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Mentor:
Dr. P. Andrew Karplus (Department Of Biochemistry & Biophysics, OSU)
In Collaboration With:
Dr. Weng-Keen Wong (Department Of Computer Science, OSU)
Dr. Donald Berkholz (Department of Biochemistry and Molecular Biology, M
Dr. Dale Tronrud (Department of Biochemistry & Biophysics, OSU)
Understand
structure,
understand function
Ptr Tox A
conformation of the
planar peptide (amino
acid) in regards to other
peptides
One amino acid two
angles
Ramachandran Plot
Voet, Voet & Pratt Biochemistry
(Upcoming 4th Edition)
310 Helix
-Helix
Form
Can
of artificial intelligence
Visual
example
Mt. Hood
(11,239 Feet)
Mt. Jefferson
(10,497 Feet)
Three Sisters
(10,358-10,047 Feet)
LU
LO
AS
TS
OCHOCO
S T RAW B E R R I E S
PAU LI NA
MTS
J AC K AS S
MTS
NS
MAH O GANY
MTS
HAR T MTN
ST
SISKIYOUS
( K ALAM AT H )
AL
EE
C A S C
A D E S
T U ALAT I N
HILLS
C OAS T
R AN G
TROUT CREEK
MTS
helix
PI
Complications
Our
4D to 2D distance conversions
What
No definitive source
Abundance / Peak Heights
Machine
2) Run cuevas
to remove bias
Everest Method
Locate highest peak
first
Bad pun : Mt. Alpha-rest
peak
Locate third.
Identifying motifs
Search for peaks while
Results:
Definitive list of common
Points Per
Circle r=10 Degree2
5644
247
173
147
125
117
88
55
51
43
40
36
35
34
31
31
30
29
24
20
20
20
19
17
15
14
11
10
9
9
8
8
7
6
6
6
18.07
0.7909
0.5540
0.4707
0.4003
0.3747
0.2818
0.1761
0.1633
0.1377
0.1281
0.1153
0.1121
0.1089
i
-63.4
-125.5
-69.9
-65.5
-70.4
-57.2
-88.3
-88.1
-91.8
93.5
-133.9
-82.4
54.9
-122.3
i
-42
132.4
157.4
-21.4
153.6
131
-2
1.3
-1.9
-0.1
164.3
-26.8
38.3
119.6
i+1
-64
-118
-61
-90.3
-60.4
82.4
-64.7
87.9
-58.4
-71.7
-62.2
-146.3
84.5
52.7
i+1
Residue
i
i+1
-40.6
130.2
-36.3
1.5
143
-0.6
136.9
5.7
-42.5
146
-34.1
152.1
0.8
41
PII
PII
PII
L
L
PII`
L
PII
L
`
PII`
PII`
0.0993
0.0993
-136.1
65.3
70.4
28.3
-65
-67.2
-19
140.8
0.0961
0.0929
0.0769
0.0640
0.0640
0.0640
0.0608
0.0544
0.0480
0.0448
82.6
56.7
78
-78.3
-96.6
50.5
-69.9
-129.1
53.7
-87.6
5.6
-133.5
0.5
116
0.9
49.9
-32.3
80.8
48
61
-103.1
-73.7
-67.5
-89.1
-133.8
-61.2
-129.8
-70.3
-118.9
-140.3
137.5
-10.7
-43.1
-31.1
156.3
148.3
73.1
141.9
126.6
149.5
0.0352
0.0320
0.0288
0.0288
0.0256
0.0256
0.0224
0.0192
0.0192
0.0192
76.3
78.8
-138.5
92.8
-107.6
84.6
-85.8
-102.4
-77.9
83.8
-169.3
171.1
165.7
165.9
16.8
8.1
71.8
-9
-8.6
-166.3
-61.4
-69.3
57.7
-62.5
80
-143
-83.1
92.6
86.7
-121.9
138.3
-29.6
-137.8
-35.7
-177
169.3
163.5
163.3
174.2
132.1
L
`
PII`
Cluster Size
Motif Name
PII
L
PII
L
PII
L
L
1
1
1
1
1
1
1
1
1
1
1
2
1
1
PII
PII
PII
1
1
-helix / 310-helix
-strand
PII- Helix N-Cap / Capping Box
Type I Turn#
PII
Type II Turn
Type I Turn Cap
Schellman Motif
Reverse Type I Turn
Reverse Type II Turn
Turn
Classic Beta Bulge
Type I` Turn
L
P
G1 Beta Bulge
L
Type II` Turn
L
Type VIa1 Turn (S)
Classic Beta Bulge (S)
Wide Beta Bulge (S)
PII
L (S)
` Turn
PII` PII
PII` (S)
PII`
(S)
PII`
PII
PII`
PII`
PII
1
3
1
1
1
1
2
1
1
1
2
1
2
1
1
1
3
4
1
1
New Motif
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Motif shapes
Each motif analyzed by
Results:
New insight into each
motifs structure
Context
Comparisons
Distributions show
differences between
the two structures
Nearly four years in
the making
The results go on
Motif analysis
Viral forming of Pangea
proteins