27. Lambrughi M, Lucchini M, Pignataro M,
Sola M, Bortolotti CA (2016) The dynamics
of the β-propeller domain in Kelch protein
KLHL40 changes upon nemaline myopathyassociated
mutation.
RSC
Adv
6:34043–34054. https://doi.org/10.1039/
C6RA06312H
28. Singh B, Bulusu G, Mitra A (2016) Effects of
point mutations on the thermostability of
B. subtilis lipase: investigating nonadditivity. J
Comput Aided Mol Des 30:899–916. https://
doi.org/10.1007/s10822-016-9978-0
29. Otaki H, Taguchi Y, Nishida N (2018) Molecular dynamics simulation reveals that switchable combinations of β-sheets underlie the
prion-like properties of α-synuclein amyloids.
https://doi.org/10.1101/326462
30. Pasi M, Tiberti M, Arrigoni A, Papaleo E
(2012) xPyder: a PyMOL plugin to analyze
coupled residues and their networks in protein
structures. J Chem Inf Model 52:1865–1874.
https://doi.org/10.1021/ci300213c
31. The PyMOL Molecular Graphics System, Version 2.0 Schro ¨dinger, LLC.
32. Vijayan RSK, Arnold E, Das K (2014) Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and
resistance by connection mutations. Proteins
82:815–829. https://doi.org/10.1002/prot.
24460
33. Hashem S, Tiberti M, Fornili A (2017) Allosteric modulation of cardiac myosin dynamics
by omecamtiv mecarbil. PLoS Comput Biol
13:e1005826. https://doi.org/10.1371/jour
nal.pcbi.1005826
34. Guizado TRC (2014) Analysis of the structure
and dynamics of human serum albumin. J Mol
Model 20:43. https://doi.org/10.1007/
s00894-014-2450-y
35. Papaleo E, Renzetti G, Invernizzi G, A ´ sgeirsson B (2013) Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted
homodimeric enzyme. A case study of the vibrio alkaline phosphatase. Biochim Biophys Acta
Gen Subj 1830:2970–2980. https://doi.org/
10.1016/j.bbagen.2012.12.011
36. Lambrughi M, Papaleo E, Testa L, Brocca S,
De Gioia L, Grandori R (2012) Intramolecular
interactions stabilizing compact conformations
of the intrinsically disordered kinase-inhibitor
domain of Sic1: a molecular dynamics investigation. Front Physiol 3:435. https://doi.org/
10.3389/fphys.2012.00435
37. Invernizzi G, Tiberti M, Lambrughi M,
Lindorff-Larsen K, Papaleo E (2014) Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding
loops. PLoS Comput Biol 10:e1003744.
https://doi.org/10.1371/journal.pcbi.
1003744
38. Invernizzi G, Lambrughi M, Regonesi ME,
Tortora P, Papaleo E (2013) The conformational ensemble of the disordered and
aggregation-protective 182-291 region of
ataxin-3.
Biochim
Biophys
Acta
1830:5236–5247. https://doi.org/10.1016/
j.bbagen.2013.07.007
39. Nigro P, Pompilio G, Capogrossi MC (2013)
Cyclophilin A: a key player for human disease.
Cell Death Dis 4:e888–e888. https://doi.org/
10.1038/cddis.2013.410
40. Papaleo E, Sutto L, Gervasio FL, LindorffLarsen K (2014) Conformational changes and
free energies in a proline isomerase. J Chem
Theory Comput 10:4169–4174. https://doi.
org/10.1021/ct500536r
41. Schlegel J, Armstrong GS, Redzic JS, Zhang F,
Eisenmesser EZ (2009) Characterizing and
controlling the inherent dynamics of
cyclophilin-A. Protein Sci 18:811–824.
https://doi.org/10.1002/pro.89
42. Holliday MJ, Camilloni C, Armstrong GS,
Vendruscolo M, Eisenmesser EZ (2017) Networks of dynamic allostery regulate enzyme
function. Structure 25:276–286. https://doi.
org/10.1016/j.str.2016.12.003
43. Doshi U, Holliday MJ, Eisenmesser EZ,
Hamelberg D (2016) Dynamical network of
residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and
mutation. Proc Natl Acad Sci U S A
113:4735–4740. https://doi.org/10.1073/
pnas.1523573113
44. Rodriguez-Bussey I, Yao X-Q, Shouaib AD,
Lopez J, Hamelberg D (2018) Decoding allosteric communication pathways in cyclophilin a
with a comparative analysis of perturbed conformational ensembles. J Phys Chem B
122:6528–6535. https://doi.org/10.1021/
acs.jpcb.8b03824
45. Fraser JS, Clarkson MW, Degnan SC, Erion R,
Kern D, Alber T (2009) Hidden alternative
structures of proline isomerase essential for
catalysis. Nature 462:669–673. https://doi.
org/10.1038/nature08615
46. Piana S, Lindorff-Larsen K, Shaw DE (2011)
How robust are protein folding simulations
with respect to force field parameterization?
Biophys J 100:L47–L49. https://doi.org/10.
1016/j.bpj.2011.03.051
47. Jelesarov I, Karshikoff A (2009) Defining the
role of salt bridges in protein stability. Methods
Mol Biol 490:227–260. https://doi.org/10.
1007/978-1-59745-367-7_10
Interaction Networks with PyInteraph
173
Sola M, Bortolotti CA (2016) The dynamics
of the β-propeller domain in Kelch protein
KLHL40 changes upon nemaline myopathyassociated
mutation.
RSC
Adv
6:34043–34054. https://doi.org/10.1039/
C6RA06312H
28. Singh B, Bulusu G, Mitra A (2016) Effects of
point mutations on the thermostability of
B. subtilis lipase: investigating nonadditivity. J
Comput Aided Mol Des 30:899–916. https://
doi.org/10.1007/s10822-016-9978-0
29. Otaki H, Taguchi Y, Nishida N (2018) Molecular dynamics simulation reveals that switchable combinations of β-sheets underlie the
prion-like properties of α-synuclein amyloids.
https://doi.org/10.1101/326462
30. Pasi M, Tiberti M, Arrigoni A, Papaleo E
(2012) xPyder: a PyMOL plugin to analyze
coupled residues and their networks in protein
structures. J Chem Inf Model 52:1865–1874.
https://doi.org/10.1021/ci300213c
31. The PyMOL Molecular Graphics System, Version 2.0 Schro ¨dinger, LLC.
32. Vijayan RSK, Arnold E, Das K (2014) Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and
resistance by connection mutations. Proteins
82:815–829. https://doi.org/10.1002/prot.
24460
33. Hashem S, Tiberti M, Fornili A (2017) Allosteric modulation of cardiac myosin dynamics
by omecamtiv mecarbil. PLoS Comput Biol
13:e1005826. https://doi.org/10.1371/jour
nal.pcbi.1005826
34. Guizado TRC (2014) Analysis of the structure
and dynamics of human serum albumin. J Mol
Model 20:43. https://doi.org/10.1007/
s00894-014-2450-y
35. Papaleo E, Renzetti G, Invernizzi G, A ´ sgeirsson B (2013) Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted
homodimeric enzyme. A case study of the vibrio alkaline phosphatase. Biochim Biophys Acta
Gen Subj 1830:2970–2980. https://doi.org/
10.1016/j.bbagen.2012.12.011
36. Lambrughi M, Papaleo E, Testa L, Brocca S,
De Gioia L, Grandori R (2012) Intramolecular
interactions stabilizing compact conformations
of the intrinsically disordered kinase-inhibitor
domain of Sic1: a molecular dynamics investigation. Front Physiol 3:435. https://doi.org/
10.3389/fphys.2012.00435
37. Invernizzi G, Tiberti M, Lambrughi M,
Lindorff-Larsen K, Papaleo E (2014) Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding
loops. PLoS Comput Biol 10:e1003744.
https://doi.org/10.1371/journal.pcbi.
1003744
38. Invernizzi G, Lambrughi M, Regonesi ME,
Tortora P, Papaleo E (2013) The conformational ensemble of the disordered and
aggregation-protective 182-291 region of
ataxin-3.
Biochim
Biophys
Acta
1830:5236–5247. https://doi.org/10.1016/
j.bbagen.2013.07.007
39. Nigro P, Pompilio G, Capogrossi MC (2013)
Cyclophilin A: a key player for human disease.
Cell Death Dis 4:e888–e888. https://doi.org/
10.1038/cddis.2013.410
40. Papaleo E, Sutto L, Gervasio FL, LindorffLarsen K (2014) Conformational changes and
free energies in a proline isomerase. J Chem
Theory Comput 10:4169–4174. https://doi.
org/10.1021/ct500536r
41. Schlegel J, Armstrong GS, Redzic JS, Zhang F,
Eisenmesser EZ (2009) Characterizing and
controlling the inherent dynamics of
cyclophilin-A. Protein Sci 18:811–824.
https://doi.org/10.1002/pro.89
42. Holliday MJ, Camilloni C, Armstrong GS,
Vendruscolo M, Eisenmesser EZ (2017) Networks of dynamic allostery regulate enzyme
function. Structure 25:276–286. https://doi.
org/10.1016/j.str.2016.12.003
43. Doshi U, Holliday MJ, Eisenmesser EZ,
Hamelberg D (2016) Dynamical network of
residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and
mutation. Proc Natl Acad Sci U S A
113:4735–4740. https://doi.org/10.1073/
pnas.1523573113
44. Rodriguez-Bussey I, Yao X-Q, Shouaib AD,
Lopez J, Hamelberg D (2018) Decoding allosteric communication pathways in cyclophilin a
with a comparative analysis of perturbed conformational ensembles. J Phys Chem B
122:6528–6535. https://doi.org/10.1021/
acs.jpcb.8b03824
45. Fraser JS, Clarkson MW, Degnan SC, Erion R,
Kern D, Alber T (2009) Hidden alternative
structures of proline isomerase essential for
catalysis. Nature 462:669–673. https://doi.
org/10.1038/nature08615
46. Piana S, Lindorff-Larsen K, Shaw DE (2011)
How robust are protein folding simulations
with respect to force field parameterization?
Biophys J 100:L47–L49. https://doi.org/10.
1016/j.bpj.2011.03.051
47. Jelesarov I, Karshikoff A (2009) Defining the
role of salt bridges in protein stability. Methods
Mol Biol 490:227–260. https://doi.org/10.
1007/978-1-59745-367-7_10
Interaction Networks with PyInteraph
173