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Introduction to Proteins and Enzymes

CHAPTER MENU

• 1.1 Protein Structure
• 1.2 Enzymes
  • References

1.1 Protein Structure

Proteins are the central functional molecules of life, encoded by DNA, translated, and expressed to carry out the essential functions of the cell. The building blocks for proteins are amino acids: every amino acid contains a positively charged amine group (N-terminus), a negatively charged carboxyl group (C-terminus), a hydrogen atom, and an R group, all centered around a chiral carbon (alpha carbon, Ca) (Figure 1.1). The presence of a chiral carbon results in stereoisomerism; naturally occurring amino acids are L-isomers, and D-isomers can arise during chemical synthesis. There are 20 different R groups, which give rise to 20 different amino acids (Figure 1.2). Amino acids can be charged (negatively and positively), polar and non-polar. These different properties contribute to different bonding interactions and architecture of the protein (Section 1.1.4) [1, 2].

1.1.1 Primary Structure

Each protein is formed of a unique sequence of amino acids, which determines the properties of the protein. These are linked by covalent peptide bonds between the amino group of one residue and the carboxyl group of the next, forming long polypeptide chains of amino acids. The number and sequence of amino acids in a polypeptide chain is known as the primary (1°) structure of a protein and is determined by the DNA sequence of the gene. Mutations to the DNA sequence may lead to changes in the amino acids in the polypeptide chain, thus altering the primary structure of the protein [1, 2].

1.1.2 Secondary Structure

The secondary structure of proteins describes the layout of the protein backbone in three dimensions. This structure is formed from the individual peptide bonds between residues, which usually are planar and trans (with the exception of proline). There are common elements that often combine to contribute to the protein backbone describing its overall fold. Rotations around the peptide bond enable hydrogen bond formation between the carbonyl oxygen group and amide hydrogen atom of spatially adjacent amino acids, resulting in folding of the polypeptide chains into secondary (2°) structures. Hydrogen bonding can also occur between amino acid side chains. Common secondary structures include the alpha helix, the beta sheet, loops, and many protein structures contain a combination of all elements [1].

Figure 1.1 General amino acid structure.

Figure 1.2 Chemical structure of amino acids.

1.1.2.1 The Alpha Helix

One of the most important structural features is the alpha helix (Figure 1.3). This is a right-handed helical structure containing 3.6 amino acid residues in each turn. It is formed when each N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues before it in the polypeptide chain. This occurs as the C=O groups in the helix are parallel to the axis and are directionally aligned with the N-H groups to which the hydrogen bond is formed. The amino acid side chains are positioned away from the axis. Alpha helices can vary in length, although there are few examples of proteins where the helix length extends beyond 40 residues. Clearly, the first and last residue of an alpha helix cannot make hydrogen bonds to contribute to the helix, so these residues are often amino acids that can make hydrogen bonds with other parts of the protein or with the solvent. Some residues are more likely to form alpha helices than others, with alanine, leucine, arginine, methionine, and lysine having the highest propensity, although the tendency to form helices will depend on the identities of the neighboring residues. Conversely, residues such as aspartate, glycine, and proline tend not to form alpha helices. Proline cannot donate an amide hydrogen bond and also interferes sterically with the backbone of the preceding turn. However, proline may sometimes be positioned as the first residue in an alpha helix, providing structural rigidity to the helix. Often, alpha helices display an amphipathic nature, with hydrophobic residues located on one side and hydrophilic residues on the other. Another feature of alpha helices is that they tend to have a macrodipole, with the Nterminus being the positive pole. This arises as the individual microdipoles from the carbonyl groups of the peptide bonds in the helix align along the axis [1, 2].

Figure 1.3 The alpha helix.
The structure of the alpha helix is shown: the backbone of the helix is represented in cartoon, and sticks show the amino acid side chains protruding from the backbone. The colors used are from the Clustal-X color scheme (Table 1.1).

1.1.2.2 The Beta Sheet

Another common structural motif in proteins is the beta sheet (Figure 1.4). When the backbone of a protein exists in an extended conformation (beta strand), it is possible for residues to make complementary hydrogen bonds with another beta strand. These interactions may occur when the chains are aligned in the same or opposite directions. When the chains are aligned in the same direction, the arrangement is termed a parallel beta sheet, and when the chains alternate in direction, it is termed an antiparallel beta sheet. Usually, an extensive hydrogen bond network is established where the N-H groups in the backbone of one strand establish hydrogen bonds with the C=O groups in the backbone of the adjacent strand. Often, beta sheets contain around 10 residues but can be much shorter (as low as 2 or 3 residues). Beta sheets often contain large aromatic residues (tyrosine, phenylalanine, and tryptophan) and branched amino acids (threonine, isoleucine, and valine) [1, 2].

Figure 1.4 The beta sheet.
The structure of a beta sheet is shown: the backbone of the sheet is represented in cartoon, and sticks show the amino acid side chains protruding from the backbone.

1.1.2.3 Loops

There are segments of a protein that connect the alpha helix and beta sheet elements together, which in themselves do not have recognizable regular structural patterns. These secondary structural elements are termed loops (Figure 1.5). Loops are an important component of secondary structure, often containing as much as half of the total number of residues in a protein [3]. Loops often contribute significantly to the overall shape, dynamics, and physicochemical properties of the protein [4]. Loops are frequently located on the protein's surface in solvent-exposed regions and are often involved in important interactions. Despite the lack of patterns, loops do not appear to be completely random structures, and they have been classified in various ways, including their geometrical shape [5]. However, even though their importance is recognized, loop structure remains difficult to predict.

Figure 1.5 Loop region.
The structure of a loop region is shown: the backbone of the sheet is represented in cartoon, and sticks show the amino acid side chains protruding from the backbone.

Table 1.1 Clustal-X color scheme for coloring amino acids.

The primary structure of a protein influences the secondary structure, with certain residues more likely to form one structure over the other; for example, proline residues are often called "helix breakers" as their cyclic nature induces a kink in the polypeptide chain and prevent alpha helix formation. Glycine residues, for example, also are frequently involved in tight turns as they are small and flexible [2].

The image for the loop structure has been colored by structure (in the program MOE2022; red: alpha helix, yellow: beta sheet, loop: white, turn: blue). The alpha helix and beta sheet above (Figures 1.3 and 1.4) have been colored using the Clustal-X color scheme (Table 1.1).

1.1.3 Tertiary Structure

The three-dimensional (3D) structure of a protein is defined by the position of all the atoms of the polypeptide chain arranged in 3D space. This is termed the tertiary (3°) structure, and it comprises the arrangement of the secondary structural elements, as described in Section 1.1.2,...