RMSD from Ideal Protein Geometry - University of Delaware...1 RMSD from Ideal Protein Geometry RMSD...
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1 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 Peptide Plane Reduces the Number of Parameters Tortion angles PHI PSI Tortion kinemage: C1basics.kin
Transcript of RMSD from Ideal Protein Geometry - University of Delaware...1 RMSD from Ideal Protein Geometry RMSD...
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RMSD from Ideal Protein GeometryRMSD from ideal geometryfor htADH structure
bonds (Å) 0.007
angles (°) 1.30
dihedrals (°) 23.60
impropers (°) 0.85
Peptide Plane Reduces the Number of Parameters
Tortion angles
PHI
PSI
Tortion kinemage:C1basics.kin
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Ramachandran Plot to Evaluate Outliers of “Good Protein Geometry”
Ramachandran plotfrom htADH
core (%) 91.3 %
allowed (%) 8.2 %
generously allowed 0.4 %
disallowed none
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 Sequence1 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
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Molecular Dynamic Simulation ofa 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
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Helical Wheel – for alpha helix
http://www.umass.edu/molvis/tutorials/hemoglobin/hbsstruc.htm
amphipathic-helix
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NN
N
O
H O
H OH
O
NN-term
H
NN
NN
O
HO
HO
H
H
C-term
O
R R
R R
R R
RR
Anti-parallel -sheet
Protein Folding
Richard Dawkins analogy (pg. 56 text) “Methinks it is like a weasel.”
Nucleation (2º struct.) vs. hydrophobic collapse (molten globule)
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Build model
and refine
Purified Protein
Solve Phase
Macromolecular Protein Crystallography
Diffraction
Light Microscope 400-700 nm- uses lense to focus diffracted light -into an imageX-ray crystallography uses X-rays of 0.154 nm (1.54 Å); no x-ray lense available. First structure solved 1959 by John Kendrew and Max Perutz of myoglobin and hemoglobin
Need to know wavelength, for Cu sources its 1.54 Å
Need to measure Amplitude of Diffracted Reflections- Intensity is proportional to A2
Need to estimate the relative phase
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Proteins can form an ordered lattice
Growing Protein Crystals:by Vapor Diffusion
• Hanging drop method– Widely used
• Fast• Simple• Inexpensive Test for growth in a
variety of conditionsA1 A2 A3 A4 A5 A6B1 B2 B3 B4 B5 B6C1 C2 C3 C4 C5 C6D1 D2 D3 D4 D5 D6
[X]
[Y]Sitting drop
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Overview of X-ray Experiment
Protein crystal in a loop
X-ray Equipment in CBC at Delaware
RU-H3RX-ray generator
Area Detector
Crystal mounted on a loop here
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Zoom into a single reflection
Movie of a Data Collection
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Active Site and Complete Model of IDH
2Fo – Fc map
What does electron density look like at different limits of resolution?
