242 Protein Structure Function Student f2013
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Transcript of 242 Protein Structure Function Student f2013
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Over the next 2 lectures, our goal is to
- understand the chemistry of proteins and
protein folding
- recognize different structural levels of proteins and
the role of structure on protein function
- recognize and analyze the relationship between
similar proteins in terms of protein domains and
protein families
- understand how protein function is regulated
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1. Protein composition
Amino acids
2. Protein shape and structure
Bonding
other small molecules
3. How proteins work: binding to other molecules
Protein-Protein interactionsProtein-Small Molecule interactions
4. Protein domains and Protein families
5. How protein function is controlled
A. Multiple binding sites
B. Phosphorylation
C. Nucleotide binding and hydrolysis
D. Proteolytic cleavage
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Water is an important component in all cells, along with other stuff:
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We are organic beings: carbon-based.
Macromolecules are synthesized from the appropriate
precursors.
Link monomers to generate polymers.
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Table 4-2 Essential Cell Biology( Garland Science 2010)
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What do proteins do?
Enzymatic reactions - covalent bond formation and breakage
Structural proteins - support cells and tissuesTransport proteins - carry small molecules, ions
Motor proteins - generate movement in cells and tissues
Storage proteins - store small molecules and ions
Signal proteins - carry signals from one cell to another
Receptor proteins - detect and send signals to cell response
machinery
Gene regulatory proteins - interact with DNA and control gene
expression
Special-purpose proteins - variable (glow, antifreeze,attachment, etc)
How do they do all those things???
Protein Struc ture = Protein Func t ion
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Amino Acids:
One rendition
(Alanine):
Another rendition:
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10/45Figure 4-1 Essential Cell Biology( Garland Science 2010)
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11/45Figure 2-22 Essential Cell Biology( Garland Science 2010)
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2. Shape and Structure: Polypeptide chain = 1o structure
Figure 4-2 Essential Cell Biology( Garland Science 2010)
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13/45Figure 4-5 Essential Cell Biology( Garland Science 2010)
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14/45Figure 4-6 Essential Cell Biology( Garland Science 2010)
Multiple interactions between AAs
and peptide backbone:
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15/45Figure 4-10ac Essential Cell Biology( Garland Science 2010)
Common 2o structure: -helix
Hydrogen bonding of backbone N-H to C=O, 4 peptide bonds apart
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The -helices may interact to form
coiled-coils
(ie keratin, DNA transcription factors)
helices are common in
proteins that cross membranes
(transmembrane proteins)
Figure 4-12 , 13 Essential Cell Biology( Garland Science 2010)
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Figure 4-10df Essential Cell Biology( Garland Science 2010)
2o Structure: -pleated sheet
AAs above, below plane
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Anti-parallel or parallel structure
Confer rigidity, strength
(silk, biological antifreeze)Figure 4-14, 15 Essential Cell Biology( Garland Science 2010)
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Chemical nature of the amino acids will cause interactions
between them, non-covalent bonds. Contribute to structure.
Figure 4-4 Essential Cell Biology( Garland Science 2010)
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3. 3o structure: a three dimensional globular polypeptide chain
Figure 4-17 Essential Cell Biology( Garland Science 2010)
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Figure 2-31 Essential Cell Biology( Garland Science 2010)
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Figure 4-26 Essential Cell Biology( Garland Science 2010)
Covalent disulfide bonds contribute to stabilizing protein structure:
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Figure 4-25b Essential Cell Biology( Garland Science 2010)
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Bovine insulin:
S S
G-I-V-E-Q-C-C-A-S-V-C-S-L-Y-Q-L-E-N-Y-C-NS SS S
F-V-N-Q-H-L-C-G-S-H-L-V-E-A-L-Y-L-V-C-G-E-R-G-F-F-Y-T-P-L-A
Cysteine:
SH
CH2
H2N-C-COOH
H
Proline:
CH2
CH2 CH2
H2N-C-COOH
H
Presence of Proline in a structure can make
a kink in the polypeptide chain.
S-E-G-G-A-L- P
N
Q
V
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04_22_protein subunit.jpg
4o structure: more than
one polypeptide chain
interacting in complex
Homodimer
Homotetramer
Hemoglobin: 4 subunits
2 chains
2 chains
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Macromolecular interaction through various bonds:
The stronger the bonds, the more stable the interaction.
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04_07_Denatured prot.jpg
Protein structure can be denatured,
and may reanneal to regain function.
Not all denaturing agents can be reversed - HEAT.
If you alter STRUCTURE, you can alter FUNCTION.
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Figure 4-28 Essential Cell Biology( Garland Science 2010)
Binding sites (or pockets) within a protein:
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04_30_selective binding.jpg
3. How Proteins Work: interact with other proteins and/or small
molecules in very specific fashion. Interaction determined by structure!
Thingthat
binds
Region
of
binding
4.27
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Some proteins require small molecule binding to be functional:
Hemoglobin (Fe2+)
Other examples:
Botulinum toxin (protease) binds Zinc
Transcription factors (DNA binding) bind Zinc
Amylase (digestive enzyme) binds Cl-
Without associated factor, protein not functional.
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Figure 4-21 Essential Cell Biology( Garland Science 2010)
Protein subunits (polypeptide chains) can assemble into filaments
sheets, or spheres. Self-organizing structures when proper elements
present.
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Mathews and van Holde, Biochemistry
An example of self-assembly gone awry
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Proteins with similaroverall structure may have similarfunction
can be grouped as a protein family.
Elastase and chymotrypsin are family members of a group of
enzymes that digest other proteins (proteases).
4. Protein domains and Protein families
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Proteins can have regions of amino acid sequence that have
a particular structure/function within the protein as a whole.
These microfunction regions are protein domains.
For example:
Phosphorylated Tyrosine Binding
PTB Domain SH2 Domain
Phospholipid Binding
BAR Domain BEACH Domain C1 Domain C2 Domain
GLUE Domain GRAM Domain PH Domain PX Domain
Protein Degradation
F-Box Domain HECT Domain RING Domain SOCS Domain
Proline-Rich Sequence BindingEVH1 Domain GYF Domain SH3 Domain WW Domain
Ubiquitin Binding
CUE Domain GAT Domain MIU Domain NZF Domain
Vesicle Trafficking
EH Domain SNARE Domain
http://www.cellsignal.com/reference/domain/ptb.htmlhttp://www.cellsignal.com/reference/domain/sh2.htmlhttp://www.cellsignal.com/reference/domain/bar.htmlhttp://www.cellsignal.com/reference/domain/beach.htmlhttp://www.cellsignal.com/reference/domain/c1.htmlhttp://www.cellsignal.com/reference/domain/c2.htmlhttp://www.cellsignal.com/reference/domain/glue.htmlhttp://www.cellsignal.com/reference/domain/gram.htmlhttp://www.cellsignal.com/reference/domain/ph.htmlhttp://www.cellsignal.com/reference/domain/px.htmlhttp://www.cellsignal.com/reference/domain/fbox.htmlhttp://www.cellsignal.com/reference/domain/hect.htmlhttp://www.cellsignal.com/reference/domain/ring.htmlhttp://www.cellsignal.com/reference/domain/socs.htmlhttp://www.cellsignal.com/reference/domain/evh1.htmlhttp://www.cellsignal.com/reference/domain/gyf.htmlhttp://www.cellsignal.com/reference/domain/sh3.htmlhttp://www.cellsignal.com/reference/domain/ww.htmlhttp://www.cellsignal.com/reference/domain/cue.htmlhttp://www.cellsignal.com/reference/domain/gat.htmlhttp://www.cellsignal.com/reference/domain/miu.htmlhttp://www.cellsignal.com/reference/domain/nzf.htmlhttp://www.cellsignal.com/reference/domain/eh.htmlhttp://www.cellsignal.com/reference/domain/snare.htmlhttp://www.cellsignal.com/reference/domain/snare.htmlhttp://www.cellsignal.com/reference/domain/eh.htmlhttp://www.cellsignal.com/reference/domain/nzf.htmlhttp://www.cellsignal.com/reference/domain/miu.htmlhttp://www.cellsignal.com/reference/domain/gat.htmlhttp://www.cellsignal.com/reference/domain/cue.htmlhttp://www.cellsignal.com/reference/domain/ww.htmlhttp://www.cellsignal.com/reference/domain/sh3.htmlhttp://www.cellsignal.com/reference/domain/gyf.htmlhttp://www.cellsignal.com/reference/domain/evh1.htmlhttp://www.cellsignal.com/reference/domain/socs.htmlhttp://www.cellsignal.com/reference/domain/ring.htmlhttp://www.cellsignal.com/reference/domain/hect.htmlhttp://www.cellsignal.com/reference/domain/fbox.htmlhttp://www.cellsignal.com/reference/domain/fbox.htmlhttp://www.cellsignal.com/reference/domain/fbox.htmlhttp://www.cellsignal.com/reference/domain/px.htmlhttp://www.cellsignal.com/reference/domain/ph.htmlhttp://www.cellsignal.com/reference/domain/gram.htmlhttp://www.cellsignal.com/reference/domain/glue.htmlhttp://www.cellsignal.com/reference/domain/c2.htmlhttp://www.cellsignal.com/reference/domain/c1.htmlhttp://www.cellsignal.com/reference/domain/beach.htmlhttp://www.cellsignal.com/reference/domain/bar.htmlhttp://www.cellsignal.com/reference/domain/sh2.htmlhttp://www.cellsignal.com/reference/domain/ptb.html -
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Example of a Protein Domain: SH2 domainsSrc-homology 2 (SH2) domains are modules of approximately 100 amino acids that
bind to specific phosphotyrosine (pY)-containing peptide motifs.
Src SH2 domain bound to
phosphotyrosine peptidehttp://www.cellsignal.com
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While they have similar structure/function, their different specificities are due to
the differences in their amino acid sequences in the site that cleaves the
target proteins.
These members of the protease enzyme family could have similar structures,
similar functions, and similarprotein domain composition, but have unique
differences related to the specificity of their function.
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How are these differences generated? Mutation and selection
GONE:
UONE GNNE GONJ GOZE
GONH GOLE GFNE XONENONE GKNE GJNE DONE
GCNE GOVB GOIE GGNE
GONI GFNE GPNE GENEBONE GOWE OONE GYNE
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Example: evolution of resistance of malarial parasite to drug pyrimethamine
In the original DHFR protein before the drug was widely used:
Amino acid 108 = Serine (S)
Amino acid 59 = Cysteine ( C)
Amino acid 51 = Asparagine (N)
Amino acid 164 = Isoleucine (I)
First, Amino acid 108 = Serine (S) was replaced with asparagine (N)then, Amino acid 59 = Cysteine ( C) was replaced with arginine ( R)
then, Amino acid 51 = Asparagine (N) was replaced with isoleucine (I)
finally, Amino acid 164 = Isoleucine (I) was replaced with leucine (L)
NCSI to NCNI to NRNI to IRNI to IRNL
5 How proteins are controlled/regulated:
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5. How proteins are controlled/regulated:
Why do they need
to be regulated?
Figure 4-35 Essential Cell Biology( Garland Science 2010)
A Multiple binding sites: cooperative binding is allosteric
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A. Multiple binding sites: cooperative binding is allosteric.
The protein exists in 2 or more conformations depending on the
binding of a molecule to the protein at a location apart from the
catalytic site.
Figure 4-37 Essential Cell Biology( Garland Science 2010)
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B. Phosphorylation
Protein kinase has 2 ligand sites:
One for ATP
One for substrate protein
ATP
Substrate
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C. Nucleotide binding/hydrolysis
Figure 4-39 Essential Cell Biology( Garland Science 2010)
Some proteins use GTP: bind GTP, hydrolyze to GDP + released Phosphate group
Some proteins use ATP: bind ATP, hydrolyze to ADP + released Phosphate group
Some proteins use CTP: bind CTP, hydrolyze to CDP + released Phosphate group
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Figure 3-31 Essential Cell Biology( Garland Science 2010)
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Figure 4-42 Essential Cell Biology( Garland Science 2010)
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D. Proteolytic cleavage:
Low potency
Botulinum neurotoxinHigh potency
Botulinum neurotoxin