Download Protein Architecture: Four Levels

Protein Architecture: Four Levels
Monday, January 28, 13
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DNA à Proteins
?
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Tailspike Protein: change one amino acid – obtain a different structure
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Sequence comparison: hemoglobin alpha chain vs beta chain
window size: 31
match: +5
dismatch: -4
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Sequence comparison: hemoglobin alpha chain vs beta chain
window size: 31
match: +5
dismatch: -4
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Phylogenetic Trees
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log frequencies of amino acids in seconday structure elements
A.A.
A
R
N
D
C
Q
E
G
H
I
L
K
M
F
P
S
T
W
Y
V
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P<a>
1.42
0.98
0.67
1.01
0.70
1.11
1.51
0.57
1.00
1.08
1.21
1.16
1.45
1.13
0.57
0.77
0.83
1.08
0.69
1.06
P<b>
0.83
0.93
0.89
0.54
1.19
1.10
0.37
0.75
0.87
1.60
1.30
0.74
1.05
1.38
0.55
0.75
1.19
1.37
1.47
1.70
P<t>
0.66
0.95
1.56
1.46
1.19
0.98
0.74
1.56
0.95
0.47
0.59
1.01
0.60
0.60
1.52
1.43
0.96
0.96
1.14
0.50
Hp
1.80
-4.50
-3.50
-3.50
2.50
-3.50
-3.50
-0.40
-3.20
4.50
3.80
-3.90
1.90
2.80
-1.60
-0.80
-0.70
-0.90
-1.30
4.20
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Protein structures in the Protein Data Bank
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Protein folding motifs
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Peptide bond geometry; Ramachandran Plot
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non-polar
surface area
[A^2]
Trp
Leu
Ile
Phe
Met
Val
Pro
Lys
Tyr
His
Thr
Arg
Ala
Glu
Gln
Ser
Cys
Gly
Asp
Asn
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236
164
155
194
137
135
124
122
154
129
90
89
86
69
66
56
48
47
45
42
estimated
hydrophobic effect
[kcal/mol]
4.11
4.10
3.88
3.46
3.43
3.38
3.10
3.05
2.81
2.45
2.25
2.23
2.15
1.73
1.65
1.40
1.20
1.18
1.13
1.05
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Overview: Computational Biophysics: Concepts & Methods
L08/P08: Quantum mechanics methods: basic concepts
L09/P09: Hartree-Fock, density functional theory
L10/P10: Free energy calculations, force probe simulations
L11/P11: Rate theory
L12/P12: Non-equilibrium thermodynamics
L13/P13: Electrostatics in proteins
L14/P14: Enzymatic catalysis: molecular details
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