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, (-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 AcidsAmino 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, 7th Edition, 2011; Berg JM, Tymoczko JL, Stryer L, Biochemistry, 5th Edition, 2002
Formation of PolypeptidesFormation of Polypeptides• Polypeptides and proteins are created through formation of
peptide bonds between amino acids– Condensation reaction
Polypeptide
Peptide linkages
O-
O
R
CCH
R
O
NHCNH3
+ CH
R
O
CNHCH
http://en.wikipedia.org/wiki/File:AminoacidCondensation.svg
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 C 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 Catom.
The “Handedness" of Amino Acids.
• Looking down the H-Cbond from the hydrogen atom, the L-form has CO, R, and N substituents from C 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 AcidsAmino 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,
-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,
-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
-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 -helix
Chemical Structure of Phe
• Phenylalanine Phe F Fenylalanine• Relative abundance
3.5 %
• hydrophobic, unreactive, polarizableabsorbance 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, H-bonding 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, H-bonding 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 forcleavage 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• Glutamic Acid
Glu
E
GluEtamic• pKa = 4.07• Relative abundance 6.2
%
• carboxylic acid,
ligand for Ca2+ binding, acts as a general acid/base in catalysis for lysozyme, proteinase
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/RNAforms schiff base with aldehydes (-N-N=CH-)
• a catalytic residue in some enzymes
Chemical Structure of Arg• Arginine
ArgR
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• 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
Distribution of Amino AcidsDistribution 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 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 Catoms 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 C-C' bond and its N-C bond.
• The angle of rotation around the N-C bond is called phi () and that around the C-C' bond is called psi ().
• The conformation of the main-chain atoms is determined by the values of these two angles for each amino acid.
Torsion Angles Phi and Psi
Ramachandran Plots
• Ramachandran plots indicate allowedcombinations of the conformational angles phi and psi.
• Since phi () and psi () refer to rotations of two rigid peptideunits around the same C atom, mostcombinations produce stericcollisions either between atoms in different peptide groups orbetween a peptide unit and the side chain attached to C. Thesecombinations are therefore not allowed.
• Colored areas show sterically allowed regions. The areas labeled andLcorrespond approximately to conformational angles found for theusual right-handed helices, strands, and left-handed helices,respectively.
Calculated Ramachandran Plots for Amino Acids
• (Left) Observed values for all residue types except glycine. Each point represents and 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 that are not allowed for other amino acids. (From J. Richardson, Adv. Prot. Chem. 34: 174-175,1981.)
Gly with only one H atom as a sidechain, can adopt a much wider range of conformations thanthe other residues.
Certain Side-chain Conformations are Energetically Favorable
• The staggered conformations are the most energetically favored conformations of two tetrahedrally coordinated carbon atoms.
3 conformations of Val
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-C 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-C 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 C 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 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.