Protein Structure and Folding Lectures 2 PDF

Protein Structure and Folding Lectures 2 Dr.Ali H.Dosky Session2: References • Marks’ Basic Medical Biochemistry Chapter 7 • Medical Biochemistry Chapters 2, 5 • Lippincott’s Illustrated Reviews: Biochemistry Chapters 2, 3 MGD 2017/ DR. AL-BARQAAWI Lecture 3: Learning outcomes At the end of th...

Protein Structure and Folding Lectures 2 Dr.Ali H.Dosky Session2: References • Marks’ Basic Medical Biochemistry Chapter 7 • Medical Biochemistry Chapters 2, 5 • Lippincott’s Illustrated Reviews: Biochemistry Chapters 2, 3 MGD 2017/ DR. AL-BARQAAWI Lecture 3: Learning outcomes At the end of this session, student should be able to: 1.Describe what is meant by the primary, secondary, tertiary and quaternary structure of proteins. 2. Describe the types of bonds and forces involved in protein structure. 3.Explain the key features of the two major secondary structure elements of proteins (α-helix and β -sheet). MGD 2017/ DR. AL-BARQAAWI 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. (as shown in last lecture). • The amino acid units on a peptide chain are referred to as amino acid residues. • A peptide chain may consists 2-50 amino acids. MGD 2017/ DR. AL-BARQAAWI Peptides & Proteins • A 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, which has the following sequence of amino acids. Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu • By convention, the amino terminus (N-terminus) is taken as the first residue, and the sequence of amino acids is written from left to right. MGD 2017/ DR. AL-BARQAAWI Protein 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 • Proteins do not exist as linear polypeptides but rather fold to adopt a unique 3dimensional structure. The shape of the protein is important for defining the role that protein plays. • The linear sequence of the linked amino acids contains the information necessary to generate a protein molecule with a unique three-dimensional shape. MGD 2017/ DR. AL-BARQAAWI Levels of protein structure: The complexity of protein structure is best analyzed by considering the molecule in terms of four organizational levels, namely; primary, secondary , tertiary , and quaternary. Primary Structure Of Proteins • The sequence of amino acids in a protein is called the primary structure of the protein. • 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. MGD 2017/ DR. AL-BARQAAWI Primary Structure Of Proteins • The bonds responsible for the stabilization of primary structure is only the peptide bonds. • 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. MGD 2017/ DR. AL-BARQAAWI Secondary Structure of Proteins • 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 , and β-bend are examples of secondary structures. • Collagen helix , another example of secondary structure , will discussed in the future. • The Alpha Helix Is a Coiled Structure Stabilized by Intra- chain Hydrogen Bonds. MGD 2017/ DR. AL-BARQAAWI Secondary structure: α- Helix • Essentially all α - helices found in proteins are right handed. • In the α - helix, the CO group of residue n forms a hydrogen bond with the NH group of residue n+ 4 MGD 2017/ DR. AL-BARQAAWI Amino acids per turn of α- Helix Each turn of an α-helix contains 3.6 amino acids, and has a 0.54nm pitch. Thus , amino acid residues spaced three or four apart in the primary sequence are spatially close together when folded in the α-helix. MGD 2017/ DR. AL-BARQAAWI Amin o 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. MGD 2017/ DR. AL-BARQAAWI Secondary Structure: β- Sheet β-Sheet is an Extended conformation in which the side chains (green) are alternately above and below the plane of the strand. β Sheet: 1. Parallel 2. Antiparallel MGD 2017/ DR. AL-BARQAAWI Secondary structure: 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. MGD 2017/ DR. AL-BARQAAWI Secondary Structure: 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. MGD 2017/ DR. AL-BARQAAWI Secondary Structure: Bends or Turns The CO group of residue i of the polypeptide hydrogen chain bonded is to the NH group of residue i + 3 to stabilize the turn MGD 2017/ DR. AL-BARQAAWI Tertiary Structure • The overall 3-dimensional structure of a protein is referred to as the tertiary structure. This involves folding up of the secondary structures so that amino acids far apart in the primary sequence may interact. • Larger proteins (~200 amino acids or greater) tend to have distinct domains. These are regions of the polypeptide that have distinct structures and often serve particular roles (e.g. ligand binding, interaction with other proteins etc.) MGD 2017/ DR. AL-BARQAAWI Tertiary Structure: Bonds Involved Covalent (disulphide) bonds MGD 2017/ DR. AL-BARQAAWI Hydrophobic interactions Tertiary Structure: Bonds Involved Ionic interactions, Hydrogen bonds &Van der Waals interaction MGD 2017/ DR. AL-BARQAAWI Protein Folding • Interactions between the side chains of amino acids determine how a long polypeptide chain folds into the complex three-dimensional shape of the functional protein. • Protein folding, occurs within the cell in seconds to minutes. • The information needed for correct protein folding is contained in the primary structure of the polypeptide. MGD 2017/ DR. AL-BARQAAWI Role o f chaperones in protein folding • Why most proteins when denatured (see below) do not take up again their native conformations under favorable environmental conditions? • One answer to this problem is that a protein begins to fold in stages during it s synthesis, rather than waiting for synthesis of the entire chain to be totally completed. • In addition, a specialized group of proteins, named "chaperones," are required for the proper folding of many species of proteins. MGD 2017/ DR. AL-BARQAAWI Quaternary Structure • 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. • Proteins can be categorised into 2 major groups depending of their higher order structure: globular or fibrous. • Most enzymes and regulatory proteins inside a cell tend to be globular proteins whereas fibrous proteins tend to provide structure, support and protection. MGD 2017/ DR. AL-BARQAAWI 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. • Denaturing agents include heat, organic solvents, mechanical mixing, strong acids or bases , and ions of heavy metals such as lead and mercury. MGD 2017/ DR. AL-BARQAAWI Protein Denaturation Role of β-Mercapto-ethanol in Reducing Disulfide Bonds. Note that, as the disulfides are reduced, the β-mercapto-ethanol is oxidized and forms dimers Reduction and Denaturation Ribonuclease MGD 2017/ DR. AL-BARQAAWI of Thank you for listening