Chapter 4
Native Proteins – biologically active (preferred) conformation of a protein
o Any structure is acceptable as long as the covalent binds aren’t
broken.
o Having lowest free energy; most stable conformation, proteins
need multiple stable forms to be deemed stable
o Structure is critical to function/ exceptions do occur that rely on
entropy
o Physiological conditions range 5-65 kJ/mol
o Unfolded protein is subject to higher conformational entropy –
bummer
Interactions and bonds play large roles
Covalent disulfide
o Uncommon but very strong
o Fading away due to the environments more than likely containing
oxygen
o Found in extracellular proteins with reductants (glutathione) I.E
hormone insulin
Weak interactions are important in production of different structures;
secondary, tertiary, quaternary
200-46 kJ/mol to break a SINGLE covalent bond.
o Contrast a weak bond 0.4-30 kJ/mol
Hydrophobic amino acids
o Solvation layer – ultimate layer of hydrogen bonds that act as a shield
to protect the protein
o Account for physiological conditions; hydrogen bonds in a protein is
made by the same entropic effect
Ion pairs or salt bridges can be 50/50
o Focus on dipoles +/-
o salt bridges increases closer to a LOWER dielectric constant
o salt bridge (ionic bonds)
Vander-waals interactions are put together to promote the folding function
Structural pattern RULES :
1. Hydrophobic residues are largely buries in the protein interior away
from water.
2. # of hydrogen bond/ionic interactions in a protein is maximized->
reducing the # of unpaired ionic groups
Peptide bonds
o Rigid and planar
o C-C-N-C alpha carbon residues
o 6 atoms of a peptide group lie in a single plane
Secondary Structures – polypeptide focused on the alpha helix and beta
sheets
o 1948 Pauling – simplest for of maximized used of the internal hydrogen
bonding.
o A basic spiral – left helix rotates counter clockwise and right helix
rotates clockwise
o Characteristics of dihedral angles
Alpha helix
Constraint produces Proline and Glycine residue
Proline
o Has a amine bond which cannot bend thus ‘kink’ in the
proceeded helix
o Thus not commonly found in secondary structures
Glycine
o is only C-H bonds which in turn bends MORE than other amino
acids
Constraints: bulkiness of the R groups, interactions/ lack there of
between spaced out R groups
Beta formation
1951 Pauling and Corey – extended the conformation of polypeptide
chains
o Zig-zag rather than helix
o Backbone is hydrogen bonds
Adjacent backbones produce ‘sheets’
R-Groups of adjacent AA protrude creating an alternating pattern
structure
o Beta and Alpha exsist unanimously as the protein develops
In class :
Single monomers don’t present with anything above tertiary structure
Beta sheets are mostly more stable than alpha helixes
Beta-alpha-Beta arranged a/b barrel
Motif (fold) of proteins can be a basis for a protein structural classification:
organized by families and superfamilies.
Families ~4000 strong evolutionary connection
Superfamilies – folded similarly but not much coding in common
Oligomer – multi-
repeating structural unit=promoter
Proteostasis ( Protein maintenance of the active set of cellular Pro under
given set of condition ) protein ‘cell cycle’
Renaturation (refolding) Anfinsen experiment added urea to disulfide,
completely unfolded,
Due to protein folds and unfolds - > neurodegenerative disorders.
Cystic Fibrosis – defects in membrane bound protein CFTransmembrane
conductance regulator)
Prion – misfolded brain proteins – chronic/death
Ideals to discover and observe protein isolation/activation
Protein Crystallography
Nuclear spins NMR Spectrophy
2D NMR techs.
o NOESY – distance heavy
o TOCSY – bonds observation coupling
Cryo-EM ; good for extremely large structures (i.e ribosomes)