Relationship between Bitterness of Peptides and their Chemical Structures

Various peptides and derivatives of peptides and amino acids were synthesized and tasted, systematically, to elucidate the relationship between bitterness and chemical structures of peptides.

We have found that: 1. Peptides become more bitter than the original amino acids when their amino and carboxyl groups are blocked and when peptide bond is formed. 2. A peptide molecule with a high content of amino acids with hydrophobic side chains will develop bitter taste. 3. The amino acids in a peptide chain independently contribute to bitterness regardless of amino acid sequences and configuration.     

Electrophysiological responses of taste cells to nutrient mixtures in the polyphagous caterpillar of Grammia geneura

In a normally feeding insect, the taste receptors are exposed to complex mixtures of chemicals, not single compounds. We investigate the responses of neurons in the galeal sensilla of the caterpillar of Grammia geneura to mixtures of nutrient compounds at concentrations occurring in plants. Compounds that stimulated the same neuron were generally additive in their effects in binary mixtures. Amino acids that did not stimulate usually had no effect in mixtures with a stimulating compound, but glutamic acid reduced the response to serine in the medial sensillum. Nutrient compounds that stimulated different cells in a sensillum acted independently of each other. Complex mixtures of amino acids resembling samples of free amino acids from three host plants were less stimulating than expected from their molar concentrations. In host plant selection, the response from the medial sensillum is probably dominated by sucrose; unless sucrose levels are low, amino acids will contribute little to sensory input because they stimulate the same cell as sucrose. In the lateral sensillum, amino acids act independently of sugars. The limited contact chemosensory array of caterpillars seems inadequate to allow them to make fine distinctions between plants on the basis of their free amino acids.     

A significant pool of amino acids is adsorbed on blood cell membranes

It is well known that the amino acids in the blood are distributed between the plasma and inside the cells. This study was conducted to determine whether amino acids can be located adsorbed on blood cell membranes. The amino acid concentration in the deproteinized haemolysed blood was higher than that in the fraction of blood after removal of the blood cell membranes by centrifugation. These results showed that a pool of amino acids representing 21.1% of the whole blood cell amino acids was adsorbed on the blood cell membranes of adult Wistar rats. The non-polar amino acids showed high adsorption on the membrane, whereas out of the polar amino acid group, only the non-ionic amino acids did adsorb.Bioquimica i Biologia Molecular. Dept. de Biologia Fonamental i Ciencies de la Salut.     

Effect of amino acids on collagen biosynthesis

Summary The effect of various amino acids on collagen biosynthesis was studied in organ cultures of chicken embryo tibiae. Competitive interrelationship between selected amino acids influences independently the uptake of proline and lysine, precursors of hydroxyproline and hydroxylysine, respectively, which are the two amino acids characteristics of collagen. On the basis of these influences, the possibility of biosynthesis of anomalous collagens is stressed. Parallel studies of biosynthesis of hydroxyproline and hydroxylysine are necessary.     

Is there a twenty third amino acid in the genetic code?

The universal genetic code includes 20 common amino acids. In addition, selenocysteine (Sec) and pyrrolysine (Pyl), known as the twenty first and twenty second amino acids, are encoded by UGA and UAG, respectively, which are the codons that usually function as stop signals. The discovery of Sec and Pyl suggested that the genetic code could be further expanded by reprogramming stop codons. To search for the putative twenty third amino acid, we employed various tRNA identification programs that scanned 16 archaeal and 130 bacterial genomes for tRNAs with anticodons corresponding to the three stop signals. Our data suggest that the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely.     

Functional characterization of constituent enzyme fractions of mycobacillin synthetase.

The enzyme fraction A, a constituent enzyme of the three-fraction enzyme mycobacillin synthetase, independently and sequentially activated five amino acids starting from L-proline, producing the pentapeptide Pro(Asp1,Glu1,Tyr1)Asp. The fractions B and C were unable to function independently. However, the fraction B synthesized the nonapeptide Pro(Asp3,Glu1,Tyr2,Ser1)Leu, sequentially activating the pentapeptide and next four amino acids, whereas the fraction C synthesized mycobacillin by the sequential activation of the nonapeptide and the remaining four amino acids. The pH optima of the above enzymes are almost identical (pH 7.8), but their Km values are a little different.     

An intracellular perfusion system linking pools and protein synthesis

A working model is proposed accounting for the relationship between pools and protein synthesis in heterotrophic eukaryotic cells. A constant intracellular perfusion system moves amino acids past the selection mechanism for protein synthesis but operates quite independently of the latter. By maintaining as high a flux as possible, the cell maximizes its chances of retrieving all the required amino acids for protein synthesis even under adverse conditions such as gross imbalances or restriction of the availability of amino acids. The intracellular acid soluble pool is largely, probably completely for most amino acids, on the efferent limb of the proposed cyclical perfusion system, i.e. amino acids in this pool are no longer directly retrievable for protein synthesis.     

Analysis of distributions of amino acids in the primary structure of tumor suppressor p53 family according to the random mechanism

It is well known that the evolutionary process leads to the majority of amino acids clustering in some regions rather than being homogenously distributed along a protein. Among numerous factors affecting the evolutionary process is chance, whose impact therefore should be present in a protein primary structure. The issue of how to measure the random distribution of amino acids in a primary structure is of importance for the understanding of protein structure and functions. In this study, we use the random principle as a tool to analyze and compare the distributions of amino acids in the primary structure of the p53 protein family. The results, for example, show that the amino acids are distributed more randomly in mouse p53 and less randomly in common tree shrew p53, the distribution ranks of amino acids are relatively lower in the functional regions (about 0.5 on average) than in the whole sequences (about 1.2 on average) except for mouse p53. From the probabilistic distribution view, the composition of human p53 is relatively stable in the functional regions rather than in the whole sequence, which may suggest one of the potential effects on the mutations inducing human cancers. In general, we can use the distribution probability to present quantitatively a type of distribution of amino acids in a protein, to compare quantitatively the magnitude of clusters between different proteins and to track the effect of chance on the evolutionary process.     

Structure and function of mutants in the P gene of bacteriophage lambda leading to the pi phenotype

The location of 14 independently isolated spontaneous pi A and pi B point mutants in the lambda P gene and their base exchanges were determined. It was found that the pi B mutation is one unique type mapping close to other pi A mutants. The number of possible pi A mutation sites could be estimated. The mutation sites are distributed asymmetrically in the gene. The N-terminal half of the protein is unchanged. It is assumed to be required for the interaction with the lambda O protein. The P protein can be changed by substitution of a limited number of amino acids at the C-terminus. All functional proteins of this type have pi character. pi proteins do not appear to have altered intracellular levels or stabilities as compared to wild-type P protein. The plating characteristics of our mutants on two groP- mutants located in the dnaJ and dnaK genes, respectively, are strikingly different.     

Distribution of mapping points of 20 amino acids in the tetrahedral space

Summary Based on the genetic codes and a simple theorem for the geometrical property of the regular tetrahedron, each amino acid is mapped onto a unique point in a 3-dimensional tetrahedral space. The distribution of the 20 mapping points for 20 amino acids is studied in detail. It is found that the mapping points for the hydrophobic and hydrophilic amino acids are distributed at distinct regions in the 3-dimensional space. A plane separating the two kinds of points satisfactorily based on the Fisher's algorithm has been calculated. It is shown that the codons coding for the hydrophobic amino acids are constituted dominantly by the bases of keto group, i.e., G and T. While the codons coding for the hydrophilic amino acids are constituted dominantly by the bases of amino group, i.e., A and C. The biological implication of the mapping points and the separating plane has been discussed in some details.     

Insulin and amino acids independently stimulate skeletal muscle protein synthesis in neonatal pigs

Infusion of physiological levels of insulin and/or amino acids reproduces the feeding-induced stimulation of muscle protein synthesis in neonates. To determine whether insulin and amino acids independently stimulate skeletal muscle protein synthesis in neonates, insulin secretion was blocked with somatostatin in fasted 7-day-old pigs (n = 8-12/group) while glucose and glucagon were maintained at fasting levels and insulin was infused to simulate either less than fasting, fasting, intermediate, or fed insulin levels. At each dose of insulin, amino acids were clamped at either the fasting or fed level; at the highest insulin dose, amino acids were also reduced to less than fasting levels. Skeletal muscle protein synthesis was measured using a flooding dose of l-[4-(3)H]phenylalanine. Hyperinsulinemia increased protein synthesis in skeletal muscle during hypoaminoacidemia and euaminoacidemia. Hyperaminoacidemia increased muscle protein synthesis during hypoinsulinemia and euinsulinemia. There was a dose-response effect of both insulin and amino acids on muscle protein synthesis. At each insulin dose, hyperaminoacidemia increased muscle protein synthesis. The effects of insulin and amino acids on muscle protein synthesis were largely additive until maximal rates of protein synthesis were achieved. Amino acids enhanced basal protein synthesis rates but did not enhance the sensitivity or responsiveness of muscle protein synthesis to insulin. The results suggest that insulin and amino acids independently stimulate protein synthesis in skeletal muscle of the neonate.     

Sequence similarities of protein kinase peptide substrates and inhibitors: comparison of their primary structures with immunoglobulin repeats

Forty original sequences of peptide substrates and inhibitors of protein kinases and phosphatases were aligned in a chain matrix without artificial gaps. Fifteen protein kinase peptide substrates and inhibitors (PKSI peptides) contained a common dipeptide ArgArg and also additional important tetra-, tri- and dipeptide homologies. Three further peptide substrates were significantly similar to these peptides but lacked the ArgArg dipeptide. Sequence comparison of individual PKSI peptides revealed probabilistically restricted consensus sequence—PKSI motif—comprising 8 homologous and 13 non-randomly distributed amino acids without considering mutation analysis. This template motif was compared with the consensus sequences of 12 different immunoglobulin domains. In 11 of 12 these domains, the starts of homologous segments were found at nearly the same domain related sites, beginning with serine. A single-triplet mutation, of any of the first two triplet bases that encode equally localized amino acids in each of the two sequence sets (PKSI and Ig) revealed additional homologies with the other set. A primary derived motif version composed of 9 homologous and seven non-randomly distributed amino acids was consequently established by its feedback projection into the original sequence sets. This procedure yielded a second preliminary motif version (revised motif) formed by a sequence of 9 homologous amino acids and two non-randomly distributed amino acids. In addition, three shorter oligopeptide motifs called important stereotypes were derived, based on repeated homology between Ig chains and the revised motif. The most extensive similarities in terms of these stereotypes occurred in the CH2 and CH4 domains of Ig peptides, and inhibitors of cAMP dependent protein kinase and protein kinase A. Further comparisons based on a reference sequence set arranged with the aid of feedback projection revealed a lower similarity between variable Ig chains reflected in a decreased number of homologous amino acids. Two final motif versions, FMC and FMV, were found in two different subsets of constant and variable Ig chains, respectively. FMC was composed of seven homologous and one non-randomly distributed amino acids forming the dispersed structure STLR(C)LVSD, whereas 6 homologous and one questionable amino acid constituted FMV. Only CH4 and CH1 domain segments contained all five high-incidence amino acids, which represented a higher level of similarity than homologous amino acids of all preliminary and final motifs. Four such amino acids were present also in three PKSI peptides. All similarities described here occur in domain segments positionally overlapping with the CDR1 region of variable chains. The results are discussed in terms of immunoglobulin evolution, the position of Fc receptor binding sites and degeneration or mutability of the triplets of motif-constituting amino acids.     

Differential localization of ICAD-L and ICAD-S in cells due to removal of a C-terminal NLS from ICAD-L by alternative splicing

CAD/CPAN/DFF40 is an apoptotic nuclease that is associated with the regulatory subunit ICAD/DFF in healthy cells. ICAD has two forms, ICAD-L/DFF45 and ICAD-S/DFF35, which are transcribed from a single gene by alternative splicing. They differ at the C-terminus: 70 amino acids of ICAD-L are replaced by 4 different amino acids in ICAD-S. We previously showed that both transfected and endogenous ICAD-L are nuclear; however, the localization of ICAD and CAD remains controversial and an important issue to clarify. Here we present the evidence that ICAD-L is nuclear due to the presence of an autonomous nuclear localization signal located in the C-terminal 20 amino acids. This NLS is missing from ICAD-S, which is distributed throughout the cell. We also showed that a GFP:CAD fusion protein is located in the nucleus of transfected cells.     

The meaning of the genetic code: reconstruction of the stage of prebiologic evolution

According to a certain order in sets of the two first codon bases, 20 common amino acids can be divided into 5 families each containing 4 amino acids; the corresponding order in the distribution of codon bases can be easily detected, if common amino acids are distributed for the numbers of hydrogen atoms per molecule (Sukhodolets, 1980). In the present paper, the order in the distribution of codon bases is explained on the basis of the hypothesis claiming the prebiological existence of crystalline associates composed of amino acids and bases as free molecules. In these heterogeneous crystalline associates amino acids were analogs to the base douplets and the arrangement of molecules followed a certain rule, namely: 40 protons per molecular complex forming a standard structural compartment. It is proposed that the crystalline associates existed as lyotropic liquid crystals with hydrocarbons as solvent. The genetical code allows to discover two different original crystallization types for bases and amino acids. Therefore, the life possibly originates from combining in the same structure different crystallization patterns, which resulted in formation of a finite crystalline associate.     

Transfer of Asymmetry between Proteinogenic Amino Acids under Harsh Conditions

The heating above 400 °C of serine, cysteine, selenocysteine and threonine leads to a complete decomposition of the amino acids and to the formation in low yields of alanine for the three formers and of 2-aminobutyric acid for the latter. At higher temperature, this amino acid is observed only when sublimable α-alkyl-α-amino acids are present, and with an enantiomeric excess dependent on several parameters. Enantiopure or enantioenriched Ser, Cys, Sel or Thr is not able to transmit its enantiomeric excess to the amino acid formed during its decomposition. The presence during the sublimation-decomposition of enantioenriched valine or isoleucine leads to the enantioenrichment of all sublimable amino acids independently of the presence of many decomposition products coming from the unstable derivative. All these studies give information on a potentially prebiotic key-reaction of abiotic transformations between α-amino acids and their evolution to homochirality.     

Different ubiquitin signals act at the Golgi and plasma membrane to direct GAP1 trafficking

The high capacity general amino acid permease, Gap1p, in Saccharomyces cerevisiae is distributed between the plasma membrane and internal compartments according to availability of amino acids. When internal amino acid levels are low, Gap1p is localized to the plasma membrane where it imports available amino acids from the medium. When sufficient amino acids are imported, Gap1p at the plasma membrane is endocytosed and newly synthesized Gap1p is delivered to the vacuole; both sorting steps require Gap1p ubiquitination. Although it has been suggested that identical trans-acting factors and Gap1p ubiquitin acceptor sites are involved in both processes, we define unique requirements for each of the ubiquitin-mediated sorting steps involved in delivery of Gap1p to the vacuole upon amino acid addition. Our finding that distinct ubiquitin-mediated sorting steps employ unique trans-acting factors, ubiquitination sites on Gap1p, and types of ubiquitination demonstrates a previously unrecognized level of specificity in ubiquitin-mediated protein sorting.     

C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes

Phenotypic convergence is a widespread and well-recognized evolutionary phenomenon. However, the responsible molecular mechanisms remain often unknown mainly because the genes involved are not identified. A well-known example of physiological convergence is the C4 photosynthetic pathway, which evolved independently more than 45 times [1]. Here, we address the question of the molecular bases of the C4 convergent phenotypes in grasses (Poaceae) by reconstructing the evolutionary history of genes encoding a C4 key enzyme, the phosphoenolpyruvate carboxylase (PEPC). PEPC genes belong to a multigene family encoding distinct isoforms of which only one is involved in C4 photosynthesis [2]. By using phylogenetic analyses, we showed that grass C4 PEPCs appeared at least eight times independently from the same non-C4 PEPC. Twenty-one amino acids evolved under positive selection and converged to similar or identical amino acids in most of the grass C4 PEPC lineages. This is the first record of such a high level of molecular convergent evolution, illustrating the repeatability of evolution. These amino acids were responsible for a strong phylogenetic bias grouping all C4 PEPCs together. The C4-specific amino acids detected must be essential for C4 PEPC enzymatic characteristics, and their identification opens new avenues for the engineering of the C4 pathway in crops.     

Requirement for lysosomal localization of mTOR for its activation differs between leucine and other amino acids

The mammalian target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth and metabolism. It controls many cell functions by integrating nutrient availability and growth factor signals. Amino acids, and in particular leucine, are among the main positive regulators of mTORC1 signaling. The current model for the regulation of mTORC1 by amino acids involves the movement of mTOR to the lysosome mediated by the Rag-GTPases. Here, we have examined the control of mTORC1 signaling and mTOR localization by amino acids and leucine in serum-fed cells, because both serum growth factors (or, e.g., insulin) and amino acids are required for full activation of mTORC1 signaling. We demonstrate that mTORC1 activity does not closely correlate with the lysosomal localization of mTOR. In particular, leucine controls mTORC1 activity without any detectable modification of the lysosomal localization of mTOR, indicating that the signal(s) exerted by leucine is likely distinct from those exerted by other amino acids. In addition, knock-down of the Rag-GTPases attenuated the inhibitory effect of amino acid- or leucine-starvation on the phosphorylation of mTORC1 targets. Furthermore, data from cells where Rag expression has been knocked down revealed that leucine can promote mTORC1 signaling independently of the lysosomal localization of mTOR. Our data complement existing models for the regulation of mTORC1 by amino acids and provide new insights into this important topic.     

Genetic incorporation of unnatural amino acids into proteins in mammalian cells

We developed a general approach that allows unnatural amino acids with diverse physicochemical and biological properties to be genetically encoded in mammalian cells. A mutant Escherichia coli aminoacyl-tRNA synthetase (aaRS) is first evolved in yeast to selectively aminoacylate its tRNA with the unnatural amino acid of interest. This mutant aaRS together with an amber suppressor tRNA from Bacillus stearothermophilus is then used to site-specifically incorporate the unnatural amino acid into a protein in mammalian cells in response to an amber nonsense codon. We independently incorporated six unnatural amino acids into GFP expressed in CHO cells with efficiencies up to 1 mug protein per 2 x 10(7) cells; mass spectrometry confirmed a high translational fidelity for the unnatural amino acid. This methodology should facilitate the introduction of biological probes into proteins for cellular studies and may ultimately facilitate the synthesis of therapeutic proteins containing unnatural amino acids in mammalian cells.