scholarly journals Thermodynamic Impact of Mineral Surfaces on Amino Acid Polymerization: Aspartate Dimerization on Ferrihydrite, Anatase and γ-alumina

2021 ◽  
Author(s):  
Norio Kitadai ◽  
Kumiko Nishiuchi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Model Parameters ◽  
Mineral Surfaces ◽  
Adsorbed State ◽  
Interfacial Conditions ◽  
Wide Range ◽  
Equilibrium Ratio ◽  
Surface Liquid ◽  
Emergence Of Life

The ubiquity of amino acids in carbonaceous meteorites has suggested that amino acids are widespread in the Universe, serving as a common class of components for the emergence of life. However, parameters for modeling amino acid polymerization at mineral–water interfaces remain limited, although the interfacial conditions inevitably exist on planets with surface liquid water. Here, we present a set of extended triple-layer model parameters for aspartate (Asp) and aspartyl-aspartate (AspAsp) adsorptions on ferrihydrite, anatase, and γ-alumina determined based on the experimental adsorption data. By combining the parameters with the reported thermodynamic constants for amino acid polymerization in water, the impacts of these minerals on Asp dimerization are calculable over a wide range of environmental conditions. It was predicted, for example, that ferrihydrite strongly increases the AspAsp/Asp equilibrium ratio in neutral to acidic pH; the ratio in the adsorbed state reaches 40% even from a low Asp concentration (0.1 mM) at pH 4. This percentage is approximately 5 × 107 times higher than that attainable without mineral (8.5 × 10–6%). Our exemplified approach enables us to screen wide environmental settings for abiotic peptide synthesis from a thermodynamic perspective, thereby narrowing down the geochemical situations to be explored for life’s origin on Earth and Earth-like habitable planets.

scholarly journals Thermodynamic Impact of Mineral Surfaces on Amino Acid Polymerization: Aspartate Dimerization on Two-Line Ferrihydrite, Anatase, and γ-Alumina

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 234
Author(s):  
Norio Kitadai ◽  
Kumiko Nishiuchi ◽  
Wataru Takahagi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Model Parameters ◽  
Mineral Surfaces ◽  
Adsorbed State ◽  
Interfacial Conditions ◽  
Wide Range ◽  
Evolution Of Life ◽  
Adsorption Data ◽  
Surface Liquid

The presence of amino acids in diverse extraterrestrial materials has suggested that amino acids are widespread in our solar system, serving as a common class of components for the chemical evolution of life. However, there are a limited number of parameters available for modeling amino acid polymerization at mineral–water interfaces, although the interfacial conditions inevitably exist on astronomical bodies with surface liquid water. Here, we present a set of extended triple-layer model parameters for aspartate (Asp) and aspartyl-aspartate (AspAsp) adsorptions on two-line ferrihydrite, anatase, and γ-alumina determined based on the experimental adsorption data. By combining the parameters with the reported thermodynamic constants for amino acid polymerization in water, we computationally demonstrate how these minerals impact the AspAsp/Asp equilibrium over a wide range of environmental conditions. It was predicted, for example, that two-line ferrihydrite strongly promotes Asp dimerization, leading to the AspAsp/Asp ratio in the adsorbed state up to 41% even from a low Asp concentration (0.1 mM) at pH 4, which is approximately 5 × 107 times higher than that attainable without mineral (8.5 × 10−6%). Our exemplified approach enables us to screen wide environmental settings for abiotic peptide synthesis from a thermodynamic perspective, thereby narrowing down the geochemical situations to be explored for life’s origin on Earth and Earth-like habitable bodies.

scholarly journals Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

2019 ◽  
Author(s):  
Siva Dasetty ◽  
John K. Barrows ◽  
Sapna Sarupria
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Force Field ◽  
Force Fields ◽  
Principal Component ◽  
Free Energies ◽  
Adsorbed State ◽  
Free Energy Of Adsorption ◽  
Density Based Clustering ◽  
Structural Preferences

<div> <div> <div> <p>We compare the free energies of adsorption (∆Aads) and the structural preferences of amino acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force fields, the trends in the free energy of adsorption with amino acids are similar across the studied force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with graphene–water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption of proteins and peptides would be described consistently across different force fields, the structural preferences of peptides and proteins on graphene will be force field dependent. </p> </div> </div> </div>

scholarly journals Analysis of Htra Gene from Zebrafish (Danio Rerio)

2015 ◽  
Vol 10 (2) ◽  
Author(s):  
M. Murwantoko ◽  
Chio Oka ◽  
Masashi Kawaichi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Danio Rerio ◽  
Serine Proteases ◽  
Catalytic Domain ◽  
Fruit Fly ◽  
Wide Range ◽  
Igf Binding ◽  
Bacterial Homolog

HtrA which is characterized by the combination of a trypsin-like catalytic domain with at least one C-terminalPDZ domain is a highly conserved family of serine proteases found in a wide range of organisms. However theidentified HtrA family numbers varies among spesies, for example the number of mammalian, Eschericia coli,fruit fly-HtrA family are 4, 3 and 1 gene respectively. One gene is predicted exist in zebrafish. Since no completeinformation available on zebrafish HtrA, in this paper zebrafish HtrA (zHtrA) gene was analyzed. The zHtrA isbelonged to HtrA1 member and predicted encodes 478 amino acids with a signal peptide, a IGF binding domain,a Kazal-type inhibitor domain in the up stream of HtrA-bacterial homolog. At the amino acid sequence the zHtrA1showed the 69%, 69%, 68%, 54% and 54% with the rat HtrA1, mouse HtrA1, human HtrA1, human HtrA3 andmouse HtrA4 respectively. The zHtrA1 is firstly expressed at 60 hpf and mainly in the vertebral rudiments in thetail region.

An Automated Detection System for Most L-α-Amino Acids

1969 ◽  
Vol 15 (2) ◽  
pp. 154-161 ◽  
Author(s):  
K Van Dyke ◽  
C Szustkiewicz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Detection System ◽  
Automated System ◽  
Acid Oxidase ◽  
Enzymatic Reactions ◽  
Amino Acid Oxidase ◽  
Automated Method ◽  
Wide Range

Abstract An automated system for the determination of the L-α form of the majority of amino acids is presented. The method is based upon oxidative deamination of the amino acid coupled with oxidation of o-dianisidine by hydrogen peroxide. This procedure can be used comparatively for the determination of a mixture of L-α-amino acids or for the majority of separated L-α-amino acids (especially in conjunction with column separations from urine and blood which give falsely positive identification with ninhydrin detection). The stereospecific nature of the L-α-amino acid oxidase enables the investigator to quantitate the amount of L-α-amino acid in the presence of the D-α form. From an academic viewpoint, the extreme sensitivity and wide range of the detection system make it advantageous for the study of the enzyme itself. This automated method also may be employed to follow enzymatic reactions—e.g., those catalyzed by peptidases or racemases. The methodology is extremely convenient with good reagent stability and is much more sensitive than manometric technics.

The Synthesis of a Cubane-Substituted Dipeptide

2012 ◽  
Vol 65 (6) ◽  
pp. 690 ◽  
Author(s):  
Quentin I. Churches ◽  
Roger J. Mulder ◽  
Jonathan M. White ◽  
John Tsanaktsidis ◽  
Peter J. Duggan
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
High Sensitivity ◽  
Pure Form ◽  
Bioactive Molecules ◽  
Side Chains ◽  
Cyclic Hydrocarbon ◽  
Wide Range ◽  
Effective Synthesis ◽  
Dipeptide Derivative

Amino acids and peptides bearing cyclic hydrocarbon side-chains are of interest in the development of a wide range of bioactive molecules. The preparation of an amino acid and a dipeptide derivative bearing an unfunctionalised cubane substituent is described. Attempts to prepare a cubylalanine derivative via the corresponding dehydroalanine were unsuccessful due to the high sensitivity of this vinyl cubane compound. Conversely, the addition of cubyllithium to a (RS)-glyoxylate sulfinimine led to an effective synthesis of a cubylglycine derivative and a cubane-substituted dipeptide in diastereomerically pure form.

The relationships between the concentrations of individual amino acids and protein in wheat and barley grain grown at selected locations throughout Manitoba

1996 ◽  
Vol 76 (2) ◽  
pp. 163-169 ◽  
Author(s):  
R. J. Boila ◽  
S. C. Stothers ◽  
L. D. Campbell
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Barley Grain ◽  
Regression Equations ◽  
Acid Protein ◽  
Wide Range ◽  
Indispensable Amino Acids ◽  
Protein Amino Acids ◽  
Barley Protein ◽  
Amino Acid Concentrations

The concentrations of protein and individual amino acids were determined in the grain from three cultivars of wheat and three cultivars of barley, each grown at 12 locations throughout Manitoba over 3 consecutive years. Protein concentration differed (P < 0.05) among the cultivars of wheat but not (P > 0.05) among cultivars of barley. Although the concentrations of several amino acids differed (P < 0.05) among cultivars of wheat or barley the differences among cultivars of each grain were not considered to be critical in relation to the requirements for indispensable amino acids for swine or poultry. The percentage of an ammo acid in the DM of wheat and barley increased (P < 0.05) linearly with an increase in percentage of protein in the grain. The wide range of r2 (0.29 to 0.88) obtained for this amino acid-protein relationship may be due to the different effect of environment (location and year of growth) on the concentration of individual amino acids, compared to protein, among cultivars of wheat or barley. The percentage of total variance due to an interaction between cultivar and environment was low for protein but was several fold higher for individual amino acids. The error in the prediction of amino acid concentrations with regression equations may be no different than the error associated with predicting the mean concentrations of amino acids in the protein of wheat or barley as g (100 g protein)−1, and obtained from tabulations of analyses. However, regression equations for lysine in wheat and barley did account for the significant (P < 0.05) decrease in concentration of lysine in the protein as the percentage of protein in these grains increased. Key words: Grain, wheat, barley, protein, amino acids, Manitoba

Use-dependent block of excitatory amino acid currents in cultured neurons by ketamine

1987 ◽  
Vol 58 (2) ◽  
pp. 251-266 ◽  
Author(s):  
J. F. MacDonald ◽  
Z. Miljkovic ◽  
P. Pennefather
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aspartic Acid ◽  
Excitatory Amino Acids ◽  
Hippocampal Neurons ◽  
Excitatory Amino Acid ◽  
Outward Current ◽  
Bathing Solution ◽  
Wide Range ◽  
Repeated Applications

1. Mouse hippocampal neurons grown in dissociated cell culture were patch clamped using a whole cell voltage clamp (discontinuous switching clamp) technique. The currents generated by pressure applications of excitatory amino acids were studied over a wide range of holding potentials, and current-voltage curves were plotted. Excitatory amino acids that activated the N-methyl-D-aspartic acid (NMDA) receptor demonstrated some degree of desensitization with repeated applications, whereas the currents observed in response to kainic acid (KAI) did not. Desensitization could be minimized by keeping the frequency of application sufficiently low (i.e., less than 0.1 Hz). 2. The short-acting dissociative anaesthetic, ketamine (2–50 microM), selectively blocked L-aspartic acid (L-Asp), NMDA, and L-glutamic acid (L-Glu) currents while sparing those in response to KAI. Therefore, ketamine is a relatively selective blocker of the NMDA response versus that (those) activated by KAI. 3. The block by ketamine of excitatory amino acid currents is highly voltage dependent. Concentrations of ketamine that had little effect on outward current responses at depolarized potentials were quite effective at blocking inward current responses at hyperpolarized potentials. In contrast, DL-2-amino-5-phosphonovaleric acid (APV) was equally effective at blocking both inward and outward currents (voltage independent). The voltage dependence of ketamine (a positively charged molecule) could be accounted for if ketamine blocked the NMDA response by binding to a site that experienced 55% of the membrane field. 4. In the presence of ketamine, peak inward currents evoked by repeated applications of NMDA, L-Asp, or L-Glu progressively declined to a steady-state level of block (use-dependent block). This decrement occurred at frequencies much lower than those that were employed to demonstrate desensitization (in the absence of ketamine). Moving the membrane potential to depolarized values did not, in itself, relieve the ketamine block. However, if the appropriate excitatory amino acid (L-Asp, NMDA, L-Glu) was applied during the period of depolarization, a relief of the block could be demonstrated. No recovery from the blockade occurred with periods of rest (no amino acid application) as long as 5 min. Furthermore, no recovery was observed even when ketamine was washed out of the bathing solution until the appropriate agonist was applied. Thus recovery from blockade, like development of blockade, was use dependent.(ABSTRACT TRUNCATED AT 400 WORDS)

A Study of Relations between the Absorption of Amino Acids, Dipeptides, Water and Electrolytes in the Normal Human Jejunum

1975 ◽  
Vol 49 (5) ◽  
pp. 401-408 ◽  
Author(s):  
D. B. A. Silk ◽  
P. D. Fairclough ◽  
Nicola J. Park ◽  
Annette E. Lane ◽  
Joan P. W. Webb ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Sodium Chloride ◽  
Human Subjects ◽  
Sodium Content ◽  
Sodium Chloride Solutions ◽  
Electrolyte Absorption ◽  
Wide Range ◽  
Osmotic Solution ◽  
Normal Human

1. A double-lumen perfusion technique was used to study the effect of a wide range of concentrations of the dipeptide glycyl-l-alanine and its constituent amino acids on water and electrolyte absorption from iso-osmotic solutions in the upper jejunum of normal human subjects. 2. There was no significant absorption of water and electrolytes from sodium chloride solution (150 mmol/l) but the presence of the dipeptide or its constituent amino acids stimulated water and electrolyte absorption. 3. Water absorption reached a peak at increasing amino acid and dipeptide concentrations and then tailed off. Our data suggest that the tailing off is not solely due to the diminished sodium content of the solutions. 4. During perfusion of the dipeptide-sodium chloride and amino acid-sodium chloride solutions solute and water were absorbed as an iso-osmotic solution. Analysis of the results indicates that this could occur at high dipeptide concentrations only if the majority of the dipeptide enters the cell intact.

Sorbitol and proline as intracellular osmotic solutes in the green alga Stichococcus bacillaris

1978 ◽  
Vol 56 (6) ◽  
pp. 676-679 ◽  
Author(s):  
Lewis M. Brown ◽  
Johan A. Hellebust
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
High Salinity ◽  
Single Amino Acid ◽  
Salinity Range ◽  
Wide Range ◽  
Osmotic Solutes ◽  
Steady State Levels ◽  
Total Amino Acids ◽  
Stichococcus Bacillaris

A freshwater isolate of Stichococcus bacillaris Naeg. (strain UTEX 314) was evaluated for its ability to grow, photosynthesize, and osmoregulate over a wide range of salinity. The growth and photosynthetic measurements indicate that it is a euryhaline organism. Studies of the soluble organic metabolite pools showed that the steady-state levels of two solutes varied with salinity; sorbitol (a polyol) and proline (an amino acid). Intracellular proline levels increased from 0.002 to 0.28 M over the salinity range of 0 to40%c whereas the sorbitol level increased from 0.10 to 0.52 M. The level of total amino acids (excepting proline) remained relatively constant. No single amino acid of this group exceeded an intracellular concentration of 0.04 M. The changes in the concentrations of these solutes accounted for at least 75% of the required increase in intracellular osmolality in cells following adaptation to high salinity media. Sorbitol and proline are very soluble, nontoxic, and are efficient osmotic solutes. These properties make them ideal solutes for osmoregulation.

scholarly journals Amino acids in Arctic aerosols

2012 ◽  
Vol 12 (7) ◽  
pp. 17367-17396 ◽  
Author(s):  
E. Scalabrin ◽  
R. Zangrando ◽  
E. Barbaro ◽  
N. M. Kehrwald ◽  
J. Gabrieli ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Water Cycle ◽  
Amino Acid Content ◽  
Boreal Summer ◽  
Total Amino Acid ◽  
Radiation Balance ◽  
Polar Regions ◽  
Wide Range ◽  
Amino Acid Concentrations

Abstract. Amino acids are significant components of atmospheric aerosols, affecting organic nitrogen input to marine ecosystems, atmospheric radiation balance, and the global water cycle. The wide range of amino acid reactivities suggest that amino acids may serve as markers of atmospheric transport and deposition of particles. Despite this potential, few measurements have been conducted in remote areas to assess amino acid concentrations and potential sources. Polar regions offer a unique opportunity to investigate atmospheric processes and to conduct source apportionment studies of such compounds. In order to better understand the importance of amino acid compounds in the global atmosphere, we determined free amino acids (FAAs) in seventeen size-segregated aerosol samples collected in a polar station in the Svalbard Islands from 19 April until 14 September 2010. We used an HPLC coupled with a tandem mass spectrometer (ESI-MS/MS) to analyze 20 amino acids to quantify compounds at fmol m−3 levels. Mean total FAA concentration was 1070 fmol m−3 where serine and glycine were the most abundant compounds in almost all samples and accounted for 45–60% of the total amino acid relative abundance. The other eighteen compounds had average concentrations between 0.3 and 98 fmol m−3. The higher amino acid concentrations were present in the ultrafine aerosol fraction (<0.49 μm) and accounted for the majority of the total amino acid content. Local marine sources dominate the boreal summer amino acid concentrations, with the exception of the regional input from Icelandic volcanics.

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