PyInteraph: a framework for the analysis of
interaction networks in structural ensembles
of
proteins.
J
Chem
Inf
Model
54:1537–1551.
https://doi.org/10.1021/
ci400639r
9. Bhattacharyya M, Ghosh S, Vishveshwara S
(2016) Protein structure and function: looking
through the network of side-chain interactions.
Curr Protein Pept Sci 17:4–25
10. Di Paola L, De Ruvo M, Paci P, Santoni D,
Giuliani A (2013) Protein contact networks: an
emerging paradigm in chemistry. Chem Rev
113:1598–1613. https://doi.org/10.1021/
cr3002356
11. Yan W, Zhou J, Sun M, Chen J, Hu G, Shen B
(2014) The construction of an amino acid network for understanding protein structure and
function. Amino Acids 46:1419–1439.
https://doi.org/10.1007/s00726-014-17106
12. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48.
https://doi.org/10.1016/j.sbi.2015.03.001
13. Hu G, Zhou J, Yan W, Chen J, Shen B (2013)
The topology and dynamics of protein complexes: insights from intra- molecular network
theory. Curr Protein Pept Sci 14:121–132
14. Sethi A, Eargle J, Black AA, Luthey-Schulten Z
(2009) Dynamical networks in tRNA:protein
complexes. Proc Natl Acad Sci U S A
106:6620–6625. https://doi.org/10.1073/
pnas.0810961106
15. Pandini A, Fornili A, Fraternali F, Kleinjung J
(2012) Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB J 26:868–881. https://
doi.org/10.1096/fj.11-190868
16. Pandini A, Fornili A, Fraternali F, Kleinjung J
(2013) GSATools: analysis of allosteric communication and functional local motions
using a structural alphabet. Bioinformatics
29:2053–2055. https://doi.org/10.1093/bio
informatics/btt326
17. Potapov V, Cohen M, Inbar Y, Schreiber G
(2010) Protein structure modelling and evaluation based on a 4-distance description of sidechain interactions. BMC Bioinformatics
11:374.
https://doi.org/10.1186/14712105-11-374
18. Jo ´ nsdo ´ttir LB, Ellertsson BO ¨ , Invernizzi G,
Magnu ´ sdo ´ ttir M, Thorbjarnardo ´ttir SH,
Papaleo E, Kristja ´nsson MM (2014) The role
of salt bridges on the temperature adaptation of
aqualysin I, a thermostable subtilisin-like proteinase.
Biochim
Biophys
Acta
1844:2174–2181. https://doi.org/10.1016/
j.bbapap.2014.08.011
19. Lambrughi M, De Gioia L, Gervasio FL,
Lindorff-Larsen K, Nussinov R, Urani C,
Bruschi M, Papaleo E (2016) DNA-binding
protects p53 from interactions with cofactors
involved in transcription-independent functions. Nucleic Acids Res 44:9096–9109.
https://doi.org/10.1093/nar/gkw770
20. Marino V, Scholten A, Koch K-W, Dell’Orco D
(2015) Two retinal dystrophy-associated missense mutations in GUCA1A with distinct
molecular properties result in a similar aberrant
regulation of the retinal guanylate cyclase.
Hum Mol Genet 24:6653–6666. https://doi.
org/10.1093/hmg/ddv370
21. Papaleo E, Parravicini F, Grandori R, De
Gioia L, Brocca S (2014) Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by
atomistic simulations and biophysical methods.
Biochim Biophys Acta 1844:2203–2213.
https://doi.org/10.1016/j.bbapap.2014.09.
018
22. O ´ skarsson KR, Nygaard M, Ellertsson BO ¨ ,
Thorbjarnardo ´ ttir SH, Papaleo E, Kristja ´nsson
MM (2016) A single mutation Gln142Lys
doubles the catalytic activity of VPR, a cold
adapted subtilisin-like serine proteinase. Biochim Biophys Acta 1864:1436–1443. https://
doi.org/10.1016/j.bbapap.2016.07.003
23. Nygaard M, Terkelsen T, Vidas Olsen A,
Sora V, Salamanca Viloria J, Rizza F,
Bergstrand-Poulsen S, Di Marco M,
Vistesen M, Tiberti M, Lambrughi M,
J€ a€ attel€ a M, Kallunki T, Papaleo E (2016) The
mutational landscape of the oncogenic MZF1
SCAN domain in cancer. Front Mol Biosci
3:78. https://doi.org/10.3389/fmolb.2016.
00078
24. Michetti D, Brandsdal BO, Bon D, Isaksen GV,
Tiberti M, Papaleo E (2017) A comparative
study of cold- and warm-adapted endonucleases A using sequence analyses and molecular dynamics simulations. PLoS One 12:
e0169586. https://doi.org/10.1371/journal.
pone.0169586
25. Salamanca Viloria J, Allega MF, Lambrughi M,
Papaleo E (2017) An optimal distance cutoff
for contact-based protein structure networks
using side-chain centers of mass. Sci Rep
7:2838. https://doi.org/10.1038/s41598017-01498-6
26. Marino V, Dell’Orco D (2016) Allosteric communication pathways routed by Ca2+/Mg2+
exchange in GCAP1 selectively switch target
regulation modes. Sci Rep 6:517. https://doi.
org/10.1038/srep34277
172
Matteo Lambrughi et al.
interaction networks in structural ensembles
of
proteins.
J
Chem
Inf
Model
54:1537–1551.
https://doi.org/10.1021/
ci400639r
9. Bhattacharyya M, Ghosh S, Vishveshwara S
(2016) Protein structure and function: looking
through the network of side-chain interactions.
Curr Protein Pept Sci 17:4–25
10. Di Paola L, De Ruvo M, Paci P, Santoni D,
Giuliani A (2013) Protein contact networks: an
emerging paradigm in chemistry. Chem Rev
113:1598–1613. https://doi.org/10.1021/
cr3002356
11. Yan W, Zhou J, Sun M, Chen J, Hu G, Shen B
(2014) The construction of an amino acid network for understanding protein structure and
function. Amino Acids 46:1419–1439.
https://doi.org/10.1007/s00726-014-17106
12. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48.
https://doi.org/10.1016/j.sbi.2015.03.001
13. Hu G, Zhou J, Yan W, Chen J, Shen B (2013)
The topology and dynamics of protein complexes: insights from intra- molecular network
theory. Curr Protein Pept Sci 14:121–132
14. Sethi A, Eargle J, Black AA, Luthey-Schulten Z
(2009) Dynamical networks in tRNA:protein
complexes. Proc Natl Acad Sci U S A
106:6620–6625. https://doi.org/10.1073/
pnas.0810961106
15. Pandini A, Fornili A, Fraternali F, Kleinjung J
(2012) Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB J 26:868–881. https://
doi.org/10.1096/fj.11-190868
16. Pandini A, Fornili A, Fraternali F, Kleinjung J
(2013) GSATools: analysis of allosteric communication and functional local motions
using a structural alphabet. Bioinformatics
29:2053–2055. https://doi.org/10.1093/bio
informatics/btt326
17. Potapov V, Cohen M, Inbar Y, Schreiber G
(2010) Protein structure modelling and evaluation based on a 4-distance description of sidechain interactions. BMC Bioinformatics
11:374.
https://doi.org/10.1186/14712105-11-374
18. Jo ´ nsdo ´ttir LB, Ellertsson BO ¨ , Invernizzi G,
Magnu ´ sdo ´ ttir M, Thorbjarnardo ´ttir SH,
Papaleo E, Kristja ´nsson MM (2014) The role
of salt bridges on the temperature adaptation of
aqualysin I, a thermostable subtilisin-like proteinase.
Biochim
Biophys
Acta
1844:2174–2181. https://doi.org/10.1016/
j.bbapap.2014.08.011
19. Lambrughi M, De Gioia L, Gervasio FL,
Lindorff-Larsen K, Nussinov R, Urani C,
Bruschi M, Papaleo E (2016) DNA-binding
protects p53 from interactions with cofactors
involved in transcription-independent functions. Nucleic Acids Res 44:9096–9109.
https://doi.org/10.1093/nar/gkw770
20. Marino V, Scholten A, Koch K-W, Dell’Orco D
(2015) Two retinal dystrophy-associated missense mutations in GUCA1A with distinct
molecular properties result in a similar aberrant
regulation of the retinal guanylate cyclase.
Hum Mol Genet 24:6653–6666. https://doi.
org/10.1093/hmg/ddv370
21. Papaleo E, Parravicini F, Grandori R, De
Gioia L, Brocca S (2014) Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by
atomistic simulations and biophysical methods.
Biochim Biophys Acta 1844:2203–2213.
https://doi.org/10.1016/j.bbapap.2014.09.
018
22. O ´ skarsson KR, Nygaard M, Ellertsson BO ¨ ,
Thorbjarnardo ´ ttir SH, Papaleo E, Kristja ´nsson
MM (2016) A single mutation Gln142Lys
doubles the catalytic activity of VPR, a cold
adapted subtilisin-like serine proteinase. Biochim Biophys Acta 1864:1436–1443. https://
doi.org/10.1016/j.bbapap.2016.07.003
23. Nygaard M, Terkelsen T, Vidas Olsen A,
Sora V, Salamanca Viloria J, Rizza F,
Bergstrand-Poulsen S, Di Marco M,
Vistesen M, Tiberti M, Lambrughi M,
J€ a€ attel€ a M, Kallunki T, Papaleo E (2016) The
mutational landscape of the oncogenic MZF1
SCAN domain in cancer. Front Mol Biosci
3:78. https://doi.org/10.3389/fmolb.2016.
00078
24. Michetti D, Brandsdal BO, Bon D, Isaksen GV,
Tiberti M, Papaleo E (2017) A comparative
study of cold- and warm-adapted endonucleases A using sequence analyses and molecular dynamics simulations. PLoS One 12:
e0169586. https://doi.org/10.1371/journal.
pone.0169586
25. Salamanca Viloria J, Allega MF, Lambrughi M,
Papaleo E (2017) An optimal distance cutoff
for contact-based protein structure networks
using side-chain centers of mass. Sci Rep
7:2838. https://doi.org/10.1038/s41598017-01498-6
26. Marino V, Dell’Orco D (2016) Allosteric communication pathways routed by Ca2+/Mg2+
exchange in GCAP1 selectively switch target
regulation modes. Sci Rep 6:517. https://doi.
org/10.1038/srep34277
172
Matteo Lambrughi et al.