S TRUCTURE OF P ROTEIN 1. Primary Structure

Primary structure is the sequence of amino acid residues in proteins and is decided by the genetic codes in genes. The primary structure decides the higher structures of proteins. All proteins are composed of 20 amino acids and the combination of these components leads to the occurrence of tremendous number of proteins with different spatial structures and biological functions.

2.2. Higher Structures

The polypeptide chains of proteins occur as folded and twisted conformation under suitable conditions and these conformations determine the biological and physicochemical properties of the molecules in addition to their amino acid sequences.

2.2.1. Secondary Structure

Secondary structure is the three-dimensional form of local segments of polypeptides.

This term does not involve the conformation of the side chains of amino acid residues. Two forms of periodic secondary structures have been found: α-helices and β-sheet.

The α-helical structure is characterized by the following:

(1) Multiple peptide bond planes rotate through the α-carbon atom spin, twisting each other into a tight solid right-handed helix.

(2) Each helical rotation involves 3.6 amino acid residues. Each residue extends the axial length by 1.5 Å and the angle of rotation per residue is 100°.

(3) α-Helices are stabilized by hydrogen bonding. In this structure, each backbone N-H group is hydrogen bonded to the C=O group of the fourth preceding residue in the same chain.

(4) The side chains of amino acid residues are located on the outer of the helix and their shape, size, and charge affect helix formation. α-Helix is often not found in areas with abundant acidic or basic amino acids due to charge repulsion or areas consisting more amino acids with large side chains, such as tryptophan and isoleucin. Proline is generally not

involved in α-helix formation, because it cannot rotate or hydrogen bond with other amino acids readily. The presence of glycine affects helix stability, because its side chain (H) occupies the minimum space.

The β-sheet structure is characterized by the following:

(1) The β-sheet structure is an extended structure. Amino acid residues involved are arranged in a zigzag pattern and their residues are located on the upside or downside of the pleat plane. The angle between adjacent peptide bond planes is 110°.

(2) The conformation is stabilized by hydrogen bonding of C=O and –NH between adjacent strands of a peptide.

(3) When adjacent strands run in the same direction, the peptide chains are parallel.

When the chains run in opposite directions, a planar, antiparallel sheet structure is stabilized.

Both parallel and antiparallel sheets can occur in one peptide.

(4) In parallel β-sheet, the distance between any two adjacent residues is 0.65 nm and that in anti-parallel β-sheet is 0.7 nm.

2.2.2. Tertiary Structure

The secondary structures of a polypeptide chain can further fold to form a compact three-dimensional structure termed as tertiary structure. The tertiary structure of proteins are stabilized mainly by secondary bonds, including hydrogen bond, hydrophobic interaction, salt linkage, and Vander Wasls force, as shown in Figure 5-1. These secondary bonds might occur between the side chains of amino acid residues that are quite far away in primary structure.

Secondary bonds are non covalent bonds and are affected by the pH, temperature, and ionic strength of the environment and are hence subject to change. Disulfide bond is not a secondary bond, but it can connect two segments of a peptide that are far away in a peptide chain. Hence, disulfide bonds are very important for stabilizing tertiary structures.

Proteins can be divided into two large groups on the basis of conformation: fibrous and globular proteins. Fibrous proteins, such as fibroinare, the slender molecules with axial ratio are greater than 10. Plasma albumin, globulin, and myoglobin, are examples of globular proteins. In globular proteins, hydrophobic groups are located on the interior of a protein and the hydrophilic groups are distributed on the surface. Hence, globular proteins are hydrophilic molecules and most enzymes are globular proteins. The distribution of the side chains leads to the formation of special areas with special biological functions, such as the active center of enzymes. Figure 5-2 shows the folding patterns of two proteins.

2.2.3. Quaternary Structure

Multiple folded peptide chains can combine with each other through secondary bonding to form a more complex structure. This structure is called the quaternary structure of proteins.

Each peptide chain with specific tertiary structures is a subunit of the protein. Hence, quaternary structure is also defined as the arrangement and interaction of subunits. The secondary bonds involved in subunits interaction are loose than those in secondary and tertiary structures and proteins with quaternary structure can dissociate to separate subunits with their conformation unchanged under certain conditions.

a electrovalent bond;

b hydrogen bond;

c hydrophobic bond;

d Vander Wasls force;

e disulfide bond.

Figure 5-1. Secondary bonds involved in tertiary structure stabilization [1].

Figure 5-3 shows the combination pattern of the subunits of hemoglobin. The structures of subunits in a protein may be the same or different. For example, the coat protein of tobacco streak virus consists of 2200 identical subunits and normal hemoglobin A is a tetramer containing two α subunits and two β subunits. The smallest subset of different subunits of a protein is defined as the protomer. For example, the aspartate carbamyl transferase contains six protomers and each protomer consists of one catalytic subunit and one regulatory subunit.

Some proteins can further aggregate into polymers and each repeating unit is called a monomer. According to the number of monomers, protein polymers can be divided into dimer, trimer, oligomer and multimer. For example, insulin might occur as dimer and hexamer in human body.

Figure 5-2. Tertiary structures of myoglobin and triosephosphate isomerase [2].

Figure 5-3. Binding pattern of hemoglobin subunits [3].

2.3. Structure-Function Relationships

2.3.1. Relationship between Primary Structure, Conformation and Function

Primary structure determines the spatial arrangement of peptide chains and the conformation is mainly maintained by various secondary bonds of side chains in amino acid residues. Once a polypeptide chain is synthesized in vivo, the protein folds automatically to the correct conformation.

Proteins with similar primary structure have similar conformations and functions. For instance, proteins of same functions isolated from different organisms only differ slightly in primary structure and the difference is much smaller between organisms with closer evolutionary relationships.

2.3.2. Relationship between Spatial Conformation and Function

The diverse functions of proteins are closely related to their spatial conformations. Once the conformations changed, the functional activities vary accordingly. The relationship between conformation and function of proteins can be evidenced by protein denaturation and renaturation, which will be detailed later.

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