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

Globular ProteinsGlobular Proteins

• Usually water soluble, compact, roughly spherical

• Hydrophobic interior, hydrophilic surface

• Globular proteins include enzymes,carrier and regulatory proteins

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

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

Four Levels of Protein Structure:Four Levels of Protein Structure:

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

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

““transtrans” and “” and “ciscis” conformations” conformations

• Nearly all peptide groups in proteins are in the trans conformation

Rotation around the N-CRotation around the N-C and C and C-C bonds -C bonds

that link peptide groupsthat link peptide groups

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 ()

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)

Stereo view of right-handed Stereo view of right-handed helixhelix

Helix in horse liver Helix in horse liver alcohol dehydrogenasealcohol dehydrogenase

Helical wheel diagram

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

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)

-Sheets -Sheets (a) parallel, (b) antiparallel(a) parallel, (b) antiparallel

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

Reverse turnsReverse turns

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

Supersecondary Structures Supersecondary Structures (Motifs)(Motifs)

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

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

Urea and guanidinium chloride Urea and guanidinium chloride (chaototropic agents)(chaototropic agents)

Hydrogen BondingHydrogen Bonding

• Contributes to cooperativity of folding

• Helps stabilize secondary structures and native conformation

Examples of hydrogen bondsExamples of hydrogen bonds

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

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)

Stereo view of human Stereo view of human Type III collagen triple helixType III collagen triple helix

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

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