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Amino acid compatibility

Amino acid compatibility


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The (human) genetic code encodes 20 amino acids. They form a protein using peptide bonds. Each amino acid has a carboxyl group (COOH) and an amino group (NH2) that can potentially form a peptide bond.


Source: The Culture of Chemistry

Does this property of amino acids means that each amino acid can form a peptide bond in any combination? In other words, are there certain amino acid doublets in existence that never pair up?


Short answer: there are no restrictions in principle on which amino acids can follow which. That means that in principle you can have polypeptide in any configuration: AAAA, WQWQWQ etc.

Problem is that polypeptides must be functional and, because they are in aqueous solution, it puts restrictions on how polypeptide form secondary and tertiary structure. It means that having very rigid hydrophobic surface is energetically unfavorable. If cell where to produce such polypeptide, it might be either degraded or cause problems for cell, such as aggregates or other form of toxicity.

That means that polypeptides has more restrictions than just linkage (C-N bonding) order. And of course it has been studied: Probabilistic analysis of the frequencies of amino acid pairs within characterized protein sequences.

Authors analyzed protein databases to find out which doublets of amino acids are more and less common. First of all, not all amino acids (of which there are 20 considered) have same occurrence, e.g. P(L, leucine)=0.096, P(W, tryptophan)=0.0118.

And, of course, not doublets are equally distributed (16 pairs out of 400 were picked as statistically significant):


It seems like you may be thinking along the lines of DNA, where adenine pairs only with thymine and guanine with cytosine.

Unlike DNA, amino acid chains are single-stranded…

… so there is no pairing of compatible types like there is in DNA. Neighboring amino acids in the chain can be in any combination (as you say, because each has a carboxyl group and an amino acid group), just as neighboring nucleotides in DNA (ie those next to, not across from, each other) can come in any order.

In practical terms, the functional groups of amino acids have different chemical properties (hydrophobic, hydrophilic, aromatic), therefore some pairings are probably more commonly found than others. But in principle there is no restriction on who is next to who.


To answer your question: No, there are no restrictions to what amino acid is next ("a nearest neighbor") to its N-terminal or C-terminal neighbor.


Fluorescent amino acids as versatile building blocks for chemical biology

Fluorophores have transformed the way we study biological systems, enabling non-invasive studies in cells and intact organisms, which increase our understanding of complex processes at the molecular level. Fluorescent amino acids have become an essential chemical tool because they can be used to construct fluorescent macromolecules, such as peptides and proteins, without disrupting their native biomolecular properties. Fluorescent and fluorogenic amino acids with unique photophysical properties have been designed for tracking protein–protein interactions in situ or imaging nanoscopic events in real time with high spatial resolution. In this Review, we discuss advances in the design and synthesis of fluorescent amino acids and how they have contributed to the field of chemical biology in the past 10 years. Important areas of research that we review include novel methodologies to synthesize building blocks with tunable spectral properties, their integration into peptide and protein scaffolds using site-specific genetic encoding and bioorthogonal approaches, and their application to design novel artificial proteins, as well as to investigate biological processes in cells by means of optical imaging.


Amino Acid

To form a molecule with its functional groups, having a positive and negative charge.

1 ml Ninhydrin on 1 ml protein solution shows violet color after heating. It shows the presence of alpha-amino acids.

Sanger reagent reacts with an amino group in a mild alkaline medium under cold conditions.

Reacts with the Amino group to release nitrogen and form the corresponding hydroxyl.

Classification based on polarity

  1. Polar Amino Acids
  2. Non-polar Amino Acids
  • Polar amino acids:
  1. In this category there are 11 amino acids listed down:
  2. Polar Uncharged: Serine, Threonine, Cysteine, Asparagine, Glutamine, and Tyrosine.
  3. Polar Charged: Histidine, Lysine, Arginine, Aspartate, and Glutamate
  • Non-polar amino acid
  1. In this category there are 9 amino acids:
  2. Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Tryptophan, Phenylalanine, and Methionine.

Essential and non-Essential amino acids

based on the requirement of our body:

  • What are the Essential amino acids?
  1. Out of 20 amino acids, there are 9 are in the list of essential amino acids. We need to take these amino acids from outside (food sources).
  2. Isoleucine, Valine, Lysine, Phenylalanine, Methionine, Threonine and Tryptophan
  • What are the Non-essential amino acids?
  1. These amino acids can be made by our body.
  2. Arginine, Cysteine, Glutamine, Tyrosine, Glycine, Proline, Serine, Alanine, Aspartate, and Asparagine.

What is the isoelectric point?

The pH when the total charge of an amino acid is zero, known as an isoelectric point.


Abstract

The compatibility of d -amino acids with peptide elongation during translation has been examined in several studies. However, some of the studies have reported that d -amino acids are incompatible with translation, whereas others have reported that d -amino acids are incorporated into polypeptides. Here, we have reevaluated the incorporation of a series of d -amino acids into the nascent chain of short peptides with a reprogrammed genetic code by using the flexible in vitro translation (FIT) system. The FIT system enables the compatibility of each d -amino acid with elongation to be assessed quantitatively in the absence of potential competitors. The incorporation efficiencies were determined by Tricine-SDS-PAGE and the full-length peptide was detected by MALDI-TOF-MS. The d -amino acids were categorized into three groups based on their incorporation efficiencies relative to the corresponding l -amino acid. The d -isomers in group I showed efficiencies of 40% or higher (Ala, Ser, Cys, Met, Thr, His, Phe, and Tyr), and those in group II showed efficiencies of 10–40% (Asn, Gln, Val, and Leu). The d -amino acids in group III produced truncated peptides or no detectable full-length peptides (Arg, Lys, Asp, Glu, Ile, Trp, and Pro). When group I d -amino acids were used consecutively or were alternated with l -amino acids, this completely inhibited their elongation. However, when two or three l -amino acids were inserted between the d -amino acids, the double-incorporation efficiency was restored. Our results quantitatively reveal the compatibility of d -amino acids with peptide elongation and raise new questions about the mechanism of d -amino acid selection and incorporation by the ribosome.


Imino acid

Imino acids are a group of compounds that consist both an amide(-NH2) and a carboxyl group(-COOH), bonded to the alpha carbon molecule. The difference between the amino acids and the imino acids is in the bonding of the nitrogen(N2) in the amide group. In imino acids, the nitrogen forms a double covalent bond(“=”) to another molecule, or two single bonds to two different ‘R’ groups.

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RESULTS AND DISCUSSION

Quantification of amino acids and related amines by iTRAQ-based profiling

In our previous study, norvaline was added to the reaction system to investigate the derivatization efficiency of amino acids and related amines (An et al., 2020). The results showed more than 80% norvaline could be derivatized by the iTRAQ reagent. In this study, 31 labeled amino acids and related compounds were separated and quantified with excellent peak shapes. The MRM ion chromatograms corresponding to the amino acids and their isotopic internal standards were extracted from the data. Integration and calculation were adjusted to quantify amino acid levels.

Principal component analysis (PCA) could provide clustering information in each group and possible metabolic profile changes. The concentrations were assigned as variables while the pre-storage handing conditions and freeze-thaw cycles were set as factors for the multivariate data analysis. SIMCA-P 13.0 (VersionAB, Umeå, Sweden) was employed to visually investigate the clustering of amino acids measured in serum at different pre-processing conditions. Fig. 1 shows the three-dimensional PCA score plot of serum samples stored at 4°C and 22°C with different storage times as well as samples detected immediately after processing. The model statistics indicate a low degree of fit (R2X=0.385) and low predictability (Q2=0.203). Multivariate data analysis by PCA did not show clear separation of the three groups. However, the serum samples stored at 4°C, 22°C, and the samples detected immediately after processing tended to aggregate together. This indicated that there were indeed differences among the serum samples stored at different conditions and the differences were gradually changing. The samples stored at 22°C were relatively scattered, and more variability was found in samples analyzed immediately after processing. We also performed a univariate analysis comparing the serum samples at the different storage times. Fig. 2 shows the three-dimensional PCA score plot of serum samples for different storages times (0, 1, 2, 4, 8, 12 and 24 h) at 4°C (A) and 22°C (B). The values for the two multivariate analyses at 4°C and 22°C were R2X=0.427, Q2=0.185, and R2X=0.442, Q2=0.213, respectively. Although the R2X and Q2 values from the PCA model were low, the sample aggregation at the same times and temperatures is good. The serum samples at 4°C from 0 to 24 h are scattered and distributed with increased storage time, the samples gathered at the same pre-storage times gradually deviated from immediately detected samples. When stored at 22°C, the serum samples are scattered and distributed with storage time. After 8 h, they deviate from the sample group with rapid detection significantly. Taken together, the variability stems from variations in amino acid content as a function of time and temperature. It shows that temperature and storage time have an impact on the composition of amino acids in serum.


Non Essential Amino Acids

12 nonessential amino acids are produced within the body, although many believe in providing further sources by way of amino acid supplements or high-protein diets. Humans are able to synthesize alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, taurine, and tyrosine. Inborn deficiencies of non essential amino acids and their catalyzing enzymes may cause abnormal phenotypes caused by a genetic inability to form certain proteins. This can be seen in low or nonexistent arginine and glycine amidinotransferase production that leads to mental retardation and muscular abnormalities. A lack of glutathione synthetase, even in the presence of plentiful non essential amino acids, causes sufferers to exhibit signs of oxidative stress, progressive neurologic disorders, hemolytic anemia, and metabolic acidosis.


Amino Acid Requirements of Fish

The unit of protein formation is the amino acid. 23 types of amino acids have been isolated from natural proteins. 10 of them are essential for fish. Animals cannot make essential amino acids. So these have to be taken with food. The quality of food depends not only on the amount of nutrients, but also on the quality of the protein and the accumulation of amino acids in the food. For this, amino acids are divided into the following two groups, viz

1. Essential Amino Acid

Although there are more than 200 amino acids in nature, only 20 of them are found in all living things. Of the 20 amino acids, 10 are essential amino acids that fish cannot synthesize. Therefore, they must be supplied with food, so such amino acids are called essential amino acids. The following are the names of the 10 essential amino acids:

  1. Histidine
  2. Isoleucine
  3. Leucine
  4. Lysine
  5. Methionine
  6. Phenyl alanine
  7. Threonine
  8. Tryptophan
  9. Valine
  10. Arginine

Among the essential amino acids, lysine and methionine are the first limiting amino acids. Fish meal is made from vegetable protein (soybean) and it contains low levels of methionine. Therefore, excess methionine must be added to soybean-based foods for moderate growth and good health of fish. In addition, in fish farming, it is important for every fish species to have knowledge about the combination of protein and amino acid needs.

2. Non-essential Amino Acid

Certain amino acids are non-essential which the body can make through synthesis. These play a role in the management of various physiological processes in the body. Since such amino acids are produced in one's body, it does not need to be supplied with food. Animal protein contains all the essential amino acids. Vegetable proteins, on the other hand, do not contain all the essential amino acids. The following are some of the non-essential amino acids:

  • Alanine
  • Aspartic acid
  • Asparagine
  • Cysteine
  • Glutamic acid
  • Glutamine
  • Glycine
  • Proline
  • Selenocysteine
  • Serine
  • Taurine
  • Tyrosine

Importance and Requirements of Amino Aacid in Fish

Amino acids play an important role in the body's maintenance, growth, reproduction and cell tissue transplantation. Also some amino acids are quickly converted into glucose and provide energy to the brain and blood cells. Lack of essential amino acids causes the fish to lose growth, lose weight and lose its appetite. As a result, the body's resistance to disease is reduced.

Alanine and aspartate are the main raw materials for fish glucose production and important sources of energy production. In addition, aspartate is essential for the synthesis of purine nucleotides in all cell types. Moreover, alanine is a more important nitrogen carrier for amino acid metabolism in the internal organs of fish (Mommsen et al. 1980). Aspartate and asparagine make up 10% of the amino acids in plant and animal proteins. Alanine can stimulate the diet of certain fish (Shamushaki et al. 2007). The addition of 5% pyruvate to the synthesis of Atlantic salmon and the synthesis of vitellogenin increases the level of alanine production without negative effects, resulting in an almost nitrogen-releasing environment (Olin et al. 1992). At present there is no information about adding aspartate or asparagine to fish diet. Alanine and aspartate are rapidly oxidized and are often used to maintain nitrogen balance due to lack of toxicity.

Arginine is found in large quantities in proteins (as peptide bond amino acids) and so it is needed in large quantities in fish feed. Citrulline is converted to arzinine by arginosaccinate synthase and lyase in the liver of elasmobranch and ureogenic teleost fish (Mommsen et al. 2001). In terrestrial animals, arginine is used for the synthesis of proteins, nitric oxides, urea, polyamines, proline, gutamate, creatine and agmatin (Wu and Morris 1998). Arginine also plays an important role in regulating endocrine glands and reproductive function (Jobgen et al. 2006 Yao et al. 2008).

18-20% of plant and animal proteins are leucine, isoleucine and valine. Leucine is said to be an active amino acid because it is an active effectors of certain rapamycin. It inhibits muscle protein synthesis and protein analysis in mammals (Nakashima et al. 2007).

Fish muscle and blood plasma contain large amounts of free amino acids, but gutamate and its decarboxylation products (glutamate, glutamine, and γ-aminobutyrate: GABA) are nerve stimulators that are present in the brain at high concentrations (1979). Moreover, glutamine is essential for the synthesis of purine and pyrimidine nucleotides in all cells. Glutamine also plays an important role in the production of renal ammonia in maintaining the acid-base balance in the body of fish. Glutamine and glutamate are 20% of the amino acids in plant and animal proteins, but they are completely dissociated in the gut in aquatic animals, such as in terrestrial mammals (Wu 1998). Thus, most of the glutamine and glutamate in blood plasma are synthesized from the amino acids and acetoglutrates attached to the skeletal muscle. Glutamate is used as a substrate in the synthesis of glutamine by ATP-dependent glutamine synthesis, whereas glutamine is hydrolyzed by phosphate-dependent glutamine to form glutamate (Anderson et al. 2002). Although there is an idea about this intracellular glutamine-glutamate cycle in mammals, but there is little information in fish.

Large amounts of glutamine synthetase are present in the brain, intestines, liver, muscles, gills, kidneys, and heart of fish. Cortisol (Vijayan et al.1996) or high environmental ammonia (Anderson et al. 2002) regulate liver proteins. Glutamine and glutamate are one of the most important sources of energy in fish, but tissue-based metabolism of these two amino acids has been determined in aquatic animals.

Excessive GABA in the diet interferes with the intake of food by Japanese flounders (Kim et al. 2003). On the other hand, the growth of Atlantic salmon and the addition of 5% α-chitoglutrate to the synthesis of vitellogenin almost reduced nitrogen emissions into the environment without negative effects (Olin et al. 1992). Providing gluten-rich foods to Asian carp increases fish weight, food intake, food conversion rate, and enzyme activity (Lin and Zhou 2006).

Integration of glycin and serine in the liver occurs through tetrahydrofalate dependent hydroxymethyltransferase. These two amino acids participate in glucose production, sulfur amino acid metabolism and fat digestion (Fang et al. 2002). Many fish also stimulate the intake of these two amino acids (Shamushaki et al. 2007). Glycin plays an important role in controlling the secretion of fins and shellfish (such as oysters).

Fish plasma albumin contains large amounts of histidine (Szebedinszky and Gilmour 2002). Fish muscle contains large amounts of such free amino acids or carnosine. Histidine plays a role in DNA and protein synthesis. Moreover, histidine acts as a source of energy when you are hungry. Histidine is a component of noncarbonate buffer that protects fish from starvation, abnormal swimming, and lactacidosis by altering pH values. Differences in non-carbonate buffer capacity have been observed in different fish species. This allows the fish to adapt to the environment for a long time. Interestingly, the concentration of intracellular histidine increased significantly before salmon was introduced during breeding (Mommsen et al. 1980). The metabolism of histidine in fish and its demand in food is regulated by a variety of environmental and endocrine regulators.

Lysine is one of the most important amino acids in commercial fish feed production, especially in the use of vegetable protein sources instead of fishmeal (Mai et al. 2006a). Lysine levels in the diet affect the health and growth of fish. In carnitine synthesis, lysine acts as a raw material that is required to transport long chain fatty acids from cytosol to oxidation in mitochondria. Adding carnitine to the diet leads to rapid physical growth and protects the fish from the toxins of ammonia and xenobiox. It increases fish reproduction by rapidly adapting to temperature changes and other environmental pressures (Harpaz 2005).

Phenylalanine is converted to tyrosine by tetrahydrobiopterin-based phenylalanine hydroxylase in the kidney and liver of fish.

Tyrosine is used as a raw material in the synthesis of important hormones such as thyroxine (T4), triiodothyronine, epinephrine, norepinephrine, dopamine and melanin and nerve stimulators. These elements have important controlling roles (Chang et al.2007 Yoo et al. 2000). Phenylalanine and tyrosine have a greater effect on the survival of fish in the natural environment, food intake, growth, color formation and disease prevention. Phenylalanine and tyrosine in the diet during fish conversion lead to rapid growth (Pinto et al. 2008). Furthermore, feeding thyroxine (T4) to carp, channel catfish, and flounder fish increases protein digestion, digestive enzyme activity, nutrient retention, growth rate, and feeding efficiency (Garg 2007).

Polyamines (putrescine, spermedin and spermin) are naturally occurring polysaccharides that are essential for cell growth and division. In mammals, it is synthesized from arginine derived from arginine or proline (Wu et al. 2008). Adding spermine to refined foods increases the activity of digestive enzymes and intestinal maturation, thereby increasing larval survival rates (e.g. European sea bass) (Pe´res et al.1997). Note that, high levels of polyamines are toxic to fish and have a negative effect on growth rate (Cowey and Cho 1992).

It is thought that proline is a non-essential amino acid in fish and stimulates the diet of fish. In mammals, proline is synthesized from arginine, ornithine, groutamine and groutmate (Wu and Morris 1998). Proline is currently considered a conditionally essential amino acid for fish larvae and mature stages.

Methionine is one of the most essential amino acids in some fish foods, especially high-protein vegetable protein sources such as soybean meal, almond meal, etc. (Mai et al. 2006b). Methionine and its derivative compounds can be made commercially through chemical processes. Methionine is usually found at adequate rates in the DL-phase. The natural isomer called L-methionine is quickly absorbed by animals and used efficiently.

Taurine is not associated with proteins but promotes fat digestion, anti-oxidation protection, cellular permeability, vision organs, nerves and muscular system development (Fang et al. 2002 Omura and Inagaki 2000). Fish meals and animal products contain large amounts of taurine (especially marine invertebrates) but are absent in plants. Providing taurine in the diet increases the intestinal permeability of cobia larvae which increases the efficiency of larval cultivation (Salze et al. 2008).

Threonine is a major component of small intestinal mucosa in fish. Tryptophan can be converted to serotonin (5-hydroxytryptamine it is a neurotransmitter) and melatonin (resistant to corrosion) (Fang et al. 2002). Feeding with tryptophan prevents rainbow trout from providing aggressive behavior in their larvae (Hseu et al. 2003). It reduces cannibalism and food reluctance in grouper fish larvae (Ho¨glund et al. 2007) and plays a role in counteracting environmental stress by increasing cortisol levels (Lepage et al. 2003). Long-term use of cortisol in the diet has a negative effect on increased food intake, increased protein intake, and immunity (Vijayan et al. 1996).


Reevaluation of the D-amino acid compatibility with the elongation event in translation

The compatibility of D-amino acids with peptide elongation during translation has been examined in several studies. However, some of the studies have reported that D-amino acids are incompatible with translation, whereas others have reported that D-amino acids are incorporated into polypeptides. Here, we have reevaluated the incorporation of a series of D-amino acids into the nascent chain of short peptides with a reprogrammed genetic code by using the flexible in vitro translation (FIT) system. The FIT system enables the compatibility of each D-amino acid with elongation to be assessed quantitatively in the absence of potential competitors. The incorporation efficiencies were determined by Tricine-SDS-PAGE and the full-length peptide was detected by MALDI-TOF-MS. The D-amino acids were categorized into three groups based on their incorporation efficiencies relative to the corresponding L-amino acid. The D-isomers in group I showed efficiencies of 40% or higher (Ala, Ser, Cys, Met, Thr, His, Phe, and Tyr), and those in group II showed efficiencies of 10-40% (Asn, Gln, Val, and Leu). The D-amino acids in group III produced truncated peptides or no detectable full-length peptides (Arg, Lys, Asp, Glu, Ile, Trp, and Pro). When group I D-amino acids were used consecutively or were alternated with L-amino acids, this completely inhibited their elongation. However, when two or three L-amino acids were inserted between the D-amino acids, the double-incorporation efficiency was restored. Our results quantitatively reveal the compatibility of D-amino acids with peptide elongation and raise new questions about the mechanism of D-amino acid selection and incorporation by the ribosome.


Amino Acids

Amino acids are organic acids in which one or more hydrogen atoms attached to the hydrocarbon skeleton are replaced by equal number ofamino(-NH2) groups. Each amino acid contains at least one acidic carboxyl (-COOH) group and one basic amino (-NH2) group. Some amino acids may have an additional amino and/or a carboxyl group. All amino acids are made up of C2H2O and N2 while some of them contain Sulphur(S) in addition.

Types of Amino Acids

As constituent of proteins most of the natural amino acids are found. Several natural amino acids are now known that are not found in proteins but remain in free or bound form. So many types of amino acids are known to be present in protein. Those are:
1) Lysine
2) Valine
3) leucine
4) Isoleucine
5) Threonine
6) Methionine
7) phenyl alanine
8) Tryptophan
9) Glycine
10) Alanine
11) Serine
12) Aspartic acid
13) Glutamic acid
14) Arginine
15) Cysteine
16) Cystine
17) Tyrosine
18) Histidine
19) Proline
20) Hydroxyproline
21) Hydroxylysine
22) Aspargine
23) Glutamine.

Essential Amino Acids and Non-essential Amino Acids

From nutritional point of view, amongst the abovementioned amino acids, the first eight are called essential or indispensable amino acids as they are not synthesized in our body and their presence in diet is essential.
The remaining ones are referred to as non-essential or dispensable amino acids because they can be synthesized in the body and are not necessarily to be taken through diet. In addition to the eight essential amino acids, histidine and arginine are considered as semi-essential amino acids because these two amino acids are essential for infants but not for adults.

Classification of amino acids

Amino acids may also be classified into three groups according to the number of amino and carboxyl groups present in the molecule or according to the reaction in solution as follows: —

Neutral amino acids

Neutral amino acids have equal number of basic amino and acidic carboxyl groups. These may again be of two types—(a) mono amino mono carboxylic acid e.g., glycine, alanine, serine, valine etc., and (b) diamino dicarboxylic acid e.g., cystine.

Acidic amino acids

Mono-amino dicarboxylic acids are Acidic amino acids because they contain an extra acidic carboxylic group. Example: — aspartic acid and glutamic acid.

Basic amino acids

Basic amino acids are diamino monocarboxylic acids e.g., lysine, hydroxylysine and arginine.

According to their metabolic fates, amino acids are of three types, those are: —

Glycogenic amino acids

Amino acids which can enter into the neoglucogenic pathway to produce glucose and glycogen are called glyogenic aminoacids. They comprise glycine, alanine, serine, cysteine, valine, methionine, glutamine, aspartic acid, histidine, arginine, proline and hydroxy proline.

Ketogenic amino acids

Amino acids whose carbon skeletons are converted to ketone bodies and not to glucose are called ketogenic amino acids. They comprise leucine and lysine.

Glycogenic-ketogenic amino acids

Amino acids whose carbon skeletons are converted partly to glucose and partly to ketone bodies belong to this group. They include phenyl alanine, tyrosine, tryptophan, isoleucine and threonine.
And the amino acids contain sulphur: -

Sulphur containing amino acids

There are three amino acids namely methionine, cysteine and cystine belong to this group because their molecules contain sulphur (S).