L18 Protein Structure, Folding & Modifications PDF

18 Protein structure & modifications: ILOs By the end of this lecture, students will be able to 1. Describe the different orders of protein structure 2. Deduce importance of protein folding 3. Correlate protein structure to its function 4. Classify biologically import...

18 Protein structure & modifications: ILOs By the end of this lecture, students will be able to 1. Describe the different orders of protein structure 2. Deduce importance of protein folding 3. Correlate protein structure to its function 4. Classify biologically important proteins according to their structure and function 5. Interpret the effect of denaturation on proteins’ structure and function ❖ Orders of protein structure: o Primary Structure of Proteins - The primary structure of a protein is defined by “The linear sequences of amino acid residues linked to each other by peptide bonds”. Protein contain between 50 and 2000 amino acid residues. The amino acid composition of a peptide chain has a profound effect on the physical and chemical properties of proteins. - The amino acids sequences are read from N-terminal (amino acid number 1) to C-terminal ends of the peptide. The primary structure of proteins determines the secondary and tertiary structures which are essential for protein functions. - Many genetic diseases result in proteins with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function. If the primary structures of the normal proteins are known, this information may be used to diagnose or study the disease. o Secondary Structure of proteins - The next level of structure is the secondary structure of a protein which is “The regular, recurring arrangements of adjacent amino acid residues in a polypeptide chain”. It includes coiling, folding or bending of the polypeptide chain leading to specific structure which is kept by Hydrogen bonds. There are two main types of secondary structure, the ∝ - helix and the β- pleated sheet. Both structures are held in shape by hydrogen bonds which are formed between the carbonyl O of one amino acid and the amino H of another. Both types could co- exist in the same protein. ▪ The α – helix: It is a rigid, spiral structure, consisting of a tightly packed, coiled Page 1 of 5  polypeptide backbone core, with the side chains of the amino acids extending outward from the central axis to avoid interfering with each other. ▪ β-Sheet: Another form of secondary structure in which two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. o Tertiary Structure of proteins - The three dimensional, folded and biologically active conformation of a protein is referred to as tertiary structure. The structure reflects the overall shape of the molecule. - This structure is stabilized by interactions between side chains, ionic interactions, disulfide bonds, and hydrogen bonds. - “Tertiary” refers to both the folding of domains and to the final arrangement of domains in the polypeptide. But what are the “Domains”? - Domains are the three-dimensional structural part of protein that can fold, function and exist independently of the rest of the protein chain. - Therefore, each domain has special characteristics that are structurally independent of the other domains in the polypeptide chain. - Some proteins only contain a single domain, others may have several domains. Some domains have a clearly defined function, like the coenzyme-binding domain. Other domains, are there probably just for their stability. o Quaternary Structure of proteins - Many proteins are made up of a single polypeptide chain and have only three levels of structure discussed above. However, some proteins are made up of multiple polypeptide chains, also known as subunits. - The arrangement of these polypeptide subunits is called the quaternary structure of the protein. Subunits are held together primarily by non-covalent interactions (as hydrogen bonds). They may either function independently of each other or may work cooperatively, as in hemoglobin which contains 4 chains, in which the binding of oxygen to one subunit of the tetramer increases the affinity of the other subunits for oxygen Clinical Implications: Protein folding is a complex process that can sometimes result in improperly folded molecules. These misfolded proteins are usually tagged and degraded within the cell. However, this quality control system is not perfect, and intracellular or extracellular aggregates of misfolded proteins can accumulate, particularly as aged individuals. Deposits of misfolded proteins are associated with a number of diseases, most important are Parkinson disease and Alzheimer disease. Page 2 of 5  - Chaperones are a family of proteins that guide proteins along the proper pathways for folding. They protect them when they are in the process of folding, shielding them from anything that might bind and hinder the process. Many chaperone proteins are termed "heat shock" proteins because they are made in large amounts when cells are exposed to heat. Heat, in general, destabilizes proteins and makes misfolding more common. So when it gets really hot, cells need some extra help with their proteins. ❖ What is protein “Denaturation”? Proteins have finite lifetimes. Denaturation involves the destruction of the higher level structural organization of protein in other words it is loss of secondary and tertiary structures with the retention of the primary structure. This occurs due to rupture of the non-covalent bonds while peptide bonds responsible for the primary structure are retained since denaturation reactions are not strong enough to break the peptide bonds. A denatured protein loses its native biological properties since the bonds that stabilize the protein are broken down. Thus the polypeptide chain unfolds itself and remains in the unfolded state. Causes of Denaturation: 1. Physical factors as temperature (above 70 oC), vigorous vibration and ionizing radiation, X- rays and high pressure. 2. Chemical factors as strong acids and alkalis (extremes of PH) also urea. Effects of denaturation: Biological changes: - Loss of biological activity of enzymes and protein hormones. - Changes of antigenic property of proteins. - Denatured proteins are easily digested due to unfolding of the peptide chains. Page 3 of 5  A good example for this is using strong chemicals (perms and relaxing treatments) to change the curly hair to straight, this is done by “denaturation” of the disulfide bonds in the hair that are responsible for it’s the curly appearance, leading to permanent loss of the curly texture. On the other hand using medium heat cannot break down these bonds, it’s only capable of breaking the weak hydrogen bonds which can be easily affected by heat, water and humidity. ❖ How are proteins Classified? There are many classifications for proteins most important are: ▪ Classification based on chemical composition - Simple proteins: they are made up of only amino acids. Examples are: plasma albumin the important transport protein in the blood and collagen the major component of connective tissues that make up tendons, ligaments, skin, and muscles. - Conjugated proteins : they contain in their structure a non-protein portion. Example: Glycoproteins: They are proteins that covalently bind one or more carbohydrate units to the polypeptide backbone. They play an important role in cell signaling, cell attachment and regulating the immune system. Lipoproteins: These are combinations of proteins with lipids. Plasma lipoproteins play a key role in the absorption and transport of lipids. ▪ Classification based on shape o Fibrous proteins - Fibrous proteins are elongated strand-like structures and are usually present in the form of rods or wires. They have only primary and secondary structures. - Fibrous proteins are highly resistant to digestion by enzymes, these proteins are insoluble in water, they have primarily mechanical and structural functions providing external protection, support and shape; in fact, they ensure flexibility and/or strength. - Examples include Keratins which forms nails, hair and a large part of the outer layer of the skin. The different stiffness and flexibility of these structures is a consequence of the number of disulfide bonds that contribute, together with other binding forces, to stabilize the protein structure. And this is the reason why keratins in different tissues give different degrees of flexibility as that in hair vs nails or as different hair types. o Globular proteins - Most of the proteins belong to this class. They have a compact and more or less spherical structure, more complex than fibrous proteins. They are generally soluble in water. - Globular proteins are made up of not only primary, secondary but also tertiary and quaternary structures - Unlike fibrous proteins, they act as: enzymes, hormones, membrane transporters and receptors. Examples of globular proteins are: Myoglobin: It is an oxygen carrier in muscle cells providing oxygen to the working muscle and is responsible for the color of the muscle Page 4 of 5  Hemoglobin: the protein responsible for transferring oxygen from the lungs to the tissues. ▪ Classification based on biological Value This classification provides the ability to identify proteins that provide the greatest benefit for consumption in human’s diet specially for individuals with special dietary needs as athletes, aged individuals or those with chronic diseases Proteins of high biological value (HBV): which contain all the essential amino acids e.g. meat, poultry, fish and dairy products. Proteins of low biological value (LBV): which are proteins deficient in one or more essential amino acid as plant based proteins including legumes and vegetables. Page 5 of 5