Chapter 4 The Three-Dimensional Structure of Proteins

Covalent bonds linking amino acid residues in a polypeptide chain

Primary structure

Recurring structural patterns

Secondary structure

3D folding of polypeptide

Tertiary structure

2+ polypeptide subunits

Quaternary structure

What does the function of a protein depend on?

Amino acid sequence

Amino acid sequence confers _______.

3D structure

3D structure confers ____.

Function

Most human proteins are _____.

Polymorphic

Have amino acid sequence variants

Polymorphic

classic method of sequencing amino acids

Edman degradation

A sequence variant changes several amino acid residues in a polypeptide. Which consequence best follows from the relationship among protein structure levels and function?

• It changes only the protein's recurring secondary patterns, without affecting its function.

• It may alter the protein's three-dimensional folding and thereby change its function.

• It directly creates additional polypeptide subunits in the protein.

• It changes the sequencing method used to identify the amino acid order.

• It may alter the protein's three-dimensional folding and thereby change its function.

Limited number of _______ predominate under biological conditions.

Conformations

What is the most stable conformation?

Lowest free energy (G)

Proteins in any functional, folded conformations

Native

What is a protein’s conformation largely stabilized by?

Weak interactions

Tendency of a protein to maintain a native conformation

Stability

Unfolded proteins have ____ conformational entropy.

High

What holds proteins together?

Noncovalent interactions

Chemical interactions stabilize native conformations. What is uncommon?

Strong disulfide (covalent) bonds

Chemical interactions stabilize native conformations. What is numerous?

Weak (noncovalent) interactions

What are some examples of weak (noncovalent) interactions?

Hydrogen bonds, hydrophobic effect, ionic interactions

What happens if a protein is not stable in a solution?

Precipitates out

Packing of hydrophobic amino acids away from water favors ______.

Protein folding

Predominating weak interaction

Hydrophobic effect

Highly structured shell of H₂O around a hydrophobic molecule

Solvation layer

The solvation layer _____ when nonpolar groups cluster together.

Decreases

The solvation layer _____ causes a favorable increase in net entropy.

Decrease

Hydrophobic R chains form a ________.

Hydrophobic protein core

Repeating secondary structures (alpha helices and beta sheets) optimize _____ bonding.

Hydrogen

Is a salt bridge stronger in nonpolar or polar environments?

Nonpolar environment

Interaction of oppositely charged groups

Ion pair

Ion pair =

Salt bridge

Strength (wanting to interact with each other) increases in an environment of ___ dielectric constant, E

Lower

Water has a ___ dielectric constant, which means it’s ready to be dissolved and form charges.

Higher

E ~ 80 (high dielectric constant)

Polar aqueous solvent

E ~ 4 (low dielectric constant)

Nonpolar protein interior

Would a Lysine in hydrophobic core be happy?

No, would rather be in soluble areas (+1 charge)

Which explanation best describes why folding can stabilize a protein through both its hydrophobic core and polar interactions?

• Hydrophobic clustering increases net entropy, while buried ion pairs are strengthened in the low-dielectric interior.

• Hydrophobic clustering decreases net entropy, while ion pairs are strongest in the aqueous environment.

• Hydrophobic groups form surface solvation layers, while ion pairs are weakened in the low-dielectric interior.

• Hydrophobic interactions optimize secondary-structure hydrogen bonds, while ion pairs require a high-dielectric environment.

• Hydrophobic clustering increases net entropy, while buried ion pairs are strengthened in the low-dielectric interior.

Individual van der Waals interactions are weak but combine to promote _____.

Folding

Dipole-dipole interactions over short distances

van der Waals interactions

Individual van der Waal interactions contribute ___ to overall protein stability.

Little

____ number of van der Waal interactions can be substantial.

High

What are the hydrophobic portions of an unfolded protein surrounded by?

Solvation layer (ordered shell) of water molecules

When the protein folds, these water molecules have a greater degree of freedom for movement and becomes ____ in the surrounding solvent, ______ their entropy.

Disordered, increasing

The peptide bond is ____ and ____.

Rigid and planar

3 covalent bonds separate the alpha carbons of adjacent amino acid residues:

C alpha - C - N - C alpha

There is resonance between what two atoms?

Carbonyl oxygen and amide nitrogen

Peptide C — N bonds cannot ____ freely.

Rotate

6 atoms of the ______ lie in a single plane.

Peptide group

What prevents rotation, limiting range of conformations in peptide bonds?

Partial double-bond character of C — N peptide bond

We don’t want ____ residues in same plane.

Bulky

Why is there almost no rotation around the peptide

C-N bond?

• the bond has partial double-bond character from resonance

• the R groups on either side collide

• hydrogen bonding across the bond holds it fixed

• the alpha carbons are too bulky to allow rotation

• it is a true double bond

• the bond has partial double-bond character from resonance

What are the 3 dihedral angles?

Phi, psi, and omega

between -180 and +180 degrees

Phi and psi

±180 degrees for trans

Omega

Many phi and psi values are prohibited by ______.

Steric interference

Phi and psi cannot both = ______

0 degrees

Which description best explains how peptide-backbone geometry restricts its possible conformations?

• The three dihedral angles can each vary freely between -180° and +180°.

• The trans peptide bond has omega near ±180° while steric interference excludes some phi and psi combinations, including phi = psi = 0°.

• The omega angle varies continuously, whereas pi and psi are fixed at 0° in the trans state.

• Steric interference restricts omega to 0° but allows every combination of psi and psi.

• The trans peptide bond has omega near ±180° while steric interference excludes some phi and psi combinations, including phi = psi = 0°.

Describes the spatial arrangement of the main-chain atoms in a segment of a polypeptide chain

Secondary structure

Phi and psi remain the same throughout the segment

Regular secondary structure

What are the common types of secondary structure?

Alpha helix, beta conformation, beta turn random coils

In an alpha helix, R groups point ___ from the helix.

Away

Simplest arrangement, maximum number of hydrogen bonds

Alpha helix

In an alpha helix, backbone wound around an imaginary ________ axis.

Longitudinal

In an alpha helix, ______ protrude out from the backbone.

R groups

In an alpha helix, each helical turn = ____ residues.

3.6

In an alpha helix, each helical turn = 3.6 residues, ~___ A.

5.4

Alpha helix are ______.

Right-handed

• _________

  • R groups protruding away from the helical backbone

  • Most common

Right-handed

Theoretically less stable, not observed in proteins

Extended left-handed

Are all R groups outside even if they’re polar or nonpolar?

Yes

What properties hold alpha helices together?

Hydrogen bonding

Between hydrogen atom attached to the electronegative nitrogen atom of residue n and the electronegative carbonyl oxygen atom of residue n + 4.

Intrahelical hydrogen bonds

Intrahelical hydrogen bonds confers significant ____.

Stability

A peptide segment contains oppositely charged side chains four residues apart. Which explanation best accounts for its potential a-helix stability?

• The side chains prevent backbone hydrogen bonding by increasing residue spacing.

• The carbonyl terminus forms hydrogen bonds directly with the charged side chains.

• Backbone hydrogen bonds occur from residue n to n+4, while side-chain ion pairs can add stability.

• Hydrophobic interactions destabilize the helix because residues n and n+4 align closely.

• Backbone hydrogen bonds occur from residue n to n+4, while side-chain ion pairs can add stability.

What affects the stability of the alpha helix?

Amino acid sequence

Amino acid residues have an intrinsic propensity to form an _______.

Alpha helix

What can stabilize or destabilize an alpha helix?

Interactions between R chains spaced 3-4 residues apart

Charge, size, and shape

Destabilizes an alpha helix

Formation of ion pairs and hydrophobic effect

Stabilizes an alpha helix

What two amino acids will not form an alpha helix?

Proline and glycine

• Introduces destabilizing kink in helix

• Nitrogen atom is part of rigid ring

• Rotation about N—Calpha bond not possible

Proline

High conformational flexibility, takes up coiled structures

Glycine

In an alpha helix, small electric _____ in each peptide bond align through hydrogen bonds.

Dipoles

Where are the negatively charged amino acids found in an alpha helix?

Near NH₃+ terminus

Where are the positively charged amino acids found in an alpha helix?

Near COO- terminus

An alpha helix is often stabilized by the hydrophobic effect when one side faces the hydrophobic core while the other faces the aqueous solvent. Based on ideal helical geometry, which of the following primary sequences is most likely to fold into a stable amphipathic helix?

• LAVIFWM

• EDKRSTQ

• LEAKVRI

• GPGPGPG

• VVVEEEV

• LEAKVRI

You are engineering a stable alpha helix for a synthetic protein. You decide to mutate a central Leucine residue to a Proline. Why will this specific mutation severely destabilize or break the a helix?

• Proline's side chain is too bulky, causing severe steric clash with the carbonyl oxygen of the preceding residue.

• Proline's cyclical structure forces the peptide bond into a trans configuration, which is incompatible with the right-handed twist of the helix.

• Proline lacks an available amide hydrogen to participate in the intrahelical hydrogen bonding network, and its restricted angle prevents the necessary backbone coiling.

• Proline introduces a permanent positive charge at physiological pH, causing electrostatic repulsion within the tightly packed helical core.

• Proline actively recruits water molecules into the hydrophobic core, disrupting the thermodynamic stability of the helix.

• Proline lacks an available amide hydrogen to participate in the intrahelical hydrogen bonding network, and its restricted angle prevents the necessary backbone coiling.

What organizes polypeptide chains into sheets?

Beta conformation

Backbone extends into a zigzag

Beta conformation

Single protein segment

Beta strand

Several strands in Beta conformation side by side

Beta sheet

Antiparallel beta sheet

Parallel beta sheet

Beta sheets can be ______ or _____.

Antiparallel and parallel

Opposite orieintation

Antiparallel

Occurs more frequently in beta sheet

Antiparallel

Same orientation

Parallel

Connect ends of two adjacent segments of an antiparallel beta sheet to create a 180 degree fold.

Function of beta turns

Involves exactly 4 residues. A stabilizing hydrogen bond forms between the carbonyl oxygen of the first residue and the amide hydrogen of the fourth residue.

Structure of beta turns