Lecture 20: Lehninger Ch4 Proteins PDF

4 | The Three- Dimensional Structure of Proteins © 2017 W. H. Freeman and Company  CHAPTER 4 The Three-Dimensional Structure of Proteins Learning goals: Structure and properties of the peptide bond Structural hierarchy in proteins Structure an...

4 | The Three- Dimensional Structure of Proteins © 2017 W. H. Freeman and Company  CHAPTER 4 The Three-Dimensional Structure of Proteins Learning goals: Structure and properties of the peptide bond Structural hierarchy in proteins Structure and function of fibrous proteins Structure analysis of globular proteins Protein folding and denaturation  Structure of Proteins Unlike most organic polymers, protein molecules adopt a specific three-dimensional conformation. This structure is able to fulfill a specific biological function. This structure is called the native fold. The native fold has a large number of favorable interactions within the protein. There is an entropy cost to folding the protein into one specific native fold.  Favorable Interactions in Proteins Hydrophobic effect – The release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy. Hydrogen bonds – Interaction of N−H and C=O of the peptide bond leads to local regular structures such as a helices and b sheets. London dispersion – Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein. Electrostatic interactions – long-range strong interactions between permanently charged groups – Salt bridges, especially those buried in the hydrophobic environment, strongly stabilize the protein. Four Levels of Protein Structure Primary Structure: The Peptide Bond The structure of the protein is partially dictated by the properties of the peptide bond. The peptide bond is a resonance hybrid of two canonical structures. The resonance causes the peptide bonds: – to be less reactive compared with esters, for example – to be quite rigid and nearly planar – to exhibit a large dipole moment in the favored trans configuration Resonance in the Peptide Bond The Polypeptide Is Made Up of a Series of Planes Linked at α Carbons  Secondary Structures Secondary structure refers to a local spatial arrangement of the polypeptide backbone. Two regular arrangements are common: the a helix – stabilized by hydrogen bonds between nearby residues the b sheet – stabilized by hydrogen bonds between adjacent segments that may not be nearby Irregular arrangement of the polypeptide chain is called the random coil.  The a Helix Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n + 4 amino acids. It is a right-handed helix with 3.6 residues (5.4 Å) per turn. n+4 Peptide bonds are aligned roughly parallel with the helical axis. n Side chains point out and are roughly perpendicular with the helical axis. What Is a Right-Handed Helix?  The a Helix: Top View The inner diameter of the helix (no side chains) is about 4–5 Å. too small for anything to fit “inside” The outer diameter of the helix (with side chains) is 10–12 Å. happens to fit well into the major groove of dsDNA Amino acids #1 and #8 align nicely on top of each other. What kind of sequence gives an a helix with one hydrophobic face?  Sequence Affects Helix Stability Not all polypeptide sequences adopt a-helical structures. Small hydrophobic residues such as Ala and Leu are strong helix formers. Pro acts as a helix breaker because the rotation around the N-Ca (φ-angle) bond is impossible. Gly acts as a helix breaker because the tiny R group supports other conformations. Attractive or repulsive interactions between side chains 3 to 4 amino acids apart will affect formation.  The Helix Dipole Recall that the peptide bond has a strong dipole moment. – C−O (carbonyl) negative – N−H (amide) positive All peptide bonds in the a helix have a similar orientation. The a helix has a large macroscopic dipole moment that is enhanced by unpaired amides and carbonyls near the ends of the helix. Negatively charged residues often occur near the positive end of the helix dipole.  b Sheets The planarity of the peptide bond and tetrahedral geometry of the a carbon create a pleated sheet-like structure. Sheet-like arrangement of the backbone is held together by hydrogen bonds between the backbone amides in different strands. Side chains protrude from the sheet, alternating in an up-and-down direction.  Parallel and Antiparallel b Sheets Multi b-strand interactions are called sheets. Sheets are held together by the hydrogen bonding of amide and carbonyl groups of the peptide bond from opposite strands. Two major orientations of b sheets are determined by the directionality of the strands within: – Parallel sheets have strands that are oriented in the same direction. – Antiparallel sheets have strands that are oriented in opposite directions. In parallel b sheets, the H-bonded strands run in the same direction. Hydrogen bonds between strands are bent (weaker). In antiparallel b sheets, the H-bonded strands run in opposite directions. Hydrogen bonds between strands are linear (stronger).  b Turns b turns occur frequently whenever strands in b sheets change the direction. The 180° turn is accomplished over four amino acids. The turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence. Proline in position 2 or glycine in position 3 are common in b turns.  Proline Isomers Most peptide bonds not involving proline are in the trans configuration (>99.95%). For peptide bonds involving proline, about 6% are in the cis configuration. Most of this 6% involve b turns. Proline isomerization is catalyzed by proline isomerases.  Protein Tertiary Structure Tertiary structure refers to the overall spatial arrangement of atoms in a protein. Stabilized by numerous weak interactions between amino acid side chains - largely hydrophobic and polar interactions - can be stabilized by disulfide bonds Interacting amino acids are not necessarily next to each other in the primary sequence. Two major classes: – fibrous and globular (water or lipid soluble) Fibrous Proteins  Fibrous Proteins: From Structure to Function TABLE 4-3 Secondary Structures and Properties of Some Fibrous Proteins Structure Characteristics Examples of occurrence α Helix, cross-linked by Tough, insoluble protective structures α-Keratin of hair, feathers, nails disulfide bonds of varying hardness and flexibility β Conformation Soft, flexible filaments Silk fibroin Collagen triple helix High tensile strength, without stretch Collagen of tendons, bone matrix Structure of a-Keratin in Hair Chemistry of Permanent Waving  Structure of Collagen Collagen is an important constituent of connective tissue: tendons, cartilage, bones, cornea of the eye. Each collagen chain is a long Gly- and Pro-rich left- handed helix. Three collagen chains intertwine into a right-handed superhelical triple helix. The triple helix has higher tensile strength than a steel wire of equal cross section. Many triple-helices assemble into a collagen fibril.  4-Hydroxyproline in Collagen Forces the proline ring into a favorable pucker Offers more hydrogen bonds between the three strands of collagen The posttranslational processing is catalyzed by prolyl hydroxylase and requires α-ketoglutarate, molecular oxygen, and ascorbate (vitamin C). Collagen Fibrils Collagen superstructures are formed by cross-linking of collagen triple-helices to form collagen fibrils. Crosslinks are covalent bonds between Lys or HyLys, or His amino acid residues. Water-Soluble Globular Proteins  Motifs (folds) Specific arrangement of several secondary structure elements – all a helix – all b sheet – both Motifs can be found as recurring structures in numerous proteins. Globular proteins are composed of different motifs folded together. Motifs (folds) Repeated Motifs Contribute to Final Fold  Quaternary Structure A quaternary structure is formed by the assembly of individual polypeptides into a larger functional cluster.  Protein Stability and Folding A protein’s function depends on its 3D structure. Loss of structural integrity with accompanying loss of activity is called denaturation. Proteins can be denatured by: heat or cold pH extremes organic solvents chaotropic agents: urea and guanidinium hydrochloride Proteins Folding Follow a Distinct Path Protein Misfolding Is the Basis of Numerous Human Diseases Native (correctly folded) b amyloid is a soluble globular protein, Misfolded b amyloid promotes aggregation at newly exposed protein-protein interface. Correctly folded helices are lost and peptides form b strands, b helices, and b sheets.  Chapter 4: Summary In this chapter, we learned about: the two most important secondary structures – a helices – b sheets how properties and function of fibrous proteins are related how to determine three-dimensional structures of proteins one of the largest unsolved puzzles in modern biochemistry: how proteins fold