Chapter 6 - The Three-Dimensional Structure of Proteins

What are Pauling's Four Rules for Secondary Structure?

- Bond angles and lengths should be similar to respective free amino acid
- No atoms should approach one another more closely than allowed by their van der waals radii
- Their amide group must be planar
- Noncovalent bonds stabilizes folding processes and products

What are the four types of secondary structure for proteins?

Alpha Helix
Beta Sheets
310-helix
Poly ProlineII Helix

Which direction is an alpha helix?

Right handed helix

Describe the hydrogen bonding in alpha helices

H bonding between residue i and residue (i+3) or (i+4) between carbonyl oxygen and amide proton

What is the residue/turn, pitch, and rise of alpha helices?

3.6 amino acids/turn
5.4 A Pitch
1.5 A Rise

Where are the side chains in alpha helices?

Extending outward from alpha helix

Describe the backbone atoms in the alpha helix

Backbone atoms found in central channel
• Closely packed

Describe the amphipathy of alpha helices

Often with distinct hydrophilic and hydrophobic faces
• Side chains with similar polarities every 3-4 residues

Describe the structure of beta sheets

Two or more β-strands connected by hydrogen bonds
• Can run parallel or antiparallel

Where are the hydrogen bonds in beta sheets?

Main-chain H-bonds between adjacent β-strands

What is the residues/turn in beta sheets?

2

What is the pitch and rise for a parallel beta sheet?

6.8 A pitch and 3.4 A rise

What is the pitch and rise for a antiparallel beta sheet?

6.4 A pitch and 3.2 A rise

Describe the amphipathy of beta sheets

side chains extend above or below plane. Side chains with similar polarity will be on one side while opposite polarity on the other

Which direction is a 310 helix?

Right handed helix

What is unique about a 310 helix?

It is a possible structure by Pauling's Rules but not commonly found

What is the residues/turn, pitch, and rise of a 310 helix?

3 residues/turn, 6 A pitch, 2 A rise

Compare the shape of a 310 helix to an alpha helix?

Tighter spiral and more elongated

What is unique about the polyproline II helix?

It does not follow Pauling's Rules but is present in nature

Which direction is the polyproline II helix?

Left handed helix

Compare the structure of the polyproline II helix to the other protein helices?

Most extended structure

Are hydrogen bonds in polyproline II helix?

No

Describe the amino acid profile of polyproline II helix?

Approx. 1/3 of the residues are proline

What is the residues/turn, pitch, and rise for polyproline II helix?

3.0 residues/turn
• Rise: 3.1Å/ residue
• Pitch: 9.3 Å/ turn

Where is polyproline II helix prevalent?

In the structure of collagen

Which atom in peptides allows for free rotation?

Alpha carbon

What is the phi angle?

between N and Cα

What is the psi angle?

between Cα and the carbonyl C

From which view are the phi and psi angles found?

Looking down the bond from Cα

How are the phi and psi angles restricted?

By steric hinderance

What is a Ramachandran Plot?

A plot of the angles of phi and psi angles

What does a cartoon representation of 3D structure of proteins show?

Secondary structure associated with the protein backbone

What does a stick representation of 3D structure of proteins show?

Specific interactions

What does a solvent accessible surface area representation of 3D structure of proteins show?

shows all the places a water molecule could interact with the protein

What does a monochrome representation of 3D structure of proteins show?

highlights irregularities in protein surface
- protein binding occurs at depressions

What does a color-based-on-atoms representation of 3D structure of proteins show?

shows variance in polarity

What does a color-based-on-charge representation of 3D structure of proteins show?

(+) - Blue
(-) - Red

What are the two major classes of tertiary proteins?

Fibrous and Globular Proteins

What are the general characteristics of fibrous proteins?

Elongated structures
• Simple tertiary structure
• Regular pattern of amino acids
• Insoluble in water
• Used for structural support

What are the general characteristics of globular proteins?

Compact structures
• More complex tertiary structure
• Irregular amino acid sequence
• Soluble in water
• Used for chemical reactions

Describe the amino acid profile of fibrous proteins

High abundance of certain amino acids

Describe the secondary structure profile of fibrous proteins

Sequence favors specific secondary structure

What are the three types of fibrous proteins?

1. Keratin
2. collagen
3. Fibroin

Where can keratin be found?

Hair, fingernails, feathers, scales, and intermediate filaments

Where can fibroin be found?

Silk Cocoons

What is collagen used for?

Connective tissue protein; tendons, skin
• Most abundant single protein in most vertebrates
• 1/3 of protein mass in large animals

Describe the structure of alpha keratin?

Left handed coiled coil - 2 alpha helices coiled around one another (over 300 residues)

Why is it important that the alpha keratin coiled coil is left handed?

Maximizes hydrophobic interactions

Describe the location of hydrophobic residues in the alpha keratin?

Hydrophobic residues repeat every 3-4 positions, which allows each helix to have a hydrophobic strip that spirals in the interface of the alpha keratin coiled coil

What is attached to an alpha keratin coiled coil?

small globular region

How can a keratin molecule be strengthened?

By adding disulfide bonds due to keratins high cysteine content

Why are nails harder than hair?

The keratin in nails has more disulfide bonds

If two cysteines are oxidized, what happens?

Disulfide bond is created

If two cysteines are reduced, what happens?

Disulfide bond is broken

Describe the structure of fibroin proteins

Long regions of stacked antiparallel beta sheets

Describe the amino acid profile of fibroin proteins

almost every other residue is glycine

Why is glycine important in fibroin proteins?

Allows β-sheets to stack very closely

How are Beta sheets held together in fibroin proteins?

Van der waals interactions (Allows for flexibility)

Are fibroin proteins elastic and/or flexible?

Not elastic because bond angles are already extended and it has compact folded regions

it is flexible

What is the basic unit of a collagen fiber?

tropocollagen (approx 1000 amino acids)

Describe the structure of tropocollagen

triple right handed helix made up of protein chains that are left handed helices

What is the motif for tropocollagen?

G-X-Y tripeptide motif
• X is often Pro;Y is often Pro orHydroxyproline

Where is glycine in tropocollagen?

Inside of triple helix

How is collagen formed from tropocollagen?

Tropocollagens interact to form collagen fibers

Which two amino acid residues are often found hydroxylated?

Proline and Lysine

How does hydroxylation of proline increase the stability?

Increase in hydrogen bonds

Describe lysine crosslinks

Lys or Hydroxylysine can be oxidized
• Forms an aldehyde (allysine) that can be cross-linked

Does crosslinking increase or decrease flexibility?

Decreases, which is why bones become more brittle since more crosslinking occurs over time

What is tertiary structure characterized by?

- conent of helix and sheet secondary structures, defined turns that link these secondary structures

What are the four types of secondary structure characterizations in tertiary structures?

- mostly helices
- mostly sheets
- mix of both
- not much of either

What is a supersecondary structure?

1. Combinations of secondary structures such as Alpha helixes and beta strands that form recognizably patterns. For example Beta-Alpha-Alpha-Alpha-Beta
2. These are connected by turns, loops and coils

(CALLED MOTIFS)

What are the three common principles of protein structure classification?

1. Classify based on dominant secondary structure
2. Many proteins have more than one domain
3. Domains may consist of supersecondary structures

Each domain is representative of a different _______.

Function

Describe protein motifs

• Structure made from a combination of secondary structural elements
• Connected through turns or loops
• Structural elements of a protein domain
• Not independently stable

Describe protein domains

• Folding unit that makes up the tertiary structure
• Connect by non-covalent interactions
• Gives protein a specific function
• Able to fold independently
• Proteins can have more than 1domain

What are three alpha helix motifs?

Helix turn Helix (binds DNA)
Helix loop Helix (transcription factors)
Coiled Coil (keratin)

What are three beta sheet motifs?

Beta Hairpin
Greek Key
Beta Barrel

Which two amino acids are found in turns?

Glycine and Proline

Where are beta barrels commonly found?

Proteins that transport ions across cell membranes

What are two alpha + beta motifs?

Beta-alpha-beta
Zinc Finger

Describe zinc finger motif

Another structural motif commonly found in proteins that bind RNA or DNA is the zinc finger, which contains three secondary structures - an α helix and two β strands with an antiparallel orientation - that form a fingerlike bundle held together by a zinc ion.

What does CATH stand for?

class, architecture, topology, and homologous superfamily

What does class represent in identifying domains?

• Secondary structure composition
• 4 main classes

What does architecture represent in identifying domains?

• General shape of domain structure
• Have similar arrangements of 2°structure, but connected differently
(Motif)

What does topology represent in identifying domains?

• Order in which structure is organized in main chain
• Have similar arrangements of 2° structure and connected similarly
(How motif is structured)

What does Homologous superfamily represent in identifying domains?

• Based on common ancestry

What is the first common feature of folded globular proteins?

1. Have a defined inside and outside
• Nonpolar (hydrophobic) interior and a more hydrophilic exterior

What is the second common feature of folded globular proteins?

2. β-sheets are usually twisted or wrapped into barrel structures

What is the third common feature of folded globular proteins?

3. Polypeptide chain can "turn corners"
• Allows structure to go from one segment of 2° structure to the next

Describe Beta Turns

reverse turns
H-bonding of amino acids 3 sequences apart
cause a U turn
Type I and II: Gly favored at i + 1

What is another type of protein turn?

Gamma turn

What is the fourth common feature of folded globular proteins?

Not all globular proteinseasily classified as helix,sheet, or a combination

Describe Anfinsen's Experiment

Showed that primary sequence of amino acid contains information necessary for proper protein folding

First denatured RNAaseA by reducing disulfide bonds with β-mercaptoethanol and then removing H bonds with urea

one experiment removed urea to restore H bonds then oxidized to reestablish disulfide bonds (native protein restored)

Another experiment oxidized then removed urea. (Disulfide bonds form randomly, protein folded differently and loses function)

What is the midpoint of sigmoidal transition of protein denaturation?

Melting Point

Why is protein folding favored even though conformational entropy decreases?

Protein enthalpy decreases as more interactions (salt bridges, hydrogen bonds, van der waals) are made to reduce energy.

hydrophobic effect takes place as hydrophobic chains cluster inside the protein expelling water from clathrate cages increasing solvent entropy

Why are proteins relatively unstable?

• Energy change slightly higher than a hydrogen bond (5-15 kJ/mol)
• Overall energy change equivalent to a few non-covalent bonds

How can a protein be denatured?

Proteins can be denatured (loss of shape) due to changes in pH, temperature, or extreme salt concentration (salinity).
Causes protein to lose its ability to function!

What is the role of disulfide bonds?

stabilize the already folded structure

Describe the energy profile of disulfide bonds

• Enthalpy - favorable contribution to stabilize structure
• Entropy - unfavorable in the folded state be cause it reduce s the number of possible conformations

Why don't all proteins have disulfide bonds?

Intracellular environment is reducing