Proteins are made by linking amino acids Protein Structure Review and Refinement Introduction Brian...
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Proteins are made by linking amino acids Protein Structure Review and Refinement Introduction Brian Bahnson Dept of Chemistry & Biochemistry, University of Delaware
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Transcript of Proteins are made by linking amino acids Protein Structure Review and Refinement Introduction Brian...
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
