1. Biochem Block Handout #6: Protein Structure

2. Protein Structure Levels: Definitions
1º (primary) structure: sequence of aa’s
2º (secondary) structure: local folding of a polymer to form a regular, repeating structure (local 3-D)
3º (tertiary) structure: how the 2º structures fit together (global 3-D)
4º (quaternary) structure: interactions between separate folded polypeptides ex. Hemoglobin
Proteins are held together by H-bonding interactions and other noncovalent interactions

3. The plane truth about peptide bonds
Both C and N are sp2 hybridized  planar
C-N has double bond character  can’t rotate
Because of steric constraints, only certain values of(φ,ψ) are allowed

4. Helical Parameters
Pitch: (rise) (# residues/turn)
Turn: how far one travels to reach a point on the helix directly above the starting point on the helix
Repeat: how far one travels along the helical axis in the helix before the structure exactly repeats itself (repeats is an integer value of residues)
Repeat = pitch if # residues per turn = an integer

5. α-helix
H-bonds between residues separated by 3 aa. C=O of aa #1 bonds with H-N of aa #5, aa #2 with #6, etc.
H-bonds between carbonyl oxygen and hydrogen of amide nitrogen
3.6 residues per turn
rise (vertical height between residues) = 1.5Ǻ
pitch = (# residues / turn) x (rise) = 5.4 Ǻ. This is the vertical distance of a turn as traveled along the helical axis.

6. Secondary Structure: Regular Ways to Fold the Polypeptide Chain
An antiparallel arrangement of strands forming b-sheets.
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7. Fibrous Proteins: a-keratins
Fibrous proteins have a filamentous, or elongated, form.
The a-keratins are made of a-helix and are found in hair, fingernails and skin.
Helix  filament

8. The structure of silk fibroin, a beta sheet protein
The b-sheet regions comprise almost exclusively multiple repetitions of the sequence:
[Gly-Ala-Gly-Ala-Gly-Ser-Gly-Ala-Ala-Gly-(Ser-Gly-Ala-Gly-Ala-Gly)8]
(a) A three-dimensional view of the stacked sheets of fibroin. The region shown contains only alanine and glycine residues.
(b) Interdigitation of alanine or serine side chains and glycine side chains in
fibroin. The plane of the section is perpendicular to the folded sheets.

9. Collagen fibers: the material of tendons, bone & skin
Collagen Structure:
The basic unit of the collagen fiber is the tropocollagen molecule.
A triple helix of three polypeptide chains, ~1000 residues in length.
Left-handed helices, with about 3.3 residues/turn.
The chains wrap around one another in a right-handed sense.
Hydrogen bonds are between the chains, using hydroxyproline and hydroxylysine.

10. Scurvy
Scurvy is a connective tissue disease from a deficiency in Vitamin C
(ascorbic acid).
Collagen fibers are weakened.
It is caused by failure to hydroxylate
prolines and lysines in collagen.
There is less H-bonding between the chains of tropocollagen.
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11. Post-translational Processing: Some proteins need additional modification to be functional
Example:
Biosynthesis and assembly of collagen:
Steps 1–4 occur in the endoplasmic reticulum and cytosol of collagen-synthesizing cells.
Steps 6 and 7 occur in the extracellular region.
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12. Globular Proteins: Tertiary 3o Structure
Carry out most of the chemical work of the cell
Synthesis
Transport
Metabolism
Possess secondary structures
Fold into compact tertiary structures
All globular proteins have a defined inside and outside:
hydrophobic residues are packed
mostly on the inside and the hydrophilic residues are on the surface, in contact with water.
Many carry prosthetic groups
small molecules that may be noncovalently or covalently bonded to the protein (e.g., heme in myoglobin).
The tertiary structure of BPTI:
A “stick” model showing atomic positions from X-ray diffraction.
A “cartoon” model of the backbone.
A “surface” model showing the solvent accessible surface.

13. Turns in 2o structure of proteins
b-turns
g-turn

14. Folding, Denaturation & Refolding
Most of the information for determining the 3-D structure of a protein is carried in the amino acid sequence of that protein.
Under harsh conditions, a protein loses its functional 3-D structure.
This process is called denaturation.
Denaturing conditions include:
Increased temperature
pH becomes extremely acidic or alkaline
Organic solvents or urea
This schematic drawing depicts the classic RNase A
refolding experiment of Anfinsen.

15. The Thermodynamics & Kinetics of Folding
Folding of a globular protein is clearly thermodynamically favorable in vivo
The overall free energy change for folding must be negative.
This negative ΔG is achieved by a balance of several thermodynamic factors:
Conformational Entropy
Charge–Charge Interactions
Internal Hydrogen Bonds
van der Waals Interactions
Many diseases are associated with
protein misfolding: Alzheimer’s, Parkinson’s
Mad Cow, ALS, Type II diabetes, etc.
Kinetics of folding: some proteins can fold in milliseconds;
A random fold of a 125-aa protein takes 1050 years
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16. Quaternary Structure of Proteins
Symmetries of protein quaternary structures:
Although composed of asymmetric polypeptides, proteins adopt many symmetrical patterns in forming quaternary structures.