Protein Structure
The Chemical Nature of Amino Acids
The amino acids found in proteins have the following generalized
structure:
where R can stand for a variety of constituents. The amino
group and the carboxyl group of the amino acid have PKs of about
9.6 and 2.3 respectively. Thus, the amino acid can exist in three
general forms. At low pH the amino and carboxyl groups will be
protonated and the molecules will be in the acid form.
As the pH is increased towards neutrality, the amino acids
become zwitterions having both negative and positive charges.
As the pH increases further, the molecules become basic.
In going from low to high pH:
When amino acids are joined together to form peptide bonds, water
is removed in the following reaction:
It should be noted that the joining of amino acids to form
peptide bonds eliminates the acid and basic character of the
molecules. The only ionized groups in the finished protein will
be the terminal amino and carboxyl groups and also any R groups
that happen to contain acidic or basic groups.
The Structure of Amino Acids
While there are hundreds of amino acids in nature, only 20 are
commonly found in proteins. With one exception these are a amino
acids that differ only in the nature of their R groups. In this
section the structure of each amino acids will be given and some
of the properties that are unique to that compound will be
discussed. The standard three letter abbreviations for each amino
acid will be given with its structure and these abbreviations
will be used frequently in the remainder of the text.
Glycine
Glycine is the only amino acid that does not have optical
isomers. The other amino acids do, but in proteins only the L
isomer occurs. Glycine has no ionizable groups when it is located
in peptide bounds. Glycine will spontaneously transfer from a non
aqueous to an aqueous environment with a DF
of -4.6 Kcal/mole. Because glycine contains only a hydrogen while
other amino acids contain either polar or nonpolar groups,
Tanford (1962) has suggested that glycine be utilized as a
reference compound and that other amino acids be compared to
glycine to determine the nonpolarity or hydrophobicity of their
side chains. These free energy transfer values have been
designated Hf. The value for glycine
then is by definition zero and glycine can be expected to be
found with nearly equal frequency at the interior or exterior of
a protein. Due to its small size, glycine may be placed in
portions of proteins where other amino acids can not occur due to
steric reasons. The presence of glycine residues tends to
interrupt the helical structure. Glycine is often found in
portions of proteins involve in turns.
Alanine
The next largest amino acid, alanine, contains a methyl group
rather than a hydrogen attached to its a carbon. Like glycine, it
has no ionizable groups when it is found in proteins. Its value
for Hf is 0.75 Kcal which suggests
that is mildly hydrophobic. Also like glycine, alanine tends to
be found with almost equal frequency on the surface and interior
of protein molecules. Alanine tends to promote the formation of
helical structure.
Valine
Valine has no ionizable groups when found in peptide bonds,
but has considerably more bulk than either Gly or Val. Its Hf value of 1.70 Kcal suggest that it is a
fairly hydrophobic residue. It is found almost exclusively in the
interior of proteins. The presence of valine tends to favor the
formation of helical structures.
Leucine
Leucine resembles VAL with a CH2 group before the branch. It
has no ionizable groups when found in proteins and is strongly
hydrophobic. It has a Hf of 2.40 Kcal
and is found in the interior of protein molecules. Its presence
tends to stabilize helical structures.
Isoleucine
Isoleucine is a positional isomer of LEU and thus has many of
the same characteristics. The branching at the b-carbon tends to increase its bulk and thus
its hydrophobicity. Isoleucine has the second highest Hf of 2.95 Kcal, has no ionizable groups when
found in proteins and tends to stabilize helical structures.
Serine
Serine resembles ALA with a hydroxyl group. It is a neutral
polar molecule that tends to remain on the surface of proteins (Hf < O). The presence of serine tends to
interrupt helical structures. While generally present on the
surface, serine can be found on the interior of protein when its
-OH group is involved in hydrogen bond formation. Serine can also
form noncovalant cross links between protein links between
protein chains due to hydrogen bonding.
Threonine
Threonine is closely related to SER in that only a methyl
group has been added to the molecule. The hydroxyl group tends to
make the molecule polar while the ethyl group tends to be
non-polar. Threonine has an Hf of 0.45
Kcal but tend to be found on the surface of proteins unless its
hydroxyl group is hydrogen bounded. The presence of threonine
neither favors nor inhibits the formation of helical structure
and threonine has no ionizable groups when found in protein
molecules. Like SER, threonine can be used to form hydrogen bond
cross-links between protein chains.
Phenylalanine
Phenylalanine is a bulky amino acid with a strong hydrophobic
character. Its Hf is 2.65 Kcal and
this residue is found almost exclusively in the interior of
protein molecules. It has no ionizable groups but does contain
the conjugated ring system with its p
electrons are also able to interact with other molecules
containing p electrons. Phenylalanine
neither favors nor inhibits the formation of helical structure.
This residue can be found both at the surface and interior of
protein molecules.
Tyrosine
Tyrosine strongly resembles PHE but contains a hydroxyl group
on the ring. The bulky ring gives the molecule a hydrophobic
nature with Hf of 2.85 Kcal. The
hydroxyl group is polar and will readily interact with water. The
conjugated ring's p electrons are also
able to interact with other molecules containing p electrons. Tyrosine neither favors nor
inhibits the formation of helical structure. This residue can be
found both at the surface and interior of protein molecules. When
found in the interior, its hydroxyl group is always involved in
hydrogen bonding. At very high pH values the hydroxyl of PHE can
be ionized and thus the molecule can be considered as weakly
acidic. The pk of this group is around 9.6 when tyrosine is
located in a protein and thus at neutral pH values, the molecule
is essentially unionized. Tyrosine absorbs strongly in the
ultraviolet region and thus contributes to the UV absorbance of
proteins.
Tryptophan
The tryptophan is the bulkiest amino avid and has a Hf of 3.0 Kcal. In spite of its very
hydrophobic nature, it is found both on the surface and interior
of protein molecules. Its extensive array of p
electrons allows it to interact strongly with other molecules
containing p electrons. Tryptophan has
no ionizable groups and tends to favor the formation of helical
structures. Tryptophan absorbs strongly in the region between 275
and 280 nM and makes a large contribution to the ultraviolet
absorption of protein molecules.
Cysteine
Cysteine is a slightly acidic amino acid that is slightly
hydrophobic with an Hf of 1.0 Kcal.
The presence of cysteine neither favors nor inhibits the
formation of helical structures. Probably the most important
characteristic of cysteine is its ability to stabilize protein
structure by forming disulfide linkages with other cysteine
molecules. These covalent cross links add stability to the three
dimensional structures of protein and their formation and
importance will be discussed in some detail in the next chapter.
The sulfhydryl group of cysteine is a very weak acid with a pK of
about 8.4. At a pH near neutrality, a few percent of the
sulfhydryl groups of a protein will be ionized.
Methionine
Methionine is a neutral amino acid with a Hf
of 1.3 Kcal. It is related to cysteine but can not form disulfide
linkages. Methionine tends to favor the formation of helical
structures. While not able to cross link proteins through
disulfide linkages, the molecule can form important interactions
with other constituents that may bind to proteins. The sulfur
atoms of methionine contains a pair of nonbonded electrons that
are capable of binding to metals to make methionine a metal
ligand.
Proline
Proline is not a primary amine, but rather a secondary amine
or an imine. Peptide bonds formed with proline lack a free amino
group to form hydrogen bonds and thus proline tends to strongly
inhibit a helical structure. These peptide bonds tend to fold
back upon themselves and proline is found quite often in regions
or protein that form turns. Proline has not ionizable groups and
has Hf of 2.6 Kcal.
Aspartic Acid
Aspartic acid is one of the two dicarboxylic amino acids. The
second carboxly group makes the molecule very hydrophillic. It
has a Hf < 0. The pK of the second
group is about 3.85 and thus aspartic acid contains a negative
charge at neutral pH. Removal of this charged group from the
aqueous phase requires a large expenditure of energy and thus
charged amino acids are found almost exclusively at the surface
of proteins. This group is able to form ionic bonds with
positively charged amino acids or metals and it can also form ion
dipole interactions with water. These interactions are very
important to the solubility properties of proteins. The pressures
of aspartic acid neither favors nor inhibits the formation of
helical structures.
Glutamic Acid
Glutamic acid is very similar to aspartic acid in its
structure and its properties. It contains one more CH2 group, but
still has a Hf < 0. The carboxyl
group is less acidic than is that of ASP with a pK of 4.25. The
differences are not great, however, and at neutral pH
dissociation is virtually complete. The presence of glutamic acid
tends to favor the formations of helical structures and like ASP,
it is involved in many interactions.
Asparagine
Asparagine resembles ASP but the carboxyl group has been
neutralized by formation of an amide bond., Some amino acids are
modified after the protein is assembled, eg. hydroxylation of
some proline residues, methylation of some histidines, etc. These
changes are not determined by the genetic code but rather are
performed by specific enzymes that recognize certain amino acid
sequences. This is not the case for asparagine and this amino
acid is inserted as such during protein synthesis. Even without
the free carboxyl group asparagine is a polar molecule that is
almost always found at the protein surface. It can function as a
chain crosslinker via hydrogen bond formation or it can hydrogen
bond to water at the protein surface. Asparagine tends to inhibit
the formation of helical structure and quite often is found in
protein bends.
Glutamine
Much as asparagine resembles ASP , Glutamine resembles GLU. Again
the carboxyl group has been neutralized by formation of an amide
bond. Like asparagine, glutamine is almost always found at the
protein surface. It can function as a chain crosslinker via
hydrogen bond formation or it can hydrogen bond to water at the
protein surface. Glutamine tends to favor the formation of
helical structures in proteins.
Histidine
Histidine can bind a proton to the nonbonded electron pair of
its ring nitrogen to become a weak acid at low pH. The pK of the
acid is 6.0 so that at neutral pH, histidine is about 90% in the
basic form with about 10% still in the acid form. Histidine is
the only amino acid that has a functional group that titrates in
the physiological pH range. It is a polar molecule, Hf < O that tends to favor the formation
of helical structure. Depending upon its form, which depends on
the localized pH of its environment, histidine can serve as both
a proton donor and accepter. The nonbonded electron pair of the
basic form are always available for metal chelation. This
versatility has been utilized and histidine is quite often found
at the active site of enzymes and as a point of attachment for
metal containing group.
Arginine
Arginine is a large polar molecule with a positive charge at
neutral pH. The pK of the guanidanyl group is about 12.5. Even
though the molecule has a positive charge at almost all pH
values, arginine is a very large molecule and has an Hf of 0.75 Kcal. Arginine tends to interact
with negatively charged groups, negative ions and with water.
Lysine
Lysine is a charged polar amino acid having an extra amino group. The pK of this group is about 10.5 and thus lysine will have a positive charge at the pH values that most proteins are likely to encounter. Lysine is a bulky molecule with a Hf of 1.5 Kcal. Lysine neither favors nor inhibits the formation of helical structure and is capable of interacting with groups that have negative charges and with water.
