, and dihydrofolate reductase. The reported synthesis of these Se-containing analogs is currently not efficient for commercial purposes. Thus a more efficient, concise, high-yield synthesis of selenotryptophan, as well as the corresponding, tellurotryptophan, will be necessary for wide spread use of these unnatural amino acid analogs. This research will highlight our progress towards a synthetic route of both [6,7]SeTrp and [6,7]TeTrp, which ultimately will be used to study the effect on the catalytic activity of Lignin Peroxidase (LiP).

Beauveriolides I and III, which are naturally occurring cyclodepsipeptides, have been reported to bind to sterol O-acyltransferase (SOAT), inhibiting its ability to synthesize cholesteryl esters. To facilitate an analysis of the binding site(s) of these compounds, we designed beauveriolide analogues 1a-d wherein the Leu or D-allo-Ile residue was replaced by photoreactive amino acids possessing methyldiazirine or trifluoromethyldiazirine in the side chains. The methyldiazirine moiety was installed by reaction of methyl ketones with liquid ammonia to provide imine intermediates, followed by treatment with hydroxylamine-O-sulfonic acid to provide the diaziridines. Subsequent oxidation gave methyldiazirines. In contrast, trifluoromethyldiazirine derivatives were prepared from trifluoromethyl ketones via the oxime intermediates, which were transformed into diaziridines. Subsequent oxidation afforded trifluoromethyldiazirines. The synthesized photoreactive amino acids 3a-d were coupled with 3-hydroxy-4-methyloctanoic acid 4 and dipeptide 5, followed by macrolactamization to provide beauveriolide analogues 1a-d. The SOAT inhibitory activities of 1a-d were found to be as potent as those of beauveriolides I and III. Moreover, 1a-d inhibited SOAT1 selectively rather than SOAT2, which was also consistent with the behavior of beauveriolides I and III.

Amino acyl-tRNA synthetases (AARSs) play a vital role in protein synthesis by catalyzing the aminoacylation of tRNA with its cognate amino acid. More recently, the endogenous AARS has been reported to recognize the close structural analogs of its cognate amino acid and helps in the in vitro and in vivo incorporation of analogs into recombinant proteins. By exploiting this substrate promiscuity, a number of non-canonical amino acids were successfully incorporated into the recombinant proteins. However, the incorporation efficiency varies with the different structural analogs depending on their reactivity towards the tRNA synthetases, which is due to the interaction and accommodation in the active site. Here, to analyze the incorporation efficiency of different proline analogs and to predict the active site residues responsible for the recognition, we carried out molecular docking study with the modeled Escherichia coli prolyl-tRNA synthetase (EcProRS). We also mapped the binding mode for the reported, virtually generated proline analogs and compared it with the reported crystal structure. The reactivity of the reported analogs was correlated with the biochemical data with respect to their interaction and orientation in the active site, which demonstrates the role of active site residues for the recognition of proline analogs and some new substrates such as chloro, bromo and iodoproline for EcProRS. We also rationally designed a EcProRS mutant for desired proline analog and validated by docking simulation with 3D model structure.

The racemization-free synthesis of N-phthaloyl amino acids (Pht-amino acids) from amino acid esters, by using o-methoxycarbonylbenzoyl chloride in anhydrous media, is described. The N-phthaloyl amino acids and esters from proteins were obtained in high yields. Three N-phthaloyl amino acids were synthesized for the first time: N-Pht-LTrp, N-Pht-S-Bzl-LCys and N-Pht-Nim-Bzl-LHis. In the case of some sterically hindered amino acids, LIle and α-amino-isobutyric acid, the intermediate N-(o-methoxycarbonylbenzoyl) amino acid derivative could be isolated.

Amino acid derivatives react with C60 at 110-120°C to form adduct compounds. The products were isolated by column chromatography and were identified by FD-MS, UV-Vis, FT-IR and 13C NMR spectroscopies.

Novel derivatives of poly(aspartic acid) conjugated with various amino acids and their amphiphilic copolymers were synthesized and characterized. Methyl esters of various amino acids (in their hydrochloride form) were synthesized from the reaction of amino acids with methanol in the presence of chlorotrimethylsilane (TMSCl). Aminolysis reaction onto polysuccinimide (PSI) using various amino acid methyl esters in the presence of catalyst and the followed hydrolysis provided the corresponding amino acid-conjugated poly(aspartic acid) derivatives in high reaction yield. Amino acid—conjugated amphiphilic analogs were also prepared by introducing hydrophobic alkylamine along with amino acid using a similar procedure. The chemical structures of copolymers were confirmed by FT-IR and 1H NMR spectroscopy. The physicochemical properties of amphiphilic copolymers were characterized using dynamic light scattering (DLS), fluorescence spectroscopy and field emission scanning electron microscopy (FE-SEM). In addition, the in vitro cell viability of the copolymers was examined. These polymers have potential applications in the pharmaceutical and cosmetic fields as delivery vehicles for bioactive molecules.

We report the identification of potent agonists of the Glucagon-Like Peptide-1 Receptor (GLP-1R). These compounds are short, 11 amino acid peptides containing several unnatural amino acids, including (in particular) analogs of homohomophenylalanine (hhPhe) at the C-terminal position. Typically the functional activity of the more potent peptides in this class is in the low picomolar range in an in vitro cAMP assay, with one example demonstrating excellent in vivo activity in an ob/ob mouse model of diabetes.

In protein evolution amino acid replacements occur more frequently between similar than dissimilar amino acids. Accordingly, the mutations obey a simple 'similar replaces similar' rule as disruption of the resulting protein structure is minimized by the modest alterations in the amino acid side chains. At laboratory level such non-destructive modifications have to be incorporated in a controlled manner by integrating the chemical diversity achieved in synthetic chemistry into proteins. For this purpose the most straightforward route is generation of the synthetic proteins by the cellular translational apparatus via insertion of isosteric synthetic amino acid analogs during gene expression. This leads to target proteins with chemical diversity not found in nature. Such genetic code engineering does not require any DNA mutagenesis step as it produces extensive sequence variations at the level of protein translation. It is generally achieved either by expansion of the existing amino acid repertoire or by introduction of novel coding units. Here we highlight the concept of using isosteric noncanonical amino acid analogs for in vivo protein synthesis as a useful tool to dissect, study and manipulate protein folding and conformational stability with two examples, the prion protein and green fluorescent protein. In the first example, we show how alternative translation of the single gene sequence by different synthetic amino acids enables the protein to fold into stable, but differing conformations. In particular, replacement of methionine by the isosteric analogs norleucine/metoxinine provide a chemical model to dissect the role of hydrophilicity/hydrophobicity in the alpha-->beta conversion of the prion protein structure. In the second example, proline residues in green fluorescent protein are replaced with (4S)-fluoroproline which improves folding and overall stability of the protein. Indeed, fluorination of the protein matrix creates a network of favorable local interactions absent in the parent (i.e. natural) protein. The generation of these novel properties is the first demonstration of a structural preogranisation principle in one complex globular protein molecule.

The N-phenyl methyl esters 4 of glycine, alanine, valine, leucine, isoleucine, phenylalanine, methionine, proline, serine, threonine, tyrosine, aspartic acid, and glutamic acid have been synthesized in good to excellent yields using diphenyliodonium bromide, AgNO3, and a catalytic amount of CuBr starting from the relevant amino acid ester. The chiral integrity of the amino acids 5 was maintained during these reactions, which were confirmed by the synthesis of dipeptide for each N-phenyl amino acid. The structures of the new compounds were confirmed by the analysis of their IR, 1H, and 13C NMR spectra in addition to CHN microanalysis or high-resolution mass spectrometry for the new N-phenyl amino acids 5 and the esters 4.

Synthesis of dihydroquinopymaric acid amides and their 2beta-succinyl and 2beta-phthalyl derivatives containing residues of amino acids was carried out for the first time. Antiviral properties of the compounds synthesized were investigated.

In order to study further the importance of the P'1 residue upon the activity of human PC1 and human furin, two important members of subtilisin/kexin family of enzymes, we have prepared by solid-phase Fmoc or recently introduced FastMoc chemistry a series of 10 peptidyl substrate analogs. The structures of these analogs are based upon the core sequence of pro-mPC1(83-93) namely, D-Tyr-Lys-Glu-Arg-Ser-Lys-Arg-Xaa-Val-Gln-Lys-Asp, where D-Tyr replaces the native L-Tyr residue and Xaa, representing the P'1 position, corresponds to L-Ser or to nonproteinacous amino acids such as Tle, Sarc, MLeu, Aib, D-Tic or L-Tic. Two more analogs with L-Tic at P'1 position but with one amino acid less, namely P5 Glu or P'3 Gln, and one with a Cit residue in place of Arg at P1 site of the dodecapeptide were also obtained. These peptides were all fully characterized by a combination of MS, 1H-NMR and amino acid analysis. In contrast to the Ser analog, which is an excellent substrate for both hPC1 and hfurin, these analogs displayed moderate to strong inhibition of both hPC1 and hfurin activity in a reversible competitive manner. They all exhibited higher potency for hfurin than for hPC1, with an inhibition constant (Ki) ranging from 0.8 to 10 microM and from 1.0 to 170 microM, respectively. Incorporation of L-Tic yielded an analog with a two to four-fold increased inhibition of either enzymes when compared to its D-Tic counterpart, the effect being more pronounced for hPC1 than for hfurin. Comparison of these data with those for the corresponding N-terminal Fmoc protected peptides revealed that the highly hydrophobic N-terminal Fmoc function occupying the P8 position can contribute positively or negatively towards proteinase inhibition depending on the nature of the unnatural amino acid at P'1 and the enzyme used. Finally, none of the analogs was significantly cleaved by either enzyme. FTIR data on these analogs revealed some important structural differences between the substrate and inhibitor analogs, as there appears to be a conformational shift from a more beta-sheet-like structure for the substrates to a more alpha-helical-like structure for the inhibitors.

Primary amino groups on the model peptide Xaa-Ala-Pro-Lys(ClZ)-Tyr(2BrZ), synthesized on a p-methylbenzhydryl amine resin with conventional Boc/benzyl protective group strategy, were reacted with 4,4'-dimethoxydityl chloride in dichloromethane, resulting in the introduction of the dimethoxydityl group, which is an acid-labile N-alkyl type of protective group. The secondary amino groups thereby formed can be methylated by treating the peptide-resin with formaldehyde and sodium cyanoborohydride in N,N-dimethylformamide. After the removal of the dimethoxydityl group with trifluoroacetic acid, the resulting N-methylated amino acid residues with a free secondary amino groups are accessible for acylation with the next activated Boc amino acid. With this method majority of the 20 common amino acids can be monomethylated directly on the resin and, in most cases, with very low levels of the side reactions. In the cases where the complete methylation is difficult to achieve, the remaining primary amino groups can be selectively acylated in the presence of secondary amino groups with trimethylacetic acid 1-hydroxybenzotriazole ester. The method provides a convenient general route to synthesize N-methylated derivatives of most of the occurring and synthetic amino acids.

Crystal structure data of 31 different globular proteins were analysed. Potentials for all 400 pairs of 20 amino acid residues in helix, extended structure, chain reversals and coil state were obtained. Analysis of these potentials showed that tripeptides of amino acid residues are not linear combinations of amino acids. The association effect of these tripeptides depends on the types of amino acids associated, the position of amino acids in the pair and the secondary structure in which the pair exists. This built-in information in tripeptides should be used in polypeptide and protein folding studies.

The synthesis of analogs of tetra-L-alanine containing 3-fluoro-L-alanine selectively incorporated at each position is described. The standard procedures in the literature used to couple L-alanine peptides together were often found to lead to undesired products, or elimination reactions when corresponding 3-fluoro-L-alanine peptide analogs were used. Several modified procedures have thus been developed for the synthesis of fluorine-substituted analogs. In addition, the pH-dependence of 19F n.m.r. spectra of 3-fluoro-L-alanine and the tetrapeptide analogs is presented.

Amino acids with aryl-keto function in their side-chains were obtained in excellent yields in the reaction of omega-carboxyamino acids with liquid HF in the presence of aromatic compounds susceptible to electrophilic substitution, such as anisole, 2-methoxybiphenyl, butyl phenyl ether or 1,3-dimethoxybenzene. The new amino acids were converted smoothly into N-tert-butyloxycarbonyl or N-fluorenylmethoxycarbonyl derivatives and then incorporated into peptides by conventional coupling methods. During the coupling step, no formation of cyclic Schiff bases was observed for aryl-keto amino acids derived from DL-alpha-aminopimelic acid and from L-alpha-aminosuberic acid. In the crude products, truncated peptides terminated at the keto amino acids were not detected by liquid chromatography-mass spectrometry.

Non-canonical amino acids (NAA), as building blocks for peptides and proteins during ribosomal translation, represent a nearly infinite supply of novel functions. The specific selection, activation and tRNA-charging of amino acids by aminoacyl-tRNA synthetases (AARS) in the aminoacylation reaction are essential steps. In most cases, aminoacylation of NAA is a good indication that the related amino acid will participate in ribosomal translation as well. However, testing the translational capacity of amino acid analogs has technical limitations. Therefore, a rapid and reliable in silico test for NAA recognition by AARS would be advantageous in experimental design. We chose tryptophanyl-tRNA synthetase from Escherichia coli as a model system for docking studies with various tryptophan analogs using the FlexX-Pharm strategy. We were able to calculate relative binding energies for Trp analogs in TrpRS that correlate well with their translational activities in E. coli. In particular, FlexX-Pharm predicted the binding sites of fluoro-, amino-, hydroxyl- and aza-containing Trp analogs within 1.5 Å of Trp in the homology model of E. coli TrpRS. Therefore, the use of ligand docking prior to NAA incorporation experiments might provide a straightforward means for determining NAA that can be efficiently incorporated into a protein.

A direct solid-phase synthesis of a series of substituted benzimidazole-containing peptides is described. The method involves on-resin formation of new amino acids containing benzimidazole derivatives in the side chain. The heterocycle conjugates were obtained by reaction between aldehydes and peptides containing beta-(3,4-diaminophenyl)alanine residue, immobilized on a polymeric solid support.

Despite astounding diversity in their structure and function, proteins are constructed from 22 protein or 'canonical' amino acids. Hundreds of amino acid analogues exist; many occur naturally in plants, some are synthetically produced or can be produced in vivo by oxidation of amino acid side-chains. Certain structural analogues of the protein amino acids can escape detection by the cellular machinery for protein synthesis and become misincorporated into the growing polypeptide chain of proteins to generate non-native proteins. In this review we seek to provide a comprehensive overview of the current knowledge on the biosynthetic incorporation of amino acid analogues into proteins by mammalian cells. We highlight factors influencing their incorporation and how the non-native proteins generated can alter cell function. We examine the ability of amino acid analogues, representing those commonly found in damaged proteins in pathological tissues, to be misincorporated into proteins by cells in vitro, providing us with a useful tool in the laboratory to generate modified proteins representing those present in a wide-range of pathologies. We also discuss the evidence for amino acid analogue incorporation in vivo and its association with autoimmune symptoms. We confine the review to studies in which the synthetic machinery of cell has not been modified to accept non-protein amino acids. © 2008 Elsevier Ltd. All rights reserved.

The L-type amino acid transporter 1 (LAT1, SLC7A5) is an Na+-independent neutral amino acid transporter the expression of which is located in retinal endothelial cells. Due to its broad substrate selectivity, LAT1 has been proposed to mediate the transport of amino acid-related drugs across the blood-tissue barriers. Here, we have investigated the transport screening of amino acid-mustards using a conditionally immortalized rat retinal capillary endothelial cell line (TR-iBRB2) which expresses LAT1. We synthesized 5 amino acid-mustards: tyrosine-mustard, phenylglycine-mustard, alanine-mustard, ornithine-mustard, and lysine-mustard. LAT1-mediated [3H]L-phenylalanine (Phe) uptake by TR-iBRB2 cells was inhibited in a competitive manner by tyrosine-mustard and phenylglycine-mustard as well as melphalan (phenylalanine-mustard). Phenylglycine-mustard was able to induce the efflux of [3H]Phe preloaded into the TR-iBRB2 cells expressing LAT1 through the obligatory exchange mechanism, although tyrosine-mustard, alanine-mustard, ornithine-mustard, lysine-mustard, and melphalan did not induce any significant efflux. These findings suggest that phenylglycine-mustard is a better substrate for LAT1 than melphalan and other amino acid-mustards.

We report on a simple synthetic route to a novel anthracene-based bis-armed amino acid derivative as a useful fluorescent probe. Various photophysical studies of this amino acid derivative are also described. Here, Suzuki-Miyaura cross-coupling reaction has been used as a key step for carbon-carbon bond formation.

Three kinds of poly amino acids, poly-γ-glutamic acid, poly(ɛ-L-lysine) and multi-L-arginyl-poly (L-aspartic acid) can be synthesized by enzymatic process independently from ribosomal protein biosynthesis pathways in microorganism. These biosynthesized polymers have attracted more and more attentions because of their unique properties and various applications. In this review, the current knowledge on the biosynthesis, biodegradations and applications of these three poly amino acids are summarized.

Fifteen naturally occurring amino acids representing basic, neutral and acidic members were interacted with 4,4′-dimethoxydiquinone (I). Basic amino acids reacted readily to give amino acid substituted carbazoloquinones (III), while neutral and acidic amino acids reacted only after addition of an acid binding agent. Using an excess of any of the amino acids resulted in the substitution of the quinonoid methoxyl group in compounds (III) by an amino acid moiety. In the case of basic amino acids, this substitution reaction was preferentially influenced by a terminal amino or guanidino amino rather than by an α-amino group. Moreover, basic amino acids could be reacted with two moles of (I) to produce dicarbazoloquinones (X). The i.r. and u.v.-visible spectra of the various carbazoloquinone products were determined and discussed.

Entirely amino acid-based polymers were prepared by side-chain attachment to polysuccinimide derived from the thermal polycondensation of aspartic acid. Following deprotonation of various amino acid ester hydrochlorides by a secondary amine, the restored primary amino groups initiated the ring-opening of succinimide to form amide bonds. 1H and 13C NMR measurements revealed that the mole fraction of the introduced amino acid side chains could be controlled by the reaction time, while no hydrolysis of methyl ester groups was observed. The synthesized polymers contain exclusively amino acids, which makes them promising candidates as base materials of controlled drug delivery systems.

Proteins are the central functional constituents in all living organisms ranging from viruses, bacteria, yeast, and plants to mammals. All of these biopolymers that are formed by natural biosynthetic pathways are composed of a genetically determined sequence of the 20 so-called natural amino acids. The physical and chemical properties of proteins are a reflection of the side chains of each of the component amino acids. However, for some purposes it would be very desireable to have amino acids with side chains of various selected physical chemical properties, such as a keto group, a crosslinker, or a NMR probe group, incorporated into the protein. Although chemical and biochemical methods for modifying amino acid moieties in proteins have been achieved, recent successes in incorporating unnatural amino acids in vivo open entirely new avenues for determining protein functions in vivo and for the creation of unnatural proteins with novel functionalities. Several examples by employing the novel activity of unnatural amino acids have shown significant roles in both basic research and biotechnology.

LAT1 (L-type amino acid transporter 1), one of the L-type amino acid transporters, transports the branched and aromatic amino acids. LAT1 requires the heavy chain of 4F2 antigen (4F2hc) for the functional expression as an amino acid transporter. The expression of this transporter is up-regulated in tumor cells and rapidly-growing cells to support their proliferation. Here, we studied the expression of LAT1 and 4F2hc in human cultured cells by real-time PCR and Western blot, and found that human brain astrocytomas, U343MGa, highly expressed LAT1 and 4F2hc mRNAs and proteins. The uptake of [14C]leucine by U343MGa cells is Na+-independent and inhibited by BCH (2-amino-2-norbornane carboxylic acid), and branched and aromatic amino acids, indicating that the LAT1 is expressed at the cell surface. Pulse chase labeling and surface labeling experiments of this cell line indicate that the protein synthesis of LAT1 and 4F2hc is slow, however, the heterodimeric complex assembled in the cells is very stable, and that the disulfide bond between the LAT1 and 4F2hc is not directly involved in the stability of the heterodimer.

The general amino acid permease, Gap1p, of Saccharomyces cerevisiae transports all naturally occurring amino acids into yeast cells for use as a nitrogen source. Previous studies have shown that a nonubiquitinateable form of the permease, Gap1pK9R,K16R, is constitutively localized to the plasma membrane. Here, we report that amino acid transport activity of Gap1pK9R,K16Rcan be rapidly and reversibly inactivated at the plasma membrane by the presence of amino acid mixtures. Surprisingly, we also find that addition of most single amino acids is lethal to Gap1pK9R,K16R-expressing cells, whereas mixtures of amino acids are less toxic. This toxicity appears to be the consequence of uptake of unusually large quantities of a single amino acid. Exploiting this toxicity, we isolated gap1 alleles deficient in transport of a subset of amino acids. Using these mutations, we show that Gap1p inactivation at the plasma membrane does not depend on the presence of either extracellular or intracellular amino acids, but does require active amino acid transport by Gap1p. Together, our findings uncover a new mechanism for inhibition of permease activity in response to elevated amino acid levels and provide a physiological explanation for the stringent regulation of Gap1p activity in response to amino acids.

Drug design can benefit from the use of non-coded amino acids, such as alpha-amino isobutyric acids (Aib) or sarcosine (N-methyl-glycine). Non-coded amino acids can confer resistance to enzymatic degradation and increase the conformational stability of the peptides. We have simulated the conformational effects of combining N-methylation, bulky groups on the Calpha atom and/or thioamides using the class II CFF91 force field and our thioamide force field parameters. Although single amino acid substitutions (e.g. Aib) can restrict the available conformations, they do not necessarily lead to unique conformers, however, we predict that some of the amino acids described in this report will fold to a single phi, psi conformation (e.g. N-methylated and thioamide penicillamine). Several other amino acid/thiopeptide combinations were designed, which are predicted to prefer only two conformations. Novel amino acids of this type should prove useful for designing peptides with defined conformations.

The proton coupled amino acid transporter PAT1 expressed in intestine, brain, and other organs accepts L- and D-proline, glycine, and L-alanine but also pharmaceutically active amino acid derivatives such as 3-amino-1-propanesulfonic acid, L-azetidine-2-carboxylic acid, and cis-4-hydroxy-D-proline as substrates. We systematically analyzed the structural requirements for PAT1 substrates by testing 87 amino acids, proline homologs, indoles, and derivatives. Affinity data and effects on membrane potential were determined using Caco-2 cells. For aliphatic amino acids, a blocked carboxyl group, the distance between amino and carboxyl group, and the position of the hydroxyl group are affinity limiting factors. Methylation of the amino group enhances substrate affinity. Hetero atoms in the proline template are well tolerated. Aromatic alpha-amino acids display low affinity. PAT1 interacts strongly with heterocyclic aromatic acids containing an indole scaffold. The structural requirements of PAT1 substrates elucidated in this study will be useful for the development of prodrugs.

In this paper, we describe the synthesis of novel endomorphin-2 analogs, containing N-methylated amino acids, consecutively in each position. The receptor-binding profile of the new analogs and their stability against enzymatic cleavage by commercially available peptidases, carboxypeptidase Y and aminopeptidase M, and a rat brain homogenate are reported. The best analog of this series, [Sar2]endomorphin-2, was almost equipotent with the parent peptide in the mu-receptor-binding assay and was also highly resistant to enzymatic degradation. This analog may be a suitable candidate for the in vivo antinociceptive studies.

In this study, we analyze the amino acid pairs in human protein C precursor to determine which amino acid pairs are more susceptible to 71 variants from missense mutant human protein C precursor. The results show 85.92% of 71 variants occur at randomly unpredictable amino acid pairs accounting for 61.96% of amino acid pairs in protein C.

The post-translational modification of an L- to a D-amino acid has been documented in relatively few gene products, mostly in small peptides under 10 amino acids in length. In this report, we demonstrate that a 46-amino acid polypeptide toxin has one D-phenylalanine at position 44, and that the epimerization from an L-Phe to a D-Phe has a dramatic effect on the excitatory effects of the peptide. In one electrophysiological assay carried out, the D-Phe-containing peptide was extremely potent, whereas the unmodified polypeptide had no biological activity, demonstrating that the chirality of the post-translationally modified amino acid is functionally significant. The peptide toxin analyzed, r11a, belongs to the I-gene superfamily of conotoxins that has four disulfide cross-links. The D-Phe in r11a is at the third amino acid from the C terminus, the same relative position from the C-terminal end as the d-amino acid in omega-agatoxin TK from a spider, an unrelated peptide. Thus, although post-translational amino acid isomerization appears to have no strong specificity for the chemical nature of the amino acid side chain, the few peptides where this modification has been established suggest that there may be favored positions near the N or C terminus that are preferential sites for isomerization to a D-amino acid.

S-Ethyl 2-azidohexanethioate (N3-Hex-SEt), an unnatural amino acid analog of leucine, is coupled with L-cysteine ethyl ester (NH2-Cys-OEt) to obtain N3-Hex-Cys-OEt by native chemical ligation. Coupling of this dipeptide with N-t-butoxycarbonyl-2-diphenylphosphinoethanethioglycinate produces the tripeptide, t-Boc-Gly-Hex-Cys-OEt, in high yield. These reactions suggest an approach for the incorporation of unnatural amino acids into proteins by successive native chemical ligation and Staudinger ligation.

We summarize here results of studies designed to elucidate basic mechanisms of reactive oxygen (ROS)-mediated oxidation of proteins and free amino acids. These studies have shown that oxidation of proteins can lead to hydroxylation of aromatic groups and aliphatic amino acid side chains, nitration of aromatic amino acid residues, nitrosylation of sulfhydryl groups, sulfoxidation of methionine residues, chlorination of aromatic groups and primary amino groups, and to conversion of some amino acid residues to carbonyl derivatives. Oxidation can lead also to cleavage of the polypeptide chain and to formation of cross-linked protein aggregates. Furthermore, functional groups of proteins can react with oxidation products of polyunsaturated fatty acids and with carbohydrate derivatives (glycation/glycoxidation) to produce inactive derivatives. Highly specific methods have been developed for the detection and assay of the various kinds of protein modifications. Because the generation of carbonyl derivatives occurs by many different mechanisms, the level of carbonyl groups in proteins is widely used as a marker of oxidative protein damage. The level of oxidized proteins increases with aging and in a number of age-related diseases. However, the accumulation of oxidized protein is a complex function of the rates of ROS formation, antioxidant levels, and the ability to proteolytically eliminate oxidized forms of proteins. Thus, the accumulation of oxidized proteins is also dependent upon genetic factors and individual life styles. It is noteworthy that surface-exposed methionine and cysteine residues of proteins are particularly sensitive to oxidation by almost all forms of ROS; however, unlike other kinds of oxidation the oxidation of these sulfur-containing amino acid residues is reversible. It is thus evident that the cyclic oxidation and reduction of the sulfur-containing amino acids may serve as an important antioxidant mechanism, and also that these reversible oxidations may provide an important mechanism for the regulation of some enzyme functions.

Aligned amino acid sequences of three functionally independent samples of transmembrane (TM) transport proteins have been analyzed. The concept of TM-kernel is proposed as the most probable transmembrane region of a sequence. The average amino acid composition of TM-kernels differs from the published amino acid composition of transmembrane segments. TM-kernels contain more alanines, glycines, and less polar, charged, and aromatic residues in contrast to non-TM-proteins. There are also differences between TM-kernels of bacterial and eukaryotic proteins. We have constructed amino acid substitution matrices for bacterial TM-kernels, named the BATMAS (BActerial Transmembrane MAtrix of Substitutions) series. In TM-kernels, polar and charged residues, as well as proline and tyrosine, are highly conserved, whereas there are more substitutions within the group of hydrophobic residues, in contrast to non-TM-proteins that have fewer, relatively more conserved, hydrophobic residues. These results demonstrate that alignment of transmembrane proteins should be based on at least two amino acid substitution matrices, one for loops (e.g., the BLOSUM series) and one for TM-segments (the BATMAS series), and the choice of the TM-matrix should be different for eukaryotic and bacterial proteins.

糖-アミノ酸ハイブリッドは単純なアミノ酸の構造特性と単純な糖の構造特性を併せ持つ分子である。このハイブリッドは高度に置換された多官能性のビルディングブロックであり、糖ミメティック、人工アミノ酸、人工ペプチドとしての用途が期待される新規物質を創製するのに用いられる。糖-アミノ酸ハイブリッドは天然にも種々の形で存在し、いくつかの抗生物質、抗ウイルス剤、抗菌剤の成分である。非天然型の糖-アミノ酸ハイブリッドは、糖由来の5員環もしくは6員環スキャフォールドをアミノ酸の側鎖に組み込むことにより合成できる。糖部分をさらに改変すれば、ハイブリッド体の物理的および力学的特性を調節可能である。ペプチドのアミノ酸ビルディングブロックを糖-アミノ酸ハイブリッドで置換すれば、合成ペプチドに糖結合部位を組み込むことができる。これは、酵素によるタンパク質分解、分子輸送能の低さ、非選択的レセプター認識といった、ペプチドを基にしたドラッグデザインの欠点を克服する有用な手段になり得る。

reports. The likely requirements for intravenous amino acids were clearly spelt out and numerous commercial preparations (mostly for adults) became available in Europe. The composition of these preparations, however, was mainly based on oral requirement data in healthy man. The major nutrition efforts were directed to improve tolerance of the nitrogen load in the presence of illness rather than to provide specific nutrients for individual organs or tissues. At most instances, the efficacy of an amino acid therapy was monitored in blood (plasma). However, as shown over the past 20 years, changes in plasma-free amino acid concentrations may parallel those in intracellular compartment, but they frequently differ either quantitatively or qualitatively. The importance of this area was recognised early in the history of ESPEN when in the 1984 Arvid