In conclusion the structural property and the assortativity property
of the interfaces influence the assortativity property of the induced
hot spot network.
Acknowledgement
The authors would like to thank the CNRS and the MITI for the
support within the project 80|Prime.
References
1. Janin J, Bahadur RP, Chakrabarti P (2008)
Protein-protein interaction and quaternary
structure. Q Rev Biophys 41(2):133–180
2. Lesieur C (2014) The assembly of protein oligomers—old stories and new perspectives with
graph
theory.
In:
Lesieur
C
(ed) Oligomerization of chemical and
biological compounds. InTech
3. Lesieur C, Vuillon L (2014) From tilings to
fibers: bio-mathematical aspects of fold plasticity. In: Lesieur C (ed) Oligomerization of
chemical and biological compounds. InTech.
ISBN: 978-953-51-1617-2 https://doi.org/
10.5772/58577
4. Baraba ´si A-L, Po ´sfai M (2016) Network science. Cambridge University Press, Cambridge
5. Bagler G, Sinha S (2007) Assortative mixing in
protein contact networks and protein folding
kinetics. Bioinformatics 23(14):1760–1767
6. Karsai M, Kivel€ a M, Pan RK, Kaski K,
Kerte ´sz J, Baraba ´si A-L, Saram€ aki J (2011)
Small but slow world: how network topology
and burstiness slow down spreading. Phys Rev
E Stat Nonlinear Soft Matter Phys 83:025102
7. Newman MEJ (2002) Assortative mixing in
networks. Phys Rev Lett 89:208701
8. Newman MEJ (2003) Mixing patterns in networks. Phys Rev E 67:026126
9. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
10. Vuillon L, Lesieur C (2015) From local to
global changes in proteins: a network view.
Curr Opin Struct Biol 31:1–8
11. Viloria JS, 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
(1):2838
12. Feverati G, Achoch M, Vuillon L, Lesieur C
(2014) Intermolecular β-strand networks
avoid hub residues and favor low interconnectedness: a potential protection mechanism
against chain dissociation upon mutation.
PLoS One 9(4):e94745
13. Berman HM, Westbrook J, Feng Z,
Gilliland G, Bhat TN, Weissig H, Shindyalov
IN, Bourne PE (2000) The protein data bank.
Nucleic Acids Res 28(1):235
14. Reinhard D (2000) Graph theory, graduate
texts in mathematics, vol 173. Springer-Verlag,
Berlin
15. Achoch M, Dorantes-Gilardi R, Wymant C,
Feverati G, Salamatian K, Vuillon L, Lesieur C
(2016) Protein structural robustness to mutations: an in silico investigation. Phys Chem
Chem Phys
16. Lesieur C, Cliff MJ, Carter R, James FL, Clarke
AR, Hirst TR (2002) A kinetic model of intermediate formation during assembly of cholera
toxin b-subunit pentamers. J Biol Chem 277
(19):16697–16704
17. Shoemaker BA, Portman JJ, Wolynes PG
(2000) Speeding molecular recognition by
using the folding funnel: the fly-casting mechanism. Proc Natl Acad Sci 97(16):8868–8873
18. Zrimi J, Ng Ling A, Arifin EGR, Feverati G,
Lesieur C (2010) Cholera toxin b subunits
assemble into pentamers-proposition of a
fly-casting mechanism. PLoS One 5(12):
e15347
19. Achoch M, Feverati G, Vuillon L,
Salamatian K, Lesieur C (2014) Protein subunit association: NOT a social network. In:
TABIS. Institute of Physics, Belgrade, Belgrade
Topology Results on Adjacent Amino Acid Networks of Oligomeric Proteins
135
of the interfaces influence the assortativity property of the induced
hot spot network.
Acknowledgement
The authors would like to thank the CNRS and the MITI for the
support within the project 80|Prime.
References
1. Janin J, Bahadur RP, Chakrabarti P (2008)
Protein-protein interaction and quaternary
structure. Q Rev Biophys 41(2):133–180
2. Lesieur C (2014) The assembly of protein oligomers—old stories and new perspectives with
graph
theory.
In:
Lesieur
C
(ed) Oligomerization of chemical and
biological compounds. InTech
3. Lesieur C, Vuillon L (2014) From tilings to
fibers: bio-mathematical aspects of fold plasticity. In: Lesieur C (ed) Oligomerization of
chemical and biological compounds. InTech.
ISBN: 978-953-51-1617-2 https://doi.org/
10.5772/58577
4. Baraba ´si A-L, Po ´sfai M (2016) Network science. Cambridge University Press, Cambridge
5. Bagler G, Sinha S (2007) Assortative mixing in
protein contact networks and protein folding
kinetics. Bioinformatics 23(14):1760–1767
6. Karsai M, Kivel€ a M, Pan RK, Kaski K,
Kerte ´sz J, Baraba ´si A-L, Saram€ aki J (2011)
Small but slow world: how network topology
and burstiness slow down spreading. Phys Rev
E Stat Nonlinear Soft Matter Phys 83:025102
7. Newman MEJ (2002) Assortative mixing in
networks. Phys Rev Lett 89:208701
8. Newman MEJ (2003) Mixing patterns in networks. Phys Rev E 67:026126
9. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
10. Vuillon L, Lesieur C (2015) From local to
global changes in proteins: a network view.
Curr Opin Struct Biol 31:1–8
11. Viloria JS, 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
(1):2838
12. Feverati G, Achoch M, Vuillon L, Lesieur C
(2014) Intermolecular β-strand networks
avoid hub residues and favor low interconnectedness: a potential protection mechanism
against chain dissociation upon mutation.
PLoS One 9(4):e94745
13. Berman HM, Westbrook J, Feng Z,
Gilliland G, Bhat TN, Weissig H, Shindyalov
IN, Bourne PE (2000) The protein data bank.
Nucleic Acids Res 28(1):235
14. Reinhard D (2000) Graph theory, graduate
texts in mathematics, vol 173. Springer-Verlag,
Berlin
15. Achoch M, Dorantes-Gilardi R, Wymant C,
Feverati G, Salamatian K, Vuillon L, Lesieur C
(2016) Protein structural robustness to mutations: an in silico investigation. Phys Chem
Chem Phys
16. Lesieur C, Cliff MJ, Carter R, James FL, Clarke
AR, Hirst TR (2002) A kinetic model of intermediate formation during assembly of cholera
toxin b-subunit pentamers. J Biol Chem 277
(19):16697–16704
17. Shoemaker BA, Portman JJ, Wolynes PG
(2000) Speeding molecular recognition by
using the folding funnel: the fly-casting mechanism. Proc Natl Acad Sci 97(16):8868–8873
18. Zrimi J, Ng Ling A, Arifin EGR, Feverati G,
Lesieur C (2010) Cholera toxin b subunits
assemble into pentamers-proposition of a
fly-casting mechanism. PLoS One 5(12):
e15347
19. Achoch M, Feverati G, Vuillon L,
Salamatian K, Lesieur C (2014) Protein subunit association: NOT a social network. In:
TABIS. Institute of Physics, Belgrade, Belgrade
Topology Results on Adjacent Amino Acid Networks of Oligomeric Proteins
135