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The Peptide
Bond Joins
Two Amino
Acid
Residues
Basic Biophysical Chemistry
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Electrostatic Interactions
Van der Waals Interactions
Hydrogen-bonded Interactions
Hydrophobic Interactions
Gab = H - T S
Gab = - RT ln Kab
Dihedral Angles in Polypeptides
Ramachandran
Plot of Polypeptide
Conformation
n = # residues / turn
Ac-L-Ala-NHMe
Ac-Gly-NHMe
Alpha helix
The Right-Handed
Alpha Helix
(3.613 Helix)
3.6 residues / turn
5.4 Ang / turn
13 atoms / Hbond loop
Righthanded
alpha
helix
Alpha Helix
3.6 residues / turn
13 atoms / H-bonded loop
Helix Dipole
Helical Wheels
Amphipathic
Helices - every 3-4
residues is
hydrophobic
Four Helical Bundle
With Antiparallel Helices
Amphipathic
Helices forming a
Hydrophobic Core
Beta-Sheets
Top - antiparallel
Bottom - parallel
Ramachandran
Plot of Polypeptide
Conformation
n = # residues / turn
Beta-Turns
(tight turns)
Beta-Turns
(tight turns)
Principal
Classes of
Proteins
- Globular
- Membrane
- Fiberous
Representations of
Protein Stuctures
a - full atom
b,c - strands /
helices
d - Topology
diagrams
Storing Protein Structure
Information
Cartesian Coordinates
Dihedral Angles
- x,y,z coordinate for each
atom
- 3 per atom / 30 - 100 per
residue
- assumes fixed bond
lengths and fixed bond
anges
- 3 - 8 per residue
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
1
49.88
2
50.35
3
50.04
4
49.13
5
46.62
6
41.99
7
43.24
8
53.00
9
57.79
10
62.94
C
O
CH3
N
CA
C
O
CB
OG
N
ACE
0
1GKY 67
ACE
0
1GKY 68
ACE
0
1GKY 69
SER
1
1GKY 70
SER
1
1GKY 71
SER
1
1GKY 72
SER
1
1GKY 73
SER
1
1GKY 74
SER
1
1GKY 75
ARG
2
1GKY1515
9.401
30.166
60.595
1.00
10.432
30.832
60.722
1.00
8.876
29.767
59.226
1.00
8.753
29.755
61.685
1.00
9.242
30.200
62.974
1.00
10.453
29.500
63.579
1.00
10.593
29.607
64.814
1.00
8.052
30.189
63.974
1.00
7.294
31.409
63.930
1.00
11.360
28.819
62.827
1.00
Principal Protein Fold Classes
All alpha
alpha + beta
All beta
alpha / beta
Classification
of Protein
Folds
- SCOP
- CATH
- DALI / FSSP
Protein Domains
“Independent Folding Units”
50 - 350 residues
Mean size - 125 residues
Alpha folds; Beta Folds;
Alpha+Beta Folds; Alpha/Beta Folds
Cadherins
Cadherin Proteins in Caenorhabditis elegans
CDH-4
Cadherin Proteins in Drosophila melanogaster
233
3 2 2 3 1 2 3 1 3 2 0 0 3 1 2 3 0 3 1 2 3 3 1 3 3 1 3 3 3 3 2
S
CDH-3
3 3 2 1 2 1 3
1 3
3 3 3 0 3 3 3
95
S
CDH-12
2
S
3
0 3 1 0 1 0 3 1 3 3 1
3 0 0 3
HMR-1a
3 2
120
1 1 0 3 0 3 3 2 3 0 3 3 3 3 3 3 3 2
120
S
HMR-1b
S
CDH-1
124
3 3 0 3 0 3 0 3 3 3 0 1 0 2 0 1 3 0 3 3 1 3 0 2
207
S
CDH-6
143
3 3 3 3 2 3 3
S
CDH-10
S
0
3
3 3 3
CDH-8
3
2 2 1 3 3 0 1 3 1 1 3 2
S
CDH-5
3 3 3
3 2 3
56
64
156
S
CDH-7
S
1 1 1 2 2 3 3
CDH-11
S
76
4307
CG7749
3017
1223
2920
2775
CDH-9
S
3 3 0 0
Stan
S
CadN
3 3 2 3 3 3 3 2 3 3 3
613
3 3 3 3 3 3 1 3 3 3 3 3 3 3 1 3 3 3 1 3 3 3 1 3 3 2
437
1 3 2 3 0 3 3 3 3 1 3 3 3 3 3 3 3 3
CG14900
1671
CG15511/CG7805
1507
CG6445
3 3 3 3
S
S
332
3 3 3 3 3 3 3 3 3 3 2 3 3 3
132
3
3 3
3 1 3 2 3 3 3 1 3
S
S
3 3 3 3 3 3 3 1 3 3 2 3 3
2? 3 3 3 3 3 3
Shg
984
3191
3 3 3 3 2 3
3
CG7527
1156
Y37E11A.94.a
158
S
CG4655/CG4509
623
320
S
Ds
2302
T01D3.1
S
3 2 1 3 3 1 3 3 3 3 3 1 3 3 3 3 3 3 2 1 3 2 1 3 2 3 3 3 3 3 3 3 1
S
CG3389
2610
82
538
3 3 3 3 3 3 0 3 3 3 2 3 3 3 1 3 3 3 3 3 3 3 3 2 3 3 3 1 1 3 3 3 3
S
3343
113
2
Fat
S
CG6977
968
286
43
227
3 0 3 3 3 3 3
158
3 2 3 3 3 3 2 3 3 3 3 ?
4643
3666
3503
3097
2204
2005
1963
1821
1820
1783
1507
1346
518
Ret
1120
411 CG11059
S
80
3
978
503
CG10244/HD-14
838
S
CG10421
S
5147
2? 3 3 3
Signal peptide
T ransmembrane Helix
Classic cytoplasmic domain
Cadherin
7 Pass T ransmembrane Domain
T yrosine Kinase cytoplasmic domain
EGF
HormR
T ype 1 Cytoplasmic domain
EGF_CA
GPS
T ype 2 Cytoplasmic domain
Laminin G
Merge Position
Other Cytoplasmic domain
189
678
courtesy of C. Chothia
Most proteins in biology have been
produced by the duplication,
divergence and recombination of
the members of a small number of
protein domain families.
courtesy of C. Chothia
Domain Combinations in Genome Sequences
In bacteria close to
1/3 of proteins consist of one domain and
2/3 consist of two or more domains.
In eukaryotes close to
1/4 of proteins consist of one domain and
3/4 consist of two or more domains.
courtesy of C. Chothia