LEVELS OF PROTEIN STRUCTURE
1. Sequence of amino acids represents the primary structure of a polypeptide.
[As we have said, a critical feature of a protein is its ability to fold into a 3-Dimensional conformation. Each protein exists in a unique conformation (or sometimes in a series of alternate conformations. The conformation is described in terms of several levels of structure.]
2. Secondary structure is generated by the folding of the primary sequence. This is possible because of the ability to move about bonds of free rotation. Secondary structure refers to the path that the polypeptide backbone of the protein follows in space.
Protein structures are extremely versatile but certain types of secondary structure are relatively common. They result from hydrogen bonding between the NH and CO groups of the polypeptide backbone.
The two most common types of secondary structure observed are the alpha helix & beta-sheet
ALPPHA HELIX
Imagine the polypeptide backbone as winding in a coil on the surface of a cylinder, with the side-groups protruding from the cylindrical surface. The a helix is stabilized by hydrogen bonds formed between the C=O group of one peptide bond and the NH group of the peptide bond four residues farther along the polypeptide chain. So, one turn of helix for ~ every 4 amino acids.
Remember, interactions are not between side chains in this case. In fact if reactive side chains are present in the polypeptide this will interfere with the helical structure. Polyglycine which has only H as an R group forms an helix its entire length.
See Figure in Text
The alpha helix is a common component of protein secondary structures. Individual segments of alpha helix may be quite short.
beta sheet
A polypeptide chain can be extended into a sheet-like structure by hydrogen bonding with another chain that runs in the same or opposite direction. Once again, the hydrogen bonding involves the C=O group of one peptide bond and the NH group of another. Beta-sheet structure.
See Figure in text
As well as occurring between two different polypeptide chains, this type of structure can be formed between two sections of a single polypeptide chain arranged so that the adjacent regions are in reverse orientation.
Discuss principle of parallel vs anti-parallell
Tertiary Structure Refers to the organization in three dimensions of all the atoms in the polypeptide chain, including the R groups as well as the polypeptide backbone. In a protein consisting of a single polypeptide chain, this level describes the complete structure. Proteins can be divided into two general types on the basis of their tertiary structure:
Fibrous proteins and Globular Proteins
Fibrous
Fibrous proteins are elongated structures, with the polypeptide chains arranged in long strands (parallel strands along a single axis). Long fibers or sheets. Physically tough. The tertiary structure may be based on alpha helix or Beta sheet. The particular form of secondary structure may stretch through a large part of the protein. The fibrous proteins are major structural components of the cell or tissue, for example, they are prominent in connective tissues. Thus their role tends to be static in providing a structural framework.
Examples: collagen (tendon, cartilage, and bone), elastin (skin), tubulin and actin (cell shape, motility, muscle movement)
Globular
Tightly folded polypeptide chains, having a much more compact structure. The tertiary structure is generally rather irregular, often containing many different types of secondary structure. Many globular proteins consist of partly helical and partly non-helical secondary structures. Globular proteins include most enzymes and most of the proteins involved in gene expression and regulation with which we will be involved. Their roles tend to be dynamic, involving the ability to catalyze reactions or change conformation.
If globular proteins loose their 3D structure (i.e. become denatured) there will be a corresponding loss in the activity of the protein.
FORCES WHICH STABILIZE TERTIARY STRUCTURE:
-In many proteins, one of the important features responsible for establishing the tertiary structure is the formation of disulfide bonds S-S bonds (between cysteines).
See Figure in Text (p.51)
A major force underlying the acquisition of 3D conformation in all proteins is the formation of noncovalent bonds. The formation of noncovalent bonds is strongly influenced by the aqueous environment. A major factor that influences these reactions is the structure of water itself, which forms a transient network of connections between individual molecules. The major force in this network is the hydrogen bond.
-The polarization of the (C=O ) and (N-H or O-H )bonds allows the formation of a hydrogen bond between the two groups. Hydrogen bonds commonly form between the NH and CO groups of the peptide backbone.
-Hydrogen bonds also form between amino acids with polar side groups.
-Ionic interactions occur between amino acids with oppositely charged groups (i.e. between acidic and basic amino acids). The strength of the ionic bond is enormously affected by circumstances. In a solid crystal, the interaction between Na and Cl has a strength comparable to a covalent bond. In solution, water molecules interact with the charged groups - the water molecules shield the charge - and the strength is weakened substantially. The basic amino acids, Lysine, arginine, and histidine, may interact with the acidic amino acids, aspartic acid and glutamic acid. Therefore, a typical ionic interaction in a protein or between two proteins might involve attraction between acidic and basic amino acids.
-Hydrophobic interactions occur between amino acids with nonpolar side chains. Tend to aggregate and form the interior of a polypeptide where they are inaccessible to water.
Protein structures do exist largely in water where hydrogen and ionic bonds are somewhat shielded. Dynamic
- reemphasize
Quaternary Structure
The highest level of organization, recognized in mutimeric proteins. Aggregates of more than one polypeptide chain. Quaternary structure is the overall 3D structure assumed by the mutimeric protein. The individual polypeptide chains that make up multimeric proteins are often called protein subunits i.e. hemoglobin has 2 each of 2 different subunits
Immunoglobulin molecule (IgG)
Two types of subunits or polypeptide chains
2 light chains (~25,000 D)
2 heavy chains (~50,000 D)
For a given antibody molecule, the two heavy chains are identical to one another in amino acid sequence. The two light chains are identical to one another in amino acid sequence. However, the H and L chains are different in amino acid sequence from every other antibody molecule.
Most protein molecules retain their biological activity only within a very limited rnage of temperature and pH. Globular proteins are especially susceptible to these effects. Denaturation is generally observed at Temperatures >60-70C
denaturation - unfolding of the characteristic native folded structure of the polypeptide chain. Resulting loss in biological activity. Also resulting decrease in solubility.
renaturation - unfolded protein spontaneously returns to its native biologically active form.
Hydrolysis: Breaking covalent bonds (peptide bonds) by the addition of water. Complete hydrolysis of a protein requires 6N HCl. There are proteins (enzymes) which can hydrolyze other proteins (proteolytic enzymes or proteases). Characterized by cleaving only some peptide bonds because they are specific for particular amino acids.
Examples include:
-trypsin which has a specificity for Lysine or arginine
-chymotrypsin which has a specificity for phenylalanine, tryptophan
So, if you subject a protein to proteolysis by proteolytic enzymes what you end up with are peptide fragments.
Also, many proteins have nonpeptide components such as carbohydrate moieties (glycoproteins)
metalloproteins (have metal groups attached)
lipoproteins (have lipid groups attached)
Interesting note: not all polypeptides have a stable folded pattern. If you construct an amino acid chain randomly, result is generally a loose, flexible coil. Proteins found in biological systems are a subset of polypeptides selected for their stability of structure.