What Is the Protein Sequence?
A protein sequence, defined as the arrangement of amino acids in a protein molecule, constitutes the primary structure of the protein, also known as its basic structure. This sequence not only determines the protein's three-dimensional conformation but also influences its biological function within the organism.
Protein Sequence—Types of Amino Acids
Proteins are macromolecules made up of 20 standard amino acids linked by peptide bonds. These amino acids include glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), serine (Ser), threonine (Thr), cysteine (Cys), methionine (Met), aspartic acid (Asp), asparagine (Asn), glutamic acid (Glu), glutamine (Gln), lysine (Lys), arginine (Arg), histidine (His), phenylalanine (Phe), tryptophan (Trp), and tyrosine (Tyr). The sequence of these amino acids determines the protein's primary structure, which subsequently affects its higher-order structure and function. Amino acids differ in their side chains (R groups), which confer distinct physicochemical properties, such as polarity, charge, and hydrophobicity. These properties play a critical role in protein folding and interactions with other biomolecules.
Protein Sequence and Protein Structure
Protein function is often closely tied to its specific three-dimensional structure, which is determined by its primary structure, i.e., the amino acid sequence. According to the "Central Dogma," the DNA sequence encodes the RNA sequence, which guides the synthesis of the protein and dictates the amino acid sequence. This sequence then undergoes folding and self-assembly to form secondary structures (e.g., α-helices, β-sheets), tertiary structures (the overall 3D conformation), and quaternary structures (complexes composed of multiple polypeptide chains).
Protein folding is a highly organized process regulated by various forces, including hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bonds, and van der Waals forces. These interactions collectively drive the transition from an unordered linear chain to a functional three-dimensional conformation.
Relationship between Protein Sequence and Protein Function
Proteins serve a wide range of functions, including enzyme catalysis, structural support, signal transduction, transport, and immune response. These functions are intimately connected to their amino acid sequence. For example, the active site of an enzyme often contains specific amino acid residues that facilitate substrate transformation through mechanisms such as acid-base catalysis or nucleophilic attack. Structural proteins, which provide support for cells and tissues, are enriched in rigid amino acids such as proline and glycine, which enable the formation of stable helical or folded structures.
Furthermore, the function of a protein can be modulated by post-translational modifications of amino acid residues, such as phosphorylation, glycosylation, and acetylation. These modifications can alter the protein's physicochemical properties and influence its interactions with other molecules, thereby impacting its overall function.
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