Partial atomic charges of amino acids in proteins

Using a semiempirical quantum mechanical procedure (FCPAC) we have calculated the partial atomic charges of amino acids from 494 high-resolution protein structures. To analyze the influence of the protein's environment, we considered each residue under two conditions: either as the center of a tripeptide with PDB structure geometry (free) or as the center of 13-16 amino acid clusters extracted from the PDB structure (buried). The partial atomic charges from residues in helices and in sheets were separated. The FCPAC partial atomic charges of the Cbeta and Calpha of most residues correlate with their helix propensity, positively for Cbeta and negatively for Calpha (r2 = 0.76 and 0.6, respectively). The main consequence of burying residues in proteins is the polarization of the backbone C=O bond, which is more pronounced in helices than in sheets. The average shift of the oxygen partial charges that results from burying is -0.120 in helix and -0.084 in sheet with the charge of the proton as unit. Linear correlations are found between the average NMR chemical shifts and the average FCPAC partial charges of Calpha (r2 = 0.8-0.85), N (r3 = 0.67-0.72), and Cbeta (r2 = 0.62) atoms. Correlations for helix and beta-sheet FCPAC partial charges show parallel regressions, suggesting that the charge variations due to burying in proteins differentiate between the dihedral angle effects and the polarization of backbone atoms.     

Changes in carbohydrates,amino acids and proteins in developing seed of chickpea

Developing seeds of chickpea cultivars G-130, L-550 and 850-3/27 grown under field conditions were sampled at different stages of maturity and analysed for soluble sugars, starch, soluble nitrogen, protein nitrogen and amino acids. Fr. wt of seeds of all three cultivars decreased after 28 days of flowering while the dry wt continued to increase. Rapid starch accumulation was observed between 14 and 28 days after flowering. Starch as per cent of seed dry wt started to decrease after 28 days, while starch per seed increased till maturity. The percentage of salt-soluble proteins decreased with maturation of seed. The electrophoretic pattern revealed that deposition of seed storage protein in cotyledons occurred 14 days after flowering. Most of the biochemical activity apparently occurred between 14 and 28 days after flowering.     

Changes in brain temperature and free amino acids in normal and protein deprived suckling rats exposed to room temperature

Previous reports on early-induced protein-calorie malnutrition (PCM) in rats have indicated alterations in the concentration of free amino acids and of protein synthesis in the brain. Recently it was shown that early-induced protein deprivation (PD) retards the development of thermoregulation. This resulted in a failure to maintain a normal rectal temperature after short exposure to room temperature (+22°C) still at the age of 20–25 days corresponding to changes seen in normal rats at an age of 10–15 days. In the present study, 20-day old PD and normal rats where examined with regard to the effect of exposure to room temperature on brain temperature and on brain free amino acids. The results show a similar reduction in brain and rectal temperature of the PD rats occuring within 30 minutes after exposure to room temperature. The reduction was in the range of 5°C. PD rats kept in room temperature for 5 hours and then allowed to recover at 32.5°C showed a slow increase in brain and rectal temperature but normal temperatures were not reached even after 1 hour. The concentration of free amino acids in the brain was examined in rats kept for 1 hour at room temperature or at 32.5°C. In the PD rats kept at 32.5°C, free aspartate and glutamate were reduced whereas taurine, GABA and glycine were increased as compared to their corresponding control rats. As a result of the reduced brain temperature in PD rats exposed to room temperature there was a reduction in free asparagine. The lability of the pool of asparagine may be related to the low levels of aspartate and glutamate in PD rats. On the basis of the present findings it is recommended that temperature-sensitive parameters are examined in PCM rats at a normal body temperature.Special Issue dedicated to Prof. Holger Hydén     

Photoacoustic spectroscopy of aromatic amino acids in proteins

This paper concerns the use of photoacoustic spectroscopy (PAS) to study the presence of aromatic amino acid in proteins. We examined the aromatic amino acids in six proteins with well-known structures using absorption spectra of near ultraviolet PAS over the wavelength range 240–320 nm. The fundamental understanding of the physical and chemical properties that govern the absorption of light and a subsequent release of heat to generate a transient pressure wave was used to test the concept of monitoring aromatic amino acids with this method. Second derivative spectroscopy in the ultraviolet region of proteins was also used to study the regions surrounding the aromatics and the percentage area in each band was related in order to determine the contribution in function of the respective molar extinction coefficients for each residue. Further investigation was conducted into the interaction between sodium dodecyl sulphate (SDS) and bothropstoxin-I (BthTx-I), with the purpose of identifying the aromatics that participate in the interaction. The clear changes in the second derivative and curve-fitting procedures suggest that initial SDS binding to the tryptophan located in the dimer interface and above 10 SDS an increased intensity between 260 and 320 nm, demonstrating that the more widespread tyrosine and phenylalanine residues contribute to the SDS/BthTx-I interactions. These results demonstrate the potential of near UV-PAS for the investigation of membrane proteins/detergent complexes in which light scattering is significant.     

Correlations of amino acids in proteins

A correlation analysis among 20 amino acids is performed for four protein structural classes (, β, /β, and +β) in a total of 204 proteins. The correlation relationships among amino acids can be classified into the following four types: (1) strong positive correlation, (2) strong negative correlation, (3) weak correlation, and (4) no correlation. The correlation relationships are different for different proteins and are correlated with the features of their structural classes. The amino acids with the weak correlation relationship can be treated as the independent basis functions for the space where proteins are defined. The amino acids with large correlation coefficients are linear correlative with each other and they are not independent. The strong correlation among amino acids reflects their mutual constrained relationship, as exhibited by their relevant structural features. The information obtained through the correlation analysis is used for predicting protein structural classes and a better prediction quality is obtained than that by the simple geometry distance methods without taking into account the correlation effects.     

Changes with aging in the levels of amino acids in rat CNS structural elements II. Taurine and small neutral amino acids

Taurine (Tau) and the small neutral amino acids glycine (Gly), serine (Ser), threonine (Thr), and alanine (Ala) were measured in 53 brain areas of 3- and 29-month-old male Fisher 344 rats. The ratio of highest to lowest level was 34 for Tau, 9.1 for Thr, 7.6 for Gly and Ser, and 6.5 for Ala. The heterogeneity was found in numerous areas; for example, Tau levels were more than 90 nmol/mg protein in 6 areas, and less than 20 nmol/mg protein in 10 areas. Similar heterogeneity was found with the other amino acids. The relative distribution of the small neutral amino acids showed several similarities; Tau distribution was different. With age, four amino acids decreased in 10–18 areas, and increased in only 1–3, while Thr increased in more areas than it decreased. The five amino acids of this paper, and the four of the previous paper, are among the amino acids at highest level in the brain; the sequence in their levels shows considerable regional heterogeneity.     

Selenium containing amino acids and proteins in marine algae

The unicellular marine algae, Dunaliella primolecta Butcher, Chlorella sp. and Porphyridium cruentum (S.F. Grey) were grown in artificial sea water containing a sublethal concentration of selenite, 10^?2 g Se/1. Both free-and protein-bound seleno-amino acids were identified. The initial steps of selenium incorporation seem to involve the use of the sulfur enzymatic machinery resulting in the replacement of some of the sulfur by selenium in both free amino acids and proteins. At relatively low selenium concentrations, selenium-specific enzymes seem to be in operation.     

The contribution from the choroid plexus and the periventricular CNS to amino acids and proteins in the human CSF

During neurosurgery the freshly secreted extracellular fluid (ECF) from the choroid plexus was sampled with small pieces of application paper in three patients with intractable epilepsy. The samples were analyzed for free amino acids and for soluble proteins. The results were compared with corresponding data on extracellular fluid from the brain surface obtained with dialysis-perfusion as well as with the cerebrospinal fluid (CSF) acquired by lumbar punction. The dialysis data were calibrated against the paper results. The choroid plexus secretion had a high concentration of transthyretin as well as of an unidentified protein with an isoelectric point of 7.4. The cortical ECF exhibited high concentrations of tau-globulin and gamma-trace protein. Among the amino acids, glutamine had lower concentration in the choroid plexus secretion and higher concentrations in the ECF of the brain compared to the CSF. The amino acid derivative ethanolamine exhibited a similar pattern. This was interpreted to demonstrate that these compounds enter the CSF from the brain tissue. In contrast, alanine, serine, and taurine had a lower concentration in the CSF than in the plexus secretion which suggests that they are removed from the CSF by brain tissue.     

Analysis of the interactions of sulfur‐containing amino acids in membrane proteins

The interactions of Met and Cys with other amino acid side chains have received little attention, in contrast to aromatic–aromatic, aromatic–aliphatic or/and aliphatic–aliphatic interactions. Precisely, these are the only amino acids that contain a sulfur atom, which is highly polarizable and, thus, likely to participate in strong Van der Waals interactions. Analysis of the interactions present in membrane protein crystal structures, together with the characterization of their strength in small‐molecule model systems at the ab‐initio level, predicts that Met–Met interactions are stronger than Met–Cys ≈ Met–Phe ≈ Cys–Phe interactions, stronger than Phe–Phe ≈ Phe–Leu interactions, stronger than the Met–Leu interaction, and stronger than Leu–Leu ≈ Cys–Leu interactions. These results show that sulfur‐containing amino acids form stronger interactions than aromatic or aliphatic amino acids. Thus, these amino acids may provide additional driving forces for maintaining the 3D structure of membrane proteins and may provide functional specificity.     

Solid phase isotope exchange with spillover hydrogen in amino acids,peptides, and proteins

We summarize here information on the theoretical and experimental study of high-temperature (150–200°C) solid phase catalytic isotope exchange (HSCIE) carried out with amino acids, peptides, and proteins under the action of spillover hydrogen. Main specific features of the HSCIE reaction, its mechanism, and its use for studying spatial interactions in polypeptides are discussed. A virtually complete absence of racemization makes this reaction a valuable preparative method. The main regularities of the HSCIE reaction with the participation of spillover tritium have been revealed in the case of peptides and proteins, and the dependence of reactivity of peptide fragments on the spatial organization of their molecules has been studied. An important peculiarity of this reaction is that HSCIE proceeds at 150–200°C with a high degree of chirality retention in amino acids and peptides. This is provided by its reaction mechanism, which consists in a synchronous one-center substitution at the saturated carbon atom characterized by the formation of pentacoordinated carbon and a three-center bond between the carbon and the incoming and outgoing hydrogen atoms.Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 1, 2005, pp. 3–21.Original Russian Text Copyright © 2005 by Zolotarev, Dadayan, Borisov.     

Changes with aging in the levels of amino acids in rat CNS structural elements I. Glutamate and related amino acids

Glutamate and related amino acids were determined in 53 discrete brain areas of 3-and 29-month-old male Fischer 344 rats microdissected with the punch technique. The levels of amino acids showed high regional variation-the ratio of the highest to lowest level was 9 for aspartate, 5 for glutamate, 6 for glutamine, and 21 for GABA. Several areas were found to have all four amino acids at very high or at very low level, but also some areas had some amino acids at high, others at low level. With age, in more than half of the areas, significant changes could be observed, decrease occurred 5 times more frequently than increase. Changes occurred more often in levels of aspartate and GABA than in those of glutamate or glutamine. The regional levels of glutamate and its related amino acids show severalfold variations, with the levels tending to decrease in the aged brain.     

Free and bound amino acids and proteins in developing grains of rice with enhanced lysine/proteins

 Free amino acids were determined in developing seed of a rice mutant with enhanced grain lysine. This phenotype frequently has enhanced protein. Some free amino acids of developing seed are inversely related to the level of total amino acids in proteins of the mature grain. Amino acids that were enhanced in protein, including aspartic acid, threonine, methionine and lysine, were notably lower in the free amino-acid pool. Our conclusion is that mutant-developing grains process aspartate amino acids more rapidly than the controls. Conversely, arginine, valine and glutamic acid/glutamine accumulate as free amino acids with mutant/control ratios of 1.39, 1.29 and 1.12, respectively. Glutamic acid/glutamine in proteins of mature seeds is lower in the mutant than the control. ³H-lysine incorporation showed enhanced isotope incorporation into at least four proteins. One mutant protein was less actively labelled than analogous controls. The ³Hlysine pattern indicates processing modifications in this useful rice mutant. Received: 14 October 1996/Accepted: 8 November 1996     

Free amino acids in Japanese eel eggs obtained by hormonal inducement

Restriction proteolysis of the yolk proteins during the final oocyte maturation appears to result in the low content of free amino acids (FAA) and the unique FAA profile in Japanese eel Anguilla japonica eggs obtained by hormonal inducement.     

Studies on the mechanism of induction of hypercholesterolemia in rabbits by high dietary levels of amino acids

Increasing the proportion of an amino acid mixture corresponding to casein in a low-fat, cholesterol-free, semipurified diet fed to rabbits causes a progressive increase in serum total and low density lipoprotein cholesterol, and the effect appears to be due primarily to the essential amino acids in the mixture. Our recent studies have also shown that the variations in serum cholesterol in response to different levels of the amino acid mixture are not associated with any changes in fecal excretion of cholesterol or bile acids. Further attempts to understand the mechanism of action of dietary amino acids on serum cholesterol levels have shown the following: (1) no correlation with levels of plasma amino acids, either in the fasting or postprandial state: (2) no correlation with serum levels of thyroid hormones: (3) no relationship to activity of hepatic or intestinal microsomal hydroxymethylglutaryl coenzyme A reductase: (4) no corresponding effects on the activities of cholesterol esterifying enzymes of intestinal mucosa: and (5) no correlation with the degree of esterification of cholesterol in very low or low density lipoproteins. Further studies are required to identify the specific amino acids responsible for the hypercholesterolemic effects and to determine the mechanisms involved.     

Heterogeneous distribution of functionally important amino acids in brain areas of adult and aging humans

The regional distribution of seven amino acids thought to have inhibitory neurotransmitter or neurotransmitter precursor function—GABA, glycine, taurine, serine, threonine, phenylalanine, and tyrosine—was determined in 52 discrete areas from brain of adult and old humans. Significant heterogeneity was found, with 3- to 16-fold differences in levels in the various regions analyzed. The patterns of distribution were somewhat different from those in the adult or old rat brain. Relatively few changes were seen in old brain. Heterogeneity in distribution has to be taken into account in assessing physiological changes in amino acid levels and metabolism.Special issue dedicated to Dr. Claude Baxter.     

Study of the resolution of amino acids and aminoalcohols in organic solvents

Summary The enzymatic resolution of racemic phenylglycine, phenylglycinol and phenylalaninol has been studied in organic solvents under a variety of experimental conditions. Subtilisin in 3-methyl-3-pentanol was effective for the resolution of phenylglycine esters, via N-acylation with trifluoroethyl butyrate. Porcine pancreatic lipase in ethyl acetate gave satisfactory results in the resolution of phenylglycinol and phenylalaninol; the or position of the phenyl group was found to influence both the rate and the chemioselectivity of the reaction.     

Changes in growth,proteins and free amino acids of developing seed and pod of fenugreek

The growth and development under field conditions of the pods and seeds of two cvs of Trigonella foenum graecum are described. Samples were harvested at different stages of ripeness for the determination of dry matter, protein and free amino acid content. During maturation, reserves of solutes are established in the pod wall before the seeds begin their exponential phase of growth. Later, these reserves disappear, providing about 20% of the seed's requirements for nitrogen. SDS-electrophoresis was used to follow the formation of proteins and it was shown that the synthesis of storage proteins takes place prior to dehydration of the seed. Production soluble nitrogenous compounds precedes protein accumulation. Free amino acids follow the same pattern. 4-Hydroxyisoleucine represents nearly 80% of free amino acid of dry seeds. The concentration does not decrease in the later stages of maturation of the seed but this unusual amino acid is absent in the storage proteins of the seeds.     

Distribution patterns of palatal taste buds and their responses to amino acids in salmonids

The distribution pattern of the palatal taste buds and their electrical response characteristics to amino acids were studied in five salmonid species: Arctic grayling ( Thymallus arcticus ), lake whitefish ( Coregonus clupeaformis ), Atlantic salmon ( Salmo salar ), brown trout ( Salmo trutta ), and kokanee ( Oncorhynchus nerka ). In these fish the most dense taste bud populations were found on ridges in tine area around the palatine teeth. With the exception of lake whitefish, the ridges adjacent to the teeth on the head and shaft of the prevomer were also dense in taste buds, which appear to be largely responsible for amino acid detection. All species, except for lake whitefish, responded well to l -proline ( l -Pro) and l -α-amino- β -guanidinopropionic acid ( l -AGPA), with thresholds at 10⁻⁸-10⁻⁷ and 10⁻⁵-10⁻⁴ M, respectively. These species also responded to varying degrees to hydroxy- l -proline ( l -Hpr) and l -alanine ( l -Ala), believed to be agonists for l -Pro receptors. In addition, kokanee detected l -phenylalanine, l -leucine and betaine. Of six lake whitefish examined, only one specimen responded to l -Pro, l -AGPA and l -arginine. We concluded that in these five salmonid species l -Pro and l -AGPA receptors play a major role in amino acid gustation, and further proposed a hypothesis that salmonids may have initially evolved these two gustatory receptors. With phylogenetic advancement, they gained greater response capabilities by (1) acquiring new receptor types, and (2) by losing the specificity of existing receptors.     

Feeding pigs amino acids as protein-bound or in free form influences postprandial concentrations of amino acids,metabolites, and insulin

Dietary proteins need to be digested first while free amino acids (AAs) and small peptides are readily available for absorption and rapidly appear in the blood. The rapid postprandial appearance of dietary AA in the systemic circulation may result in inefficient AA utilisation for protein synthesis of peripheral tissues if other nutrients implicated in AA and protein metabolism are not available at the same time. The objective of this experiment was to compare the postprandial concentrations of plasma AA and other metabolites after the ingestion of a diet that provided AA either as proteins or as free AA and small peptides. Twenty-four male growing pigs (38.8 ± 2.67 kg) fitted with a jugular catheter were assigned to one of three diets that provided AA either in protein form (INT), free AA and small peptides (HYD), or as free AA (FAA). After an overnight fast and initial blood sampling, a small meal was given to each pig followed by serial blood collection for 360 min. Postprandial concentrations of plasma AA, glucose, insulin, and urea were then measured from the collected blood. Non-linear regression was used to summarise the postprandial plasma AA kinetics. Fasting concentrations of urea and some AA were higher (P < 0.05) while postprandial plasma insulin and glucose were lower (P < 0.01) for INT than for HYD and FAA. The area under the curve of plasma concentration after meal distribution was lower for INT for most AAs (P < 0.05), resulting in a flatter curve compared to HYD and FAA. This was the result of the slower appearance of dietary AA in the plasma when proteins are fed instead of free AA and small peptides. The flatter curve may also result from more AAs being metabolised by the intestine and liver when INT was fed. The metabolism of AA of the intestine and liver was higher for HYD than FAA. Providing AA as proteins or as free AA and small peptides affected the postprandial plasma kinetics of AA, urea, insulin, and glucose. Whether the flat kinetics when feeding proteins has a positive or negative effect on AA metabolism still needs to be explored.     

Effects of branched-chain amino acids on plasma amino acids in amyotrophic lateral sclerosis

Summary Although the cause of amyotrophic lateral sclerosis (ALS) remains unknown, biological findings suggest that the excitatory amino acid glutamate contributes to the pathogenesis of ALS. In previous studies of ALS, the therapeutic effect of the branched-chain amino acids (BCAAs) leucine, valine and isoleucine has been evaluated. The present study aimed at investigating the acute effect of BCAAs on plasma glutamate levels in ALS patients. Following two oral doses of BCAAs, significantly increased plasma levels were seen for valine (500%), isoleucine (1,377%) and leucine (927%), however the plasma level of glutamate was not affected. The plasma level of several other amino acids (tryptophan, tyrosine, phenylalanine and methionine) were found decreased after oral BCAAs, which may indicate a diminution in the rate of degradation of muscle protein and/or an increase in tissue disposal of amino acids.