Elements
Primary to Quaternary Structure
Learning Objectives
After this lesson you should be able to:
Surface Interior
Hydrophobic vs. Hydrophilic
Globular protein (in Membrane protein
solution)
Myoglobin Aquaporin
Hydrophobic vs. Hydrophilic
Globular protein (in Membrane protein
solution)
Cross-section Cross-section
Myoglobin Aquaporin
From Unfolded to Native State
Transition state
one or more
DG = DH - TDS E
narrow
ensembles
------------------------- T
DG: Free (Gibbs)
energy
DH: Enthalpy U
(interactions) DG F
DS: Entropy
(conformations/ Native
Unfolded state, fold, one
states) ensemble structure
Protein Stability & Dynamics
Folded proteins are:
Dynamic
Breathing motions on pico- to nanosecond scale.
Allows substrates/products to enter/leave enzymes.
Allows allosteric regulation of activity.
Amino Acids
Proteins are built from
amino acids
Ce
Amino group and acid Sd
group
Cg
Side chain at Ca Cb
A Ala M Met
C Cys N Asn
D Asp P Pro
E Glu Q Gln
F Phe R Arg
G Gly S Ser
H His T Thr
I Ile V Val
K Lys W Trp
L Leu Y - Tyr
Based on
Blosum62
matrix
Measure of
evolutionary
substitution
probability
Backbone Properties
Amide bond planarity 2 degrees of rotational
freedom per residue
Ramachandran Plot
Allowed backbone torsion angles in proteins
Peptide
bond
Residue
Torsion Angles
Characteristics of Helices
C
Backbone
interactions
are local
Aligned
peptide units
Dipolar
moment
N
Helix Types
b-Sheets
Multiple strands Antiparallel Parallel
sheet
Parallel vs. antiparallel
Twist
Flexibility
Vs. helices
Folding
b-Sheets
Thioredoxin
b-Sheets
Thioredoxin
b-Sheets
Thioredoxin
b-Sheets
Thioredoxin
Not All b-Sheets Are Flat
Nitrophorin Thioredoxin
Residue Patterns
Helices C Sheets
Helix capping Amphiphilic residue
Amphiphilic residue patterns
patterns Residue preferences at
N edges vs. middle
Special residues
Proline
Helix breaker
Glycine
In turns/loops/bends
Turns, Loops & Bends Revisited
Between helices
and sheets
On protein surface
Intrinsically
unstructured
proteins
Summary
The backbone of polypeptides form regular
secondary structures.
Helices, sheets, turns, bends & loops.