1. 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)

2. 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)

3. 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 signaling)

4. Quaternary Structure Definition: Organization of multiple chain associations  Oligomerization- Homo (self), Hetero (different)   Used in organizing single proteins and protein machines Specific structures result from long-range interactions  Electrostatic (charged) interactions  Hydrogen bonds (O  H, N  H, S  H)   Hydrophobic interactions  Disulfides only VERY infrequently

5. Quaternary Structure The classic example- hemoglobin  2 -  2

6. Protein Folding Folded proteins are only marginally stable!!  ~0.4 kJmol -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

7. 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

8. Protein Folding Random folding has too many possibilities  Backbone restricted but side chains not  A 100 residue protein would require 10 87 s to search all conformations (age of universe < 10 18 s)  Most proteins fold in less than 10 s!! *Proteins fold along specific pathways*

9. 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

10. 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

11. Relationships Among Proteins Many sequences can give same structure  Side chain pattern more important than sequence 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*