Primary structure of proteins

The primary structure of a polypeptide chain is its amino acid sequence.

Main chain and side residues (R). Note the start in the amino-terminal and the completion in the carboxi-terminal.

The primary structure is the amino acid sequence of a polypeptide chain. proteins across the ribosome. Amino acids are covalently linked by peptide bonds. Due to the fact that the formation of the peptide bond occurs by a condensation reaction, a water molecule is released, product of the -OH of the carboxyl and of an -H of the amino group, and we speak properly of the sequence of residues of amino acids (or simply residues). The main chain is formed by the succession of peptide bonds that forms a backbone of the polypeptide chain. The first residue has its free α-NH₂ group and the last residue has its free α-COOH group. Thus, the N-terminus and C-terminus are established, with which the sequence of residues begins and ends.

The way of folding, and therefore the function of the polypeptide chain is determined by the sequence of the residues. The amino acid sequence determines the other structural levels and the properties of each polypeptide, since the side chains of each amino acid present particular physicochemical properties. Thus, amino acids interact by various intermolecular forces of attraction with water, hydrophobic compounds, and the side chains of nearby amino acids.

Primary structure is the most basic way to describe proteins. The other levels of protein structure are secondary structure and tertiary structure. The association of several polypeptide chains that results in a functional protein originates a higher level of organization, the so-called quaternary structure.

When a protein undergoes hydrolysis, the amino acids that constitute it are released, which can be identified in a certain amount.

Between the primary structure and the three-dimensional shape of proteins

The amino acid sequence of a polypeptide chain determines the type of non-covalent interactions that will occur (both between the protein itself and with its environment) and the degree of freedom to adopt different stable conformations at physiological temperature. Some effects of certain amino acids on the structure of the chain are:

• alphatic hydrophobic amino acids (Alanine (Ala), Valina (Val), Isoleucina (Ile), Leucina (Leu)): They are found in the internal region of proteins or, in the case of membrane proteins, interacting with hydrophobic tails of fatty acids. They can also keep proteins in reversible form and allow the union with hydrophobic substrates in enzymes (P.E.g.: the binding of phospholipases (PL) with its substrate, the phospholipids of the membranes, is stabilized by the interaction of hydrophobic amino acids with hydrophobic glues of fatty acids). Some protein structures formed by hydrophobic amino acids are leucine zippers, hydrophobic pockets, hydrophobic helice alpha.

• amino acids aromatic hydrophobic (Fenilalanine (Phe), Tyrosine (Tyr), Triptófano (Trp)): Like alphatic hydrophobic amino acids, protein is often found in regions where they are not in contact with water. In the case of tyrosine and tryptophan, as they have a polar group in their lateral chain, they could present some interaction with polar substances.

• polar amino acids without net charge (Treonin (Thr), Serina (Ser), Asparagine (Asn), Glutamine (Gln)), acids (Aspartate (Asp), Glutamato (Glu)) and basic (Histidina (His), Lisine (Lys), Arginine (Arg)): They are located on the protein surface in contact with water, ions and other polar molecules. They are found on the surface of the holes in membrane proteins forming ionic channels and other polar molecules. They enable the solubility of protein in the aqueous environment.

• Cisteine (Cys): It is a sulfur amino acid that can be oxidized to form disulfuro bridges (-S-S-) with a second cysteine located in the same polypepidic chain or in a different chain. This gives the protein structure greater stability by limiting its deformation.

• Glicina (Gly): By the small size of its lateral residue can be located in very narrow places within the protein, allowing it a more compact form. In certain structures such as propellers can be a destabilizing factor because it allows greater freedom of movement.

• Prolina (Pro): Due to its cyclical structure, it allows abrupt changes in the direction of the polypeptide chain and limits the possibility of random movement of the chain. It is in structures such as beta spins and gamma spins.

Post-translational modifications

Some lateral residues of amino acids in certain proteins are modified after translation by acetylation, methylation, carboxylation, hydroxylation, glycosylation and phosphorylation, among others, changing their electronic properties. Some examples are:

• Fosfoserina
• 4-hydroxyproline
• γ-hydroxylisine
• Acid γ-caboxiglutamic
• Acetyl lisine
• 3-metilhistidina

Why know the primary structure of proteins

Knowing the primary structure of a protein is important to understand its function (since this depends on the amino acid sequence and the form it adopts), as well as in the study of genetic diseases. It is possible that the origin of a genetic disease lies in an abnormal sequence. This abnormality, if severe, could result in the protein's function not performing properly, or even not performing at all.

At the same time, the comparative study of the primary structure of proteins in organisms of different species makes it possible to identify evolutionary patterns at the molecular level. Differences between the sequences of two or more proteins that have identical or similar functions can be the product of natural selection or other evolutionary mechanisms (such as genetic drift or neutralistic evolution). On the other hand, conserved sequences usually correspond to regions structurally or functionally essential for the biological function of said proteins. From these studies, protein families are established.

Deduction of the primary structure

The amino acid sequence is specified in DNA by the nucleotide sequence. There is a conversion system, called the genetic code, which is used to deduce the amino acid sequence of a polypeptide chain from the nucleotide sequence of the gene. However, certain modifications during DNA transcription, produced by alternative splicing or splicing, do not always allow this conversion to be done directly.

To obtain the amino acid sequence from a purified protein sample, methods such as the sequencing technique from the N-terminal by Edman degradation, or the fragmentation of the chain into small peptides and their subsequent identification by mass spectrometry.

Effect of genetic mutations on the primary structure of proteins

Point-type genetic mutations can alter the amino acid sequence of the polypeptide chain. These modifications can produce:

• conservative changes: in which the nature of the lateral chain is maintained (e.g., if an Asparagine residue is replaced by one of Glutamine); in this case, the changes in the structure and protein function are not so significant.
• changes not conservative: where the mutation replaces the amino acid with another of different properties (e.g., an Arginine residue is replaced by another of Prolina). The latter type of changes in the peptide chain may alter the function of the protein and if they occur in sexual cells they may become perpetuated in future generations, being a very important factor in evolutionary processes.
• No change: Silent or synonym mutations in the gene produce the same sequence of amino acids. This is because the genetic code is degenerated, that is, it contains codones that are redundant. For example, amino acid glycine has four condoms: GGA, GGU, GGG and GGC, which means that if a mutation occurs that alters the third position nucleotide, the amino acid that is incorporated into the protein will always be glycine.

Other types of mutations, such as deletion, insertion, duplication, and inversion, generally produce proteins that are altered in size (larger or smaller, depending on the region of the gene where the mutation occurred) or three-dimensional structure, or both. In almost all of these cases, the aberrant proteins lead to severe physiological problems.