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The analysis of free amino acids present in food samples, body fluids such as urine, serum and blood, amino acid hydrolysates, from proteins, or primary and secondary amines is an important, standardized method routinely performed in biochemical, medical and biological labs. It has been, and still is used for the accurate quantification and characterization of proteins and peptides, as well as recombinant gene products. It is considered the method of choice to determine the purity and chemical composition of a protein or peptide.
1. Types of amino acid analysis
A. Hydrolysate analysis
Composition studies: Determination of amino acid content of proteins, peptides, foods, beverages, cosmetics, and others.
Quality control: Verification of product composition
B. Physiological analysis
Nutrition studies: Determination of free amino acid content in food supplements, and others.
Clinical assays: Determination of amino acid content in serum, tissue, and other body fluids.
Amino acid analysis (AAA) is a method for breaking down a protein or peptide into its components (amino acids) and determining their identities and relative quantities of the freed amino acids. Absolute quantities of amino acids released from the protein or peptide can also be determined.
AAA can be used in combination with protein sequence analysis to verify if the total sequence of the protein in question has been determined. It also helps to identify modified amino acids like phosphor-tyrosine, the presence of amino acids modified with carbohydrates, if amino sugars are found, and others.
Knowledge of the number of methionines or tryptophanes present allows for the design of peptide mapping strategies employing enzymatic or chemical cleavage methods to generate a limited number of longer peptides. These peptides may then be sequenced and used for the design of primers. Knowledge of the number of Lys, Arg, Asp, and Glu residues allows one to select the most appropriate protease for further experiments.
Even today, AAA is still the most practical method for accurately quantifying amino acid, peptide and protein concentrations. Accurate measurements are essential for calculating extinction coefficients of proteins or to determine the turnover number for an enzyme. Although instrumentation performance has improved over the years, the basic concepts of amino acid analysis have not changed since Stein and Moore (1963) developed the original method based on ion exchange resins.
2. Sample preparation
The preparation of samples to be used in AAA can be a quite difficult but very important experimental step for a successful amino acid analysis. Contamination with other proteins, amino acids, and other molecular weight solutes that interfere with the analysis chemistry are the most serious. To get accurate results the purity of the sample is much more critical than for sequencing or mass analysis.
2.1. Contamination with traces of undesired proteins:
In the case of proteins a 10% contamination of the desired protein with an undesired byproduct such as a different protein may render the data useless.
2.2. Low molecular weight compounds
Compounds containing primary or secondary amino groups are a very serious problem. They can be found in abundance in every laboratory and are difficult to completely eliminate. Tris and glycine are two good examples. Contamination is the major factor limiting increases in the sensitivity of analysis. The rule of thumb here is: the more steps used prior to analysis the more contamination one can pick up.
Non-amine compounds including many buffers, detergents, and inorganic salts, especially high salt concentrations may interfere with the analysis and need to be removed prior to analysis.
2.4. Sample treatment for physiological samples
Physiological samples need to be treated differently than proteins prior to loading on to the derivatizer unit. To avoid losses of labile amino acids present in the sample, keep sample solutions on ice and store in freezer below -20 ºC between use or better (if enough sample is at hand), prepare aliquots and store frozen in freezer prior to analysis.
Precipitation of proteins with 5-sulfocalicylic acid (SSA): Human urine, serum and rat brain tissue extracts are treated with sulfosalicylic acid to precipitate protein: 20 µl of 35% sulfosalicylic acid is added to 200 µl of each sample. These solutions are vortexed and allowed to sit at room temperature at least 20 minutes before proceeding. The samples are then spun in a microfuge for 2 minutes and the supernatants are collected. Collagen samples are hydrolyzed in 6 N HCl, 110 oC for 24 hours. The hydrolysates are then dried down and resuspended in 250 µg/ml K4EDTA. Ant hemolymph does not need to be pretreated before analysis. Samples are loaded onto the analyzer as follows: Urine - 10 µl of a 1:2 dilution of the supernatant, Serum - 10 µl of undiluted supernatant, Rat brain extract - 10 µl of the undiluted supernatant, Collagen hydrolysate - 1.2 µg in 15 µl, Fire ant hemolymph - 4 µl of a 1:9 or 1:10 dilution. Our current knowledge that approximately 30,000 human genes appear to code for up to 1 million or more proteins has generated new interest in independent ‘de novo’ protein and peptide sequencing of gene products. Two methods are available for this task, the classical Edman chemistry based method, or the newer, more recent method which utilizes LC-MS/MS based sequencing. The second method is considered to be faster and more sensitive.
When sufficient quantities are at hand, samples may be desalted by dialysis or size exclusion chromatography using deionized water or a volatile buffer like 1 N acetic acid. These two methods are not recommended to be used for quantities below 1 nanomole. Reversed phase-HPLC may be used for smaller sample quantities. But even this method can be tricky.
3. Hydrolysis methods
The second part of the analysis is the hydrolysis process. Many methods have been investigated to ensure optimal recoveries for the different amino acids analyzed.
3a. Standard hydrolysis conditions are 6N HCl from 20 to 96 hours at 110 ºC in vacuo.
Limitations and recovery improving modifications of the method are listed below:
Side chain hydroxyl group is modified during hydrolysis (eg. esterification, dehydration). Typical losses using standard hydrolysis conditions are 15-20% for serine and 10-15% for threonine.
A typical method for quantitation is to run multiple hydrolyses at different hydrolysis times and plot the serine and threonine recovery versus length of hydrolysis (hydrolyzed for 30, 60 and 90 min). Extrapolate the recovery to time = 0 to yield an accurate quantitation.
Table 2: Derivatization Chemistries for Amino Acids and Amine Analysis
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