Protein Structure. Hierarchy of Protein Structure. Tertiary structure. independently stable structural unit. includes disulfide bonds

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1 Protein Structure Hierarchy of Protein Structure 2 3 Structural element Primary structure Secondary structure Super-secondary structure Domain Tertiary structure Quaternary structure Description amino acid sequence of protein helices, sheets, turns and loops association of secondary structures independently stable structural unit folded structure of whole polypeptide includes disulfide bonds assembled complex (oligomer) homo-oligomeric ( protein type) hetero-oligomeric (> type) Primary Structure Linear amino acid sequence -Can be chemically sequenced Sanger insulin 955 -Can usually be translated from gene B - inteins Aminoacid 2 Equine hemoglobin primary structure VLSAADKTVKAAWSKVGGHAGEYGAEALEMF LGFPTTKTYFPHFDLSHGSAQVKAHGKKVADGL TLAVGHLDDLPGALSDLSLHAHKLVDPVFK LLSHCLLSTLAVHLPDFTPAVHASLDKFLSSV STVLTSKY Aminoacid

2 Secondary Structure Defined by main chain angles - Helix - Sheet Distinct hydrogen bonding patterns - Turn - Loop (or coil) amachandran Plot Alpha Helix Super-Secondary Structure TIM barrel composed of strand-helix-strand motifs Tertiary Structure Three main categories: - all alpha - all beta - alpha/beta May contain one or more domains Lipoxygenase 2 2

3 Quaternary Structure Homodimer S-adenosyl homocysteine hydrolase Homotrimer of heterodimers b a b F0F ATPase a a b Main Chain Angles (eview) Omega (peptide bond) is ~80 and can be 0 for proline 2 3 Omega is angle between two planes: -Plane made by atoms,2,3 -Plane made by atoms 2,3, Main Chain Angles (Phi) Phi is angle between two planes: -Plane made by atoms,2,3 -Plane made by atoms 2,3, o Phi for proline 3

4 Main Chain Angles (Psi) 2 3 Psi is angle between two planes: -Plane made by atoms,2,3 -Plane made by atoms 2,3, 2 3 amachandran Plot Describes allowable areas for 8 amino acids (not G and P) Psi estrictions 2 3 Clash between and Clash between and

5 Phi estrictions 3 2 Clash between C and C Clash between C and, Interactions Limit Main Chain Conformational Space Secondary Structure Elements alpha-helix beta-sheet Helices (30, alpha, pi) Sheets (parallel, anti-parallel) Turns (beta, gamma) Loop/Coil (everything else) coil (usually exposed on the surface of proteins) ribonuclease A 5

6 alpha Helices 3.0 pi amino acids per turn: frequency 3.6 ~97% 3.0 ~3%. rare H-bonding i, i+ i, i+3 i, i+5 Helical Main Chain Angles Collagen, PolyProline 3 0 Helix Alpha Helix Pi Helix a-helices -Local interactions -ight handed rise per residue,.5 Å -esidue per turn, 3.5Å -Alpha helices are about 0 residues on average -Side chains staggered -Linus Pauling (obel Prize in Chemistry, 95) figured out the structure of alpha-keratin helix. 6

7 a-helix Dipole Moment d- -Hydrogen bond between C=O(i)...H-(i+) -Dipole moment arises due to the orientation of peptide bond (3.5 Debye) d+ Dipole moment Helical Wheels - a tool to visualize the position of amino acids around an alpha-helix - allows for quick visualization of whether a side of a helix posses specific chemical properties - example shown is a helix that forms a Leucine-Zipper Hydrophobic residues on one side interact with helix displaying same pattern Amphipathic Helices Amphipathic: hydrophilic & hydrophobic - these helices posses hydrophilic amino acids on one side and hydrophobic residues on the other. Hydrophobic -these -helices can interact with membrane Hydrophilic hydrophilic head group aliphatic carbon chain lipid bilayer 7

8 b-sheets Antiparallel b-sheet Parallel b-sheet b-sheets fulfill the hydrogen bonding potential of the main-chain atoms, except at the edges. Sheet are composed of individual beta strands. Adjacent strands are usually close in sequence. b-sheets Antiparallel b-sheet Parallel b-sheet Properties: -Parallel beta-strands (3.25 Å between adjacent Ca s) -Anti-parallel beta-strands (3.7 Å between adjacent Ca s) -Distance between strands ~.6 Å -o significant net dipole moment -Strands are not flat. They have a characteristic right-handed twist ight Handed Twist parallel - beta-sheets can form various higher-level structures, such as a beta-barrel anti-parallel twisted Green Fluorescent Protein (GFP) 8

9 Beta Strand Main Chain Angles Antiparallel Parallel Side Chains Extend Above and Below Beta-Sheets Silk An example of complex beta-sheets: Silk Fibroin - multiple pleated sheets provide toughness & rigidity to many structural proteins. 9

10 Beta Bulge C H 3 O H H 0 O O O H O 2 H - H O H O 3 0 H O 2 H O Beta bulge C C H 3 O H O O H 2 O H 0 H O H O 3 H 0 O 2 H O C Anti-parallel strands -Beta bulges occur on the last strand (edge) of an anti-parallel beta sheet -An additional amino acid is present in the last strand -Bulges cause bending of otherwise straight anti-parallel beta strands Beta - Turns Same side There are two classes of beta-turns: - type I - type II Type I turns have the amino acids on the same side Opposite sides Type II turns have the amino acids on the opposite sides Hydrogen-bonding between backbones of residue and Gamma-Turns Proline A 3 amino acid turn utilizing proline at the turn. Hydrogen-bonding with C=O of residue and -H of residue 2 0

11 Conformational Preferences of the Amino Acids Helical Preference Strand Preference Turn Preference Williams, W et al., Biochim. Biophys. Acta 987, 96: 200- Conformational Preferences of the Amino Acids Extended flexible side chains Bulky side chains, beta-branched estricted conformations, side Chain main chain interactions Williams, W et al., Biochim. Biophys. Acta 987, 96: 200- Helical Preference Extended flexible side chains

12 Strand Preference Bulky side chains, beta-branched B B B Bulky residues better tolerated above and below sheet Turn Preference estricted conformations, side chain main chain interactions End of Secondary Structure 2

13 Super Secondary Structure Motifs These simple arrangements of secondary structural elements account for most protein domains. In all cases the stabilizing interactions occur within a local area of the sequence (this is convenient for evolution). ote also that all of these motifs are chiral and are observed almost exclusively in these arrangements Tertiary Structure PDB 3

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