Protein Structure and Function
Proteins consist of strings of individual subunits called amino acids that are chemically bonded together with peptide bonds. Once amino acids are bonded, the resulting molecule is called a polypeptide. The properties and arrangement of the amino acids in the polypeptide cause it to fold into a specific shape or conformation that is required for proper protein function. Proteins have been called the “workhorses” of the cell because they perform most of the activities encoded in the genes of the cell. Proteins function by binding to other molecules, frequently to other proteins. The precise three-dimensional shape of a protein determines the specific molecules it will be able to bind to, and for many proteins binding is specific to just one other specific type of molecule.
In 1973, Christian B. Anfinsen
performed experiments that showed that the three-dimensional structure of a protein is determined by the sequence of its amino acids. He used a protein called ribonuclease (RNase), an enzyme that degrades RNA in the cell. The ability of ribonuclease to degrade RNA is dependent upon its ability to fold into its proper three-dimensional shape. Anfinsen showed that if the enzyme was completely unfolded by heat and chemical treatment (at which time it would not function), it formed a linear chain of amino acids. Although there were 105 possible conformations that the enzyme could take upon refolding, it would refold into the single correct functional conformation upon removal of heat and chemicals. This established that the amino acid sequences of proteins, which are specified by the genes of the cell, carry all of the information necessary for proteins to fold into their proper three-dimensional shapes.
To understand protein conformation better, it is helpful to analyze the underlying levels of structure that determine the final three-dimensional shape. The primary structure of a polypeptide is the simplest level of structure and is, by definition, its amino acid sequence. Because the primary structure of polypeptides ultimately determines all succeeding levels of structure, knowing the primary structure should theoretically allow scientists to predict the final three-dimensional structure. Building on a detailed knowledge of the structure of many proteins, scientists have developed computer programs that are able to predict three-dimensional shape with some degree of accuracy.
Primary Protein Structure
There are twenty naturally occurring amino acids that are commonly found in proteins, and each of these has a common structure consisting of a nitrogen-containing amino group (—NH2), a carboxyl group (—COOH), a hydrogen atom (H), and a unique functional group referred to as an R group, all bonded to a central carbon atom (known as the alpha carbon, or Cα) as shown in the following figure:
The uniqueness of each of the twenty amino acids is determined by the R group. This group may be as simple as a hydrogen atom (in the case of the amino acid glycine) or as complex as a ring-shaped structure (as found in the amino acid phenylalanine). It may be charged, either positively or negatively, or it may be uncharged.
Cells join amino acids together to form peptides (strings of up to ten amino acids), polypeptides (strings of ten to one hundred amino acids), or proteins (single or multiple polypeptides folded and oriented to one another so they are functional). The amino acids are joined together by covalent bonds, called peptide bonds (in the box in the following figure), between the carbon atom of the carboxyl group of one amino acid (—COOH) and the nitrogen atom of the amino group (—NH2) of the next adjacent amino acid:
During the formation of the peptide bond, a molecule of water (H2O) is lost (an -OH from the carboxyl group and an -H from the amino group), so this reaction is also called a dehydration synthesis. The result is a dipeptide (a peptide made of two amino acids joined by a peptide bond) that has a “backbone” of nitrogens and carbons (N—Cα—C—N—Cα—C) with other elements and R groups protruding from the backbone. An amino acid may be joined to the growing peptide chain by formation of a peptide bond between the carbon atom of the free carboxyl group (on the right of the preceding figure) and the nitrogen atom of the amino acid being added. The end of a polypeptide with an exposed carboxyl group is called the C-terminal end, and the end with an exposed amino group is called the N-terminal end.
The atoms and R groups that protrude from the backbone are capable of interacting with each other, and these interactions lead to higher-order secondary, tertiary, and quaternary structures.
Secondary Structure
The next level of structure is secondary structure, which involves the formation of hydrogen bonds between the oxygen atoms in carboxyl groups with the hydrogen atoms of amino groups from different parts of the polypeptide. Hydrogen bonds are weak bonds that form between atoms that have a very strong attraction for electrons (such as oxygen or nitrogen), and a hydrogen atom that is bound to another atom with a very strong attraction for electrons. Secondary structure does not involve the formation of bonds with R groups or atoms that are parts of R groups, but involves bonding just between amino and carboxyl groups that are in the peptide bonds making up the backbone of polypeptides.
These hydrogen bonds between backbone molecules lead to the formation of two major types of structures: alpha helices and beta-pleated sheets. An alpha helix is a rigid structure shaped very much like a telephone cord; it spirals around as the oxygen of one amino acid of the chain forms a hydrogen bond with the hydrogen atom of an amino acid five amino acids away on the protein strand. The rigidity of the structure is caused by the large number of hydrogen bonds (individually weak but collectively strong) and the compactness of the helix that forms. Many alpha helices are found in proteins that function to maintain cell structure.
Beta sheets are formed by hydrogen bonding between amino acids in different regions (often very far apart on the linear strand) of a polypeptide. The shape of a beta-pleated sheet may be likened to the bellows of an accordion or a sheet of paper that has been folded multiple times to form pleats. Because of the large number of hydrogen bonds in them, beta sheets are also strong structures, and they form planar regions that are often found at the bottom of “pockets” inside proteins to which other molecules attach.
In addition to alpha helices or beta-pleated sheets, other regions of the protein may have no obvious secondary structure; these regions are said to have a “random coil” shape. It is the combinations of random coils, alpha helices, and beta sheets that form the secondary structure of the protein.
Tertiary Structure
The final level of protein shape (for a single polypeptide or simple protein) is called tertiary structure. Tertiary structure is caused by the numerous interactions of R groups on the amino acids and of the protein with its environment, which is usually aqueous (water based). Various R groups may either be attracted to and form bonds with each other, or they may be repelled from each other. For example, if an R group has an overall positive electrical charge, it will be attracted to R groups with a negative charge but repelled from other positively charged R groups. For a polypeptide with one hundred amino acids, if amino acid number 6 is negatively charged, it could be attracted to a positively charged amino acid at position 74, thus bringing two ends of the protein that are linearly distant into close proximity. Many of these attractions lead to the formation of hydrogen, ionic, or covalent bonds. For example, sulfur is contained in the R groups of a few of the amino acids, and sometimes a disulfide bond (a covalent bond) will be formed between two of these. It is the arrangement of disulfide bonds in hair proteins that gives hair its physical properties of curly versus straight. Hair permanent treatments actually break these disulfide bonds and then reform them when the hair is arranged as desired. Many other R groups in the protein will also be attracted to or repelled from each other, leading to an overall folded shape that is most stable. In addition, because most proteins exist in an aqueous environment in the cell, most proteins are folded such that their amino acids with hydrophilic R groups (R groups attracted to water) are on the outside, while their amino acids with hydrophobic R groups (R groups repelled from water) are tucked away in the interior of the protein.
Quaternary Structure
Many polypeptides are nonfunctional until they physically associate with another polypeptide, forming a functional unit made up of two or more subunits. Proteins of this type are said to have quaternary structure. Quaternary structure is caused by interactions between the R groups of amino acids of two different polypeptides. For example, hemoglobin, the oxygen-carrying protein found in red blood cells, functions as a tetramer, with four polypeptide subunits.
Because secondary, tertiary, and quaternary interactions are caused by the R groups of the specific amino acids, the folding is ultimately dictated by the amino acid sequence of the protein. Although there may be numerous possible final conformations that a polypeptide could take, it usually assumes only one of these, and this is the conformation that leads to proper protein function. Many polypeptides are capable of folding into their final conformation spontaneously. More complex ones may need the assistance of other proteins, called chaperones, to help in the folding process.
Impact and Applications
The function of a protein may be altered by changing its shape, because proper function is dependent on proper conformation. Many genetic defects are detrimental because they represent a mutation that results in a change in protein structure. Changes in protein conformation are also an integral part of metabolic control in cells. Normal cellular processes are controlled by “turning on” and “turning off” proteins at the appropriate time. A protein’s activity may be altered by attaching a molecule or ion to that protein that results in a change of shape. Because the shape is caused by R group interactions, binding of a charged ion such as calcium to the protein will alter these interactions and thus alter the shape and function of the protein. One molecular “on/off” switch that is used frequently within a cell involves the attachment or removal of a phosphate group to or from a protein. Attachment of a phosphate will significantly alter the shape of the protein by repelling negatively charged amino acids and attracting positively charged amino acids, which will either activate the protein to perform its function (turn it on) or deactivate it (turn it off).
Cancer and diseases caused by bacterial infections or viral infections are often the result of nonfunctional proteins that have been produced with incorrect shapes or that cannot be turned on or off by a molecular switch. The effects may be minor or major, depending upon the protein, its function, and the severity of the structural deformity. Understanding how a normal protein is shaped and how it is altered in the disease process allows for the development of drugs that may block the disease. This may be accomplished by blocking or changing the effect of the protein of interest or by generating drugs or therapies that mimic the normal functioning of the protein. Thus, understanding protein structure is essential for understanding proper protein function and for developing molecular-based disease treatments.
Key terms
amino acid
:
the basic subunit of a protein; there are twenty commonly occurring amino acids, any of which may join together by chemical bonds to form a complex protein molecule
enzymes
:
proteins that are able to increase the rate of chemical reactions in cells without being altered in the process
hydrogen bond
:
a weak bond that helps stabilize the folding of a protein
polypeptide
:
a chain of amino acids joined by chemical bonds
R group
:
a functional group that is part of an amino acid that gives each amino acid its unique properties
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