nodes and edges and more. It allows performing network analysis
by calculating and visualizing hubs, connected components, and
paths between selected residues on the structure. It also allows to
calculate the difference matrix between two loaded matrices and
visualize it as well. Finally, it supports customizing colors, thickness, and scale of the plotted interactions to produce publicationready figures. xPyder has been used in a number of studies for the
analysis and visualization of different types of networks, including
those generated by PyInteraph [21, 32–38].
1.7 Our Test System:
Cyclophilin A
We have used Cyclophilin A as a test case for our protocol. CypA is a
peptidyl prolyl cis-trans isomerase involved in different biological
functions and an important therapeutic target due to its involvement in pathological processes such as viral infection, cancer, cardiovascular diseases, neurodegeneration, aging, and others
[39]. Different studies investigated CypA’s dynamics and allosteric
mechanisms and how these are coupled to catalysis and substrate
recognition to shed light on its functions and exploit them for
inhibitor drugs development and protein engineering [40–44]. It
has been shown that dynamics of this enzyme happen on the same
timescale as the catalytic turnover and that they are coupled to
protein function, including long-range structural communication
effects. Mutations of residue Ser99, 14 A ˚ away from the active site,
influence the dynamics of the catalytic residue Arg55 and affect
reaction rates through a dynamic network of residues [40, 45]. Further experimental and computational works allowed to identify
different dynamic pathways and distal regions in CypA that are
involved in allosteric communication with the active site. For example, distal regions around the Val29 and Val6 residues have been
recently identified to be involved in allosterically coupled dynamic
networks in CypA and mutations of these key hotspot residues alter
dynamics at the active site, modulating enzymatic function through
allosteric networks [42, 44]. These reasons make CypA particularly
suitable to be a good test case for our protocol.
2 Materials
The PyInteraph software was downloaded from https://github.
com/ELELAB/PyInteraph and the xPyder PyMOL plug-in from
https://github.com/ELELAB/xPyder. These packages were
installed according to the installation instructions included with
each. PyInteraph is written for Python 2.7 and includes C and
Cython extensions, which need to be compiled during installation
(see Note 1 for more details). xPyder is a PyMOL plug-in and thus
requires the PyMOL software to run.
We have used a 1 μs molecular dynamics simulation trajectory
of wild-type CypA to demonstrate our protocol, whose set up is
detailed elsewhere [25, 40]. Notably, this simulation was
158
Matteo Lambrughi et al.
by calculating and visualizing hubs, connected components, and
paths between selected residues on the structure. It also allows to
calculate the difference matrix between two loaded matrices and
visualize it as well. Finally, it supports customizing colors, thickness, and scale of the plotted interactions to produce publicationready figures. xPyder has been used in a number of studies for the
analysis and visualization of different types of networks, including
those generated by PyInteraph [21, 32–38].
1.7 Our Test System:
Cyclophilin A
We have used Cyclophilin A as a test case for our protocol. CypA is a
peptidyl prolyl cis-trans isomerase involved in different biological
functions and an important therapeutic target due to its involvement in pathological processes such as viral infection, cancer, cardiovascular diseases, neurodegeneration, aging, and others
[39]. Different studies investigated CypA’s dynamics and allosteric
mechanisms and how these are coupled to catalysis and substrate
recognition to shed light on its functions and exploit them for
inhibitor drugs development and protein engineering [40–44]. It
has been shown that dynamics of this enzyme happen on the same
timescale as the catalytic turnover and that they are coupled to
protein function, including long-range structural communication
effects. Mutations of residue Ser99, 14 A ˚ away from the active site,
influence the dynamics of the catalytic residue Arg55 and affect
reaction rates through a dynamic network of residues [40, 45]. Further experimental and computational works allowed to identify
different dynamic pathways and distal regions in CypA that are
involved in allosteric communication with the active site. For example, distal regions around the Val29 and Val6 residues have been
recently identified to be involved in allosterically coupled dynamic
networks in CypA and mutations of these key hotspot residues alter
dynamics at the active site, modulating enzymatic function through
allosteric networks [42, 44]. These reasons make CypA particularly
suitable to be a good test case for our protocol.
2 Materials
The PyInteraph software was downloaded from https://github.
com/ELELAB/PyInteraph and the xPyder PyMOL plug-in from
https://github.com/ELELAB/xPyder. These packages were
installed according to the installation instructions included with
each. PyInteraph is written for Python 2.7 and includes C and
Cython extensions, which need to be compiled during installation
(see Note 1 for more details). xPyder is a PyMOL plug-in and thus
requires the PyMOL software to run.
We have used a 1 μs molecular dynamics simulation trajectory
of wild-type CypA to demonstrate our protocol, whose set up is
detailed elsewhere [25, 40]. Notably, this simulation was
158
Matteo Lambrughi et al.