1. Polypeptide and protein structure
Nafith Abu Tarboush
DDS, MSc, PhD

2. Protein conformation
Many conformations are possible for proteins due to flexibility of amino acids linked by peptide bonds
At least one major conformations has biological activity, and hence is considered the protein’s native conformation or the native protein

3. Levels of Protein Structure
1°structure: sequence and number, from N to C
2°structure: the ordered 3-dimensional arrangements (conformations) in localized regions of a polypeptide chain, backbone interactions through hydrogen bonding;
e. g., -helix and -pleated sheet
3˚ structure: 3-D arrangement of all atoms
4˚ structure: arrangement of monomer subunits with respect to each other

4. Primary Structure of Proteins
Zigzag arrangement
R-groups
Determination?
1o Sequence & 3-D conformation; relation to functional properties (MW& genetic mutations)
Site-directed mutagenesis and structure function relationship

5. Shape-Determining Interactions in Proteins
Is it ordered or spaghetti?
Hydrogen, ionic, covalent, & hydrophobic

6. Secondary Structure of Proteins
What is the secondary structure of proteins? “folding of the backbone”
What are the bonds that have a free rotation? What is the implication? These angles repeat themselves in regular secondary structures
Two main kinds: α-helix and β-pleated sheet
They are periodic; their features repeat at regular intervals
Stability of secondary structure

7. The α-helix H-bonds are parallel to the helix axis, same segment
C=O binds N—H four residues away
linear arrangement of H-bonds (maximum strength and stability)
Turns occur every 3.6 residues, right handed, clockwise
The pitch (linear distance between corresponding points on successive turns) is 5.4 Å
Proteins have varying amounts of α-helical structures
What factors affect the helix (specific amino acids, electrostatic repulsion, steric repulsion)

8. The β-sheets Backbone is almost completely extended
R groups extending above and below the sheet
H-bonds are intra-chain or inter-chain bonds
Perpendicular to the direction of the protein chain
Parallel vs. anti-parallel
Zigzag structure

9. Others regular ones Why do we have them? Loops vs. turns
Also known as β-bends
Involve 4 amino acids (H-bond: C=O of 1 & N–H of 4)
A motif is a repetitive super-secondary structure. Regardless of function
Domains; protein conformations with similar functions (leucine zipper)

10. -Helices and -Sheets
Supersecondary structures: a combination of - and -sections
b unit: (parallel)
 unit: (helix-turn-helix), anti-parallel
-meander: an anti-parallel sheet formed by a series of tight reverse turns connecting stretches of a polypeptide chain
Greek key: a repetitive super-secondary structure formed when an anti-parallel sheet doubles back on itself
-barrel: created when -sheets are extensive enough to fold back on themselves

12. Fibrous Proteins Fibroin, β-sheets, alternating glycine and alanine
α-keratins, bundles of α-helices
Fibrous Proteins
Contain polypeptide chains organized approximately parallel along a single axis:
Consist of long fibers or large sheets
Mechanically strong
Insoluble
play an important structural role
Examples are
Keratin
Collagen
fibroin

13. Globular Proteins Folded to, a more or less, spherical shape Soluble
Polar vs. non-polar, exterior vs. interior
Most of them have substantial sections of -helix and -sheet

14. 3˚ Structure
The 3-dimensional arrangement of all the atoms in the molecule
Simple vs. conjugated
Backbone hydrogen bonding, side chains hydrogen bonding, hydrophobic interactions, electrostatic attraction, electrostatic repulsion, metal coordination
Not every protein have all kinds of interactions (myoglobin & hemoglobin; no disulfides) (trypsin & chymotrypsin, no metal complexes)
Interactions between side chains also plays a role

15. Forces That Stabilize Protein Structure

16. 3°& 4°Structure
Tertiary (3°) structure: the arrangement in space of all atoms in a polypeptide chain
It is not always possible to draw a clear distinction between 2°and 3°structure
Quaternary (4°) structure: the association of polypeptide chains into aggregations (dimers, trimers, tetramers,…etc). Non-covalent interactions. Simple or conjugated

17. Determination of 3°Structure
X-ray crystallography
uses a perfect crystal; that is, one in which all individual protein molecules have the same 3D structure and orientation
exposure to a beam of x-rays gives a series diffraction patterns
information on molecular coordinates is extracted by a mathematical analysis called a Fourier series
2-D Nuclear magnetic resonance
can be done on protein samples in aqueous solution

18. X-Ray and NMR Data
High resolution method to determine 3˚ structure of proteins (from crystal)
Diffraction pattern produced by electrons scattering X-rays
Series of patterns taken at different angles gives structural information
Determines solution structure
Structural info. Gained from determining distances between nuclei that aid in structure determination
Results are independent of X-ray crystallography

19. Complex Protein Structures
Covalent conjugation to carbohydrates (glyco-proteins): post-translational, function, N-linked (-N of Asn) & O-linked (-OH of Ser or Thr) & occasionally to the –OH of hydroxy-lysine
Lipoproteins: Non-covalent, store & transport lipids and cholesterol
Extremely important: ex. Erythrocytes & blood groups (glycoshpingolipids)
Phosphoproteins: contain phosphate groups esterified to Ser, Thr, or Tyr.; the phosphate group usually regulates protein function

20. Chemical Properties of Proteins
1. Protein Hydrolysis
The reverse of protein synthesis
Digestion of proteins is hydrolyzing peptide bonds
Takes place in the stomach and small intestine

21. 2. Protein Denaturation How the protein preserve its shape?
What is denaturation? It affects physical, chemical, and biological properties, such as enzymes
Solubility decreased, ex. eggs
Heat (≈≥50 οC)
Mechanical agitation
Detergents
Organic compounds: acetone, ethanol, bacterial proteins
pH change: disrupt salt bridges, milk turns sour because it has become acidic
Most denaturation is
irreversible

22. Protein Folding & prediction
The integration of biochemistry and computing has led to bioinformatics
Predicting the 3˚ structure (limitations)
First step is to search for sequence homology

23. Hydrophobic Interactions & Chaperons
Hydrophobic interactions are spontaneous
Chaperones aid in correct & timely folding of many proteins
hsp70 were the first chaperone proteins discovered
Chaperones exist in organisms from prokaryotes to humans

24. Structure & diseases (prion, Alzheimer)
Mad-cow disease (bovine spongiform encephalopathy), and human spongiform encephalopathy (Creutzfeldt-Jakob disease)
The cause is a small (28-kDa) protein called a prion (Met129)
Alzheimer's Disease: buildups of plaques and fibers of hard insoluble material
Amyloid protein mis-folded and broken down (≈40 a.a, Ab protein) and aggregates