242 Protein Structure Function Student f2013

7/29/2019 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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2. Shape and Structure: Polypeptide chain = 1o structure

Figure 4-2 Essential Cell Biology( Garland Science 2010)



Multiple interactions between AAs

and peptide backbone:


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.



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3. 3o structure: a three dimensional globular polypeptide chain



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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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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

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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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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?


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.



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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


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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D. Proteolytic cleavage:

Low potency

Botulinum neurotoxinHigh potency

Botulinum neurotoxin

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242 Protein Structure Function Student f2013