Analysis of hydration structures in protein-protein interfaces
1
Namgoong
Yoon
– Dr. Adrian
1
2
Singapore American School - Department of Biochemistry, University of Iowa
Objective
Background
References
12.5: Nucleophilic acyl substitution reactions involving peptide bonds. Figure 6. (2013, October
01). Retrieved July 25, 2016, from
http://chemwiki.ucdavis.edu/Textbook_Maps/Organic_Chemistry_Textbook_Maps/
Map:_Organic_Chemistry_With_a_Biological_Emphasis_(Soderberg)/
12:_Acyl_substitution_reactions/
12.5:_Nucleophilic_acyl_substitution_reactions_involving_peptide_bonds
Hong, S., & Kim, D. (2015, 11). Interaction between bound water molecules and local protein
structures: A statistical analysis of the hydrogen bond structures around bound water molecules.
Proteins Proteins: Structure, Function, and Bioinformatics, 84(1), 43-51. doi:10.1002/prot.24953
Nittinger, E., Schneider, N., Lange, G., & Rarey, M. (2015, 04). Evidence of Water Molecules—A
Statistical Evaluation of Water Molecules Based on Electron Density. Journal of Chemical
Information and Modeling J. Chem. Inf. Model., 55(4), 771-783. doi:10.1021/ci500662d
Rakers, C., Bermudez, M., Keller, B. G., Mortier, J., & Wolber, G. (2015, 07). Computational close
up on protein-protein interactions: How to unravel the invisible using molecular dynamics
simulations? Wiley Interdisciplinary Reviews: Computational Molecular Science WIREs Comput
Mol Sci, 5(5), 345-359. doi:10.1002/wcms.1222
Results
Figure 3 (left): A
histogram of all the 1D
angles formed from a
water molecule + two
different polar atoms of
the protein.
1600
1400
1200
1000
800
600
Image from:
http://wps.prenhall.com/
Anomaly
400
0
0
6
12
18
24
30
36
42
48
54
60
66
72
78
84
90
96
102
108
114
120
126
132
138
144
150
156
162
168
174
180
200
Figure 4 (right):
Histograms sorted by
protein chain categories.
Green: angles of water
molecules that were
between two polar
atoms of different
protein chains. Red:
angles of water
molecules that were
bound to polar atoms of
the same chain.
Anglesofinter-chainandintrachainwatermolecules
1000
900
800
700
600
500
400
300
200
100
0
IntraChain
InterChain
AnglesofintrawaterandcombinaCon
ofdifferentpolaratoms
400
Arginine
350
INTRAN-N
300
INTRAO-O
Aspar+c
Acid
250
200
150
100
50
0
N-N interactions rare!
Figure 10 (right):
Histograms of intra-chain
waters sorted by
combinations of backbone
nitrogen and oxygen that
waters are bonded to. As
expected, 48 degree
anomalies of side chain
structures disappeared.
The anomalies at 60degrees are due to waters
stabilizing tightly coiled
backbone conformations.
Anglesofintrawater+different
polaratomsinbackboneonly
180
SideChainIgnoredIntra
N-N
160
140
SideChainIgnoredIntra
O-O
120
100
SideChainIgnoredIntra
N-O
80
60
40
0
Angle B
Tetrahedral angle range
AnglesofinterwaterandcombinaCon
ofbackboneorsidechain
500
INTERS-S
450
INTERB-B
400
INTERB-S
350
300
250
200
150
100
Angle A
Rare
Figure 5 (left):
Histograms of inter-chain
waters sorted by
combinations of side
chain and backbone of a
protein. No anomalies
present and the
distribution is centered
around 110 degrees.
H2O
All waters (front view)
Almost no N-N backbone
interactions!
Figure 11 (left): An example structure
of two water molecules bonded
between two polar atoms. A total of 3
angles: angle A, angle B, and dihedral
All waters (side view)
50
0
Impossible angles
Tetrahedral angle range
Figure 6 (above): An example of a short
poly peptide chain formed of a backbone
chain and several side chains.
Rare
Figure 12 and 13 (above): A 3D density distribution graph of all angles calculated
from the water bound structures in figure 11. The y-axis (green) shows value of angle
A (refer to figure 11), the x-axis (red) shows values of angle B (refer to figure 11), and
the z-axis (blue) shows the values of dihedral angles ranging from 0 to 360 degrees.
Dark red regions show the most dense parts (regions of most frequent values) and
blue regions are plotted points of all data values.
Backbone
Inter waters (front view)
Intra waters (front view)
Side chain
AnglesofintrawaterandcombinaCon
ofbackboneorsidechain
Figure 7 (right):
Histograms of intra-chain
waters sorted by
combinations of side
chain and backbone of a
protein. Anomalies shown
as expected.
450
INTRAS-S
400
INTRAB-B
350
INTRAB-S
300
250
200
150
100
50
0
Impossible angles
Tetrahedral angle range
Rare
²  Water molecules in protein-protein interfaces have
favorable 1D bond angle, but do not have strongly
favorable dihedral angle.
²  Water molecules tend to maintain tetrahedral
structures
²  Water molecules of intra-chain and inter-chain display
different characteristics
²  Important to note most water mediated interactions are
between backbone and side chain (see figure 16). This
is true for both inter-chain and intra-chain interactions.
²  Important to note which polar atoms the water
molecules are interacting with. Especially in most intrachain situations, bond angle between two nitrogen or
two oxygen and a water molecule will be shallow due
to the presence of certain amino acid side chains such
as Arginine and Glutamic Acid.
Count of backbone and
side chain interactions
10000
9000
8000
7000
6000
5000
4000
3000
2000
1000
0
47.0%
Figure 14 and 15 (above): A 3D density distribution graph of inter-chain angles
(figure 14) and intra-chain angles (figure 15). The y-axis (green) shows value of
angle A (refer to figure 11), the x-2axis (red) shows values of angle B (refer to figure
11), and the z-axis (blue) shows the values of dihedral angles ranging from 0 to 360
degrees. Dark red regions show the most dense parts (regions of most frequent
values) and blue regions are plotted points of all data values. However difference
are slight, the inter-chain prefers a dihedral angle of 180 degrees and the intrachain prefers a dihedral angle of 0 degrees.
27.3%
25.7%
#ofB-B
20
H2O
Impossible angles
INTRAN-O
0
4
8
12
16
20
24
28
32
36
40
44
48
52
56
60
64
68
72
76
80
84
88
92
96
100
104
108
112
116
120
124
128
132
136
140
144
148
152
156
160
164
168
172
176
180
1800
Histogramofanglesforallwaters
Figure 9 (right): Histograms
of intra-chain waters sorted
by combinations of nitrogen
and oxygen that waters are
bonded to. Anomalies shown
in figure 4 and 6 were
present. Enough data was
collected to speculate that
the 48 degrees anomalies
were due to waters
simultaneously bonding with
certain amino acid chains.
0
6
12
18
24
30
36
42
48
54
60
66
72
78
84
90
96
102
108
114
120
126
132
138
144
150
156
162
168
174
180
Figure 2 (above): An example structure of a water molecule bonded
to two different polar atoms illustrating the angle measured.
0
6
12
18
24
30
36
42
48
54
60
66
72
78
84
90
96
102
108
114
120
126
132
138
144
150
156
162
168
174
180
²  Download experimental data of all PPI water molecules
confirmed based on electron density (Nittinger et al.,
2015).
²  Construct script to identify polar atoms that are
separated by one or two hydrogen bonded water
molecules (distance cut off: 3Å)
²  For polar atoms separated by one water molecule,
calculate angle between the polar atoms and water
molecule to make 1D distribution (see results).
²  For polar atoms separated by two water molecules,
calculate two angles and one dihedral angle and make
3D density distribution (see results).
²  Confirm the accuracy of the script by comparing with
manual calculations from a program with a GUI
²  Analyze the trend of the data by observing histograms
and density maps and perform further analysis.
H2O
0
6
12
18
24
30
36
42
48
54
60
66
72
78
84
90
96
102
108
114
120
126
132
138
144
150
156
162
168
174
180
Methods
Conclusions
The objective of the research is to determine the effect of water on protein-protein interactions. In order
to develop better simulation software with more accurate energy functions, the study of favorable
geometries of water molecules at the protein-protein interface is essential.
0
4
8
12
16
20
24
28
32
36
40
44
48
52
56
60
64
68
72
76
80
84
88
92
96
100
104
108
112
116
120
124
128
132
136
140
144
148
152
156
160
164
168
172
176
180
To expedite drug discoveries, biochemists have used
Molecular Dynamics (MD) simulation software to study
Protein-Protein Interactions (Rakers et al., 2015).
In most cases, this simulation software depends on
proper alignment of force field parameters and numerical
algorithms to simulate the forces between particles and
represent their potential energies accurately. However,
these energy functions and force field parameters often
ignore the effect of water molecules in PPIs. Since almost
all protein-protein interactions in real life occur in water,
the polar properties of water mean that it will interact with
polar atoms within protein chains. In order to better
simulate protein-protein interactions, it is essential to
understand the role that water plays in these processes
and include those parameters in the simulations. One way
to develop such an understanding is to examine the
geometries of water molecules in protein-protein
interfaces in crystal structures of protein complexes. This
project reports such an analysis and shows that water
molecules adopt restricted geometries in protein-protein
interfaces. Accounting for this behavior will be crucial for
developing better computational models of protein-protein
interactions.
2
Elcock
#ofB-S
Figure 16: A count of all the
combinations of backbone
and side chain interactions.
Data shows most
interactions are between
one polar atom from
backbone and the other
from a side chain.
#ofS-S
Future Studies
With more experimental data to work with as further study
is done regarding this field, a more detailed analysis can
be done. For example, separate analyses could be
performed for different types of residues.
Further studies could also consider water molecules that
are between proteins in crystal contact (CC) instead of
only at PPI interfaces. Although both PPI and CC
interfaces constitute physical interfaces between protein
molecules, the PPI and CC interfaces have evolved to
provide different biological functions. Bound water
molecules with three or four hydrogen bonds have been
shown to be more favorable in PPI interfaces but less
favorable in CC interfaces (Hong, 2015). Due to their
similar yet contrasting characteristics, it will be interesting
to see how the data results will differ in CC from PPI.
Figure 17 (left): A
example crystal
structure of protein
PDB ID ‘2YOG’.
Image created using
PyMol. This CC
structure can be
exported as a PDB
file for analysis.
Results from the intra-chain water molecules could also
be used to study more of protein folding and improve the
accuracy of protein folding simulations. This would help
scientists better understand specific functions
of proteins.
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