Amino acids in interstitial waters from ODP Sites 126-790 and 126-791

Sites 790 and 791 lie in the eastern half graben of the Sumisu Rift, a backarc graben west of the active Izu-Bonin arc volcanoes Sumisu Jima and Tori Shima, at 30°54.96'N, 139°50.66'E, in 2223 m water depth and 30°54.97'N, 139°52.20'E, in 2268 m water depth, respectively. A small decrease in the sulfate concentration in the interstitial waters from these sites suggests fairly low microbial activity by sulfate-reducing bacteria. The values of the dissolved free amino acids (DFAA) in the interstitial waters from both sites range from 1.26 to 6.82 µmol/L, with an average of 3.81 µmol/L. The acidic, basic, neutral, aromatic, and sulfur-containing amino acids have average values of 0.32, 0.50, 2.71, 0.15, and 0.09 µmol/L, respectively. The relative abundances of the acidic, basic, neutral, aromatic, and sulfur-containing amino acids average 8, 13,72, 4, and 1 mol%, respectively. Glycine, serine, alanine, ornithine, and aspartic acid are major constituent amino acids. The dissolved combined amino acids (DCAA) values range between 1.25 and 44.35 µmol/L, with an average of 10.36 µmol/L. The mean concentrations and relative abundances of the acidic, basic, neutral, aromatic, and sulfur-containing amino acids are 2.29 (22 mol%), 0.60 (6 mol%), 6.70 (65 mol%), 0.09 (1 mol%), and 0.00 µmol/L (0 mol%), respectively. Glycine is the most abundant amino acid residue, followed by glutamic acid, serine, and alanine. The predominance of DCAA over DFAA present in the interstitial waters from Sites 790 and 791 is consistent with previous results from interstitial-water and seawater analyses. The most plausible source for the DCAA is biogenic calcareous debris. A much greater depletion of aspartic acid and the basic fraction, except for ornithine, is found in the DCAA. The decomposition of the basic amino acid fraction or its incorporation to clay minerals would result in a decrease in its relative abundance, whereas ornithine is produced during early diagenesis. The characteristics of the amino acids in the interstitial waters are (1) a greater depletion of the acidic amino acid fraction in the DFAA than in the DCAA and (2) the enrichment of glycine and serine in both. The adsorption or reaction of the amino acids in interstitial waters with biogenic carbonates would be responsible for the lower relative abundance of the acidic fraction of the DFAA. The production of glycine during early diagenesis and its stability in solution would raise its relative abundance in the interstitial waters.

Amino acids in the interstitial waters from ODP Hole 113-695A

Site 695 lies on the southeast margin of the South Orkney microcontinent on the northern margin of the Weddell Sea, at 62°23.48'S, 43°27.10'W in 1305 m water depth. The inorganic properties of interstitial waters at this site, including sulfate reduction, biogenic methane production, and high concentrations of ammonia and phosphate, imply high microbial activity. However, no clear relationship between amino acid composition and concentration and the type of microbial activity (e.g., sulfate reduction or methane production) can be identified. The THAA (total hydrolyzable amino acids) values range between 2.45 and 17.31 µmol/L, averaging 7.14 µmol/L. The mean concentrations and relative abundance values of acidic, basic, neutral, aromatic, and sulfur-containing amino acids are 1.34 (18%), 1.09 (15%), 3.93 (54%), 0.50 (8%), and 0.02 (0%) µmol/L, respectively. Glycine is the most abundant amino acid residue, with serine, glutamic acid, and ornithine next. The DFAA (dissolved free amino acids) values range from 0.10 to 12.73 µmol/L, averaging 4.07 µmol/L. The acidic, basic, neutral, aromatic, and sulfurcontaining amino acids are on average 0.21, 0.79, 2.56, 0.41, and 0.01 µmol/L, respectively. The relative abundances of acidic, basic, neutral, and aromatic amino acids average 4%, 18%, 58%, and 15%, respectively. Predominance of DFAA over DCAA (dissolved combined amino acids) in interstitial waters of Lithologic Units I and II is contrary to the predominance of DCAA over DFAA in other interstitial waters and seawater. The comparison of amino acid compositions between DCAA and siliceous plankton suggests that the DCAA in interstitial waters originally comes from amino acids derived from siliceous plankton. However, other sources which are much enriched in glutamic acid contribute to the DCAA composition.

Organic properties of sediments and amino acids in iterstitial waters of ODP Holes 111-677A and 111-678B

The basement at Ocean Drilling Program (ODP) Sites 677 and 678 originated from the Galapagos spreading center of the Costa Rica Rift and has moved about 200 km over the last 6 m.y. (Fig. 1) (Shipboard Scientific Party, 1987, 1988; Scientific Drilling Party, 1987). Sediments about 300 m thick cover basement so young that basal sediments at Sites 677 and 678 have been reheated up to 60?-70?C at Site 677 and altered to limestone and/or chert (Shipboard Scientific Party, 1988). Sediments from both sites indicate (1) a high sedimentation rate (about 48 m/m.y.) and (2) biogenic silica and carbonate as the main constituents of sediments (Table 1) (Shipboard Scientific Party, 1988). Heatflow observations and measurements of interstitial water chemistry around the sites show that Site 677 is in a lower heatflow zone (166 mW/m**2; 1°12.14'N, 83°44.22'W) whereas Site 678 is located in a zone of higher heat flow (250 mW/m**2; 1°13.01'N, 83°43.39'W) (Langseth et al., 1988; Shipboard Scientific Party, 1988). In the flank hydrothermal systems, circulating solution is moving upward through the sedimentary column in zones of higher heat flow while it is moving downward in zones of lower heat flow (Anderson and Skilbeck, 1981). The chemistry of the interstitial waters is modified by several processes such as (1) diagenetic reactions and (2) advective and (3) diffusive transports of dissolved constituents. Analyses of Ca2+ and Mg2+ in interstitial waters from Sites 677 and 678 show that their profiles are mainly controlled by advective transport (Shipboard Scientific Party, 1988). In contrast, the interstitial-water profiles for NH4+, Si, and PO4[3-] are highly affected by reactions in the sediments. Site 677 offers a good opportunity to investigate amino acids in the interstitial waters because sediments of similar compositions have been deposited at constant rates of sedimentation. There are few previous works on amino acid distributions in interstitial waters (Henrichs and Parrington, 1979; Michaelis et al., 1982; Henrichs et al., 1984; Henrichs and Farrington, 1987; Ishizuka et al., 1988). In this chapter, we report (1) Rock-Eval analysis and (2) the composition of total hydrolyzable and dissolved free amino acids (THAA and DFAA, respectively) in the interstitial waters. Our objectives are to discuss (1) the possible origin of organic materials, (2) the characteristics of THAA and DFAA, and (3) their relationships in interstitial waters.

Isoselenocyanates derived from Boc/Z-amino acids: synthesis, isolation,characterization, and application to the efficient synthesis of unsymmetrical selenoureas and selenoureidopeptidomimetics

Isoselenocyanates derived from Boc/Z-amino acids are prepared by the reaction of the corresponding isonitriles with selenium powder in presence of triethylamine at reflux. The utility of these new classes of isoselenocyanates in the preparation of selenoureidodipeptidomimetics possessing both amino as well as carboxy termini has been accomplished. The H-1 NMR analysis confirmed that the protocol involving the conversion of isonitriles to isoselenocyanates and their use as coupling agents in assembling selenour-eido derivatives is free from racemization. (C) 2010 Elsevier Ltd. All rights reserved.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Identification and determination of muscle's fatty acids and amino acids in Cobia and Indian squid

The present study aims to find the effect of freezing Time on the quality of Cobia (Rastrelliger kanagurta) and Indian Squid in commercial scale during freezing and subsequent frozen storage (−18◦C). Total time for freezing was significantly different (P<0.05) between the Cobia and Indian squid samples. The difference in the freezing time could be attributed to the varied quality of the 2 samples. Upon freezing, the moisture content decreased in Indian Squide samples compared to Cobia freezer where protein content decreased in both the samples. Upon freezing and during frozen storage, lipid oxidation products (peroxide value, and free fatty acid value) and volatile bases (total volatile base nitrogen) showed an increasing trend in both the samples with values slightly higher in Indian squid samples compared to cobia frozen samples. The total plate counts showed a significantly (P<0.05) decreasing trend in both the samples. K value did not show any significant (P<0.05) difference between the samples whereas the histamine formation was significantly (P<0.05) increased in Indian squid frozen samples compared to cobia samples. The taste and overall acceptability was significantly different (P<0.05) in cobia samples compared to Indian squid frozen samples on 5th month. Both samples were in acceptable condition up to 5 month but the Cobia frozen samples quality was slightly better than the air blast frozen samples.

Protection of DNA against low-energy electrons by amino acids: A first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.

Effect of plasma insulin and branched-chain amino acids on skeletal muscle protein synthesis in fasted lambs

The increase in fractional rate of protein synthesis (K-s) in the skeletal muscle of growing rats during the transition from fasted to fed state has been explained by the synergistic action of a rise in plasma insulin and branched-chain amino acids (BCAA). Since growing lambs Also exhibit an increase in K-s with level of feed intake, the objective of the present study was to determine if this synergistic relationship between insulin and BCAA also occurs in ruminant animals. Six 30 kg fasted (72 h) lambs (8 months of age) received each of four treatments, which were based on continuous infusion into the jugular vein for 6 h of: (1) saline (155 mmol NaCl/l); (2) a mixture of BCAA (0.778 mumol leucine, 0.640 mumol isoleucine and 0.693 mumol valine/min.kg); (3) 18.7 mumol glucose/min.kg (to induce endogenous insulin secretion): (4) co-infusion of BCAA and glucose. Within each period all animals received the same isotope of phenylalanine, (Phe) as follows: (1) L-[1-C-13]Phe; (2) L-phenyl-[ring H-2(5)]-alanine; (3) L-[N-15]Phe; (4) L-[ring 2,6-H-3]Phe. Blood was sampled serially during infusions to measure plasma concentrations of insulin, glucose and amino acids, and plasma free Phe isotopic activity; biopsies were taken 6 h after the beginning of infusions to determine K-s in in. longissimus dorsi and vastus muscle. Compared with control (saline-infused) lambs, K-s was increased by an average of 40% at the end of glucose infusion, but this effect was not statistically significant in either of the muscles sampled. BCAA infusion, alone or in combination with glucose, also had no significant effect on K-s compared with control sheep. K-s was approximately 60% greater for vastus muscle than for m. longissimus dorsi (P<0.01), regardless of treatment. It is concluded that there are signals other than insulin and BCAA that are responsible for the feed-induced increase in K-s in muscle of growing ruminant animals.

Influence of sulfur amino acids on the volatile and nonvolatile components of cooked salmon (Salmo salar)

Volatile and nonvolatile compounds, which could contribute to flavor, were analyzed in salmon. One hundred twenty-three volatile compounds were identified in the headspace of two different samples of cooked salmon, including lipid-derived volatiles, Maillard-derived volatiles, sulfur volatiles, Strecker aldehydes, nitrogen heterocyclic compounds, terpenes, and trimethylamine. Significant differences between samples were found for 104 of the volatiles. Although the levels of free cysteine and methionine were low in the salmon, sulfur volatiles were formed in the cooked fish, demonstrating that there were sufficient sulfur amino acids present for their formation. Notable differences in sulfur compounds between the samples suggested that small changes in sulfur amino acids could be responsible. When this hypothesis was tested, salmon heated with cysteine had increased levels of many thiophenes, thiazoles, alicyclic sulfides, and nitrogen heterocycles. With the addition of methionine, levels of dimethyl sulfides, two alicyclic sulfides, pyrazines, some unsaturated aldehydes, and alcohols and 2-furanmethanethiol increased. The largest difference found among the nonvolatile (low molecular weight water-soluble) compounds was in inosine monophosphate.

Polyamines, amino acids, IAA and ABA contents during Ocotea catharinensis seed germination

The aim of this work was to Study biochemical variations of IAA (indole-3-acetic acid), ABA (abscisic acid). PAs (polyamines) and amino acids at endogenous levels, during seed germination in Ocotea catharinensis. Seeds were germinated in a vermiculite substratum (100%), samples being collected after 15, 30 and 60 days. Total amino acid levels decreased during the first 15 days. Followed by all increment at the end of germination. Among amino acids, higher concentration was observed in asparagine, this being the predominant amino acid during the whole germination period. Total PAs (free + conjugated) content increased during the first 15 days, followed by a decrease and stabilization between 30 and 60 days of germination. Among the PAs, free putrescine levels rose during the first 15 days, followed by a drop and Stabilization up to 60 days of germination, while spermidine and spermine (spm) contents diminished during the period. Only spin was detected in a conjugated form, with increasing concentrations starting from 30 days on. IAA levels increased during tire first 15 days. followed by a decrease and stabilization until the end of germination (60 days), while ABA contents dwindled during the first 15 days, with similar Values until the end of germination.

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

Investigation of the non-covalent interaction of biomolecules with aqueous graphene interfaces is a rapidly expanding area. However, reliable exploitation of these interfaces in many applications requires that the links between the sequence and binding of the adsorbed peptide structures be clearly established. Molecular dynamics (MD) simulations can play a key role in elucidating the conformational ensemble of peptides adsorbed at graphene interfaces, helping to elucidate these rules in partnership with experimental characterisation. We apply our recently-developed polarisable force-field for biomolecule-graphene interfaces, GRAPPA, in partnership with advanced simulation approaches, to probe the adsorption behaviour of peptides at aqueous graphene. First we determine the free energy of adsorption of all twenty naturally occurring amino acids (AAs) via metadynamics simulations, providing a benchmark for interpreting peptide-graphene adsorption studies. From these free energies, we find that strong-binding amino acids have flat and/or compact side chain groups, and we relate this behaviour to the interfacial solvent structuring. Second, we apply replica exchange with solute tempering simulations to efficiently and widely sample the conformational ensemble of two experimentally-characterised peptide sequences, P1 and its alanine mutant P1A3, in solution and adsorbed on graphene. For P1 we find a significant minority of the conformational ensemble possesses a helical structure, both in solution and when adsorbed, while P1A3 features mostly extended, random-coil conformations. In solution this helical P1 configuration is stabilised through favourable intra-peptide interactions, while the adsorbed structure is stabilised via interaction of four strongly-binding residues, identified from our metadynamics simulations, with the aqueous graphene interface. Our findings rationalise the performance of the P1 sequence as a known graphene binder.

Effects of Diets Supplemented with Branched-Chain Amino Acids on the Performance and Fatigue Mechanisms of Rats Submitted to Prolonged Physical Exercise

This study aimed to determine the effects of diets chronically supplemented with branched-chain amino acids (BCAA) on the fatigue mechanisms of trained rats. Thirty-six adult Wistar rats were trained for six weeks. The training protocol consisted of bouts of swimming exercise (one hour a day, five times a week, for six weeks). The animals received a control diet (C) (n = 12), a diet supplemented with 3.57% BCAA (S1) (n = 12), or a diet supplemented with 4.76% BCAA (S2) (n = 12). On the last day of the training protocol, half the animals in each group were sacrificed after one hour of swimming (1H), and the other half after a swimming exhaustion test (EX). Swimming time until exhaustion was increased by 37% in group S1 and reduced by 43% in group S2 compared to group C. Results indicate that the S1 diet had a beneficial effect on performance by sparing glycogen in the soleus muscle (p < 0.05) and by inducing a lower concentration of plasma ammonia, whereas the S2 diet had a negative effect on performance due to hyperammonemia (p < 0.05). The hypothalamic concentration of serotonin was not significantly different between the 1H and EX conditions. In conclusion, chronic BCAA supplementation led to increased performance in rats subjected to a swimming test to exhaustion. However, this is a dose-dependent effect, since chronic ingestion of elevated quantities of BCAA led to a reduction in performance.

Novel porphyrin amino acids as building blocks for artificial photosynthetic reaction centers : photoinduced energy and electron transfer

This thesis reports on the synthesis and characterisation of trans-(M)AB2C meso-substituted porphyrin amino acid esters (PAr) (M = 2H or Zn) with tunable electron donating and electron withdrawing Ar substituents at B positions (Ar = 4-C6H4OnBu, 4-C6H4OMe, 2,4,6-C6H2Me3, 4-C6H4Me, C6H5, 4-C6H4F, 4-C6H4CF3, C6F5). These porphyrins were used as key building blocks for photosynthetic LHC (LHC = light-harvesting antenna complex) and RC (RC = reaction center) model compounds.rnBased on free-base or zinc(II) porphyrin amino acid esters and porphyrin acids several amide linked free-base bis(porphyrins) PAr1-PAr2 (Ar1 = 2,4,6-C6H2Me3, C6F5 and Ar2 = 2,4,6-C6H2Me3, 4-C6H4F, 4-C6H4CF3, C6F5), mono metallated bis(porphyrin) PAr1-(Zn)PAr2 (Ar1 = 2,4,6-C6H2Me3 and Ar2 =4-C6H4F) and its doubly zincated complexes (Zn)PAr1-(Zn)PAr2 were prepared. In the fluorescence spectra of free-base bis(porphyrins) the porphyrin with the strongest electron donating power of Ar substituents at B positions is the light emitting unity. The emission of mono metallated bis(porphyrin) occurs only from the free-base porphyrin building block. This phenomenon is caused by an efficient energy transfer likely via the Dexter through-bond mechanism.rnLinking of anthraquinone (Q) as electron acceptor (A) to the N-terminus of porphyrin amino acid esters ((M)PAr) and aminoferrocene (Fc) as electron donor (D) to the C-terminus of the porphyrin resulting in Q-(M)PAr-Fc triads (M = 2H or Zn, Ar = 4-C6H4OnBu, 4-C6H4OMe, 2,4,6-C6H2Me3, 4-C6H4Me, C6H5, 4-C6H4F, 4-C6H4CF3, C6F5) with tunable electron density at the porphyrin chromophore. In these triads initial oxidative PET (Q←(M)PAr) and reductive PET ((M)PAr→Fc) (PET = photoinduced electron transfer) are possible. Both processes leads to an emission quenching of (M)PAr. The efficiency of the PET pathways occurring in the Marcus normal region is controlled by the specific porphyrin electron density.rnAmide-linked conjugates PAr-Fc (Ar = 2,4,6-C6H2Me3, C6F5) and Fmoc-Fc-PAr1 (N-Fmoc-Fc = N-Fmoc protected 1,1’-ferrocene amino acid; Ar1 = C6H5, 4-C6H4F, 4-C6H4CF3, C6F5) as well as hinges PAr2-Fc-PAr1 (Ar1 = C6H5, 4-C6H4F and Ar2 = 2,4,6-C6H2Me3) were studied with respect to the reductive PET. The PET driving force (−GET) in dyads increases with the increasing electron withdrawing character of Ar substituents. Additionally, intramolecular energy transfer between porphyrins PAr1 and PAr2 is feasible in the hinges via the Förster mechanism.rn

Amino acids and carbohydrates in sediments and interstitial waters of ODP Site 112-681

Total organic carbon (TOC), dissolved organic carbon (DOC), total hydrolyzable amino acids (THAA), amino sugars (THAS), and carbohydrates (THCHO) were measured in sediments and interstitial waters from Site 681 (ODP Leg 112). TOC concentrations vary between 0.75% and 8.2% by weight of dry sediment and exhibit a general decrease with depth. DOC concentrations range from 6.1 to 49.5 mg/L, but do not correlate with TOC concentrations in the sediment. Amino compounds (AA and AS) and sugars account for 0.5% to 8% and 0.5% to 3% of TOC, respectively, while amino compounds make up between 2% and 27% of total nitrogen. Dissolved hydrolyzable amino acids (free and combined) and amino sugars were found in concentrations from 3.7 to 150 µM and from 0.1 to 3.7 µM, respectively, and together account for an average of 8.5% of DOC. Dissolved hydrolyzable carbohydrates are in the range of 6 to 49 µM. Amino acid spectra are dominated by glycine, alanine, leucine, and phenylalanine; nonproteinaceous amino acids (gamma-amino butyric acid, beta-alanine, and ornithine) are enriched in the deeper part of the section, gamma-amino butyric acid and beta-alanine are thought to be indicators of continued microbial degradation of TOC. Glycine, serine, glutamic acid, alanine, aspartic acid, and ornithine are the dominating amino compounds in the pore waters. Spectra of carbohydrates in sediments are dominated by glucose, galactose, and mannose, while dissolved sugars are dominated by glucose and fructose. In contrast to the lack of correlation between abundances of bulk TOC and DOC in corresponding interstitial waters, amino compounds and sugars do show some correlation between sediments and pore waters: A depth increase of aspartic acid, serine, glycine, and glutamic acid in the pore waters is reflected in a decrease in the sediment, while an enrichment in valine, iso-leucine, leucine, and phenylalanine in the sediment is mirrored by a decrease in the interstitial waters. The distribution of individual hexoseamines appears to be related to zones of bacterial decomposition of organic matter. Low glucoseamine to galactoseamine ratios coincide with zones of sulfate depletion in the interstitial waters.