,
,
Results clearly show that the structure isnt in equilibrium. Right after the simulation start there
is a large change in structure in less than 0.3ns. Another large change occurs after 0.75ns and
even after that the peptide doesnt keep its structure in equilibrium as can be seen in the RMSD
plot after 1ns. The RMSD keeps changing in the range of 7-10. In order to explain these
changes there is a need of further analysis.
Figure 9 Root Mean Square Deviation throughout molecular dynamics
4.3 Hydrogen Bonds Analysis
Analysis of the hydrogen bonds during the simulation gives an indications of a very large
involvement of hydrogen bonds in the changes during the simulation. The percentage of
hydrogen bonds from the initial number drops in average to less than 50%, though there are
peaks of ~80% in certain occurrences.
0
2
4
6
8
10
12
0.0 0.5 1.0 1.5 2.0 2.5 3.0
R
M
S
D
[
]
Time [ns]
RMSD vs. Time
9
Figure 10 Percentage of hydrogen bonds compared to t=0ns throughout molecular dynamics
As can be seen in Figure 11, at the beginning there is a noticeable occurrence: after a large
increase in RMSD, where hydrogen bonds break, there is some formation of hydrogen bonds
with a decrease in RMSD. It is important to realize that these arent the same hydrogen bonds,
as the bonds that break in the first half of the simulation are mostly ones related to salt bridges,
as will be shown in section 4.5. In the second half of the simulation this trend is less apparent,
meaning that something else is happening to stabilize the protein.
Figure 11 Correlation between RMSD and percentage of hydrogen bonds
It is important to mention that the number of hydrogen bonds refer to the absolute number but
doesnt take into account the identity of the bonds. In total, hydrogen analysis counts all the
hydrogen bonds during the molecular dynamics and it is revealed that there are 30 different
bonds when counting residues that interact using hydrogen bonds, while differentiating
between main and side-chain hydrogen bonds. There are hydrogen bonds related to salt bridges
that change during the molecular dynamics as will be discussed in the next section.
0
10
20
30
40
50
60
70
80
90
100
0.0 0.5 1.0 1.5 2.0 2.5 3.0
%
H
y
d
r
o
g
e
n
B
o
n
d
s
Time [ns]
%Hydrogen Bonds vs. Time
%Hydrogen bonds Moving average
0
2
4
6
8
10
12
0.0 0.5 1.0 1.5 2.0 2.5 3.0
0
10
20
30
40
50
60
70
80
90
100
R
M
S
D
[
]
Time [ns]
%
H
y
d
r
o
g
e
n
B
o
n
d
s
Correlation between RMSD and %Hydrogen Bonds
%Hydrogen bonds RMSD Moving average
10
4.4 Distances Between the Backbones of Residues
A change in distance between backbones of residues can indicate of a process that is happening
during molecular dynamics. Looking at the alpha carbons of residues 11-15 and their distance
to the alpha carbon of residue 3 shows an interesting trend. After approximately 2ns, there is a
sudden decrease in distance for all distances. A change as large as this indicates a change in
the surface of protein, and a surface analysis should reveal more, as is shown in section 4.7.
Figure 12 Distance of -Carbons throughout molecular dynamics
4.5 Salt Bridges
Another important factor determining protein structural stability is salt bridges. In this case, the
salt bridges are breaking apart throughout the molecular dynamics as depicted in Figure 13 Salt
Bridge Distances throughout molecular dynamicsFigure 13. This is possible as a result of a
stabilizing interactions of the charged side chains and bulk water. Although, breakage of salt
bridges isnt always favorable. This might indicate that salt bridge breakage allows for other
changes in the protein as a result of decrease in stress of the backbone. One important factor
that salt bridges are related to is the number of hydrogen bonds. In this case, the salt bridges
have a number of hydrogen bonds with which they can interact, shown in appendix 6.1.
Figure 13 Salt Bridge Distances throughout molecular dynamics
0
2
4
6
8
10
12
14
16
18
20
0.0 0.5 1.0 1.5 2.0 2.5 3.0
A
l
p
h
a
C
a
r
b
o
n
D
i
s
t
a
n
c
e
[
]
Time [ns]
Alpha Carbon Distances vs. Time
TYR3-ARG11 TYR3-ASP12 TYR3-CYS13
TYR3-VAL14 TYR3-MET15
0
2
4
6
8
10
12
14
0.0 0.5 1.0 1.5 2.0 2.5 3.0
D
i
s
t
a
n
c
e
[
]
Time [ns]
Salt Bridge Distances vs. Time
ASP12-LYS8
ASP12-ARG11
11
4.6 Ramachandran Plot
The Ramachandran plot is an indication of the secondary structure that an amino acid is part
of. Changes in the psi and phi angles that define the backbone structure will result in amino
acids changing their location on the Ramachandran plot. Analysis of the Ramachandran plot
reveals that most amino acids dont change very much. Residues that do change somewhat are
LEU18 and GLY19. LEU18 is mostly in a turn or an undefined secondary structure, but
sometimes is in a region of a beta sheet structure. GLY19 is able to change as much as it does
(at least in terms of the psi angle) as a consequence of its small side chain. This allows for
LEU18 some flexibility as well as both residues are neighbors.
Figure 14 Ramachandran plot of LEU18 (right) and GLY18 (left)
4.7 Solvent Accessible Surface Analysis
Analysis of the solvent accessible surface area (solvent ASA) can give an indication of what
changes in the core of the protein lead to the formation of surface phenomena which might be
of interest. As shown in Figure 15, the ASA varies to a large degree throughout the molecular
dynamics. as shown before, a little before 1ns the second salt bridge starts to break and thus
the ASA increases rapidly. As show both in Figure 16 and in Figure 17, polar ASA doesnt
vary a lot, while non-polar ASA changes in the same trend as the total ASA. This is explained
in that the decrease in contact between non-polar areas and water can happen only with certain
strains in the structure are relived through the breakage of salt bridges on the other side of the
protein, as can be indicated by Figure 18 that shows an increase in charged ASA, as well as
earlier discussed in sections 4.4 and 4.5.
12
Figure 15 Total accessible surface area throughout molecular dynamics
Figure 16 Polar\non-polar accessible surface area throughout molecular dynamics
Figure 17 Polar\non-polar side chains accessible surface area throughout molecular dynamics
2500
2550
2600
2650
2700
2750
2800
2850
2900
2950
3000
0.0 0.5 1.0 1.5 2.0 2.5 3.0
S
o
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v
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t
A
c
c
e
s
s
i
b
l
e
S
u
r
f
a
c
e
A
r
e
a
[
2
]
Time [ns]
Total ASA vs. Time
Total ASA Moving average
0
200
400
600
800
1000
1200
1400
1600
1350
1400
1450
1500
1550
1600
1650
1700
0.0 0.5 1.0 1.5 2.0 2.5 3.0
P
o
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a
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A
S
A
[
2
]
N
o
n
-
p
o
l
a
r
A
S
A
[
2
]
Time [ns]
Polar\non-polar ASA vs. Time
Non-polar ASA Polar ASA
0
100
200
300
400
500
600
700
800
900
1000
900
1000
1100
1200
1300
1400
1500
0.0 0.5 1.0 1.5 2.0 2.5 3.0
P
o
l
a
r
S
i
d
e
C
h
a
i
n
A
S
A
[
2
]
N
o
n
-
p
o
l
a
r
S
i
d
e
C
h
a
i
n
A
S
A
[
2
]
Time [ns]
Polar\non-polar side chains ASA vs. Time
Non-polar side chain ASA Polar side chain ASA
13
Figure 18 Charged accessible surface area throughout molecular dynamics
5 Conclusions
The changes occurring throughout the molecular dynamics show that there are many factors to
the structure of a protein. At the beginning, the salt bridges between ASP12 and ARG11, and
between ASP12 and LYS8 break, probably as a result of stabilizing interactions with water. As
this happens, the backbone of the protein is allowed to move more freely, allowing for the
formation of cavities and specifically the cavity involving residue 3 and 11-15. During this
process non-polar residues decrease their contact with water and turn into the core of the
protein, while charged residues increase their surface area with water. As a matter of summing
things up, all these changes allow for the increase in ASA even though it might increase the
potential energy, in order to allow for changes in the residues 11-15&3 area in order to create
a cavity which allows for non-polar surface areas to hide from water, and thus stabilizing the
protein structure. The total change is portrayed in Figure 19 that shows the structures of the
protein in selected timestaps.
0
50
100
150
200
250
300
0
20
40
60
80
100
120
140
0.0 0.5 1.0 1.5 2.0 2.5 3.0
P
o
s
i
t
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v
e
l
y
C
h
a
r
g
e
d
A
S
A
[
2
]
N
e
g
a
t
i
v
e
l
y
C
h
a
r
g
e
d
A
S
A
[
2
]
Time [ns]
Charged ASA vs. Time
Negatively charged
Positively charged
14
Figure 19 blue indicates side chains, green indicates backbone. the white indicates residues 1 and 11-15. Top: structure at
t=0.03ns; Bottom Right: structure at t=2.81ns; Bottom Left: structure at t=2.47ns. It is clrealy seen that these residues get
closer and form a cavity during the molecular dynamics.
15
6 Appendices
6.1 Hydrogen Bonds According To Donor-Acceptor Residues
Donor Acceptor Occupancy Atoms
CYS16-Main CYS13-Main 1.67% 232 198 233
CYS27-Main VAL5-Main 24.33% 379 80 380
CYS22-Main GLY19-Main 2.00% 305 274 306
LYS8-Main ASP12-Side 20.00% 105 186 106
LYS8-Side ASP12-Side 12.00%
121 185 122
121 185 123
121 186 122
121 186 123
ARG11-Side ASP12-Side 0.67% 169 185 170
GLY17-Main VAL14-Main 1.00% 242 214 243
SER21-Main ASP10-Side 32.00%
294 149 295
294 150 295
CYS30-Main CYS27-Main 4.67% 413 388 414
GLY19-Main ASP10-Side 2.33% 268 149 269
THR31-Main GLN28-Main 2.00% 423 405 424
TYR3-Main TYR26-Side 0.67% 30 371 31
CYS7-Main GLY25-Main 10.33% 95 357 96
ASP12-Main THR9-Main 2.33% 177 140 178
TYR26-Side THR31-Side 1.00% 371 429 372
GLY17-Main CYS13-Main 6.00% 242 198 243
CYS13-Main ASP10-Main 7.67% 189 152 190
LYS23-Side ASN24-Side 3.33%
331 345 332
331 345 333
331 345 334
THR31-Main CYS27-Main 0.33% 423 388 424
THR31-Side CYS27-Main 6.00% 429 388 430
VAL14-Main ARG11-Main 0.33% 199 176 200
THR9-Main ASP12-Side 3.33% 127 186 128
TYR26-Main LYS23-Main 1.67% 358 336 359
LYS23-Side GLN28-Side 0.33% 331 400 332
ASN6-Side GLY25-Main 11.67% 90 357 92
THR31-Side GLN28-Main 3.67% 429 405 430
THR31-Side TYR26-Side 2.00% 429 371 430
LYS23-Main GLY19-Main 1.00% 315 274 316
GLN28-Main TYR26-Main 0.67% 389 378 390
SER21-Side ASP10-Side 0.67% 301 150 302
16
6.2 Script used to run multiple runs of Surface Racer
As the program input allow only for single frames input, there is a need to divide multiple-
frame PDBs (or PSF with DCD trajectories) into multiple files each holding a single frame.
Dividing the multiple frame file into separate files was done using the splitmultiframepdb.tcl
script from the VMD project website. In order to automate the process of the analysis using
Surface Racer, the following Batch script was used:
7 References
[1] Xiang Chen et al., "Solution structure of BmP08, a novel short-chain scorpion toxin from
Buthus martensi Karsch," Biochemical and Biophysical Research Communications, vol.
330, no. 4, pp. 1116-1126, 2005.
[2] Yifat Miller, Buyong Ma, and Ruth Nussinov, "Polymorphism in Alzheimer Abeta
amyloid organization reflects conformational selection in a rugged energy landscape,"
Chemical Reviews, vol. 110, no. 8, pp. 4820-4838, 2010.
[3] Yoav Raz and Yifat Miller, "Interactions between A and Mutated Tau Lead to
Polymorphism and Induce Aggregation of A-Mutated Tau Oligomeric Complexes,"
PLoS One, vol. 8, no. 8, p. e73303, 2013.
[4] Yoav Raz et al., "Effects of mutations in de novo designed synthetic amphiphilic -sheet
peptides on self-assembly of fibrils," Chemical Communications, vol. 49, pp. 6561-6563,
2013.
[5] Laxmikant Kal et al., "NAMD2: Greater Scalability for Parallel Molecular Dynamics,"
Journal of Computational Physics, vol. 151, no. 1, pp. 283-312, 1999.
[6] Brooks BR et al., "CHARMM: The Biomolecular Simulation Program," Journal of
Computational Chemistry, vol. 30, no. 10, pp. 1545-1615, 2009.
[7] A. D., Jr. MacKerell et al., "All - Atom Empirical Potential for Molecular Modeling and
Dynamics Studies of Proteins," Journal of Physical Chemistry B, vol. 102, no. 18, pp.
3586-3616, 1998.
for /l %%x in (0,1,9) do (
surfrace5_0cmd 1 split000%%x.pdb 1.4 3
)
for /l %%f in (10,1,99) do (
surfrace5_0cmd 1 split00%%f.pdb 1.4 3
)
for /l %%g in (100,1,299) do (
surfrace5_0cmd 1 split0%%g.pdb 1.4 3
)
17
[8] William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey,
and Michael L. Klein, "Comparison of simple potential functions for simulating liquid
water," The Journal of Chemical Physics, vol. 79, no. 2, pp. 926-935, 1983.
[9] Michael W. Mahoney and William L. Jorgensen, "A five-site model for liquid water and
the reproduction of the density anomaly by rigid, nonpolarizable potential functions," The
Journal of Chemical Physics, vol. 112, no. 20, pp. 8910-8922, 2000.
[10] W Humphrey, A Dalke, and K Schulten, "VMD - Visual Molecular Dynamics," Journal
of Molecular Graphics, vol. 14, no. 1, pp. 33-38, 1996.
[11] M Heinig and D Frishman, "Knowledge-based protein secondary structure assignment,"
PROTEINS, vol. 23, no. 4, pp. 566-579, 1995.
[12] OV Tsodikov, MT Jr. Record, and Sergeev YV, "A novel computer program for fast
exact calculation of accessible and molecular surface areas and average surface
curvature," Journal of Computational Chemistry, vol. 23, no. 6, pp. 600-609, 2002.
[13] Piana Stefano et al., "Evaluating the Effects of Cutoffs and Treatment of Long-range
Electrostatics in Protein Folding Simulations," PLoS ONE, vol. 7, no. 6, p. e33918, 2012.
[14] B Knapp, N Lederer, U Omastis, and W Schreiner, "vmdICE: a plug-in for rapid
evaluation of molecular dynamics simulations using VMD," Journal of Computational
Chemistry, vol. 31, no. 16, pp. 2868-2873, 2010.