Transcript Class_3: Protein - University of Illinois at Urbana

• Proteins
• Protein Structures and Shapes
• Protein Functions
Protein Structures and Shapes
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Amino acids
Peptide bonds
alpha helix and beta sheet
Domains and Modules
Classification of Families
Protein Assembly
Amino Acids form polypeptide
through peptide bond
Structural Components of a protein
The 20 Amino Acids
2 negative, 3 positive, 5 non-charged polar, 10 nonpolar
Read Page 132-133, panel 3-1
Limitations on the
bond angles
Ramachandran plot
Four major noncovalent bonds that help protein folding
1. Ionic bond 2. van der Waals 3. Hydrogen bond, 4.
Hydrophobic force
Hydrophobic “forces”
The importance of hydrogen bond
Folding and Refolding
Secondary structures
a helix and b sheet
Coiled-coil
structure
a-keratin
Two types of b
sheet structures
Src Kinase
The combination of ahelix and b-sheets
Classification of protein families
Two serine proteases
Two homeodomains from different species
(yeast a2, green; drosophila engrailed protein, red)
Domains and Modules
Domain shuffling
Calcium binding domain
Kringle domain
Module Examples
The combination of Modules
Design Strategy
ECFP(1-227) SH2(from c-Src)
Linker
Substrate
EYFP
433 nm
Weak FRET
433 nm
Strong FRET
527 nm
Src Activation
Phosphatase
490 nm
Protein Subunits
Hydrophobic forces
Hemoglobin
Protein assemblies
Actin Filaments
Disulfide bonds
Extracellular matrix protein are
covalently cross-linked by
Disulfide bonds
Hexagonally packed globular protein
subunits can form flat sheets
Self-Assembly
Tobacco mosaic virus (TMV)
Model Structure
Electron Micrograph
The formation of
Virus shell
X-Ray Crystallography of different virus
(A) Tomato bushy stunt virus (B) poliovirus (C) simian virus
40 (SV40) (D) satellite tobacco necrosis virus
Three mechanisms of length determination
for self-assembly
Protein assembly aided
by assembly factors
(insulin assembly)
Protein Functions
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Protein Binding
Protein conformation
Antibody
Enzyme and substrate
Catalytic Reaction
Kinase and phosphatase
GTPase, GEF, GAP
Motor protein
Membrane-bound protein
Protein binding
Protein binding sites
Protein binding site
Cyclic AMP
Protein binding sites
1. Restriction of water entrance
2. Alteration of reactivity
Sequence Comparison to find
conserved binding sites
Sh2 domain
Three ways for two proteins to bind
Antibody
Noncovalent bonds and protein interactions
Binding Energy and Equilibrium constant
Enzyme Kinetics
Read Panel 3-3, page 165
Enzymes lower the activation energy
to accelerate chemical reactions
Lysozyme actions
Bending of the polysaccharide bond
Steps of lysozyme actions
Strategies of enzyme catalysis
Feedback inhibitions
Coupled regulation:
Positive Regulations
Coupled regulation:
negative Regulations
Coupled regulation on
multiple subunits
Aspartate transcarbamoylase
Kinase and phosphatase
Kinase Domain
Kinase families
Cyclin-dependent Kinase (CdK):
Signal integrator
threonine
tyrosine
Src Kinase
Multiple Inputs for Src
Kinase activation
GTPases
Ras Structure:
One kind of GTPases
Phosphorylation and GTP binding regulations
EF-Tu and its regulation of tRNA
Motor Protein Regulation
Myosin on Actin and Kinesin on Microtubules
Membrane Protein
Calcium Pump on
Sarcoplasmic reticulum