9.5: Protein Structure

Learning Objectives

• Describe the four levels of protein structure.
• Identify the types of attractive interactions that hold proteins in their most stable three-dimensional structure.

Each of the thousands of naturally occurring proteins has its own characteristic amino acid composition and sequence that result in a unique three-dimensional shape. Proteins are compounds of high molecular mass consisting largely or entirely of chains of amino acids. Hemoglobin is a transport protein found in the red blood cells. It transports O₂ from the lungs to the cells. Collagen is a structural protein found in tendon, cartilage, bone, blood vessels, and teeth. It make up one-third of the total protein in the human body. Collagen is strong, water insoluble and resistant to chemical change.

Levels of Protein Structure

The structure of proteins is generally described as having four organizational levels.

Primary Structure

The first of these is the primary structure, which is the sequence of amino acids in a protein’s polypeptide chain or chains, beginning with the free amino group and maintained by the peptide bonds connecting each amino acid to the next.

For peptides and proteins to be physiologically active, it is not enough that they incorporate certain amounts of specific amino acids. The order, or sequence, in which the amino acids are connected is also of critical importance. Bradykinin is a nine-amino acid peptide produced in the blood that has the following amino acid sequence:

arg-pro-pro-gly-phe-ser-pro-phe-arg

This peptide lowers blood pressure, stimulates smooth muscle tissue, increases capillary permeability, and causes pain. When the order of amino acids in bradykinin is reversed,

arg-phe-pro-ser-phe-gly-pro-pro-arg

the peptide resulting from this synthesis shows none of the activity of bradykinin.

The primary structure of insulin, composed of 51 amino acids, is shown in Figure \(\PageIndex{1}\).

Figure \(\PageIndex{1}\): Primary Structure of Human Insulin. Human insulin, whose amino acid sequence is shown here, is a hormone that is required for the proper metabolism of glucose.

Just as millions of different words are spelled with our 26-letter English alphabet, millions of different proteins are made with the 20 common amino acids. However, just as the English alphabet can be used to write gibberish, amino acids can be put together in the wrong sequence to produce nonfunctional proteins. Although the correct sequence is ordinarily of utmost importance, it is not always absolutely required. Just as you can sometimes make sense of incorrectly spelled English words, a protein with a small percentage of “incorrect” amino acids may continue to function. However, it rarely functions as well as a protein having the correct sequence. There are also instances in which seemingly minor errors of sequence have disastrous effects. For example, in some people, every molecule of hemoglobin (a protein in the blood that transports oxygen) has a single incorrect amino acid unit out of about 300 (a single valine replaces a glutamic acid). That “minor” error is responsible for sickle cell anemia, an inherited condition that usually is fatal.

Secondary Structure

A protein molecule is not a random tangle of polypeptide chains. Instead, the chains are arranged in unique but specific conformations. The term secondary structure refers to the fixed arrangement of the polypeptide backbone. On the basis of X ray studies, Linus Pauling and Robert Corey postulated that certain proteins or portions of proteins twist into a spiral or a helix. This helix is stabilized by intrachain hydrogen bonding between the carbonyl oxygen atom of one amino acid and the amide hydrogen atom four amino acids up the chain (located on the next turn of the helix) and is known as a right-handed α-helix. X ray data indicate that this helix makes one turn for every 3.6 amino acids, and the side chains of these amino acids project outward from the coiled backbone (Figure \(\PageIndex{2}\)). The α-keratins, found in hair and wool, are exclusively α-helical in conformation. Some proteins, such as gamma globulin, chymotrypsin, and cytochrome c, have little or no helical structure. Others, such as hemoglobin and myoglobin, are helical in certain regions but not in others.

Figure \(\PageIndex{2}\) A Ball-and-Stick Model of an α-Helix. This ball-and-stick model shows the intrachain hydrogen bonding between carbonyl oxygen atoms and amide hydrogen atoms. Each turn of the helix spans 3.6 amino acids. Note that the side chains (represented as green spheres) point out from the helix.

Another common type of secondary structure, called the β-sheet conformation, is a sheetlike arrangement in which two or more extended polypeptide chains (or separate regions on the same chain) are aligned side by side. The aligned segments can run either parallel or antiparallel—that is, the N-terminals can face in the same direction on adjacent chains or in different directions—and are connected by interchain hydrogen bonding (Figure \(\PageIndex{3}\)). The β-sheet is particularly important in structural proteins, such as silk fibroin. It is also seen in portions of many enzymes, such as carboxypeptidase A and lysozyme.

Figure \(\PageIndex{3}\): A Ball-and-Stick Model of the β-Pleated Sheet Structure in Proteins. The side chains extend above or below the sheet and alternate along the chain. The protein chains are held together by interchain hydrogen bonding.

Tertiary Structure

Tertiary structure refers to the unique three-dimensional shape of the protein as a whole, which results from the folding and bending of the protein backbone. The tertiary structure is intimately tied to the proper biochemical functioning of the protein. This unique folding conformation leads to a native (biologically acitive) molecule. Figure \(\PageIndex{4}\) shows a depiction of the three-dimensional structure of insulin.

Figure \(\PageIndex{4}\): A Ribbon Model of the Three-Dimensional Structure of Insulin. The spiral regions represent sections of the polypeptide chain that have an α-helical structure, while the broad arrows represent β-pleated sheet structures.

Four major types of attractive interactions determine the shape and stability of the tertiary structure of proteins.

1. Ionic bonding or Salt Bridges: Ionic bonds result from electrostatic attractions between positively and negatively charged side chains of amino acids. For example, the mutual attraction between an aspartic acid carboxylate ion and a lysine ammonium ion helps to maintain a particular folded area of a protein (part (a) of Figure \(\PageIndex{5}\)).
2. Hydrogen Bonding: Hydrogen bonding forms between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen atom attached to another oxygen atom or a nitrogen atom, such as those found in polar amino acid side chains shown below in part (b) of Figure \(\PageIndex{5}\).
3. Disulfide Bonds: Two cysteine amino acid units may be brought close together as the protein molecule folds. Subsequent oxidation of the thiol functional group and linkage of the sulfur atoms leads to the formation of intrachain disulfide linkages part (c) of Figure \(\PageIndex{5}\). The disulfide bridges have a strong stabilizing effect on the tertiary structure.

4. London's forces: These forces arise between nonpolar parts of a molecule. London's forces are weak but can be important when other types of interactions are either missing or minimal part (d) of Figure \(\PageIndex{5}\)). This is the case with fibroin, the major protein in silk, in which a high proportion of amino acids in the protein have nonpolar side chains. The term hydrophobic interaction is often used as a synonym for dispersion forces. Because nonpolar groups cannot engage in hydrogen bonding, the protein folds in such a way that these groups are buried in the interior part of the protein structure, minimizing their contact with water. This folding rule is "nonpolar in, polar out".

Figure \(\PageIndex{5}\): Tertiary Protein Structure Interactions. Four interactions stabilize the tertiary structure of a protein: (a) ionic bonding (salt bridges), (b) hydrogen bonding, (c) disulfide linkages, and (d) dispersion forces.

A prosthetic group is a nonpeptide component tightly bound to a polypeptide chain. The heme group in hemoglobin is an example of a prosthetic group. Proteins that require a prosthetic group for biological activity are called complex proteins or conjugated proteins. Simple proteins do not require a prosthetic group. At the center of heme is an iron(II) ion (Fe²⁺) which binds to an oxygen molecule.

Figure \(\PageIndex{6}\):The heme is the prosthetic group part of the protein hemoglobin.

Quaternary Structure

When a protein contains more than one polypeptide chain, each chain is called a subunit. The arrangement of multiple subunits represents a fourth level of structure, the quaternary structure of a protein. Hemoglobin, with four polypeptide chains or subunits, is a good example of a protein having quaternary structure as shown in Figure \(\PageIndex{7}\). The quaternary structure of a protein is produced and stabilized by the same kinds of interactions that maintain the tertiary structure such as the salt bridges, disulfide bonds, and IMF's such as hydrogen bonding and hydrophobic effect. Since there are four subunits in hemoglobin, there are four heme prosthetic groups with four Fe²⁺ ions. Each subunit can bind to an oxygen molecule (O₂). So hemoglobin can bind to and carry four oxygen molecules.

Figure \(\PageIndex{7}\) The Quaternary Structure of Hemoglobin. Hemoglobin is a protein that transports oxygen throughout the body.

Source: Image from the RCSB PDB (www.pdb.org(opens in new window)) of PDB ID 1I3D (R.D. Kidd, H.M. Baker, A.J. Mathews, T. Brittain, E.N. Baker (2001) Oligomerization and ligand binding in a homotetrameric hemoglobin: two high-resolution crystal structures of hemoglobin Bart's (gamma(4)), a marker for alpha-thalassemia. Protein Sci. 1739–1749).

A schematic representation of the four levels of protein structure is in Figure \(\PageIndex{8}\).

Figure \(\PageIndex{8}\): Levels of Structure in Proteins

The primary structure consists of the specific amino acid sequence. The resulting peptide chain can twist into an α-helix, which is one type of secondary structure. This helical segment is incorporated into the tertiary structure of the folded polypeptide chain. The single polypeptide chain is a subunit that constitutes the quaternary structure of a protein, such as hemoglobin that has four polypeptide chains.

Fibrous and Globular Proteins

Once proteins form and have developed all levels of their structure, they can be classified as either fibrous or globular. The two major structural classifications of proteins are based on general qualities: whether the protein is (1) fiber-like and insoluble or (2) globular and soluble. Some proteins, such as those that compose hair, skin, muscles, and connective tissue, are fiber-like.

The fibrous proteins are insoluble in water and usually serve structural, connective, and protective functions. Examples of fibrous proteins are keratins, collagens, myosins, and elastins. Hair and the outer layer of skin are composed of keratin. Connective tissues contain collagen. Myosins are muscle proteins and are capable of contraction and extension. Elastins are found in ligaments and the elastic tissue of artery walls.

Globular proteins, the other major class, are soluble in aqueous media. In these proteins, the chains are folded so that the molecule as a whole is roughly spherical. Familiar examples include egg albumin from egg whites and serum albumin in blood. Serum albumin plays a major role in transporting fatty acids and maintaining a proper balance of osmotic pressures in the body. Hemoglobin and myoglobin, which are important for binding oxygen, are also globular proteins.

Summary

Proteins can be divided into two categories: fibrous, which tend to be insoluble in water, and globular, which are more soluble in water. A protein may have up to four levels of structure. The primary structure consists of the specific amino acid sequence. The resulting peptide chain can form an α-helix or β-pleated sheet (or local structures not as easily categorized), which is known as secondary structure. These segments of secondary structure are incorporated into the tertiary structure of the folded polypeptide chain. The quaternary structure describes the arrangements of subunits in a protein that contains more than one subunit. Four major types of attractive interactions determine the shape and stability of the folded protein: ionic bonding, hydrogen bonding, disulfide linkages, and dispersion forces.