Chapter 4: The Three-Dimensional Structure of Proteins PDF

Chapter 4 The Three- Dimensional Structure of Proteins Chapter Outline (4-1) Protein structure and function (4-2) Primary structure of proteins (4-3) Secondary structure of proteins (4-4) Tertiary structure of proteins (4-5) Quaternary structure of proteins Protein Structure Biological...

Chapter 4 The Three- Dimensional Structure of Proteins Chapter Outline (4-1) Protein structure and function (4-2) Primary structure of proteins (4-3) Secondary structure of proteins (4-4) Tertiary structure of proteins (4-5) Quaternary structure of proteins Protein Structure Biologically active proteins are polymers that consist of amino acids linked by covalent peptide bonds Many conformations are possible for proteins due to flexibility of amino acids Native conformations: 3-D shapes of proteins with biological activity Many proteins have large segments of random structure as they have no obvious regular repeating structure Levels of Protein Structure Primary structure (1°): Order in which amino acids are covalently linked together Read from the N-terminal end to the C-terminal end Secondary structure (2°): Ordered 3-D arrangement in space of the backbone atoms in a polypeptide chain Tertiary structure (3°): 3-D arrangement of all atoms in a protein, including those in side chains and in prosthetic groups Quaternary structure (4°): Arrangement of subunits with respect to one another Subunits: Individual parts of a large molecule Primary Structure Amino acid sequence helps determine the 3-D conformation of a protein, which determines its properties Determination of this sequence is a routine operation in classical biochemistry Changes in one amino acid residue in a sequence can alter biological functions Example - Hemoglobin associated with sickle-cell anemia Secondary Structure Hydrogen-bonded arrangement of the polypeptide chain Peptide chains are linked at opposite corners by swivels Each amino acid residue has two bonds with free rotation that are designated by the Ramachandran angles, phi (Φ) and psi (Ψ) Bond between the α-carbon and amino nitrogen of that residue Bond between the α-carbon and carboxyl carbon of that residue Types - α-helix and β-pleated sheet arrangements Peptide Conformation α-Helix Stabilized by hydrogen bonds parallel to the helix axis within the backbone of a single polypeptide chain Helical conformation allows for a linear arrangement Provides maximum bond strength and makes the conformation stable Features Coil of the helix is clockwise or right-handed There are 3.6 residues for each turn of the helix Linear distance between corresponding points on successive turns (pitch) is 5.4 Å Each peptide bond is s-trans and planar C═O of each peptide bond is hydrogen bonded to the N—H of the fourth amino acid residue C═O≡H—N hydrogen bonds are parallel to the helical axis All R groups point outward from the helix Four Different Graphic Representations of the α-Helix Factors That Disrupt the α-Helix Bending of the polypeptide backbone because of proline Restricts rotation due to its cyclic structure Results in absence of the N—H for hydrogen bonding in the α-amino group Strong electrostatic repulsion caused by the proximity of several side chains of like charges Examples - Lys and Arg or Glu and Asp Steric repulsion, or crowding, caused by the proximity of bulky side chains Example - Val, Ile, and Thr β-Pleated Sheet Hydrogen bonds between peptide chains can be interchain or intrachain Give rise to a zigzag structure and are perpendicular to the direction of the protein chain Polypeptide chains lie adjacent to one another If chains run in the same direction, the sheet will be parallel If chains run in the opposite direction, the sheet will be antiparallel R groups alternate above and below the plane Each peptide bond is s-trans and planar Hydrogen Bonding in β-Pleated Sheets Three-Dimensional Form of the Antiparallel β-Pleated Sheet Arrangement Reverse Turns Parts of proteins where the polypeptide chain folds back on itself Contain glycine Formed because of spatial (steric) reasons Result Polypeptide chain changes direction Proline is also encountered in reverse turns because of its cyclic structure Structures of Reverse Turns Supersecondary Structures and Domains Supersecondary structures - Result from the combination of α- and β- strands βαβ unit - Two parallel strands of β-sheet are connected by a stretch of α- helix αα unit - Contains two antiparallel α-helices Also called helix-turn-helix β-meander - Antiparallel sheet is formed by a series of tight reverse turns connecting stretches of the polypeptide chain Greek key - Formed when a polypeptide chain doubles back on itself Schematic Diagrams of Supersecondary Structures Supersecondary Structures and Domains Motifs: Repetitive supersecondary structures β-barrel - Created when β-sheets are extensive enough to fold back on themselves Provide information about the folding of proteins Do not help predict the biological function of the protein Proteins that have the same type of function have similar protein sequences Domains with similar conformations are associated with a particular function Some β-Barrel Arrangements Fibrous Proteins Contain polypeptide chains organized approximately parallel along a single axis Consist of long fibers or large sheets Tend to be mechanically strong Insoluble in water and have the ability to dilute salt solutions Play important structural roles in nature Examples Keratin in hair and wool Collagen in connective tissue, including cartilage, bones, teeth, skin, and blood vessels Globular Proteins Proteins in which the backbone folds on itself to produce a more or less spherical shape Most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion–dipole interactions Most of their nonpolar side chains are buried inside Have substantial sections of α-helix and β-sheet Tend to be soluble in water and salt solutions Have compact structures Tertiary Structure of Proteins 3-D arrangement of all atoms in a molecule Includes the conformations of side chains and the positons of any prosthetic groups In fibrous proteins: Backbone of the protein does not fold back on itself Arrangement of the atoms of the side chains is not specified by the secondary structure In globular proteins: Tertiary structure helps determine the way helical and pleated-sheet sections fold back on each other Interactions between side chains play an essential role in folding Forces Involved in Tertiary Structures Tertiary structures depend on noncovalent interactions Backbone hydrogen bonding between polar side chains of amino acids Hydrophobic interaction between nonpolar side chains Electrostatic attraction between side chains of opposite charge Complexing several side chains to a single metal ion Disulfide bonds between side chains of cysteines Restrict folding patterns available to polypeptide chains Absent in myoglobin and hemoglobin but present in chymotrypsin and trypsin Forces That Stabilize the Tertiary Structure of Proteins Myoglobin Consists of a single polypeptide chain of 153 amino acid residues and a prosthetic group, heme, in a hydrophobic pocket Heme: Iron-containing cyclic compound Has a compact structure Carries eight α-helical regions, which are stabilized by hydrogen bonding in the polypeptide backbone β-pleated sheet regions are absent Exterior contains most of the polar side chains Interior contains nonpolar side chains and two histidine residues that are involved in interactions with the heme group and bound O2 Structure of Myoglobin Heme Group Presence affects conformation of the polypeptide Consists of: A metal ion, Fe(II) Has six coordination sites and forms six metal–ion complexation bonds Four sites are occupied by N atoms of the four pyrrole-type rings of the porphyrin Fifth coordination site is occupied by one of the N atoms of the imidazole side chain of histidine residue F8 O2 is bound at the sixth coordination site An organic part, protoporphyrin IX Consists of four five-membered rings based on the pyrrole structure that are linked by methine (—CH═) groups Structure of the Heme Group Oxygen: Imperfect Binding to the Heme Group More than one molecule can bind to heme Affinity of free heme for carbon monoxide (CO) is 25,000 times greater than its affinity for O2 Oxygen and Carbon Monoxide Binding to the Heme Group of Myoglobin Denaturation and Refolding Denaturation: Unraveling of the 3-D structure of a macromolecule caused by the breakdown of noncovalent interactions that can result from: Heat Large changes in pH, which alter charges on side chains Detergents, such as sodium dodecyl sulfate (SDS), which disrupt hydrophobic interactions Urea and guanidine hydrochloride, which disrupt hydrogen bonding β-mercaptoethanol Denaturation of a Protein Quaternary Structure of Proteins Pertains to proteins that consist of more than one polypeptide chain Each chain is called a subunit Oligomers: Molecules that are made up of a number of smaller subunits Include dimers, trimers, and tetramers Chains interact with one another noncovalently via electrostatic attractions, hydrogen bonds, and hydrophobic interactions Allosteric: Property of multisubunit proteins such that a conformational change in one subunit induces a drastic change in another subunit Hemoglobin Tetramer with: Two α-chains 141 residues long Two β-chains 146 residues long Overall structure - α2β2 Most amino acids of the α- chain, β-chain, and myoglobin are homologous Oxygen Binding of Hemoglobin (Hb) One molecule of myoglobin binds one O2 Hemoglobin can bind up to four molecules of O2 Binding of O2 to hemoglobin exhibits positive cooperativity When one O2 is bound, it becomes easier for the next O2 to bind Myoglobin versus Hemoglobin Myoglobin Function - Oxygen storage Requirement - Bind strongly to O2 at very low pressures Saturation - 50% at 1 torr partial pressure of O2 Hemoglobin Function - Oxygen transport Requirement - Bind strongly to O2 and release O2 easily Saturation - 100% when O2 pressure is 100 torr Structures of Hemoglobin Structure of oxygenated hemoglobin is different from that of deoxygenated hemoglobin Conformational Changes That Accompany Hemoglobin Function Ligands involved in cooperative effects when O2 binds to Hb can affect protein affinity for O2 by altering structure H+ and CO2 Effect of H+ is called the Bohr effect Increase in [H+] reduces O2 affinity of Hb and causes protonation of key amino acids Conformational Changes That Accompany Hemoglobin Function Acid–base properties of Hb Oxygenated form of Hb is a stronger acid since it has a lower pKa than its deoxygenated form Deoxygenated hemoglobin has higher affinity for H+ than the oxygenated form Oxygen Saturation Curves for Myoglobin and for Hemoglobin at Five Different pH Values Conformational Changes That Accompany Hemoglobin Function Hb is also bound to 2,3- bisphosphoglycerate (BPG) Binding is electrostatic In the absence of BPG, oxygen-binding capacity of Hb would be higher BPG plays a role in the supply of O2 to the growing fetus Binding of BPG to Deoxyhemoglobin  Hydrophobic Interactions: A Case Study in Thermodynamics Hydrophobic interactions are major factors in protein folding Folding occurs so that: Nonpolar hydrophobic side chains tend to be on the inside and away from water Polar side chains are on the outside and have access to the aqueous environment Example Liposomes: Spherical aggregates of lipids arranged so that the polar head groups are in contact with water and the nonpolar tails are sequestered from water Schematic Diagram of a Liposome Favorable versus Unfavorable Hydrophobic Interactions Hydrophobic interactions are spontaneous processes Result in increase in the entropy of the Universe ΔS univ > 0 Example Mixing liquid hydrocarbon hexane (C6H14) with water yields one layer of hexane and one layer of water Formation of the mixed solution is nonspontaneous Formation of the two layers is spontaneous Unfavorable entropy terms arise if solution formation requires the creation of ordered arrays of solvent Favorable versus Unfavorable Hydrophobic Interactions Results in high degree of order Prevents the dispersion of energy, which lowers the entropy Nonpolar substances associate with one another by hydrophobic interactions and are excluded from water