Ch. 4 - The Three-Dimensional Structure of Proteins

3D

Unlike most organic polymers, protein molecules adopt a specific _____ conformation

Native fold

The specific 3D conformation of a polypeptide is called the _____

Entropy

There is an _____ cost to folding the protein into one specific native fold

Native folding

The function of a protein is dependent on the _____

Hydrophobic effect

The release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy

Hydrogen bonds

Interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha helices and beta sheets

London dispersion

Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein. Can be established between any two atoms

Electrostatic interactions

Long-range strong interactions between permanently charged groups

Salt bridges

_____, especially those buried in the hydrophobic environment, strongly stabilize the protein

Cysteine

In order to have a disulfide bond present, we need two _____ in the chain

Leu

What is the N-terminus of this chain?
Leu-Arg-Cys-Asp-His-Ile-Glu-Ala

Ala

What is the C-terminus of this chain?
Leu-Arg-Cys-Asp-His-Ile-Glu-Ala

2

How many salt bridges are present in this chain?
Leu-Arg-Cys-Asp-His-Ile-Glu-Ala

0

What is the net overall charge of this chain?
Leu-Arg-Cys-Asp-His-Ile-Glu-Ala

7

How many peptide bonds are present in this chain?
Leu-Arg-Cys-Asp-His-Ile-Glu-Ala

Primary structure

The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain

Peptide bond

The primary structure of a protein is maintained by a _____

Resonance hybrid

The peptide bond is a _____ of two canonical structures

Rigid, planar

Resonance causes peptide bonds to be quite _____ and nearly _____

Large

Resonance causes peptide bonds to exhibit a _____ dipole moment in the favored trans configuration

True

T/F Rotation around the peptide bond is not permitted due to the resonance structure

Phi

Angle around the alpha carbon - amide nitrogen bond

Psi

Angle around the alpha carbon - carbonyl carbon bond

180

In a fully extended polypeptide, both psi and phi are _____ degrees

Secondary

The organization around the peptide bond, paired with the identity of R groups, determines the _____ structure of the protein

Steric crowding

Some psi and phi combinations are very unfavorable because of _____ of backbone atoms with other atoms in the backbone or side chains

H-bonding

Some psi and phi combinations are more favorable because of chance to form favorable _____ interactions along the backbone

Ramachandran

A _____ plot shows the distribution of psi and phi dihedral angles that are found in a protein
- Shows the common secondary structure elements
- Reveals regions with unusual backbone structure

Secondary

_____ structure refers to a local spatial arrangement of the polypeptide backbone

Alpha helix

Secondary structure arrangement stabilized by hydrogen bonds between nearby residues; most abundant in right-handed alpha helix

Right

The alpha helix is a _____-handed helix, with 3.6 residues per turn

Beta sheet

Secondary structure arrangement stabilized by hydrogen bonds between adjacent segments that may not be nearby; second most abundant in right-handed alpha helix

Random coil

The irregular arrangement of the polypeptide chain is called the _____ (lack of distinguishable motif)

Parallel

Peptide bonds are aligned roughly _____ with the helical axis in the alpha helix

Perpendicular

Side chains point out and are roughly _____ with the helical axis in the alpha helix

Ala, Leu

Small hydrophobic residues such as _____ and _____ are strong helix formers

Pro

_____ acts as a helix breaker because the rotation around the N-Ca bond is impossible

Gly

_____ acts as a helix breaker because the tiny R group supports other conformations (too flexible to keep helix in line)

Macroscopic

The alpha helix has a large _____ dipole moment that is enhanced by unpaired amides and carbonyls near the ends of the helix

Negatively

_____ charged residues often occur near the positive end of the helix dipole

Sheets

Multi ß-strand interactions are called _____

Amide, carbonyl

Sheets are held together by the hydrogen bonding of _____ and _____ groups of the peptide bond from opposite strands

Same

Parallel sheets have strands that are oriented in the _____ direction

Opposite

Antiparallel sheets have strands that are oriented in _____ directions

Bent

In parallel ß sheets, hydrogen bonds between strands are _____ (weaker)

Linear

In antiparallel ß sheets, hydrogen bonds between strands are _____ (stronger)

Beta turns

_____ occur frequently whenever strands in ß sheets change the direction

4

The 180° ß turn is accomplished over _____ amino acids

3

The ß turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton _____ residues down the sequence

Proline, glycine

_____ in position 2 or _____ in position 3 are common in ß turns

Flexible

Glycine is _____, which helps with the 180° ß turn

Stiff

Proline is _____, which helps with the 180° ß turn

Trans

Most peptide bonds not involving proline are in the _____ configuration (>99.95%)

Cis

For peptide bonds involving proline, about 6% are in the _____ configuration

Proline isomerases

Proline isomerization is catalyzed by _____

Circular dichroism

_____ (CD) measures the molar absorption difference of left- and right-circularly polarized light

Chromophores

_____ in the chiral environment produce characteristic signals

Conformation

Circular dichroism signals from peptide bonds depend on the chain _____

Tertiary

_____ structure refers to the overall spatial arrangement of atoms in a protein

Disulfide

Protein tertiary structure can be stabilized by _____ bonds

Fibrous, globular

What are the two major classes of tertiary structure?

Alpha helix, cross-linked by disulfide bonds

Tough, insoluble protective structures of varying hardness and flexibility (e.g. alpha keratin of hair, feathers, nails)

ß conformation

Soft, flexible filaments (e.g. silk fibroin)

Collage triple helix

High tensile strength, without stretch (e.g. collagen of tendons, bone matrix)

Connective tissue

Collagen is an important constituent of _____: tendons, cartilage, bones, cornea of the eye

Left

Each collagen chain is a long Gly- and Pro-rich _____-handed helix

Superhelical

Three collagen chains intertwine into a right-handed _____ triple helix

Collagen fibril

Many triple-helices assemble into a _____

Crosslinks

_____ are covalent bonds between Lys or HyLys, or His amino acid residues

Fibroin

Main protein in silk from moths and spiders with an antiparallel ß sheet structure

Ala, Gly

Small side chains of _____ and _____ allow for the close packing of sheets in fibroin

Motifs

Specific arrangement of several secondary elements

Globular

_____ proteins are composed of different motifs folded together

Disordered

_____ proteins contain protein segments that lack definable structure

Quaternary

A _____ structure is formed by the assembly of individual polypeptides into a larger functional cluster

X-ray crystallography

Steps needed:
- Purify the protein
- Crystallize the protein
- Collect diffraction data
- Calculate electron density
- Fit known amino acid residues into density

Pros

_____ of x-ray crystallography
- No size limits
- Well established

Cons

_____ of x-ray crystallography
- Difficult for membrane proteins
- Cannot resolve (see) hydrogens

Bimolecular NMR

Steps needed:
- Purify the protein
- Dissolve the protein
- Collect NMR data
- Assign NMR signals
- Calculate the structure

Pros

_____ of biomolecular NMR
- No need to crystallize the protein
- Can see many hydrogens

Cons

_____ of biomolecular NMR
- Difficult for insoluble proteins
- Works best with small proteins

Proteostasis

Maintenance of cellular protein activity is accomplished by the coordination of many different pathways

Chaperones

Proteins that assist in protein folding during post-translational processing

Ubiquitin

A protein that attaches itself to faulty or misfolded proteins and thus targets them for destruction by proteasomes

Denaturation

Loss of structural integrity with accompanying loss of activity is called _____

Denatured

Proteins can be _____ by:
- Heat or cold
- pH extremes
- Organic solvents
- Chaotropic agents (urea and guanidinium hydrochloride)

Chaotropic agents

Chemicals able to disrupt H bonds; everything above primary structure disrupted

Ribonuclease

Enzyme that breaks down RNA

Urea

_____ in the presence of 2-mercaptoethanol fully denatures ribonuclease

Renaturation

Regaining the correct tertiary structure after denaturation of a protein

Lowest-energy

Proteins fold to the _____ fold in the microsecond to second time scales

Stability

Free-Energy Funnel of Protein Folding is dependent on the _____ of motifs within the protein

True

T/F Chaperones prevent misfolding and aggregation of unfolded peptides

Heat shock protein

Chaperones start with _____ (HSP)

GroEs

Lid chaperonin

GroEl

Body of a protein folding machine

Soluble

Native (correctly folded) ß amyloid is a _____ globular protein

Misfolded

_____ ß amyloid promotes aggregation at newly exposed protein-protein interface