Post on 21-Dec-2015
Proteins are made by linking amino acids
Protein Structure Review and Refinement Introduction
Brian BahnsonDept of Chemistry & Biochemistry, University of Delaware
Several Ways to Visualize Amino Acids
20 common amino acids
NC N
C NC N
C NC N
C NC N
C
H O
H O
H O
H O
H O
H O
H O
HO R R R R
R R R R
N
C NC N
C NC
O
H O
H O
H
OH
C
O
N
N-term
H
NCN
CNCN
C
O
HO
HO
H
HC
O
N
C-term
O
R
R R
R R
R R
RR
R
H
N
C NC N
C
O
H O
H OH
C
O
N
N-term
H
R R
R R
NC C-term
OH
R
N
C NC N
C
O
H O
H OH
C
O
N
N-term
H
R R
R R
NC C-term
OH
R
-helix
anti-parallel -sheet
parallel -sheet
double headed arrows indicate hydrogen bonds
Primary Sequence Secondary Structure
Secondary Structure Tertiary Structure
Tertiary Structure Quaternary Structure
Alcohol dehydrogenase is a homotetramer
The Peptide Plane
Peptide Plane Reduces the Number of Parameters
Tortion angles
PHI
PSI
Ramachandran Plot to Evaluate Outliers of “Good Protein Geometry”
Ramachandran plotfrom htADH
core (%) 91.3 %
allowed (%) 8.2 %
generously allowed 0.4 %
disallowed none
Macromolecular Protein Crystallography
Experimental Data Points vs. Refined Parameters
X-ray Diffraction ReflectionsExperimental Data Points Electron Density Map and
Refined Model of Enzyme
RMSD from Ideal Protein Geometry
RMSD from ideal geometry
for htADH structure
bonds (Å) 0.007
angles (°) 1.30
dihedrals (°) 23.60
impropers (°) 0.85
Least Squares Refinement Summed Over all Atoms and Data Points
From Crystallography Made Crystal Clear
Molecular Dynamic Simulation of a designed mini-protein (Trp-cage)
From the Duan labhttp://www.duanlab.ucdavis.edu/
The movie shown2 slides ahead is 69.5 MBand can be downloaded here
H3NN
NN
NN
NN
NN
NN
NN
NN N
NN N
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
O
OH
H
H
H
H
H
H
H
H
H H
H
H
H
H
H
H
HH H
H
O
H2N
HO
O
NH2
NH
N1
L2
Y3
I4
Q5
W6
L7
+H3N
O-O
OH
OH
K8
D9
G10
G11
P12
S13
S14
Trp Cage Peptide Sequence
1 5 10 15 20N L Y I Q W L K D G G P S S G R P P P S
HN
+H2NNH2
OH
S20
G15
R16
P17
P18
P19
Hydrogen Bonding Connection
L2:O W6:HY3:O L7:HI4:O K8:H
G10:O S13:HG11:O S14:H
W6:HE1 R16:O
L7:O G10:HW6:O G11:H