. Tel 018-4714177 ... ASN VAL ASP GLU VAL GLY GLY
GLU ALA. LEU GLY ... MET GLY ASN PRO LYS VAL LYS ALA HIS. GLY LYS ...
Basics of protein structure
BMSF 2009
[email protected] Tel 018-4714177, 070-5988391
Four structure levels
Why structure?
Why do we need to know structure to understand macromolecules?
Sickle cell anemia is caused by the E6V mutation in the hemoglobin β-chain VAL ALA ASN LEU TRP GLY MET GLY ASP LYS LEU PRO VAL PHE GLN GLY TYR
HIS VAL VAL GLY THR ASP GLY LYS GLY GLY HIS GLU LEU GLY ALA VAL HIS
LEU THR ASP ARG GLN LEU ASN LYS LEU THR CYS ASN VAL LYS ALA ALA
THR ALA GLU LEU ARG SER PRO VAL ALA PHE ASP PHE CYS GLU TYR ASN
PRO LEU VAL LEU PHE THR LYS LEU HIS ALA LYS ARG VAL PHE GLN ALA
GLU TRP GLY VAL PHE PRO VAL GLY LEU THR LEU LEU LEU THR LYS LEU
GLU GLY GLY VAL GLU ASP LYS ALA ASP LEU HIS LEU ALA PRO VAL ALA
LYS LYS GLU TYR SER ALA ALA PHE ASN SER VAL GLY HIS PRO VAL HIS
SER VAL ALA PRO PHE VAL HIS SER LEU GLU ASP ASN HIS VAL ALA LYS
The E6V mutation creates a hydrophobic patch on the molecule surface
Hemoglobin fibers in blood vessels
Today’s lecture • Amino acids • Primary & secondary structure, p 11-25 • Tomorrow: rest of chapter 2 • Wednesday: chapter 3 • Also check appendix A: “Bonds and energetics of macromolecules” • Chapter 3 contains parts beyond this course.
Proteins consist of L amino acids
pKa ≈8
pKa ≈3
Primary structure
Direction: N-terminus => C-terminus
The polypeptide chain
α-carbon R1 H H2N
Cα
C O
N-terminus
R3 H
O
H N
C-terminus
carbonyl group
side chain
Cα H
peptide bond
R2
C
N H
O
Cα
C O
amide nitrogen
OH
H2N
Cα H
C
R4
peptide bond formed by elimination of H2O
OH
The polypeptide conformation
Partial double-bond character
Allowed backbone torsion angles: seminar 1
Ramachandran diagram: sterically allowed torsion angles
Ramachandran diagram Ala
Gly
psi
phi
Side chain conformations • Ile and Thr have chiral Cβ.
• Preferred torsion angles in side chains (rotamers) based on staggered conformations, fig 2.6.
9 Aspartic acid rotamers
α-helix (3.613 helix) Right-handed 3.6 residues per turn 13 atoms in the ring formed by H-bond
Properties of the α helix • All side chains point in the same direction C-terminus
N-terminus
Other types of right-handed helices
310 helix H-bonding to N+3
πhelix (4.116) H-bonding to N+5 Table 2.3!!
Antiparallel β-sheet
Parallel β-sheet
Mixed β-sheet Parallel
Thioredoxin
Anti-parallel
Other types of secondary structure
β-bulges
Polyproline helices (collagen)
Turns (several kinds)
