Biochemistry Ch6) The 3D Structure of Proteins

The stability of the folded structure of a globular protein depends on the interplay of which of these factors: 1) ΔH generally favors the folded state and is associated with changes in noncovalent bonding interactions. 2) ΔH of the surrounding medium, which generally favors the folded state of the protein. 3) ΔS-conformation of the protein favors the unfolded state. 4) ΔS-solvent is favorable due to the release of water from clathrates. This occurs when solvent exposed hydrophobic groups become buried within the molecule. A) 1, 3, and 4 B) 1 and 3 C) 3 and 4 D) All statements are correct

A) 1, 3, and 4

Primary Structure

Amino acid sequence

Hydrophobic Effect Proteins

Hydrophobic on inside to keep water disorganized Hydrophilic on outside

Hydroxyproline

Important for turns in collagen chain

Side chains in Alpha Helices

In the alpha helix, side chains point outward Side chains of similar polarity are frequently found together on one side of a helix -these helices are amphipathic -this allows two or more helices to associate to keep hydrophobic surfaces away from water -will dictate tertiary structure

Secondary Structure

Regular repeating structure, like a helix or a sheet

Alpha-Helices

Right-handed helix, clockwise pattern from top view N-H and C=O groups in the peptide bond align for hydrogen bonding 3.6 residues per turn, and residues of similar polarity occur every 3-4 residues (non polars will end on one side of the helix, to allow better interactions in teriary structure) The helix has its own dipole moment due to the C and N terminals of the peptide Does not contain glycine (too flexible), proline (too rigid), charged residues, and bulky R groups

Quaternary Structure

Several peptide chains (subunits) can arrange and associate themselves Two or more subunits or folded polypeptide chains Homotypic = identical/nearly identical Heterotypic = different chains Stabilizing forces between chains are the same noncovalent interactions and also sometimes disulfide bonds

Fibroin

Silkworms and spiders spin fibroin Contain stacked beta sheets with the polypeptide chains running parallel to the fiber axis The stacked sheets are held together by dispersion forces between interdigitated (intertwined fingers) side chains Repetitive chain, allows sheets to stack together, and are flexible, but do not stretch much Gly-Ala-Gly-Ala or Gly-Ser-Gly-Ser

Thermodynamics of Protein Folding

Proteins spontaneously fold when placed in intracellular conditions (-G) Entropy change -protein goes from random coil to a folded protein, and restrictions come about, so entropy decreases as order is forced -the solvent, with hydrophobic residues, will have an increase in entropy if the protein folds and hydrophobic residues cluster (will not increase without folding) Entropy of protein usually dominates solvent entropy Enthalpy is released, -H as energy is expended when proteins fold (driving factor is the IMF that form when folding occurs)

Disulfide Bond

Strong chemical side bond that joins the sulfur atoms of two neighboring cysteine amino acids to create one cystine, which joins together two polypeptide strands like rungs on a ladder

Turns

A polypeptide chain can turn corners several ways to go from helix to sheet or another

Alpha Keratin

Components of hair, nails, and skin They contain long sequences (over 300 residues) of alpha-helices Pairs of these helices coil around in each other in coils called "coiled-coils) The amino acid sequence of keratin places a nonpolar hydrophobic side chain every 3-4 residues -this leads to a continuous strip of hydrophobic residues on one face of the helix that wraps around the helix -two helices then wrap around each other to maximize the contact between the hydrophobic surface of the helices Hardened alpha keratins (nails) have more disulfide bonds

Secondary Structure Beta (Pleated) Sheets

Composed of two or more Beta strands C -> N and N -> C is an antiparallel arrangement C -> N and C -> N is a parallel arrangement The N-H and C=O groups align for hydrogen bonding in both cases Like helices, side chains of similar polarity are frequently found together on one side of a sheet (are amphipathic) -this allows two or more secondary structures to associate to keep hydrophobic surfaces away from water Sheets have every residues of alternating polarities

Proteins structure is broken down into separate levels of organization. The secondary structure of a protein is best described by which statement? A) The secondary structure of a protein arises when two or more polypeptide chains folded into tertiary structures interact to form well-defined multi-subunit complexes. B) The secondary structure of a protein is the amino acid sequence. C) The secondary structure of a protein is the assembly of local structure elements that associate along their hydrophobic surfaces to give a stably folded structure. D) Secondary structure of a protein is the adoption of a locally repeating structure.

D) Secondary structure of a protein is the adoption of a locally repeating structure.

Ubiquitin Structure

Very small protein, only 76 residues Targets other proteins for degradation Different renderings of the protein shown at pH 7 5-stranded beta sheet and alpha helix Charged residues on outside, non polar remain inside

Motif

Well known domains that are common Beta-barrel for example

Principles of Complex Protein Structures

1) Bond lengths and angles should vary as little as possible 2) No two atoms should be closer than their van der Waals radii 3) The six atoms in the peptide amine group must remain coplanar with the alpha carbons, so rotation is only possible in the bonds adjacent to alpha carbons (phi and psi) 4) Some kind of IMF (noncovalent interaction) is needed to stabilize a regular folding

What determines (and maintains) the secondary and tertiary structure?

1) Charge-charge interactions: can occur between positively and negatively charged side chains (salt bridge) -changing pH can disrupt 2) Internal H-bonds: hydroxyl groups like to bond with amino or carbonyl groups and also involving side chains -relatively weak individually but can become significant if the number large 3) VDW Interactions - weak induced dipole - induced dipole interactions -significant when protein is large 4) hydrophobic effect - clathrate structure (cages) of water form around hydrophobic substances -a protein with hydrophobic residues will fold to keep the residues together instead of having each caged by water -produces a favorable entropy change (water order -> disorder) 5) Disulfide bonds - once folding has occurred the structure can be further stabilized by disulfide bonds between two cysteine residues -covalent interaction, not an IMF

Summary of Protein Folding Thermodynamics

1) S-protein favors unfolded state 2) H-folding favors the folded state 3) Favorable S-solvent when clathrate structures are released, favors unfolded state

Which of the following statements about protein quaternary structure are correct? 1) It involves a complex of two or more proteins interacting with each other. 2) The subunits of the structure can be either identical or different. 3) The interactions between subunits can give rise to indefinite growth of polymeric complexes. 4) Most assemblies of protein subunits have one or more defined axis of rotation. A) Only statements 1, 2, and 3 are valid. B) All of the listed statements are correct. C) Only statements 1, 3, and 4 are correct. D) Only statements 2, 3, and 4 are valid.

B) All of the listed statements are correct.

Which of the following statements about globular proteins are true? 1) The protein folds to make itself as compact as possible. 2) The packing of the protein is such that hydrophilic residues appear on the surface where they can interact with an aqueous environment. 3) β sheets are usually twisted, or wrapped into barrel structures. 4) All parts of a globular protein can be classified as helix, β sheet, or turns. A) Only statement 3 is correct. B) Statements 1, 2, and 3 are correct. C) All of the listed statements are correct. D) Statements 1 and 2 are correct.

B) Statements 1, 2, and 3 are correct.

Which of the following statements regarding the folding of proteins are true? 1) The burying of hydrophobic groups within a folded protein molecule away from water leads to a stabilizing entropy increase known as the hydrophobic effect. 2) Internal hydrogen bonds stabilize the fold. 3) Salt bridges stabilize the fold. 4) Van der Waals interactions have a stabilizing, cumulative effect. A) 1 and 4 B) 1, 2, and 3 C) All statements are correct D) 2 and 4

C) All statements are correct

Which statement correctly describes amphipathic (or amphiphilic) helices and sheets? A) Sheets are typically hydrophilic on one surface, whereas helices usually have both hydrophilic and hydrophobic residues evenly distributed throughout their structure. B) Amphipathic helices and sheets have hydrophilic and hydrophobic residues evenly distributed throughout their structure. C) Amphipathic helices and sheets have predominantly hydrophilic residues on one face and predominantly hydrophobic residues on an opposite face. D) Helices are typically hydrophilic on one surface, whereas sheets usually have both hydrophilic and hydrophobic residues evenly distributed throughout their structure

C) Amphipathic helices and sheets have predominantly hydrophilic residues on one face and predominantly hydrophobic residues on an opposite face.

The basic secondary structure of which of these fibrous proteins is a β-sheet structure. A) α-keratin B) All above proteins are β-sheets C) fibroin D) collagen

C) Fibroin

Gamma Turn

Can reverse direction in 3 residues Usually includes Proline (promotes bending or breaking of helices

Quaternary Symmetry

Each polypeptide chain in a multiunit complex is asymmetric However, overall quaternary structure can exhibit symmetry Many subunits together can give indefinite growth -helical symmetry (actin and tobacco mosaic virus) Most quaternary structures are not based on helical symmetry, but on classes of point-group symmetry (based on number of axes of symmetry)

Fibrous Proteins

Fibrous proteins have a filamentous, elongated form They play structural roles like in skin, CT The primary structure determines the secondary structure which gives appropriate mechanical properties to the protein Keratin, fibroin, collagen

Tertiary Structure

Further organized secondary structure regions Less of a shape than secondary structure, usually more than 1 sheets or helices (3D)

Beta Turn

Hairpin turn Reverses direction in 4 residues (frequently includes a Glycine in type II

Domain

Many proteins are made up of more than one domain (compact locally folded region)

Beta Keratin

More beta-sheet character, found in feathers and scales

Collagen

Most abundant protein in vertebrates (1/3 of protein mass) Forms matrix in bone, tendons, part of skin Basic unit is tropocollagen, which is a triple helix, each chain is about 1000 residues -H bonds between chains -every third residue must be a glycine, otherwise residues become too bulky -also involve a lot of proline and hydroxyproline for the turns Lack of vitamin C (scurvy) can damage the collagen (reduced ability to hydroxylate proline) Each triple helix overlaps the other (tensile strength equivalent to copper wire) Strength also due to cross linking of tropocollagen triple helices (staggered) -oxidized lysine side chains can cross link and add strength -as we age, more cross-linking occurs, more brittle structure results, and less elastic availability

Globular Proteins

Working proteins used for synthesizing, transport, metabolism The protein is folded into a compact structure, not extended like a fibrous protein Within the protein, there are familiar helices and sheets These regions fold and produce a tertiary structure (big determinant of protein's function)