Protein Structure and Folding (MGD S2 Lecture 1 PDF)

Protein Structure and Folding Protein Structure Peptides& proteins In peptides and proteins, the primary amino group of one amino acid is linked to the carboxyl group of the next amino acid, forming an amide (peptide) bond. During the formation of a peptide bond, a molecule of water is eliminated....

Protein Structure and Folding Protein Structure Peptides& proteins In peptides and proteins, the primary amino group of one amino acid is linked to the carboxyl group of the next amino acid, forming an amide (peptide) bond. During the formation of a peptide bond, a molecule of water is eliminated. 2. Secondary structure: •Proteins contain between 50 and 2000 amino acid residues. •The mean molecular mass of an amino acid residue is about 110 dalton units (Da). Therefore the molecular mass of most proteins is between 5.5 and 220 kDa - I •Proteins do not exist as linear polypeptides but rather fold to adopt a unique 3- dimensional structure. The shape of the protein is important for defining the role that protein plays. •The amino acid units on a peptide chain are referred to as amino acid residues. •A peptide chain may consists 2-50 amino acids. •peptide consisting of three amino acid residues is called a tri-peptide, e.g. Glutathione (GSH), a tri-peptide with the sequence γ-glutamyl cysteinyl glycine. This peptide has an important role in antioxidant defenses. •Angiotensin, a peptide hormone that affects blood pressure, is another example of a peptide with physiological importance, There are 4 levels of protein structure: The complexity of structure is best analyzed by considering protein molecule in terms of four organizational levels, namely; primary, secondary , tertiary , and quaternary. 1. Primary structure: the linear amino acid sequence of the polypeptide chain. It contains the information necessary to generate a protein molecule with a unique threedimensional shape. •Understanding the primary structure of proteins is important because many genetic diseases result in proteins with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function. •The primary structures of the normal and the mutated proteins are known, this information may be used to diagnose or study the disease. Bonds involved : Covalent (peptide) bond •Peptide bonds are not broken by heating or high concentrations of urea. - •Prolonged exposure to a strong acid or base at elevated temperatures is required to hydrolyze these bonds The polypeptide backbone forms regular arrangements of amino acids that are located near to each other in the linear sequence. • These arrangements are termed the secondary structure of the polypeptide . • The α-helix, β-sheet ,collagen helix, and βbend are examples of secondary structures. secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone. (The backbone just refers to the polypeptide chain apart from the R groups – secondary structure does not involve R group atoms.) Bonds involved: Hydrogen bonds Types of Secondary structure : Alpha Helix A type of regular protein secondary structure. • The Alpha Helix Is a Coiled Structure Stabilized by Intra- chain Hydrogen Bonds. •It is a right-handed helix with 3.6 residues per turn and a pitch of 0.54nm. Thus, amino acid residues spaced three or four apart in the primary sequence are spatially close together when folded in the α-helix. •In the α-helix,the CO group of residue n forms a hydrogen bond with the NH group of residue n+ 4 Amino acids that disrupt an α-helix: • Proline. • Large numbers of charged amino acid. • Large numbers of amino acids with bulky side chains, such as tryptophan, or amino acids, such as valine or isoleucine, that branch at the β-carbon , . - , 0 Beta sheet A type of regular protein secondary structure where the polypeptide chains are in an extended conformation. The side chains are alternately above and below the plane of the strand. Types: 1. An Antiparallel β Sheet: - Adjacent β strands run in opposite directions. Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure. 2. A Parallel β Sheet: Adjacent β - strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand. 3. Tertiary structure: The overall 3-dimensional structure of a protein. This involves folding up of the secondary structures so that amino acids far apart in the primary sequence may interact. • The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. •Larger proteins (~200 amino acids or greater) tend to have distinct domains (regions of the polypeptide that have distinct structures and often serve particular roles e.g. ligand binding, interaction with other proteins etc.) Globular and fibrous proteins Proteins can be categorized into 2 major groups depending of their higher order structure: 1. Globular protein: a water soluble class of proteins with a compact, highly folded structure. 2. Fibrous protein: an insoluble class of proteins with an elongated structure containing repeating elements. •Most enzymes and regulatory proteins inside a cell tend to be globular proteins •whereas fibrous proteins tend to provide structure, support and protection. Bonds involved: Hydrogen bonds Van der Waals Hydrophobic interactions Covalent (disulfide) bonds Ionic interactions 4. Quaternary Structure: 3-dimensional arrangement of multi-subunit proteins. Many proteins consist of more than 1 polypeptide chain. •The polypeptide chains may be identical (homomeric proteins) or different (heteromeric proteins). The arrangement of these subunits in such proteins is referred to as the quaternary structure. •The same types of bonds that involved in tertiary structure are involved in Quaternary structure. Protein folding All the information necessary to ensure that a protein folds correctly is contained in the primary sequence of the protein itself. Most proteins fold spontaneously as they are synthesized. •Some proteins require the assistance of molecular chaperones (specialized group of proteins required for the proper folding of many species of proteins) • Misfolding of protein can cause disease states as the protein is no longer able to function effectively. Protein denaturation The loss of protein structure sufficient to cause the loss of function is known as denaturation. Denaturation is brought about by breaking the bonds that hold that maintain the protein’s tertiary and secondary structure. Bends or turns The CO group of residue i of the polypeptide chain is hydrogen bonded to the NH group of residue i + 3 to stabilize the turn. •Denaturing agents include heat, organic solvents, mechanical mixing, strong acids or bases, detergents, and ions of heavy metals such as lead and mercury. •Role of b -Mercaptoethanol in Reducing Disulfide Bonds. Note that, as the disulfides are reduced, the bmercaptoethanol is oxidized and forms dimers Video Hemi1n