Biochem-5012.2B - Center for Structural Biology

Tertiary Structure
Globular proteins (enzymes, molecular machines)
 Variety of secondary structures
 Approximately spherical shape
 Water soluble
 Function in dynamic roles (e.g. catalysis,
regulation, transport, immunity)
Tertiary Structure
Fibrous Proteins (fibrils, structural proteins)
 One dominating secondary structure
 Typically narrow, rod-like shape
 Poor water solubility
 Function in structural roles (e.g. cytoskeleton,
bone, skin)
Tertiary Structure
Membrane Proteins (receptors, channels)
 Inserted into (through) membranes
 Multi-domain- membrane spanning,
cytoplasmic, and extra-cellular domains
 Poor water solubility
 Function in cell communication (e.g. cell
Quaternary Structure
Definition: Organization of multiple chain associations
 Oligomerization- Homo (self), Hetero (different)
 Used in organizing single proteins and protein
Specific structures result from long-range interactions
 Electrostatic (charged) interactions
 Hydrogen bonds (OH, N H, S  H)
 Hydrophobic interactions
 Disulfides only VERY infrequently
Quaternary Structure
The classic example- hemoglobin a2-b2
Protein Folding
Folded proteins are only marginally stable!!
 ~0.4 kJ•mol-1 required to unfold (cf. ~20/H-bond)
 Balance of loss of entropy and stabilizing forces
Protein fold is specified by sequence
 Reversible reaction- denature (fold)/renature
 Even single mutations can cause changes
 Recent discovery that amyloid diseases (eg.
CJD, Alzheimer) are due to unstable protein folding
Protein Folding
The hydrophobic effect is the major driving force
 Hydrophobic side chains cluster/exclude water
 Release of water cages in unfolded state
Other Forces stabilizing protein structure
 Hydrogen bonds
 Electrostatic interactions
 Chemical cross links- Disulfides, metal ions
Protein Folding
Random folding has too many possibilities
 Backbone restricted but side chains not
 A 100 residue protein would require 1087 s to
search all conformations (age of universe < 1018 s)
 Most proteins fold in less than 10 s!!
*Proteins fold along specific pathways*
Protein Folding Pathways
Usual order of folding events
 Secondary structures formed quickly (local)
 Secondary structures aggregate to form motifs
 Hydrophobic collapse to form domains
 Coalescence of domains
Molecular chaperones assist folding in-vivo
 Complexity of large chains/multi-domains
 Cellular environment is rich in interacting
molecules Chaperones sequester proteins and
allow time to fold
Relationships Among Proteins
I. Homologous: very similar sequence (cytochrome c)
 Same structure
 Same function
 Modeling structure from homology
II. Similar function- different sequence (dehydrogenases)
 One domain same structure
 One domain different
III. Similar structure- different function (cf. thioredoxin)
 Same 3-D structure
 Not same function
Relationships Among Proteins
Many sequences can give same structure
 Side chain pattern more important than
When homology is high (>50%), likely to have same
structure and function (structural genomics)
 Cores conserved
 Surfaces and loops more variable
*3-D shape more conserved than sequence*
*There are a limited number of structural frameworks*