Protein Structure PDF

4 The Three- Dimensional Structure of Proteins © 2021 Macmillan Learning 4.1 Overview of Protein Structure  Protein Conformations limited number of conformations predominate under biological conditions conformations = thermodynamically the most stable, that...

4 The Three- Dimensional Structure of Proteins © 2021 Macmillan Learning 4.1 Overview of Protein Structure  Protein Conformations limited number of conformations predominate under biological conditions conformations = thermodynamically the most stable, that is, lowest free energy (G) native = proteins in any functional, folded conformations A Protein’s Conformation Is Stabilized Largely by Weak Interactions stability = tendency of a protein to maintain a native conformation unfolded proteins have high conformational entropy chemical interactions stabilize native conformations: – strong disulfide (covalent) bonds are uncommon – weak (noncovalent) interactions and forces are numerous hydrogen bonds hydrophobic effect ionic interactions Van der Waals interaction Packing of Hydrophobic Amino Acids Away from Water Favors Protein Folding hydrophobic effect solvation layer = highly structured shell of H2O around a hydrophobic molecule – decreases when nonpolar groups cluster together – decrease causes a favorable increase in net entropy hydrophobic R chains form a hydrophobic protein core Protein folding  Individual van der Waals Interactions Are Weak but Combine to Promote Folding van der Waals interactions = dipole-dipole interactions over short distances When adjacent atoms come close enough that their outer electron clouds just barely touch. This action induces charge fluctuations that result in a nonspecific, nondirectional attraction. individual interactions contribute little to overall protein stability high number of interactions can be substantial Pollev.com/yw22  Answer Which item is the predominant factor in protein stability? B. the hydrophobic effect The hydrophobic effect, derived from the increase in entropy of the surrounding water when nonpolar molecules or groups are clustered together, makes the major contribution to stabilizing the globular form of most soluble proteins.  The Peptide Bond Is Rigid and Planar 3 covalent bonds separate the α carbons of adjacent amino acid residues: Cα —C—N—Cα resonance between the carbonyl oxygen and the amide nitrogen partial negative charge and partial positive charge sets up a small electric dipole  Peptide C—N Bonds Cannot Rotate Freely 6 atoms of the peptide group lie in a single plane partial double-bond character of C—N peptide bond prevents rotation, limiting range of conformations Dihedral Angles Define Peptide Conformations 3 dihedral angles: – φ (phi) = between −180 and +180 degrees – ψ (psi) = between −180 and +180 degrees – ω (omega) = ±180 degrees for trans https://www.youtube.com/watch?v=9672qpfqDX4&t=0s 2:45 4.2 Protein Secondary Structure  Protein Secondary Structure secondary structure = describes the spatial arrangement of the main-chain atoms in a segment of a polypeptide chain – regular secondary structure = φ and ψ remain the same throughout the segment – common types = α helix, β conformation, β turn, random coils Ribbon diagram of protein structure Ribbon schematic of triose P isomerase monomer (hand- drawn by J. Richardson, 1981) (PDB: 1TIM​) Jane Shelby Richardson Duke University  The α Helix Is a Common Protein Secondary Structure α helix = simplest arrangement, maximum number of hydrogen bonds – backbone wound around an imaginary longitudinal axis – R groups protrude out from the backbone – each helical turn = 3.6 residues, ∼5.4 Å  Handedness of the α Helix right-handed: – R groups protruding away from the helical backbone – most common left-handed: less stable, less common  Intrahelical Hydrogen Bonds between hydrogen atom attached to the electronegative nitrogen atom of residue n and the electronegative n+4 carbonyl oxygen atom of residue n + 4 n confers significant stability https://www.youtube.com/watch?v=PeFdl6KmxYM  Proline and Glycine Occur Infrequently in an α Helix proline = introduces destabilizing kink in helix – nitrogen atom is part of rigid ring – rotation about N—Cα bond not possible glycine = high conformational flexibility, take up coiled structures  The β Conformation Organizes Polypeptide Chains into Sheets β conformation = backbone extends into a zigzag – β strand = single protein segment – β sheet = several strands in β conformation side by side  Adjacent Polypeptide Chains in a β Sheet Can Be Antiparallel or Parallel antiparallel = opposite orientation – occur more frequently parallel = same orientation H bonds form between backbone atoms of adjacent segments https://www.youtube.com/watch?v=jT1XvChhJ8Y  β Turns Are Common in Proteins β turns = connect ends of two adjacent segments of an antiparallel β sheet – 180° turn – involves 4 residues – hydrogen bond forms between first and fourth residue – Gly (residue 2) and Pro (residue 3) often occur in β turns  Common Secondary Structures Have Characteristic Dihedral Angles dihedral angles φ (phi) and ψ (psi) associated with each residue completely described secondary structure Ramachandran plots: – visualize all φ and ψ angles – test quality of three-dimensional protein structures Secondary Structure Conformations are Defined by φ and ψ Values  φ and ψ Values from Known Proteins Fall into Expected Regions glycine frequently falls outside the expected ranges  Activity: Properties P1. of Protein Structures Study the Ramachandran plot of a protein. P2. P3.  Activity Instructions On your own, think of answers to the question: – Which secondary structures possess φ and ψ angles that fall within regions A, B, and C, respectively? – Based on the protein structures, which protein does this plot belong to (P1, P2 or P3)? (2 minutes) Pair up to discuss your ideas. (2 minutes) Share your ideas with the class in group discussion.  Activity Solution – Which secondary structures possess φ and ψ angles that fall within regions A, B, and C, respectively? Region A corresponds to beta sheets, region B corresponds to right-handed alpha helices, region C corresponds to left- handed alpha helices. – Based on the protein structures, which protein does this plot belong to (P1, P2 or P3)? Mixed right-handed alpha helices and beta sheets P2! 4.3 Protein Tertiary and Quaternary Structures  Protein Tertiary and Quaternary Structure tertiary structure = overall three-dimensional arrangement of all the atoms in a protein – weak interactions and covalent bonds hold interacting segments in position quaternary structure = arrangement of 2+ separate polypeptide chains in three-dimensional complexes  Structural Diversity Reflects Functional Diversity in Globular Proteins globular proteins: – fold back on each other – more compact than fibrous proteins – enzymes, transport proteins, motor proteins, regulatory proteins, immunoglobulins Size of human serum albumin (585 residues) as a globular protein, compared to the approximate dimensions if it occurs as an extended beta strand or alpha helix.  The Protein Data Bank The Protein Data Bank (PDB): www.rcsb.org – archive of experimentally determined three- dimensional structures – structures assigned an identifier called the PDB ID – PDB data files describe: the spatial coordinates of each atom information on how the structure was determined information on its accuracy – structure visualization software can convert atomic coordinates to an image of the molecule Myoglobin Provided Early Clues about the Complexity of Globular Protein Structure several structural representations of myoglobin’s tertiary structure: Binding pocket α-Helical Hydrophobic R regions chains  Globular Proteins Have a Variety of Tertiary Structures Table 4-3 Approximate Proportion of α Helix and β Conformation in Some Single-Chain Proteins each globular Residues (%): Residues (%): protein has a Protein (total residues) α Helix β Conformation distinct Chymotrypsin (247) 14 45 Ribonuclease (124) 26 35 structure, Carboxypeptidase (307) 38 17 adapted for its Cytochrome c (104) 39 0 biological Lysozyme (129) 40 12 function Myoglobin (153) 78 0  The Structure of Collagen collagen = found in connective tissue – secondary structure = left-handed, repeating tripeptide unit Gly–X–Y, where X is often Pro and Y is often 4-Hyp – tertiary and quaternary structure = right-handed twisting of 3 separate polypeptides Scurvy, Vitamin C, and Collagen Formation scurvy is caused by a lack of vitamin C – characterized by general degeneration of connective tissue vitamin C is required for the hydroxylation of proline and lysine in collagen Some Proteins or Protein Segments Are Intrinsically Disordered intrinsically disordered proteins: – lack definable structure – often lack a hydrophobic core – high densities of charged residues (Lys, Arg, Glu) and Pro – facilitates a protein to interact with multiple binding partners Intrinsically Disordered Segments Can Assume Different Structures P53 protein Protein Quaternary Structures Range from Simple Dimers to Large Complexes quaternary structure = assembly of multiple peptide subunits oligomer = multimer = multisubunit protein – repeating structural unit = protomer 4.4 Protein Denaturation and Folding Pathways Involved in Proteostasis proteostasis = continual maintenance of the active set of cellular proteins required under a given set of conditions Loss of Protein Structure Results in Loss of Function denaturation = loss of three-dimensional structure sufficient to cause loss of function – can occur by heat, pH extremes, miscible organic solvents, certain solutes, detergents – often leads to protein precipitation Amino Acid Sequence Determines Tertiary Structure renaturation = process by which certain denatured globular proteins regain their native structure and biological activity Anfinsen experiment showed the amino acid sequence contains all the information required to fold the chain  Answer Denaturing followed by renaturing of a protein: B. demonstrates that primary structure dictates tertiary structure. The Anfinsen experiment provided the first evidence that the amino acid sequence of a polypeptide chain contains all the information required to fold the chain into its native, three-dimensional structure.  Polypeptides Fold Rapidly by a Stepwise Process local secondary structures fold first – ionic interactions play an important role longer range interactions follow – hydrophobic effect plays a significant role process continues until the entire polypeptide folds https://www.youtube.com/watch?v=gFcp2Xpd29I  Defects in Protein Folding Are the Molecular Basis for Many Human Genetic Disorders amyloid fiber = protein secreted in a misfolded state and converted to an insoluble extracellular fiber amyloidose diseases: type 2 diabetes, Alzheimer disease, Huntington disease, and Parkinson disease amyloid polypeptide (IAPP or amylin) deposits in islet cells Gradually less and less insulin created  type 2 diabetes  Neurodegenerative Conditions Alzheimer disease = associated with extracellular amyloid deposition by neurons, involving the amyloid-β peptide Parkinson disease = misfolded form α-synuclein aggregates into spherical filamentous masses called Lewy bodies Huntington disease = involves the intracellular aggregation of huntingtin, a protein with long polyglutamine repeat  Formation of Disease-Causing Amyloid Fibrils native = high degree of β- sheet structure misfolded β amyloid promotes aggregation, forming an amyloid fibril  Cystic Fibrosis cystic fibrosis = caused by defects in the membrane-bound protein cystic fibrosis transmembrane conductance regulator (CFTR) – deletion of a Phe residue causes improper protein folding  Death by Misfolding: The Prion Diseases prion protein (PrP) = misfolded brain protein Pyramidal cells Comparable in the human section from a cerebral cortex patient with Creutzfeldt-Jakob disease