Amino acid replacement


Amino acid replacement is a change from one amino acid to a different amino acid in a protein due to point mutation in the corresponding DNA sequence. It is caused by nonsynonymous missense mutation which changes the codon sequence to code other amino acid instead of the original.

Conservative and radical replacements

Not all amino acid replacements have the same effect on function or structure of protein. The magnitude of this process may vary depending on how similar or dissimilar the replaced amino acids are, as well as on their position in the sequence or the structure. Similarity between amino acids can be calculated based on substitution matrices, physico-chemical distance, or simple properties such as amino acid size or charge. Usually amino acids are thus classified into two types:
Physicochemical distance is a measure that assesses the difference between replaced amino acids. The value of distance is based on properties of amino acids. There are 134 physicochemical properties that can be used to estimate similarity between amino acids. Each physicochemical distance is based on different composition of properties.
Two-state charactersProperties
1-5Presence respectively of: β―CH2, γ―CH2, δ―CH2, ε―CH2 group and a―CH3 group
6-10Presence respectively of: ω―SH, ω―COOH, ω―NH2, ω―CONH2 and ―CHOH groups
11-15Presence respectively of: benzene ring, branching in side chain by a CH group, a second CH3 group, two but not three ―H groups at the ends of the side chain and a C―S―C group
16-20Presence respectively of: guanido group, α―NH2, α―NH group in ring, δ―NH group in ring, ―N= group in ring
21-25Presence respectively of: ―CH=N, indolyl group, imidazole group, C=O group in side chain, and configuration at α―C potentially changing direction of the peptide chain
26-30Presence respectively of: sulphur atom, primary aliphatic ―OH group, secondary aliphatic ―OH group, phenolic ―OH group, ability to form S―S bridges
31-35Presence respectively of: imidazole ―NH group, indolyl ―NH group, ―SCH3 group, a second optical centre, the N=CR―NH group
36-40Presence respectively of: isopropyl group, distinct aromatic reactivity, strong aromatic reactivity, terminal positive charge, negative charge at high pH
41Presence of pyrollidine ring
42-53Molecular weight of side chain, scored in 12 additive steps
54-56Presence, respectively, of: flat 5-, 6- and 9-membered ring system
57-64pK at isoelectric point, scored additively in steps of 1 pH
65-68Logarithm of solubility in water of the ʟ-isomer in mg/100 ml., scored additively
69-70Optical rotation in 5 ɴ-HCl, D 0 to -25, and over -25, respectively
71-72Optical rotation in 5 ɴ-HCI, 0 to +25, respectively
73-74Side-chain hydrogen bonding, strong donor and strong acceptor, respectively
75-76Side-chain hydrogen bonding, strong donor and strong acceptor, respectively
77-78Water structure former, respectively moderate and strong
79Water structure breaker
80-82Mobile electrons few, moderate and many, respectively
83-85Heat and age stability moderate, high and very high, respectively
86-89RF in phenol-water paper chromatography in steps of 0·2
90-93RF in toluene-pyridine-glycolchlorhydrin in steps of 0·2
94-97Ninhydrin colour after collidine-lutidine chromatography and heating 5 min at 100 °C, respectively purple, pink, brown and yellow
98End of side-chain furcated
99-101Number of substituents on the β-carbon atom, respectively 1, 2 or 3
102-111The mean number of lone pair electrons on the side-chain
112-115Number of bonds in the side-chain allowing rotation
116-117Ionic volume within rings slight, or moderate
118-124Maximum moment of inertia for rotation at the α―β bond
125-131Maximum moment of inertia for rotation at the β―γ bond
132-134Maximum moment of inertia for rotation at the γ―δ bond

Grantham's distance

Grantham's distance depends on three properties: composition, polarity and molecular volume.
Distance difference D for each pair of amino acid i and j is calculated as:
where c = composition, p = polarity, and v = molecular volume; and are constants of squares of the inverses of the mean distance for each property, respectively equal to 1.833, 0.1018, 0.000399. According to Grantham's distance, most similar amino acids are leucine and isoleucine and the most distant are cysteine and tryptophan.

Sneath's index

Sneath's index takes into account 134 categories of activity and structure. Dissimilarity index D is a percentage value of the sum of all properties not shared between two replaced amino acids. It is percentage value expressed by, where S is Similarity.

Epstein's coefficient of difference

Epstein's coefficient of difference is based on the differences in polarity and size between replaced pairs of amino acids. This index that distincts the direction of exchange between amino acids, described by 2 equations:
when smaller hydrophobic residue is replaced by larger hydrophobic or polar residue
when polar residue is exchanged or larger residue is replaced by smaller

Miyata's distance

Miyata's distance is based on 2 physicochemical properties: volume and polarity.
Distance between amino acids ai and aj is calculated as where is value of polarity difference between replaced amino acids and and is difference for volume; and are standard deviations for and

Experimental Exchangeability

Experimental Exchangeability was devised by Yampolsky and Stoltzfus. It is the measure of the mean effect of exchanging one amino acid into a different amino acid.
It is based on analysis of experimental studies where 9671 amino acids replacements from different proteins, were compared for effect on protein activity.

Typical and idiosyncratic amino acids

Amino acids can also be classified according to how many different amino acids they can be exchanged by through single nucleotide substitution.
  • Typical amino acids - there are several other amino acids which they can change into through single nucleotide substitution. Typical amino acids and their alternatives usually have similar physicochemical properties. Leucine is an example of a typical amino acid.
  • Idiosyncratic amino acids - there are few similar amino acids that they can mutate to through single nucleotide substitution. In this case most amino acid replacements will be disruptive for protein function. Tryptophan is an example of an idiosyncratic amino acid.

    Tendency to undergo amino acid replacement

Some amino acids are more likely to be replaced. One of the factors that influences this tendency is physicochemical distance. Example of a measure of amino acid can be Graur's Stability Index. The assumption of this measure is that the amino acid replacement rate and protein's evolution is dependent on the amino acid composition of protein. Stability index S of an amino acid is calculated based on physicochemical distances of this amino acid and its alternatives than can mutate through single nucleotide substitution and probabilities to replace into these amino acids. Based on Grantham's distance the most immutable amino acid is cysteine, and the most prone to undergo exchange is methionine.

Patterns of amino acid replacement

Evolution of proteins is slower than DNA since only nonsynonymous mutations in DNA can result in amino acid replacements. Most mutations are neutral to maintain protein function and structure. Therefore, the more similar amino acids are, the more probable that they will be replaced. Conservative replacements are more common than radical replacements, since they can result in less important phenotypic changes. On the other hand, beneficial mutations, enhancing protein functions are most likely to be radical replacements. Also, the physicochemical distances, which are based on amino acids properties, are negatively correlated with probability of amino acids substitutions. Smaller distance between amino acids indicates that they are more likely to undergo replacement.
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