The Three-DimensionalStructure of Proteins

Part 1

Chapter 4

Proteins: Structure, Function, Folding

– Structure and properties of the peptide bond– Structural hierarchy in proteins– Structure and function of fibrous proteins– Structure analysis of globular proteins– Protein folding and denaturation

Learning goals: to Know:

Structure of Proteins

• Unlike most organic polymers, protein molecules adopt a specific three-dimensional conformation.

• This structure is able to fulfill a specific biological function

• This structure is called the native fold• The native fold has a large number of

favorable interactions within the protein• There is a cost in conformational entropy of

folding the protein into one specific native fold

Favorable Interactions in Proteins

• Hydrophobic effect– 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 -helices and -sheets

• London dispersion – Medium-range weak attraction between all atoms contributes

significantly to the stability in the interior of the protein

• Electrostatic interactions– Long-range strong interactions between permanently charged

groups– Salt-bridges, esp. buried in the hydrophobic environment strongly

stabilize the protein

Folding Final Structure: Chymotrypsin and Glycine

75 Daltons

21,000 Daltons, 3 polypeptides

Protein Conformation

Stabilized by weak bonds:

ΔG separating folded and unfolded is small

Bond: H bonds, hydrophobic interatction, ionic interaction and –S-S-.

Proteins possess a “solvation layer”

The extent of which depends on surface amino acid R groups

Overall structural patterns:

Hydrophobic areas buried in protein interior

Number of H-bonds is maximized

The Peptide Bond

Only non-planar Bonds Rotate

Each α-Carbon has a Φ and Ψ

Getting the Angles

Many Angles are Prohibited due to Steric Overlap

Ramachandran Plot

Pauling and Corey and the Alpha Helix

How To Determine Protein StructureThe Classic Method – X-ray Crystallography

Methods to form Crystals take Proteins to their Solubility Minimum

Proteins Crystals in Electron Microscopy

X-ray Diffraction

X-ray Diffraction Pattern of Myoglobin and DNA

Fourier Transform to convert X-ray pattern to Electron Density Map

X ray Diffraction Patterns from Different Proteins

Fitting Electron Density Map to Structure

Fitting Electron Density Map to Primary Structure

X-ray Crystallography at Fine Resolution

Proton Nuclear Magnetic Resonance of a Protein

2 Dimensional NMR

NMR Structure of Myoglobin

NMR is limited to small proteins

TROSY NMRTransverse Relaxation Optimized Spectroscopy increases time overwhich NMR signals from neighboring methyl groups can be detected. The trick is to deuterate the protein then protonate methyls….

A look into a Proteasome cavity. This protein is 670 kD! (20S)

Red groups = methyls that are mobile

Yellow groups = active site…protein degradation.

C+E News Feb 5, 2007

Here Is How It Worked

Nature 445:618 Feb 8, 2007

Proteasome Function

Core Proteasome

Ubiquitin Binding Sites top and bottom

4th Edition: See pages 1075-1076, Fig 27-41

5th Edition: See pages 1107-1109, Fig 27-47, 48

Ubiquitin Targeting a Cytoplasmic Protein

Protein AminoTerminal-aa Half-life

stabilizing

M, G, A, S, T, V >20 hrs

destabilizing

I, N, Y, D, P, L, F, K, R 30 – 2 min

What’s New: Free-Electron Lasers

X-ray pulses, in series of femtoseconds on drops containing microcrystals.

Free-electron X ray source at Stanford only one ($300 million), Resolution 2Å.

Schichting, I. May, 2012 Max-Plank Gesellschaft

Alpha Helix

Stabilized by H-bonding to every 4th Amino Acid

Alpha Helix Stabilized by Dipole Moments and Hydrogen Bonds Can be Right or Left Handed

Alpha Helix H-bonding - Stability

H-bonds to every 4th amino acid

So, amino acid-8 in a 15 aa α-helix is H-bonded to aa-11 and aa-5.

What about amino acids at the N- and C-terminal ends?

Instability is brought about by:

1. electrostatic repulsion or attraction – charged R groups.

2. adjacent bulky R groups.

3. interaction with R groups 3-4 aa’s up or down the helix.

4. occurrence of G.

5. interaction of aa’s at C-terminal and N-terminal ends with any near aa-R group.

table 4-1

A

How Long is an 80 amino acid alpha helix?

FACTS to KNOW: One turn: 3.6 aa’s, 5.4 Å long

NOW DO IT

How Long is an 80 amino acid alpha helix?

FACTS to KNOW: One turn: 3.6 aa’s, 5.4 Å long

80 aa’s / (3.6 aa’s/turn) = 22.2 turns

22.2 turns x 5.4 Å/turn = 120 Å long

Sheets

• The planarity of the peptide bond and tetrahedral geometry of the -carbon create a pleated sheet-like structure

• Sheet-like arrangement of backbone is held together by hydrogen bonds between the backbone amides in different strands

• Side chains protrude from the sheet alternating in up and down direction

Beta (Pleated Sheet) Structure

Antiparallel Beta-turns

Antiparallel Beta-turns with Proline

Normal = trans In Beta-turns, Proline is cis

Ramachandran Plot showing 2o Structures

Ramachandran Plot of Pyruvate KinaseExcludes Glycines – they are too flexible

Frequency of Amino Acids in 2o Structure

Circular Dichroism Spectra

A

Difference in right handed and left handed polarized light on the extinction coefficient.

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

• Stabilized by numerous weak interactions between amino acid side chains.

Largely hydrophobic and polar interactions Can be stabilized by disulfide bonds

• Interacting amino acids are not necessarily next to each other in the primary sequence.

• Two major classes– Fibrous and globular (water or lipid soluble)

Protein Tertiary Structure

Fibrous Proteins: From Structure to Function

Alpha Keratin Structure – Almost All Alpha Helix

Biochemists at the Hairdressers

Why a Permanent is not a Temporary!

Chicken Feather α-keratin

Carbonizing (under O2 free environment) makes the fiber into a graphite-like material = light weight, high strength, low cost polymer)

Silk Fibroin is almost all Beta Structure

Silk

A

Spinnerets of a Spider – SEM, Artificially Colored

Things to Know and Do Before Class

1. The peptide bond and why it is planar.

2. Rotation around the alpha carbon, Ramachandran Plot.

3. Basic idea of X-ray crystallography and how it is used to get 3-D structure.

4. Alpha helix and B-structure.

5. Circular Dichroism spectra: what they demonstrate.

6. Fibrous proteins that are essentially all alpha helix or beta structure.

7. EOC problems 1-4. We will do some in class and a case study with music.