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![Page 1: Types of Proteins Proteomics - study of large sets of proteins, such as the entire complement of proteins produced by a cell E. coli has about 4000 different.](https://reader031.fdocuments.in/reader031/viewer/2022013101/56649e525503460f94b47eb5/html5/thumbnails/1.jpg)
Types of ProteinsTypes of Proteins• Proteomics - study of large sets of proteins,
such as the entire complement of proteins produced by a cell
• E. coli has about 4000 different polypeptides (average size 300 amino acids, Mr 33,000)
• Fruit fly (Drosophila melanogaster) about 16,000, humans, other mammals about 40,000 different polypeptides
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Globular ProteinsGlobular Proteins
• Usually water soluble, compact, roughly spherical
• Hydrophobic interior, hydrophilic surface
• Globular proteins include enzymes,carrier and regulatory proteins
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Fibrous ProteinsFibrous Proteins
• Provide mechanical support
• Often assembled into large cables or threads
• -Keratins: major components of hair and nails
• Collagen: major component of tendons, skin, bones and teeth
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Four Levels of Protein Structure:Four Levels of Protein Structure:
• Primary structure - amino acid linear sequence
• Secondary structure - regions of regularly repeating conformations of the peptide chain, such as -helices and -sheets
• Tertiary structure - describes the shape of the fully folded polypeptide chain
• Quaternary structure - arrangement of two or more polypeptide chains into multisubunit molecule
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Four Levels of Protein Structure:Four Levels of Protein Structure:
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Resonance Structures of the Peptide Resonance Structures of the Peptide BondBond
(a) Peptide bond shown as a C-N single bond
(b) Peptide bond shown as a double bond
(c) Actual structure is a hybrid of the two resonance forms. Electrons are delocalized over three atoms: O, C, N
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PlanarityPlanarity
• Rotation around C-N bond is restricted due to the double-bond nature of the resonance hybrid form
• Peptide groups (blue planes) are therefore planar
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““transtrans” and “” and “ciscis” conformations” conformations
• Nearly all peptide groups in proteins are in the trans conformation
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Rotation around the N-CRotation around the N-C and C and C-C bonds -C bonds
that link peptide groupsthat link peptide groups
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The The -Helix-Helix• Each C=O (residue n) forms a hydrogen bond with
the amide hydrogen of residue n+4
• Helix is stabilized by many hydrogen bonds (which are nearly parallel to long axis of the helix)
• All C=O groups point toward the C-terminus (entire helix is a dipole with (+) N, (-) C-termini)
• The and angles of each residue are similar:near -57o () and near -47o ()
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The The -Helix-Helix
• Pitch is 0.54nm (recurrence of equivalent positions)
• Rise - Each residue advances by 0.15nm along the long axis of the helix
• There are 3.6 amino acid residues per turn
• Most helices in proteins are right handed (backbone turns clockwise when viewed along the axis from the N terminus)
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Stereo view of right-handed Stereo view of right-handed helixhelix
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Helix in horse liver Helix in horse liver alcohol dehydrogenasealcohol dehydrogenase
Helical wheel diagram
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Strands and Strands and Sheets Sheets
• Strands - polypeptide chains that are almost fully extended
• Sheets - multiple strands arranged side-by-side
• Strands are stabilized by hydrogen bonds between C=O and -NH on adjacent strands
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Parallel and antiparallel Parallel and antiparallel -strands-strands
• Strands in a sheet are parallel or antiparallel
• Parallel sheets - strands run in the same N- to C- terminal direction
• Antiparallel sheets - strands run in opposite N- to C- terminal directions
• In antiparallel sheets the H-bonds are nearly perpendicular to the chains (more stable than parallel chains with distorted H-bonds)
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-Sheets -Sheets (a) parallel, (b) antiparallel(a) parallel, (b) antiparallel
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Loops and TurnsLoops and Turns
• Loops and turns connect helices and strands and allow a peptide chain to fold back on itself to make a compact structure
• Loops - often contain hydrophilic residues and are found on protein surfaces
• Turns - loops containing 5 residues or less
• Turns (reverse turns) - connect different antiparallel strands
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Reverse turnsReverse turns
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Tertiary Structure of ProteinsTertiary Structure of Proteins
• Tertiary structure results from the folding of a polypeptide chain into a closely-packed three-dimensional structure
• Amino acids far apart in the primary structure may be brought together
• Stabilized primarily by noncovalent interactions (e.g. hydrophobic effects) between side chains
• Disulfide bridges also part of tertiary structure
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Supersecondary Structures Supersecondary Structures (Motifs)(Motifs)
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DomainsDomains
• Independently folded, compact units in proteins
• Domain size: ~25 to ~300 amino acid residues
• Domains are connected to each other by loops, bound by weak interactions between side chains
• Domains illustrate the evolutionary conservation of protein structure
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Protein Denaturation and Protein Denaturation and RenaturationRenaturation
• Denaturation - disruption of native conformation of a protein, with loss of biological activity
• Energy required is small, perhaps only equivalent to 3-4 hydrogen bonds
• Proteins denatured by heating or chemicals
• Some proteins can be refolded or renatured
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Urea and guanidinium chloride Urea and guanidinium chloride (chaototropic agents)(chaototropic agents)
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Hydrogen BondingHydrogen Bonding
• Contributes to cooperativity of folding
• Helps stabilize secondary structures and native conformation
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Examples of hydrogen bondsExamples of hydrogen bonds
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Van der Waals and Van der Waals and Charge-Charge InteractionsCharge-Charge Interactions
• VDW contacts occur between nonpolar side chains and contribute to the stability of proteins
• Charge-charge interactions between oppositely charged side chains in the interior of a protein also may stabilize protein structure
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Protein Folding Is Assisted by Protein Folding Is Assisted by ChaperonesChaperones
• Molecular chaperones increase rate of correct folding and prevent the formation of incorrectly folded intermediates
• Chaperones can bind to unassembled protein subunits to prevent incorrect aggregation before they are assembled into a multisubunit protein
• Most chaperones are heat shock proteins (synthesized as temperature increases)
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Stereo view of human Stereo view of human Type III collagen triple helixType III collagen triple helix
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Collagen triple helixCollagen triple helix
• Multiple repeats of -Gly-X-Y- where X is often proline and Y is often 4-hydroxyproline
• Glycine residues are located along central axis of a triple helix (other residues cannot fit)
• For each -Gly-X-Y- triplet, one interchain H bond forms between amide H of Gly in one chain and -C=O of residue X in an adjacent chain
• No intrachain H bonds exist in the collagen helix
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4-Hydroxyproline and 4-Hydroxyproline and 5-hydroxylysine5-hydroxylysine
• Formed by enzyme hydroxylation reactions (require vitamin C) after incorporation into collagen
• Vitamin C deficiency (scurvy) leads to lack of proper hydroxylation and defective triple helix (skin lesions, fragile blood vessels, bleeding gums)
• Unlike most mammals, humans cannot synthesize vitamin C