BIOL 302 1st Edition Lecture 6Protein Composition and StructureOutline of Last Lecture I. Protein Composition and StructureOutline of Current Lecture II. Chemical bondsIII. Protein StructuresIV. Protein Folding, Unfolding and MIs-foldingCurrent LectureV. Chemical bonds sorted starting with strongest interactionA. CovalentB. Electrostatic interactionC. Hydrogen bondD. Van der WaalsVI. Chemical bonds sorted by their bond lengths starting with the shortestA. Covalent bondB. Electrostatic InteractionC. Hydrogen bondD. Van Der Waals interactionVII. The residue pair histidine-glutamine forms these interactions with their side chains:A. Hydrogen bondsVIII. The residue pair tryptophan-phenylalanine forms these interactions with their side chains:A. Hydrophobic interactionsIX. Summary levels of structure in proteinsThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.A. Primary Structures1. Amino acid residuesB. Secondary Structures1. Spatial arrangement of amino acid residues that are nearby in the sequnce2. α –helixa. main chain CO group of residue i forms a hydrogen bond with NH of residue i+4b. Translation- (rise) how each residue is related to one another: 1.5Ac. Rotation: 100d. 3.6 residues per turne. Pitch: length of one complete turn; equal to the product of the rise and the number of residues per turn; 5.4 Af. Screw sense- orientation of the α-helixi. Right-handed: clockwiseii. Left-handed: counterclockwise3. β – pleated sheet4. Hydrogen bonds between amides in the backboneC. Tertiary Structure1. Polypeptide Chain2. Nonpolar hydrophobic side chains are attracted to one another while repelling water3. What induces tertiary structureg. In aqueous environment: nonpolar side chains move away from water, move towards the inside of the protein, bury themselves in the center causing it to foldin on itselfi. This pairs all of the NH and CO groups by hydrogen bondingh. Van der Waals interactions occur between hydrocarbon side chainsi. Interior consists almost entirely of non-polar residues such as:i. Leucineii. Valineiii. Methionineiv. Phenylalaninej. Polar or ionic side chains on the outside such as:i. Aspartateii. Glutamateiii. Lysineiv. Argininek. Similar structure to a micellei. an electrically charged particle formed by an aggregate of molecules and occurring in certain colloidal electrolyte solutions, as those of soaps and detergents.; composed of amphipathic (pertains to a molecule containing both polar (water-soluble) and nonpolar (not water-soluble) portions in its structure )molecules with their hydrophilic heads pointing out4. 3D shapeD. Quaternary Structure1. Spatial arrangement of subunits and nature of their interactions2. More than one polypeptide chain3. Each individual polypeptide chain is called a subunit4. Most times, subunits are held together by noncovalent bondsX. Complex III of the respiratory chain – 660 kDa (660000 g/mol), Cytochrome c (boxed)– 12 kDa 12000 g/molA. Each amino acid contributes on average 110 g/mol to a protein.B. Protein sizes range from around 5 - 1000 kDa.XI. Amino acids have different propensities to form secondary structureProtein Folding, Unfolding and MisfoldingXII. Protein StabilityA. Protein stability is the net balance of forces, which determine whether a protein will be in its native folded conformation or a denatured state.B. Protein stability normally refers to the physical (thermodynamic) stability, not the chemical stabilityC. Proteins are only marginally stable : Free energies of unfolding ~5 to 15 kcal/mol !!! DG = DH - TDSXIII. Folding MechanismA. To go from a random coil to a tertiary structure the protein (1) comes together to form a nucleus with a native-like but still mobile structureB. The structure then (4) fully condenses to form the native more rigid structureC. Native structure=lowest energyD. Folding is a nucleated process, and proceeds through discreet intermediatesE. As a protein folds those segments of the chain folded correctly are retained, leading to increasing stabilizationXIV. Levinthal’s paradoxA. Consider a 100 residue proteinB. Levinthal reasons: Assume each peptide bond can adopt 3 conformations. Total possible conformations = 3100 The total number of possible structures is therefore 5× 1047. C. Now assume that it takes 10-13 s to convert one structure into another.D. Total search time = 5 × 1047 × 10-13 s = 5 × 1034 s, or 1.6 × 1027 years. E. Age of universe is estimated to be 13.75 ± 0.11 billion yearsF. Clearly, it would take much too long for even a small protein to fold properly by randomly trying out all possible conformations. G. The enormous difference between calculated and actual folding times is called Levinthal's paradox.XV. FoldingA. How can we reconcile this paradox?B. Answer: “Cumulative selection”: there are meta-stable intermediates in the folding pathway with native structure, allowing folding to occur in a step-wise manner ratherthan a random search.C. In the typing example, cumulative selection reduces the number of random key strokes required to produce a line Shakespeare from 1040 to a few thousandXVI. Folding funnel with a rugged surfaceA. As folding progresses, entropy decreases but this is offset by increasing interactions B. Folding intermediate occur in valleys along the funnel wallsC. Slope steepens toward the bottomXVII. Molecular Dynamics simulation of villin foldingXVIII. Anfinsen - sequence determines structureA. Using RNAase, Anfinsen's showed convincingly that proteins can indeed adopt their native structure spontaneously, starting from an unfolded stateB. All the information required for a protein to fold is present in the primary sequenceXIX. Protein UnfoldingA. Some ways to denature a protein1. Acid/Base treatment2. Heat3. Detergent4. Reducing agents5. Urea/Guanidinium Chloride6. Denaturants alter the equilibrium between the native (folded) and denatured (unfolded) states of the proteinB. Protein unfolding is cooperative1. Sharp transition suggests that unfolding is a cooperative process2. Conditions that lead to the disruption of any part of a protein structure are likely to unravel the protein completely3. What does it mean to have a protein solution that is half folded?XX. Denaturing Proteins: ChemicalsA. Organic Solvents1. Lowers the dielectric constant of environment2. increase the strength of all electrostatic interactions3. Weakens