Chapter 1Structure I

1
Chapter 1/Structure I

• The Building Blocks
• Chemical Properties of Polypeptide Chains

2
Level of Protein Structure

• The amino acid sequence of a protein's
  polypeptide chain is called its primary
  structure. Different regions of the sequence form
  local regular secondary structures, such as alpha
  (a) helices or beta (?) strands. The tertiary
  structure is formed by packing such 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 such
  tertiary and quaternary structures, amino acids
  far apart in the sequence are brought close
  together in three dimensions to form a functional
  region, called an active site.

3
Amino Acids

• Proteins are built up by amino acids that are
  linked by peptide bonds to form a polypeptide
  chain.
• An amino acid has several structural components
• A central carbon atom (Ca) is attached to
• an amino group (NH2),
• a carboxyl group (COOH),
• a hydrogen atom (H),
• a side chain (R).

4
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 main-chain 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.

5
The Handedness" of Amino Acids.

• Looking down the H-Ca bond from the hydrogen
  atom, the L-form 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.

6
Hydrophobic Amino Acids
7
Charged Amino Acids
8
Polar Amino Acids
9
Chemical Structure of Gly

• Glycine
• Gly
• G
• Glycine
• Relative abundance 7.5

• flexible, seen in turns

10
Chemical Structure of Ala

• Alanine
• Ala
• A
• Alanine
• Relative abundance 9.0

• hydrophobic, unreactive,
• a-helix former

11
Chemical Structure of Val

• hydrophobic, unreactive, stiff,
• b-substitution
• b-sheet former

• Valine
• Val
• V
• Valine
• Relative abundance
• 6.9

12
Chemical Structure of Leu

• Leucine
• Leu
• L
• Leucine
• Relative abundance
• 7.5

• hydrophobic, unreactive,
• a-helix, b-sheet former

13
Chemical Structure of Ile

• hydrophobic, unreactive, stiff,
• b-substitution
• b-sheet former

• Isoleucine
• Ile
• I
• Isoleucine
• Relative abundance
• 4.6

14
Chemical Structure of Met

• thio-ether,
• un-branched nonpolar,
• ligand for Cu2 binding
• a-helix former

• Methionene
• Met
• M
• Methionine
• Relative abundance 1.7

15
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
• b-sheet, b-turn former

16
Disulfide Bonds

• Disulfide bonds form between the side chains of
  two cysteine residues.
• Two SH groups from cysteine residues, which may
  be in different parts of the amino acid sequence
  but adjacent in the three-dimensional structure,
  are oxidized to form one S-S (disulfide) group.

2 -CH2SH 1/2 O2 ?? -CH2-S-S-CH2 H2O
17
Chemical Structure of Pro

• 2 amine, stiff,
• 20 cis, slow isomerization
• seen in turns
• Initiation of a-helix

• Proline
• Pro
• P
• Proline
• Relative abundance 4.6

18
Chemical Structure of Phe

• hydrophobic, unreactive, polarizable
• absorbance at 257 nm

• Phenylalanine
• Phe
• F
• Fenylalanine
• Relative abundance 3.5

19
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

20
Chemical Structure of Tyr

• aromatic,
• absorbance at 280 nm
• fluorescent at 303 nm
• can be phosphorylated hydroxyl can be nitrated,
  iodinated, acetylated

• Tyrosine
• Tyr
• Y
• tYrosine
• pKa 10.13
• Relative abundance 3.5

21
Chemical Structure of Ser

• Serine
• Ser
• S
• Serine
• Relative abundance 7.1

• hydroxyl, polar, H-bonding ability
• nucleophile in serine proteases
• phosphorylation and glycosylation

22
The Catalytic Triad of Trypsin
23
Chemical Structure of Thr

• Threonine
• Thr
• T
• Threonine
• Relative abundance 6.0

• hydroxyl, polar, H-bonding ability,
• stiff,
• b-substitution
• phosphorylation and glycosylation

24
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

25
Calcium-binding Site in Calmodulin
26
Chemical Structure of Glu

• Glutamic Acid
• Glu
• E
• GluEtamic
• pKa 4.07
• Relative abundance 6.2

• carboxylic acid,
• ligand for Ca2 bindingas acts as a general
  acid/base in catalysis for lysozyme, proteinase

27
Chemical Structure of Asn

• Polar,
• acts as both H-bond donor and acceptor
• molecular recognition site can be hydrolyzed to
  Asp

• Asparagine
• Asn
• N
• AsparagiNe
• Relative abundance 4.4

28
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

29
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-NCH-)
• a catalytic residue in some enzymes

30
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

31
Chemical Structure of His

• Histidine
• His
• H
• Histidine
• pKa 6.04
• Relative abundance 2.1

• imidazole acid or base
• pKa pH (physiological),
• member of catalytic triad in serine proteases
• ligand for Zn2 and Fe3 binding

32
Properties of the Peptide Bond

• Each peptide unit contains the C? atom and the
  C'O group of the residue n as well as the NH
  group and the C? 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 CO bond is
  delocalized over the peptide group such that
  rotation around the C-N bond is prevented by an
  energy barrier.

33
Resonance Tautomers of a Peptide
34
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 gt
• 0.1 cis.

35
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 main-chain atoms is
  determined by the values of these two angles for
  each amino acid.

36
Torsion Angles Phi and Psi
37
Ramachandran Plots

• Ramachandran plots indicate allowed
• combinations of the conformational
• 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, b, and L
• correspond approximately to
• conformational angles found for the
• usual right-handed a helices, b strands,
• and left-handed a helices,respectively.

38
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 ? and y that
  are not allowed for other amino acids. (From J.
  Richardson, Adv. Prot. Chem. 34 174-175,1981.)

39
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.

40
Side Chain Conformation

• The side chain atoms of amino acids are named
  using the Greek alphabet according to this
  scheme.

41
Side Chain Torsion Angles

• The side chain torsion angles are named chi1,
  chi2, chi3, etc., as shown below for lysine.

42
Chi1(?1) 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 Cb-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 Cb-Ca bond.
43
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.
44
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.

45
Many Proteins Contain Intrinsic Metal Atoms

• (a) The di-iron center of the enzyme
  ribonucleotide reductase. Two iron atoms form a
  redox center that produces a free radical in a
  nearby tyrosine side chain. The coordination of
  the iron atoms is completed by histidine,
  aspartic acid, and glutamic acid side chains as
  well as water molecules.
• (b) The catalytically active zinc atom in the
  enzyme alcohol dehydrogenase. The zinc atom is
  coordinated to the protein by one histidine and
  two cysteine side chains.

46
EF-hand Calcium-binding Motif

• The calcium atom is bound to one of the motifs in
  the muscle protein troponin-C through six oxygen
  atoms one each from the side chains of Asp (D)
  9, Asn (N) 11, and Asp (D) 13 one from the main
  chain of residue 15 and two from the side chain
  of Glu (E) 20. In addition, a water molecule (W)
  is bound to the calcium atom.