Download Amino Acids

Chapter 1/Structure I
• The Building Blocks
• Chemical Properties of Polypeptide Chains
Levels of Protein Structure
• The AA sequence of a protein's polypeptide chain is called its primary structure.
• Different regions of sequence form local regular secondary structures, (a-helices
or -strands).
• Tertiary structure is formed by packing structural elements into one or several
compact globular units called domains.
• The final protein may contain several polypeptide chains arranged in a quaternary
structure. By formation of structures, amino acids far apart in the sequence can be
brought closer together to form a functional region, called an active site.
Amino Acids
•
•
•
•
•
•
•
Organic compounds with amino and carboxylate functional groups
Each AA has unique side chain (R) attached to alpha (α) carbon
Crystalline solids with high MP’s
Highly-soluble in water
Exist as dipolar, charged zwitterions (ionic form)
Exist as either L- or D- enantiomers
Almost without exception, biological organisms use only the L enantiomer
Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011; Berg JM, Tymoczko JL, Stryer L, Biochemistry, 5th Edition, 2002
Formation of Polypeptides
• Polypeptides and proteins are created through formation of
peptide bonds between amino acids
– Condensation reaction
Peptide linkages
R
+
H3N
CH
NH
C
CH
O
R
O
R
C
CH
NH
Polypeptide
http://en.wikipedia.org/wiki/File:AminoacidCondensation.svg
O
C
O
-
Polypeptide
Chain
• In a polypeptide chain the carboxyl group of the amino acid
n has formed a peptide bond, C-N, to the amino group of the
amino acid n + 1. One water molecule is eliminated in this
process. The repeating units, which are called residues, are
divided into main-chain atoms and side chains. The mainchain part, which is identical in all residues, contains a
central Ca atom attached to an NH group, a C'=O group, and
an H atom. The side chain R, which is different for different
residues, is bound to the Ca atom.
The “Handedness" of Amino Acids.
• Looking down the H-Ca bond from the hydrogen atom, the Lform has CO, R, and N substituents from Ca going in a clockwise
direction. For the L-form the groups read CORN in the clockwise
direction.
• All a.a. except Gly (R = H) have a chiral center
• All a.a. incorporated into proteins by organisms are in the L-form.
Amino Acids
•
20 amino acids specified by the genetic code, grouped by different properties
associated with R group (residues)
http://courses.bio.indiana.edu/L104-Bonner/Sp11/imagesSp11/L12/Part1MPs.html
Hydrophobic Amino Acids
Charged Amino Acids
Polar Amino Acids
Chemical Structure of Gly
• Glycine
Gly
G
Glycine
• Relative abundance
7.5 %
• flexible, seen in turns
Chemical Structure of Ala
• Alanine
Ala
A
Alanine
• Relative abundance
9.0 %
• hydrophobic, unreactive,
a-helix former
Chemical Structure of Val
• Valine
Val
V
Valine
• Relative abundance
6.9 %
• hydrophobic, unreactive,
stiff,
-substitution
-sheet former
Chemical Structure of Leu
• Leucine
Leu
L
Leucine
• Relative abundance
7.5 %
• hydrophobic,
unreactive,
a-helix, -sheet former
Chemical Structure of Ile
• Isoleucine
Ile
I
Isoleucine
• Relative abundance
4.6%
• hydrophobic,
unreactive, stiff,
-substitution
-sheet former
Chemical Structure of Met
• Methionene
Met
M
Methionine
• Relative abundance
1.7 %
• thio-ether,
un-branched nonpolar,
ligand for Cu2+ binding
a-helix former
Chemical Structure of Cys
• Cysteine
Cys
C
Cysteine
• pKa = 8.33
• Relative abundance
2.8 %
• thiol, disulfide cross-links,
nucleophile in proteases
ligand for Zn2+ binding
-sheet, -turn former
Disulfide
Bonds
• Disulfide bonds form between
side chains of two cysteine
residues.
• Two SH groups from cysteine
residues, which may be in
different parts of the AA
sequence but adjacent in the 3D
structure, can be oxidized to
form one S-S (disulfide) group.
• Usually occurs in extracellular
proteins.
2 -CH2SH + 1/2 O2  -CH2-S-S-CH2 + H2O
Chemical Structure of Pro
• Proline
Pro
P
Proline
• Relative abundance
4.6 %
• 2° amine, stiff,
20 % cis, slow isomerization
seen in turns
• Initiation of a-helix
Chemical Structure of Phe
• Phenylalanine
Phe
F
Fenylalanine
• Relative abundance
3.5 %
• hydrophobic,
unreactive, polarizable
absorbance at 257 nm
Chemical Structure of Trp
• Tryptophan
Trp
W
tWo rings
• Relative abundance
1.1 %
• largest hydrophobic,
absorbance at 280 nm
fluorescent ~340 nm,
exhibits charge transfer
Chemical Structure of Tyr
• Tyrosine
Tyr
Y
tYrosine
• pKa = 10.13
• Relative abundance
3.5 %
• aromatic,
absorbance at 280 nm
fluorescent at 303 nm
• can be phosphorylated
hydroxyl can be nitrated,
iodinated, & acetylated
Chemical Structure of Ser
• Serine
Ser
S
Serine
• Relative abundance
7.1 %
• hydroxyl, polar, Hbonding ability
• nucleophile in serine
proteases
phosphorylation and
glycosylation
The Catalytic Triad of Trypsin
Chemical Structure of Thr
• Threonine
Thr
T
Threonine
• Relative abundance
6.0 %
• hydroxyl, polar, Hbonding ability,
stiff,
-substitution
phosphorylation and
glycosylation
Chemical Structure of Asp
• Aspartic Acid
Asp
D
AsparDic
• pKa = 3.90
• Relative abundance
5.5 %
• carboxylic acid,
in active sites for
cleavage of C-O bonds,
member of catalytic triad in
serine proteases, acts in
general acid/base catalysis,
ligand for Ca2+ binding
Calcium-binding Site in Calmodulin
Chemical Structure of Glu
• carboxylic acid,
• Glutamic Acid
2+ binding,
ligand
for
Ca
Glu
acts as a general acid/base
E
in catalysis for lysozyme,
proteinase
GluEtamic
• pKa = 4.07
• Relative abundance 6.2
%
Chemical Structure of Asn
• Asparagine
Asn
N
AsparagiNe
• Relative abundance
4.4 %
• Polar,
acts as both H-bond
donor and acceptor
molecular recognition site
can be hydrolyzed to Asp
Chemical Structure of Gln
• Glutamine
Gln
Q
Qutamine
• Relative abundance
3.9%
• Polar, acts as both H-bond
donor and acceptor
• molecular recognition site can
be hydrolyzed to Asp
N-terminal Gln can be
cyclized
Chemical Structure of Lys
• Lysine
Lys
K
Before L
• pKa = 10.79
• Relative abundance
7.0 %
• amine base, floppy,
charge interacts with
phosphate DNA/RNA
forms schiff base with
aldehydes (-N-N=CH-)
• a catalytic residue in some
enzymes
Chemical Structure of Arg
• Arginine
Arg
R
aRginine
• pKa = 12.48
• Relative abundance
4.7 %
• Guanidine group,
good charge coupled with acid
charge interacts with phosphate
DNA/RNA
a catalytic residue in some enzymes
Guanidine group
Chemical Structure of His
• imidazole acid or base;
• Histidine
pKa = pH (physiological),
His
member of catalytic triad in
H
serine proteases
Histidine
ligand for Zn2+ and Fe3+ binding
• pKa = 6.04
• Relative abundance
2.1 %
Distribution of Amino Acids
• Codons (3 RNA bases in sequence) determine each amino acid
that will build the protein expressed
Properties of the Peptide Bond
• Each peptide unit contains the Ca atom and the C'=O group of the
residue n as well as the NH group and the Ca atom of the residue n + 1.
• Each such unit is a planar, rigid group with known bond distances and
bond angles. R1, R2, and R3 are the side chains attached to the Ca atoms
that link the peptide units in the polypeptide chain.
• The peptide group is planar because the additional electron pair of the
C=O bond is delocalized over the peptide group such that rotation around
the C-N bond is prevented by an energy barrier.
Resonance Tautomers of a Peptide
Peptide Bond
• The peptide bonds are planer in proteins
and almost always trans.
• Trans isomers of the peptide bond are 4
kcal/mol more stable than cis isomers =>
• 0.1 % cis.
Polypeptide Chain
• Each peptide unit has two
degrees of freedom; it can rotate
around two bonds, its Ca-C'
bond and its N-Ca bond.
• The angle of rotation around the
N-Ca bond is called phi (f) and
that around the Ca-C' bond is
called psi (y).
• The conformation of the mainchain atoms is determined by
the values of these two angles
for each amino acid.
Torsion Angles Phi and Psi
Ramachandran
• Ramachandran plots indicate allowed
combinations of the conformational
Plots angles phi and psi.
• Since phi (f) and psi (y) refer to
rotations of two rigid peptide
units around the same Ca atom, most
combinations produce steric
collisions either between atoms in
different peptide groups or
between a peptide unit and the side
chain attached to Ca. These
combinations are therefore not allowed.
• Colored areas show sterically allowed
regions. The areas labeled a, , and L
correspond approximately to
conformational angles found for the
usual right-handed a helices,  strands,
and left-handed a helices,respectively.
Calculated Ramachandran Plots for Amino Acids
Gly with only one H
atom as a sidechain,
can adopt a much
wider range of
conformations than
the other residues.
• (Left) Observed values for all residue types except glycine.
Each point represents f and y values for an amino acid residue
in a well-refined x-ray structure to high resolution.
• (Right) Observed values for glycine. Notice that the values
include combinations of f and y that are not allowed for other
amino acids. (From J. Richardson, Adv. Prot. Chem. 34: 174175,1981.)
Certain Side-chain Conformations are
Energetically Favorable
3 conformations
of Val
• The staggered conformations are the most energetically favored
conformations of two tetrahedrally coordinated carbon atoms.
Side Chain Conformation
• The side chain
atoms of amino
acids are named
using the Greek
alphabet according
to this scheme.
Side Chain Torsion Angles
• The side chain torsion angles are named
chi1, chi2, chi3, etc., as shown below for
lysine.
Chi1(χ1) Angles
• The chi1 angle is subject to
certain restrictions, which arise
from steric hindrance between
the gamma side chain atom(s)
and the main chain.
• The different conformations of
the side chain as a function of
chi1 are referred to as
gauche(+), trans and gauche(-).
These are indicated in the
diagrams here, in which the
amino acid is viewed along the
C-Ca bond.
The most abundant conformation is gauche(+), in which the gamma side
chain atom is opposite to the residue's main chain carbonyl group when
viewed along the C-Ca bond.
Gauche
The second most
abundant conformation
is trans, in which the
side chain gamma atom
is opposite the main
chain nitrogen.
The least abundant conformation is gauche(-), which occurs when the
side chain is opposite the hydrogen substituent on the Ca atom. This
conformation is unstable because the gamma atom is in close contact with
the main chain CO and NH groups. The gauche(-) conformation is
occasionally adopted by Ser or Thr residues in a helices.
Chi2 (2)
• In general, side chains tend to adopt the same
three torsion angles (+/- 60 and 180 degrees)
about chi2 since these correspond to staggered
conformations.
• However, for residues with an sp2 hybridized
gamma atom such as Phe, Tyr, etc., chi2 rarely
equals 180 degrees because this would involve an
eclipsed conformation. For these side chains the
chi2 angle is usually close to +/- 90 degrees as
this minimizes close contacts.
• For residues such as Asp and Asn the chi2 angles
are strongly influenced by the hydrogen bonding
capacity of the side chain and its environment.
Consequently, these residues adopt a wide range
of chi2 angles.