Amino Acid Transport in Pseudomonas aeruginosa

Properties of the transport systems for amino acids in Pseudomonas aeruginosa were investigated. Exogenous (14)C-labeled amino acids were shown to equilibrate with the internal native amino acid pool prior to incorporation into protein. When added at low external concentrations, the majority of the amino acids examined entered the protein of the cell unaltered. The rates of amino acid transport, established at low concentrations with 18 commonly occurring amino acids, varied as much as 40-fold. The transport process became saturated at high external amino acid concentrations, was temperature-sensitive, and was inhibited by sodium azide and iodoacetamide. Intracellular to extracellular amino acid ratios of 100- to 300-fold were maintained during exponential growth of the population in a glucose minimal medium. When the medium became depleted of glucose, neither extracellular nor intracellular amino acids could be detected.     

Amino acid propensities are position-dependent throughout the length of alpha-helices

The 20 commonly occurring amino acids have been shown to have distinct position-dependent, helix-forming propensities near the ends of alpha-helices. Here, we show that the amino acids also have very strong position-dependent propensities throughout the length of a helix. Most helices are amphiphilic, and they have a strong tendency to both begin and end on the solvent-inaccessible face of the helix. These position-specific propensities should provide valuable parameters to guide de novo protein design, and should allow more precise prediction of helical topology in natural proteins.     

Light-activated amino acid transport in Halobacterium halobium envelope vesicles.

Vesicles prepared from Halobacterium halobium cell envelopes accumulate amino acids in response to light-induced electrical and chemical gradients. Nineteen of 20 commonly occurring amino acids have been shown to be actively accumulated by these vesicles in response to illumination or in response to an artificially created Na-gradient. Sodium-activated amino acid transport for 18 of these amino acids has been shown to occur in direct response to the protonmotive force generated. Glutamate is transported only in response to a sodium gradient. Michaelis constants for the uptake of these amino acids are close or identical whether the amino acids are accumulated in response to a sodium gradient or a protonmotive force (i.e., electrical gradient). On the basis of shared common carriers the transport systems can be divided into eight classes, each responsible for the transport of one or several amino acids, i.e., arginine, lysine, histidine; asparagine, glutamine; alanine, glycine, threonine, serine; leucine, valine, isoleucine, methionine; phenylalanine, tyrosine, tryptophan; aspartate; glutamate; proline. Available evidence suggests that these carriers are symmetrical in that amino acids can be transported equally well in both directions across the vesicle membranes. A tentative working model to account for these observations is presented.     

High-sensitivity amino acid analysis: methodology for the determination of amino acid compositions with less than 100 picomoles of peptides

Highly sensitive methodology is described for the determination of amino acid compositions of picomole quantities of peptides using an automated fluorescence amino acid analyzer with o-phthalaldehyde as the detection agent. All commonly occurring amino acids, including cystine, proline, and tryptophan, can be quantitated. High sensitivity is primarily achieved by using simple procedures which effectively and reliably reduce the level of interfering contamination present in buffers and reagents or introduced during sample handling. Accurate and reproducible amino acid compositions are obtained with 50 pmol or less peptide.     

Ontogenetic Changes in the Alcohol-soluble Amino Acid Fraction of the Grain, Leaves and Roots of Triticum aestivum (var. Rideau) Following Vernalization and Seedling Growth

Changes in the free alcohol-soluble amino acid fraction of theseparate organs of Rideau wheat (Triticum aestivum L.) preconditionedby vernalization were determined after 1 and 3 weeks' growthand compared with comparable organs of non-vernalized controlplants. The major components of the fraction were composed of the acidicand neutral amino acids together with asparagine and glutamine.Cystine and methionine were rarely present in more than traceamounts. Changes coincident with ontogency and growth varied considerablyboth between all seedling parts and between comparable organsof the control and vernalized series. Generally, vernalizationwas paralleled by higher levels of the acidic amino acids andthe amides. Coleoptile senescence was characterized by depletionof the total fraction but individual amino acids increased withageing. The pattern of change varied with ontogeny, age andprior grain treatment. However, within each category significantvariations in the level of one or more amino acids could berelated to the physiological status of the tissue. The amides,glutamine and asparagine were consistently absent from the stemapex and the very young fifth and sixth leaves. In stem apextissue, 17 of the commonly occurring amino acids were generallyfound present while, in coleoptiles and young leaves only eightamino acids were present.     

Influence of Carbon or Nitrogen Starvation on Amino Acid Transport in Pseudomonas aeruginosa

Pseudomonas aeruginosa was shown to utilize the majority of commonly occurring amino acids for growth as either the sole carbon or the sole nitrogen source. During carbon or nitrogen deprivation, the rates of transport of most of the amino acids remained unchanged; however, the transport rates for glutamate, alanine, and glycine increased under these conditions and the transport rates for leucine and valine decreased. Normal transport rates for these amino acids were resumed immediately upon the addition of the required nutrient. In the absence of an external source of carbon or of nitrogen, pool amino acids underwent rapid degradation. (14)C-Amino acid pulse experiments indicated that the constitutive amino acid catabolic enzymes, normally present in the organism during growth with glucose as the carbon source, were responsible for rapid pool losses. Nutrient starvation in the presence of chloramphenicol did not prevent amino acid catabolism. This enzymic activity is interpreted as providing P. aeruginosa with a selective advantage for survival during conditions of carbon or nitrogen starvation.     

Total plasma homocysteine as part of the routine aminogram by ion-exchange chromatography

Summary Ion-exchange chromatography (IEC) with ninhydrin post-column derivatisation is the only technique available for the assay of total, (free plus bound), cysteine and homocysteine which also enables the routine measurement of all other commonly occurring amino acids. IEC assay of total cysteine and homocysteine typically involves incubating buffered plasma for 60 minutes at 37°C with dithiothreitol (DTT), but these assay conditions significantly extend total analysis time and compromise other amino acid values, notably glutamine and glutamate. However, it is possible to carry out the DTT reduction in plasma virtually instantaneously and without additional buffering, thus preserving the integrity of other diagnostically important amino acids. Assay precision is adequate for cardiovascular risk assessment.     

The independent distribution of amino acid near neighbor pairs into polypeptides

With the assumption that individual amino acids are independently distributed into naturally occurring polypeptide chains, it is shown that amino acid pairs with 0–2 arbitrary intervening residues are also independently distributed, with a few possible exceptions. This is not true of N- and C-terminal amino acids.     

Studies on the coupling rates in liquid-phase peptide synthesis using competition experiments.

Competition experiments were carried out in order to determine relative reaction rates, Vrel, for the peptide-forming step. Using the liquid-phase method of peptide synthesis a model system was developed to investigate the influence of coupling method, amino component, derivatization and solvent upon Vrel. According to a standard procedure, Vrel for all 20 commonly occurring amino acids were established. A strong dependence of Vrel upon steric effects of the coupling components was found. The data obtained may serve as a guideline for optimizing the reaction conditions in peptide synthesis.     

A simple, sensitive radiomicroassay for 5'-nucleotidase

The reagent 9,10-phenanthrenequinone has been shown to react with free arginine or with arginine residues within proteins to produce a compound whose fluorescence can be used to quantitatively determine submicrogram amounts of arginine. The assay procedure, which is simple, convenient, and suitable for automation, is performed by mixing a slight excess of phenanthrenequinone with the sample at high pH followed by acidification to produce the fluorescence. None of the commonly occurring amino acids were found to interfere with the analysis. Several commonly used buffers and organic solvents also did not interfere. The arginine content of intact proteins was accurately determined by this procedure with only microgram quantities of protein required. The method is compared with other commonly used procedures for arginine and protein determination.     

Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation

During protein evolution, amino acids change due to a combination of functional constraints and genetic drift. Proteins frequently contain pairs of amino acids that appear to change together (covariation). Analysis of covariation from naturally occurring sets of orthologs cannot distinguish between residue pairs retained by functional requirements of the protein and those pairs existing due to changes along a common evolutionary path. Here, we have separated the two types of covariation by independently recombining every naturally occurring amino acid variant within a set of 15 subtilisin orthologs. Our analysis shows that in this family of subtilisin orthologs, almost all possible pairwise combinations of amino acids can coexist. This suggests that amino acid covariation found in the subtilisin orthologs is almost entirely due to common ancestral origin of the changes rather than functional constraints. We conclude that naturally occurring sequence diversity can be used to identify positions that can vary independently without destroying protein function.     

The mechanisms of amino acids synthesis by high temperature shock-waves

The mechanisms of amino acids syntheses behind high temperature shock-waves were elucidated and distinction was made between the steps occurring in the gas phase and those occurring in solution. In the presence of water vapor, aldehydes and NCN are formed separately in regions of different temperatures along the reacting gas. The aldehydes and ammonia condense to aldimines which add HCN to form α-amino nitriles, all in the gas phase. The hydrolysis to amino acids takes place in solution. In the absence of water vapor, aldimines and NCN are formed in the gas phase but condense to α-amino nitriles only in solution. A fair amount of oxygen only lowers the production of amino acids, which consequently could still be produced in the presence of oxygen in the Earth's primitive atmosphere. The waterless mechanism can operate in the Jovian atmosphere and supply it with ample amounts of amino acids, especially aspartic.     

The mechanisms of amino acids synthesis by high temperature shock-waves.

The mechanisms of amino acids synthesis behind high temperature shock-waves were elucidated and distinction was made between the steps occurring in the gas phase and those occurring in solution. In the presence of water vapor, aldehydes and HCN are formed separately in regions of different temperatures along the reacting gas. The aldehydes and ammonia condense to aldimines which add HCN to form alpha-amino nitriles, all in the gas phase. The hydrolysis to amino acids takes place in solution. In the absence of water vapor, aldimines and HCN are formed in the gas phase but condense to alpha-amino nitriles only in solution. A fair amount of oxygen only lowers the production of amino acids, which consequently could be still produced in the presence of oxygen in the Earth's primitive atmoshere. The waterless mechanism can operate in the Jovian atmosphere and supply it with ample amounts of amino acids, especially aspartic.     

The triplet genetic code had a doublet predecessor

Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and anticodons GNN. Evidence for this scenario is presented based on the properties of aminoacyl-tRNA synthetases, amino acids and nucleotide bases.     

Computational protein design with explicit consideration of surface hydrophobic patches

De novo protein design requires the identification of amino-acid sequences that favor the target-folded conformation and are soluble in water. One strategy for promoting solubility is to disallow hydrophobic residues on the protein surface during design. However, naturally occurring proteins often have hydrophobic amino acids on their surface that contribute to protein stability via the partial burial of hydrophobic surface area or play a key role in the formation of protein-protein interactions. A less restrictive approach for surface design that is used by the modeling program Rosetta is to parameterize the energy function so that the number of hydrophobic amino acids designed on the protein surface is similar to what is observed in naturally occurring monomeric proteins. Previous studies with Rosetta have shown that this limits surface hydrophobics to the naturally occurring frequency (～28%), but that it does not prevent the formation of hydrophobic patches that are considerably larger than those observed in naturally occurring proteins. Here, we describe a new score term that explicitly detects and penalizes the formation of hydrophobic patches during computational protein design. With the new term, we are able to design protein surfaces that include hydrophobic amino acids at naturally occurring frequencies, but do not have large hydrophobic patches. By adjusting the strength of the new score term, the emphasis of surface redesigns can be switched between maintaining solubility and maximizing folding free energy.     

Analysis of phenylthiohydantoin amino acid mixtures for sequencing by thermospray liquid chromatography/mass spectrometry

Phenylthiohydantoin (PTH) amino acids, the derivatives of amino acids liberated in the course of automated N-terminal sequence analysis of peptides and proteins, are most commonly identified by high-performance liquid chromatography. This communication describes an extension to the methodology for PTH amino acid identification which exploits thermospray liquid chromatography/mass spectrometry for use in the confirmation of PTH amino acid identifications previously made solely on the basis of retention times. Thermospray mass spectra of the 19 synthetic PTH amino acids corresponding to the residues commonly observed during N-terminal sequencing have been acquired. These spectra show strong signals for the protonated molecular ion, accompanied in several cases by ions produced by limited fragmentation of the amino acid side chain and/or the PTH ring system. A reverse-phase separation protocol has been adapted for use with thermospray. The method permits recognition of the protonated molecular ions of all the standard PTH amino acids at the 150-pmol level on the basis of signal-to-noise ratios of 10:1 or better with full scanning. The method has been tested on the N-terminal amino acid sequence analysis of 200 pmol of the standard protein beta-lactoglobulin A, and has been found useful in the study of selected side-products of the sequencing chemistry.     

Amino acid composition of the lymph and blood in allergic transformations of the body

The time-course of changes in the content of free amino acids and total protein in lymph of the thoracic duct and peripheral blood was studied in dogs during sensitization and anaphylactic shock (AS). Allergic rearrangement of the body during AS was accompanied by considerable disorders in redistribution of free amino acids in body fluids (blood, interstitial fluid and lymph). It is assumed that changes in the quantitative ratios occurring between individual amino acids during metabolic processes under sensitization are likely to cause protein biosynthesis disorders in the body experiencing allergic rearrangement.     

An automatic analyzer for the specific determination of amino sugars

The techniques previously employed for the extraction and determination of amino acids from different matrices are not necessarily optimal for the determination of the amino sugars. An analytical system is described which is a hybrid between the conventional amino acid analyzer and the liquid chromatographic system for the detection of reducing sugars. The major, naturally occurring amino sugars are separated in about 40 min, with sensitivites lying under the nanomole range, without interference from other co-extracted compounds such as amino acids and sugars. The reagent employed is noncorrosive and stable over long periods of time. The amino sugar analyzer can be readily constructed by simple modification of a conventional phenylketonuria or amino acid analyzer.     

Isolation and partial characterization of a 700 kilodalton human colon carcinoma associated antigen

An antigen of high molecular weight (CA-3) was isolated from the cytosol fraction of GW-39 human colon tumor cells by antibody affinity chromatography. CA-3 was characterized by an acidic pI value of 4.5-4.9, a molecular weight of 700 kilodaltons and a sedimentation coefficient of 13S. It contained all of the commonly occurring amino acids and had an acidic to basic amino acid ratio of 1.4. CA-3 was resistant to dissociation by reducing agents as well as by sodium dodecylsulfate. Quantitation of CA-3 by a radioimmunoassay employing rabbit anti-CA-3 antiserum revealed a marked elevation of CA-3 in the cytosol extracts of human primary colon carcinoma in comparison to normal colon. The molecular properties of CA-3 are compared to those of carcinoembryonic antigen, high molecular weight colon specific antigen CSAp and two other high molecular weight proteins, fibronectin and conglutinin. Colon antigen CA-3 appears to be different from these other molecules in terms of its molecular weight, sedimentation value, isoelectric point and amino acid composition.     

A possible molecular metric for biological evolvability

Proteins manifest themselves as phenotypic traits, retained or lost in living systems via evolutionary pressures. Simply put, survival is essentially the ability of a living system to synthesize a functional protein that allows for a response to environmental perturbations (adaptation). Loss of functional proteins leads to extinction. Currently there are no universally applicable quantitative metrics at the molecular level for either measuring 'evolvability' of life or for assessing the conditions under which a living system would go extinct and why. In this work, we show emergence of the first such metric by utilizing the recently discovered stoichiometric margin of life for all known naturally occurring (and functional) proteins. The constraint of having well-defined stoichiometries of the 20 amino acids in naturally occurring protein sequences requires utilization of the full scope of degeneracy in the genetic code, i.e. usage of all codons coding for an amino acid, by only 11 of the 20 amino acids. This shows that the non-availability of individual codons for these 11 amino acids would disturb the fine stoichiometric balance resulting in non-functional proteins and hence extinction. Remarkably, these amino acids are found in close proximity of any given amino acid in the backbones of thousands of known crystal structures of folded proteins. On the other hand, stoichiometry of the remaining 9 amino acids, found to be farther/distal from any given amino acid in backbones of folded proteins, is maintained independent of the number of codons available to synthesize them, thereby providing some robustness and hence survivability.