Protein Structure and Function

Protein Structure and Function

Protein Structure Classification of Proteins Based on Components Simple proteins - Proteins containing only polypeptides Conjugated proteins - Proteins containing nonpolypeptide molecules or ions 1) Apoprotein - The polypeptide part of a conjugated protein 2) prosthetic group - The nonpolypeptide part of a conjugated protein

Protein Structure Classification of Conjugated Proteins 1) Glycoproteins 2) Hemoproteins 3) Lipoproteins 4) Metalloproteins 5) Nucleoproteins 6) Phosphoproteins

Three-Dimensional Structure of Proteins The conformations of the individual bonds in all the amino acid residues within the protein produces a unique 3-D shape, which in turn produces a unique physiological function. The overall folding of a protein is described at four levels: 1º 2º 3º 4º

Levels of Protein Structure Primary structure is the amino acid sequence of a polypeptide. Secondary structure is the conformation in a local region of a polypeptide molecule. The conformation usually involves a regular coiling or layering of the protein chain. Tertiary structure exists when the polypeptide has different secondary structures in different local regions. Tertiary structure describes the threedimensional relation among the different secondary structures in different regions. Quaternary structure exists only in proteins in which two or more polypeptide molecules aggregate together. It describes the threedimensional relation among the different polypeptides.

Determinants of Protein Conformation The most stable conformation of a protein is determined by:. 1) The bonds in the linear chain a) No free rotation about the peptide bond b) Limited rotations about the bonds of the alpha carbon 2) Hydrogen-bonding between peptide amide bonds from different amino acid residues 3) Interactions of side chains with each other & with water 1º 2º a) The tendency of non-polar side chains to avoid water b) The attraction of non-polar side chains for each other c) Hydrogen bonding between polar side chains & water d) Ionic attractions between charged side chains Hydrophobic effect 3º e) Disulfide bonds between side chains

Secondary Protein Structure - The α-helix The polypeptide chain is arranged like a coiled spring with a hydrogen bond between each peptide group s C=O oxygen and the hydrogen of the N-H group of the fourth residue farther down the chain.

Secondary Protein Structure - The β-pleated Sheet Peptide chains are extended and run sideby-side each other in either a parallel or an antiparallel arrangement. Neighboring chains are held together by hydrogen bonds between an N-H on one chain and a C=O on a neighboring chain. Side chains extend alternately above and below the plain of the sheet.

Secondary Protein Structure The β-pleated Sheet

Levels of Protein Structure

Levels of Protein Structure Representation of a Simple Protein

Protein Structure Structural Classification of Proteins Fibrous Proteins Silks, Keratins, Collagens Globular Proteins Enzymes, Antibodies, Hormones 1) Elongated, water insoluble 2) Structural and contractile functions 3) No tertiary structure, but generally possess a single conformational pattern throughout most of the chain (secondary structure) 4) Most have a quaternary structure involving the aggregation of polypeptide chains 1) Remain soluble in water in order to carry out their metabolic functions 2) Spherical, Globular 3) Remain water soluble by folding up so as to segregate hydrophobic side chains in the interior of the molecule and hydrophilic side chains on the exterior of the molecule

Fibrous Proteins α-keratins The structural component of hair, horn, hoofs, nails, skin, and wool. These materials have a hierarchical structure. Coiling at higher and higher levels is a mechanism for enhancing physical strength.

Fibrous Proteins α-keratins The packing within the α-keratins is stabilized by disulfide bridges and secondary forces between different polypeptide molecules. Disulfide bridges are more important than secondary forces in imparting insolubility, strength, and resistance to stretching. Interchain disulfide bonds are often called cross-links. The degree of hardness of an α-keratin depends upon its degree of cross-linking. High cysteine content results in increased hardness (hair, horn, nail) compared to low cysteine content (skin, callus).

Fibrous Proteins Permanent Hair Waving Permanent waving of hair is accomplished by breaking and reforming cysteine cross-links within the hair fiber:

Fibrous Proteins β-keratins β-keratins and Silk Fibroins The β-keratins make up the proteins in bird feathers, reptile scales, and silk fibroin. β-keratins are almost completely composed of β- pleated sheets.

Fibrous Proteins - Collagen The most abundant protein in vertebrates is collagen. Collagen is a stress-bearing component of connective tissues such as bone, cartilage, cornea, ligament, teeth, tendons, and the fibrous matrices of skin and blood vessels. Collagen contains much more glycine and proline and much less cysteine than does α-keratin. Much of the proline present is converted into hydroxyproline. A single collagen molecule forms a lefthanded helical structure, much more elongated than an α-helix. Three left-handed collagen helices twist around each other to form a righthanded superhelix called a triple-helix or tropocollagen. Tropocollagen is further organized into fibrils and higher-level structures.

Fibrous Proteins - Collagen diameter 1.5 nm 10-300 nm 0.5-3μm

Fibrous Proteins - Collagen

Globular Proteins Globular proteins do not aggregate into macroscopic structures but remain soluble in order to carry out their metabolic functions: catalysis, transport, regulation, and protection. Globular proteins remain soluble by folding up in such a way as to segregate their hydrophobic amino acid side chains in the interior of the molecule, and their hydrophilic amino acid side chains on the exterior of the molecule, in contact with water.

Globular Proteins Myoglobin and Hemoglobin Hemoglobin in red blood cells binds oxygen in the lungs, transports it through the blood stream, and releases it in the tissues. Myoglobin has a higher affinity for oxygen than does hemoglobin and is found in muscle tissue. Myoglobin serves as a storage reserve for oxygen within the muscle.

Globular Proteins - Myoglobin Myoglobin consists of a single polypeptide chain containing 153 amino acid residues, organized into 8 α-helical regions that surround a prosthetic group called a heme group.

Heme Group The iron atom on the heme group is the site of attachment of the O2 molecule.

In 1971, Professor of Biochemistry F. R. Gurd assembled a model of myoglobin. The model was constructed of precisely bent wire segments to represent the amino acids, each fragment fastened to its neighbors using links that were screwed together. Wires were stretched throughout the structure to ensure that the various parts were held in proper alignment. A separate "space-filling" model is visible in the background. Prof. Gurd required three weeks and an entire 20 X 30 foot room to assemble the model. Today, a comparable three-dimensional model of myoglobin can be displayed in a matter of seconds. (Univ of Indiana)

Levels of Protein Structure

Globular Proteins - Hemoglobin 4 polypeptide chains 2 α-chains (141 residues each) 2 β-chains (146 residues each) Each α and β chain folded in a manner similar to that of myoglobin contains a heme group capable of carrying oxygen

HEMOGLOBIN A GLOBULAR PROTEIN WITH QUATERNARY STRUCTURE The surfaces of the α and β chains contain some hydrophobic residues which cause all 4 chains to aggregate into a tetramer. A space at the center of the tetrameric structure can bind a molecule of 2,3-bisphosphoglycerate (BPG) which regulates the affinity of the hemoglobin molecule for oxygen.

The sickle cell mutation causes hemoglobin molecules to clump t o g e t h e r i n a n a b n o r m a l manner. The valine in position 6 adheres to a notch on the o p p o s i t e s i d e o f a n o t h e r molecule of Hb, causing long chains to form.

In sickle cell anemia, the normal hemoglobin molecule mutates by exchanging the 6th amino acid on the beta chain from glutamic acid to valine. Normal Hb has the genotype SS. Sickle cell anemia occurs when an individual inherits two recessive alleles (ss). Sickle cell trait exists when one inherits the heterozygous condition (Ss). The malaria parasite (Plasmodium falciparum) does not survive in these individuals; they may have a slight anemia, but they survive better than either normal individuals (SS- who often die of malaria), or those who die of sickle cell disease (ss).

Sickle Cell Anemia

Sickle Cell Anemia Comparison of the distribution of malaria (left) and sickle-cell anaemia (right) in Africa

Globular Proteins - Denaturation Denaturation - the loss of native conformation due to a change in environmental conditions. The non-functioning protein is called a denatured protein. Denaturation results from the disruptions of the weak secondary forces holding a protein in its native conformation. (Disulfide bridges confer considerable resistance to denaturation because they are much stronger than the weak secondary forces.)

Globular Proteins - Denaturation A variety of denaturing conditions or agents lead to protein denaturation: 1) Increased temperature (or microwave radiation) 2) Ultraviolet and ionizing radiation 3) Mechanical energy 4) Changes in ph 5) Organic chemicals 6) Heavy metal salts 7) Oxidizing and reducing agents