Chapter 5 Protein function

5.0 Introduction
As said previously there are thousands of proteins structures now known. In labs
will look at a few. Biggest conceptual problem is one you see a 3D structure and
use computer to move it around you tend to think protein is a solid brick. Is really
more like jello, it moves and wiggles and jiggles. And these moves and wiggles
are critical to how it works

In this chapter focuses on details of two are three protein to illustrate the wide
range of things that can be done to make proteins work. I will just do hemoglobin
and myoglobin

Some key words/concepts

Often proteins will reversibly bind some other molecules or proteins
we call these molecules ligands
The site where it binds is called the Binding site
Usually complementary to ligand in some way including size,
shape, charge, hydrophobic or
depending on how carefully designed may be extremely selective or
somewhat promiscuous in selectivity
Protein are flexible, may see subtle changes where just one or two AA rotate
slightly, or may see massive movements of entire chunks of protein. Will often
talk of protein as ‘breathing’

Binding of a ligand often accompanied by change in protein structure that may

make binding even better (like folding around) Structural adaptation called
induced fit

Structural change accompanying binding of 1 ligand often effect binding of other

ligand, and this is used to regulate activity of protein as a whole

Enzymes (next chapter) are a special case of protein function. Not only do the
bind ligands but they make then go through chemical reactions. In Enzyme we
will call the ligands by a special name, substrates and we give the binding site a
special name, catalytic site. Otherwise is the same thing, binding, specificity,
conformational change So are learning the basic rule of how protein work, in next
chapter will add chemistry into the mix
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5.1 Reversible binding of protein to ligand O2 binding proteins

Myoglobin and hemoglobin are perhaps best studied and best understood
proteins so will look at them

A. O2 bound by heme prosthetic group

O2 not very soluble (.035g/L) need higher conc
also need to diffuse over distances > a few mm
No AA’s are good O2 binders
But metals like Fe and Cu are good O2 binders
But free Fe and O2 and H2O makes hydroxyl radicals that are bad
for cell
Need to bind Fe away from H2O
Iron frequently bound by heme prosthetic group
Prosthetic group compound permanently associated with a
protein that contributes to protein’s function

Heme Figure 5-1

Organic structure called protoporphyrin ring
Flat, planar, looks aromatic, binds a single Fe2+
Fe want 6 coordinate bonds, find 4 in heme ring
Coordination helps prevent oxidation to Fe3+
Found in many oxygen bind protein as well as many redox
proteins

Free heme will bind oxygen, but then Fe oxidizes to +3 state

In protein keep ½ of heme covered, also sequester O2
pocket makes it much harder to oxidize Fe
Binding of O2 changes electronic properties of heme (as well
as protein structure)
These account for color change in blood
Other molecule also bind to heme, CO and NO. CO binds
better than O2 that is why is poison But protein
structure helps to favor O2 over CO binding so not
quite as overpowering! (More details later)

B. Globins are a family of Oxygen Binding Proteins

Globins are a family of proteins
Similar in 1o and 3o structure
Found in most classes of eukariotes and some bacteria
Most are for O2 transport or strorage
Some used in sensing O2, NO, or CO
Humans and other mammals 4 distinct kinds of globins
Tetrameric hemoglobin for O2 transport
Momomeric myoglobin for oxygen storage
Particularly in marine mammals
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Monomeric neuroglobin for O2 storage in neurons

Monomeric Cytoglobin found in many tissues but function unknown

C. Myoglobin (Mb) (figure 5-3)

Note: we just looked at this structure last week
16,700 153 AA’s, single heme
found all mammals, primarily in muscle tissue store O2 for use when
needed
Particularly in deep sea mammals like whales
member of globin protein family
contains 8 helices that account for about 80% of structure

D. Quantitative description of Protein ligand interaction

need to look at binding behavior first before we look at atomic explanation
of behavior

Will use math to measure binding and describe how it works

Binding process is equilibrium process so let’s look at equilibria

P + L W PL

Kass or Kbinding = [PL]/[P][L] (1)

I won’t use Ka so your won’t get confused with the equilibrium
constant for an acid

Have seen this kind of K before. Now something sort of new

In Gen chem or Analytical we would calculate the % of acid in the ionized

form
% ionized =100% x [A-]/([A-]+[HA])

We want to do a similar thing to find the fraction of protein in the ligand

bound form. We call this è For the fraction of binding sites on the
protein that are occupied. If there is 1 binding site

è=[PL]/[total] = [PL]/([P]+[PL]) (2)

From equation 1: [PL] = Kass[P][L]

substitute this for [PL] in equation 2 we have:

è=Kass[P][L]/([P]+Kass[P][L])
Dividing through by P
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è=Kass[L]/(1+Kass[L])
Dividing though by Kass
è=[L]/(1/Kass+[L])

Or [L]/([L]+1/Kass)

Might recognize this as a hyperbolic function

Y=X/(X+k)

Looks like figure 5-4

Note special point, when è=.5 =[L]/2[L], so [L]=1/Kass

Can also define as Kdiss = KD

[PL]W[P] + [L]

KD = [P][L]/[PL] = 1/Kass
(You should remember this from Gen chem - K of forward and
reverse reaction)

So a simpler looking è is:

è=[L]/(Kdis+[L]) and when è=.5, [L]=Kdiss

Sketch curve, point out things below

Note at []<Kdis protein rapidly give up ligand
but at []about 5X Kdis protein is saturated and can’t bind any more

Now sketch è curve for high affinity form (low K)

And low affinity form (High K) and leave on board for next section

E. Protein structure affect ligand binding

Now have math to describe binding, now look at what happens to the
protein on binding, and compare that with the math you just learned

Complicated system ,will see lots of different stuff going on, some very
subtle
for instance said earlier CO bind to heme better than O2
Lets look at quantitavely
For free heme KdisCO is 20,000X smaller for CO than for O2
Meaning it binds CO 20,000 x better!
In protein Kdis is only 200X smaller for CO than O2 so cut down affinity for
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CO by 100!
How? Binding pocket not straight. This reinforces the binding of
O2 that prefers to bind at an angle, but interferes with binding of CO
that want to bind straight (figure 5-5)
How does it get in an out to begin with. If look at X-ray no hole big
enough!!
Protein breathing, as flexes open up hole and gaps on 10-9 time
scale to let in and out

F. Hemoglobin O2 transport in blood

Nearly all O2 in animals carried by hemoglobin in blood, specifically in red
blood cells (erythrocytes)

Do I want this??
Erythrocytes
6-9ìm biconcave disks
Derive from hemoblast stem cell
Have large amounts of hemoglobin (34% of mass)
Have lost nucleus, mitochondria, and ER
Only last about 120 days

Detail on next page, this is an Intro

Mb with hyperbolic binding curve good for holding O2
Hb, is a multimer and has a sigmoidal binding curve better suited
for transport where has to bind and give off (more in a bit)
(Show on è curve previous page)

In lungs have 96% saturation so up here on curve

in return at 64% saturation so loses abut 1/3 of O2 that it carries
100 mL of blood caries about 6.5 ml of O2 gas

G. Hemoglobin units are similar to Mb units

Hemoglobin (HB) 64,500 MW, 4 hemes, tetrahedral arrangement of 4 Mb
like monomers (figure 5-10)

2 alpha chains (141 resides)

2 beta chains (146 residues)

Only about ½ of residues are same between MB and Hb, yet structure
almost identical(figure 5-6)

Only 27 residue are identical in all three

See figure 5-7
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In Hb tetramer are many interaction between units

á1â1 30 residues need urea to break apart
á1â2 19 residues
Lots of hydrophobic interaction, but some Ion pair and H bonds at
interfaces

H. Structural change in Hb on binding O2

Observe 2 structures for hemoglobin, depending on if binds O2 or doesn’t

Call state observe without O2 the T state or ‘tense’ state

Call state observe when O2 bind the R state or ‘relaxed’ state
Tense & relaxed are old, irrelevant term refer to fact that T state
has more intersubunit salt bridges so is more tensely (tightly) held
together
In R state conformation is shifted so Hb binds O2 better (higher affinity)
than T state
Binding of O2 to T state triggers conformational change to R state
Transition involves minor change protein structure, fairly large
changes in interface contacts

Figure 5-11
Binding of O2 flattens heme, moves His, moves helix

I. Hemoglobin Binds Cooperatively

Net effect (Draw on board -then show figure 5-12)
Since T state low binding has this curve with è=.5 at high pO2
R state is high affinity so è=.5 at low pO2
As molecules move from one to other get sigmoidal kid of curve
This is called cooperativity, binding on one molecules affect binding on
another
In lungs, high O2 high affinity, sucks up all the O2 it can
In tissue, low O2 lower affinity, doesn’t hold as tightly, gives off O2
to tissue

Hemoglobin is an example of an allosteric protein

Binding of one ligand to one site affects binding at another site
Allostery can be positive or negative
Hemoglobin considered homotropic because modulator = ligand
Many cases of heterotropic modulator … ligand
Sometimes more than 1 modulator

Cooperative binding frequently observed in multimeric proteins

Allosteric, multimeric proteins are seen often in regulatory proteins
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Cooperativity depends on variation of structural stability within protein

Binding site of ligand is typically in region with both stable and
slightly unstable segments
The ligand stabilizes a particular conformation
This in turn affects conformation and reactivity of other subunits in
complex

J. Describing with math

Now let’s extend earlier math for n ligand binding sites

P + nL W PLn

Ka = [PLn]/[P][L]n

With a little math

è = [L]n/([L]n + Kd)

Rearranging

è/(1-è) = [L]n/Kd

And

Log(è/(1-è) ) = nlog([L] - log Kd

Why do this? Its called a Hill Plot

See figure 5-14
Shows cooperativity, conc where cooperative, how many
cooperative units?

(Don’t sweat the math, I don’t anticipate any Hill plot problems, other than
looking at a plot and interpreting)

K. Models for cooperative binding

2 main models have been proposed to explain cooperativity
MWC (Monod, Wyman + Changeux 1965)
Sequential (Koshland 1966)
Figure 5-15
MWC. All molecule in T or R
Sequential, 1 molecule can have bother T and R
See all the equilibria?
Make equation to describe all equilbrium
Bottom line, data yet to be good enough to say which is correct!
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L. Hb also transports H+ & CO2

Now let’s get more complicated
What else is in the blood? CO2
CO2 not very soluble, body makes soluble by converting to carbonic acid
CO2 + H2O W HCO3- + H+
A spontaneous but slow reaction, body want fast so can reverse
reaction can go forward it tie blood is in tissue and completely
reverse in time blood is in lung, have special enzyme Carbonic
Anhydrase one of the fastest enzymes known

“But wait there’s more”

Net effect, in peripheral tissue H+ high, pH lower
Body uses this effect to help unload even more O2
Called the Bohr Effect Figure 5-16
Higher [H], lower pH, less O2 bound
Effect primarily comes from changing ionization state of several ionizable
groups on Hb molecule Which one do we expect (his) you are right His
146

Hb also carries CO2 as carbamino group on terminal NH2

See left column page 171

Net Hb not only caries O2 but about 20% of CO2 and H+ generated in
peripheral tissue

M. O2 binding further regulated by 2,3 biphosphoglycerate (BPG)

Structure right hand column 171
BPG 5mM sea level, 8mM high altitude

Sea level control is for about 40% of max to be delivered to lungs

however move to 4500 m (15,000 ft) only have about ½ as much O2 in air,
so cannot deliver as much
BPG conc increases, makes HB have less affinity so kick off more
O2
So continues to deliver about 40%
See figure 5-17

Also another story in hemoglobin in fetal tissues, need and á2ã2 Hb in

fetus, because must take O2 from mother Hb and give to baby tissue

N. Sickle cell anemia

300 single site mutation of Hb known
one of them Hb S is responsible for sickle cell anemia
Glu6Val in position 6 of beta
deoxy HB has hydrophobic patch
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Starts hemoglobin aggregating to form strand and crystals

Figure 5-20
This in turn makes cells sickle and clog capillaries
Figure 5-19

For heterozygotes not too bad live normal life if avoid vigorous exercise
For momozygotes can be fatal in childhood (or later if survive)
Why is deleterious gene in gene pool?
Heterozygotes have small but significant resistance to certain kinds
of malaria!

5.2 Complementary Interaction between proteins and ligand

The immune system
A lot of good stuff, but I want to get on with proteins. It would advise the Premed
to read the section on the immune system several times, it has lots of good
information, but I must skip for now. Below are the set of notes I would use if I
taught this section

Note: I have reorganized the material in the book in a way that makes better sense to
me. I have tried to mention in the notes when I have skipped around a section

Immunoglobulins -antibodies- key protein in immune system

specifically designed to bind to other objects
Binding to objects is key part of protein function so that is tie here

But also a biochemical understanding of the immune system is also an important

subject in and of itself, so that is what part this section is about as well.

Lets start with this background

A. Immune response - specialized array of cells and proteins

Two complementary systems
Humoral system - fluid system
Designed to remove infections (bacteria and viruses) from
fluid around cells
Can also remove individual proteins that are in organism
Cellular immune system
Designed to kill host cells (the organisms own cells) that are
infected with viruses. Can also kill come parasites. Will also
be part system that recognizes and destroys foreign tissue in
a transplant.

Keys cells - Leukocytes or white blood cells

Macrophages - job is to ingest large particles and cells by
phagocytosis
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B lymphocytes - key player in Humoral system

Developed from undifferentiated stem cell in bone marrow
Called B because last part of differentiation take place in the
B or bone
Main job - produce Antibodies or Immunoglobulins (Ig’s)
Soluble proteins that bind foreign material
Material can be bacteria, virus or large
molecule
Make up 20% of all blood protein!
Soluble part means is release from cell and free in
blood

T lymphocytes - key player in cellular immune system

Also develops from undifferentiated stem cell in bone
marrow
But in this case final differentiation in the thymus
Hence the name T-cell for thymus
2 main types
cytotoxic T cells (TC cells) or killer T cells
- Receptor protein (called T-cell receptor) on
surface of T cell binds to object on
surface of infected cell or parasite
- Bulk of receptor protein found on outer
surface of cell, but extend all the way through
the cell membrane and has a portion on the
inside as well. (Will get to this in a chapter or
two)
- When binds to object, structural change takes
place on part of protein inside cell and this
triggers changes in cell that start the killer
response

Helper T cells - (TH cells)

- Produces soluble signaling proteins - called
cytokines
- This included interleukins
- This stimulates TC TH and B cells to
proliferate
Also interacts with macrophages
- So in general kicks all immune response up a
notch for those cells that are needed to fight a
particular infection
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More terminolgy
Antigen - any molecule or pathogen capable of eliciting an immune
response
- May be virus, bacterial cell wall, or other macromolecule
- Not small molecules (<5,000 MW)
- If want to make small molecule antigenic need to attach to
large molecule
These large molecules are called Haptens

Large antigens can have many binding sites for different antibodies
- An individual antibody or T-cell receptor will bind at one
particular molecular structure
- This structure is called in Epitope or an antigenic
determinate

So how do you build a protein to bind a foreign object at a randomly chosen

epitope??
(Note will discuss only structure of immunoglobins, book does not discuss
structure of T-cell receptors in this chapter)

B. Antibodies have two identical Antigen Binding sites

Note: have temporarily skipped section Section on MHC.
Five classes of immunoglobulins or antibodies
IgA, IgD, IgG, IgE and IgM
IgG is most abundant so will start with him
Structure of IgG
- 4 peptide chains
2 large chains called heavy chains
2 smaller chains called light chains
See figure 5-21
- Linked together with disulfide and noncovalent
interactions
- Make a ‘Y’- shaped molecule total mass about
150,000
- 2 heavies interact with each other at one end
- Then a flexible hinge and each heavy interacts with
a single light. This heavy/light section contains
antibody binding site

- Base part of joined heavies may be cleaved and

separated from antibody binding region by proteases
-Base fragment alone called the Fc because readily
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crystalized (Fragment, crystalizing)

- Heavy/Light section called Fab (Fragment, antigen-

binding)
Each Fab branch has a single antigen-binding
site

- Heavy chain has three domains of relatively

constant sequence (Designated CH1, CH2 and CH3),
and one region with a highly variable sequence (VH)

- The light chain has a single constant and a single

variable region (CL and VL)

- Can see that these constant regions are

characteristic beta-barrel domains with one part of
barrel coming from one chain and the other ½ from
the other chain

- Structure called the Immunoglobulin fold

- Antigen binding site is in variable regions

Makes sense want to make lots of different
binding sites for lots of different antigens

- How do you make 10,000s of different proteins to

bind 10,000 different antigen? Will save that secret
for chapter 25)

Would think that would now examine structure of binding site bound to
antigen, but to do that we have to skip ahead to:

C. Antibodies Bind tightly and specifically to Antigen

- Binding specificity is determined by sequence of variable regions (light
and heavy)
- In fact antigen binding site is hypervariable - more variable than rest of
variable region
- Specific binding conferred by complementarity between antibody and
antigen
different interaction used
Polarity, H bonding, charge, shape
Binding site flexible, will change shape to optimize interaction with
antigen
Antigen may change structure to better fit into binding site
(Will call Induced fit in next chapter)
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See figure 5-25

- Very strong and specific binding

- Kd = 10-10 M
This means that will bind when concentration of antibody and
antigen are as low as 10-5M (sqrt(10-10)
- Kd of 10-10 mean that binding energy is on the order of 65 kJ/mole

Now back to general discussion of iummunoglobulins

Functions of IgG
IgG is main antibody circulating in blood
Major early player in ‘primary’ immune response
First response to infection

- IgG is also major antibody in ‘secondary’ immune

response
- Secondary response - initiated by memory B cells
- Response to an antibody that body has already
dealt with at one time (I.E. already infected one, and
now you should be immune because your body kept a
memory of that antigen)

-First interaction is binding of antigen to antibody to

tie up antigen
- But then there are other interactions as well
- When binds antigen activates other leukocytes like
macrophages to engulf and destroy invader
-Macrophage has binding site for Fc Region of IgG
When binds IgG/antigen macrophage activates
Figure 5-24
- Also activates other parts of immune response

Differences in structure between different Ig’s

Actual differences due to sequence of heavy chains
á - IgA
ä - IgD
å - IgE
ã - IgG
ì - IgM
2 types of light chains - ê, ë
Occur in all Ig’s
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Overall structure of D, E, and G are similar

M is either monomeric , membrane bound or
crosslinked pentamer
(See figure 5-23)
A is monomer, dimer or trimer
Found in secretions like tears, saliva, milk

Early in immune response a B lyphocyte cell will make make IgG

Later will make IgD with same antigen binding site as IgG.
Function of IgD and reason for addition is not known

D. The Antibody-Antigen Interaction is the Basis of a Variety of Analytical

procedures
Since antibodies are released into the blood, can make and isolate
antibodies. For instance challenge a rabbit with a specific antigen, wait a
few days, challenge again, do this several times, then extract remove a
blood sample and isolate antibodies from blood.

Once isolate antibody now have a protein that is designed to bind to the
antigen and can do nifty analytical techniques with this antibody.

Talk about two different types of antibody preps

Polyclonal antibodies - In normal immune response get many
different B lymphocytes the recognize an antigen. Since each
lymphocyte make and antibody for a different target site on the
antigen, get a mixture of antibodies that bind in many different
places on the antigen.

Monclonal antibodies. First isolate a single lymphocyte and clone

it. Now get only antibodies to a single specific epitope

Uses for antibodies

Attach to resin to make an affinity column

Make antibody radioactive or fluorescent

Then can be used to tag and identify antigen
Can be used to see where it is in a cell or in a gel

ELISA (Enzyme linked immunosorbant assay

Figure 5-26
Say have 96 blood samples that you want to screen for Herpes
1. Put a drop of blood into 96 wells on a plastic dish
(If cell has HERPES than a HERPES protein will
adhere to plastic)
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2. Wash of excess and put a drop of nonspecific protein into

each well to cover up all possible protein binding sites
3. Wash of excess, incubate with antibody toi Herpes
protein
(Will bind to protein that is bound to dish)
4.Wash off excess now bind an antibody to the first antibody
Called a secondary antibody
This antibody has an enzyme covalently attached
Enzyme will run a reaction that makes a reagent
change color
5. Add reagent
Only those wells that have Herpes bond to antibody
bound to antibody bond to enzyme will change color

Immunoblot assay - used in electrophoresis

Transfer 1D or 2D electrophoresis gel to nitrocelluloase to bind
proteins
Treat membrane as we just did for ELISA
Will see colored bands where target protein occurs in gel.

5.3 Protein interactions of muscle

again lots of good stuff, but I will have to skip and move on
Please read if you want to understand how muscles work on the molecular level!