References
1. Lorimer GH, Horovitz A, McLeish T (2018)
Allostery and molecular machines. Philos Trans
R Soc Lond Ser B Biol Sci 373
(1749):20170173
2. Nussinov R (2016) Introduction to protein
ensembles and allostery. Chem Rev 116
(11):6263–6266
3. Ribeiro AA, Ortiz V (2016) A chemical perspective on allostery. Chem Rev 116
(11):6488–6502
4. Wagner JR et al (2016) Emerging computational methods for the rational discovery of
allosteric
drugs.
Chem
Rev
116
(11):6370–6390
5. Pauling L (1935) The oxygen equilibrium of
hemoglobin and its structural interpretation.
Proc Natl Acad Sci U S A 21(4):186–191
6. Liu J, Nussinov R (2016) Allostery: an overview of its history, concepts, methods, and
applications. PLoS Comput Biol 12(6):
e1004966
7. Collier G, Ortiz V (2013) Emerging computational approaches for the study of protein allostery. Arch Biochem Biophys 538(1):6–15
8. Feher VA et al (2014) Computational
approaches to mapping allosteric pathways.
Curr Opin Struct Biol 25:98–103
9. Verkhivker GM (2018) Computational modeling of the Hsp90 interactions with cochaperones and small-molecule inhibitors. Methods
Mol Biol 1709:253–273
10. Greener JG, Sternberg MJ (2017) Structurebased prediction of protein allostery. Curr
Opin Struct Biol 50:1–8
11. Schueler-Furman O, Wodak SJ (2016)
Computational approaches to investigating
allostery. Curr Opin Struct Biol 41:159–171
12. Suel GM et al (2003) Evolutionarily conserved
networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10
(1):59–69
13. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
14. Gunasekaran K, Ma B, Nussinov R (2004) Is
allostery an intrinsic property of all dynamic
proteins? Proteins 57(3):433–443
15. Blacklock K, Verkhivker GM (2014) Allosteric
regulation of the Hsp90 dynamics and stability
by client recruiter cochaperones: protein structure network modeling. PLoS One 9(1):
e86547
16. Verkhivker GM (2017) Network-based modelling and percolation analysis of conformational
dynamics and activation in the CDK2 and
CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. Mol
BioSyst 13(11):2235–2253
17. Stetz G, Verkhivker GM (2017) Computational analysis of residue interaction networks
and coevolutionary relationships in the Hsp70
chaperones: a community-hopping model of
allosteric regulation and communication.
PLoS Comput Biol 13(1):e1005299
18. Zhou R et al (2015) Molecular mechanism
underlying PRMT1 dimerization for SAM
binding and methylase activity. J Chem Inf
Model 55(12):2623–2632
19. Stetz G, Tse A, Verkhivker GM (2017)
Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and
communication pathways in cyclin-dependent
kinases: differentiating kinase clients of the
Hsp90-Cdc37 chaperone. PLoS One 12(11):
e0186089
20. Stetz G, Tse A, Verkhivker GM (2018) Dissecting structure-encoded determinants of allosteric cross-talk between post-translational
modification sites in the Hsp90 chaperones.
Sci Rep 8(1):6899
21. Verkhivker GM (2018) Dynamics-based community analysis and perturbation response
scanning of allosteric interaction networks in
the TRAP1 chaperone structures dissect
molecular linkage between conformational
asymmetry and sequential ATP hydrolysis. Biochim Biophys Acta 1866(8):899–912
22. Tirion MM (1996) Large amplitude elastic
motions in proteins from a single-parameter,
atomic analysis. Phys Rev Lett 77
(9):1905–1908
23. Li H et al (2016) iGNM 2.0: the Gaussian
network model database for biomolecular
structural dynamics. Nucleic Acids Res 44
(D1):D415–D422
24. Eyal E, Lum G, Bahar I (2015) The anisotropic
network model web server at 2015 (ANM 2.0).
Bioinformatics 31(9):1487–1489
25. Ming D, Wall ME (2005) Quantifying allosteric effects in proteins. Proteins 59(4):697–707
26. Atilgan C, Atilgan AR (2009) Perturbationresponse scanning reveals ligand entry-exit
mechanisms of ferric binding protein. PLoS
Comput Biol 5(10):e1000544
27. Zheng W, Brooks BR, Thirumalai D (2009)
Allosteric transitions in biological nanomachines are described by robust normal modes
34
Guang Hu
1. Lorimer GH, Horovitz A, McLeish T (2018)
Allostery and molecular machines. Philos Trans
R Soc Lond Ser B Biol Sci 373
(1749):20170173
2. Nussinov R (2016) Introduction to protein
ensembles and allostery. Chem Rev 116
(11):6263–6266
3. Ribeiro AA, Ortiz V (2016) A chemical perspective on allostery. Chem Rev 116
(11):6488–6502
4. Wagner JR et al (2016) Emerging computational methods for the rational discovery of
allosteric
drugs.
Chem
Rev
116
(11):6370–6390
5. Pauling L (1935) The oxygen equilibrium of
hemoglobin and its structural interpretation.
Proc Natl Acad Sci U S A 21(4):186–191
6. Liu J, Nussinov R (2016) Allostery: an overview of its history, concepts, methods, and
applications. PLoS Comput Biol 12(6):
e1004966
7. Collier G, Ortiz V (2013) Emerging computational approaches for the study of protein allostery. Arch Biochem Biophys 538(1):6–15
8. Feher VA et al (2014) Computational
approaches to mapping allosteric pathways.
Curr Opin Struct Biol 25:98–103
9. Verkhivker GM (2018) Computational modeling of the Hsp90 interactions with cochaperones and small-molecule inhibitors. Methods
Mol Biol 1709:253–273
10. Greener JG, Sternberg MJ (2017) Structurebased prediction of protein allostery. Curr
Opin Struct Biol 50:1–8
11. Schueler-Furman O, Wodak SJ (2016)
Computational approaches to investigating
allostery. Curr Opin Struct Biol 41:159–171
12. Suel GM et al (2003) Evolutionarily conserved
networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10
(1):59–69
13. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
14. Gunasekaran K, Ma B, Nussinov R (2004) Is
allostery an intrinsic property of all dynamic
proteins? Proteins 57(3):433–443
15. Blacklock K, Verkhivker GM (2014) Allosteric
regulation of the Hsp90 dynamics and stability
by client recruiter cochaperones: protein structure network modeling. PLoS One 9(1):
e86547
16. Verkhivker GM (2017) Network-based modelling and percolation analysis of conformational
dynamics and activation in the CDK2 and
CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. Mol
BioSyst 13(11):2235–2253
17. Stetz G, Verkhivker GM (2017) Computational analysis of residue interaction networks
and coevolutionary relationships in the Hsp70
chaperones: a community-hopping model of
allosteric regulation and communication.
PLoS Comput Biol 13(1):e1005299
18. Zhou R et al (2015) Molecular mechanism
underlying PRMT1 dimerization for SAM
binding and methylase activity. J Chem Inf
Model 55(12):2623–2632
19. Stetz G, Tse A, Verkhivker GM (2017)
Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and
communication pathways in cyclin-dependent
kinases: differentiating kinase clients of the
Hsp90-Cdc37 chaperone. PLoS One 12(11):
e0186089
20. Stetz G, Tse A, Verkhivker GM (2018) Dissecting structure-encoded determinants of allosteric cross-talk between post-translational
modification sites in the Hsp90 chaperones.
Sci Rep 8(1):6899
21. Verkhivker GM (2018) Dynamics-based community analysis and perturbation response
scanning of allosteric interaction networks in
the TRAP1 chaperone structures dissect
molecular linkage between conformational
asymmetry and sequential ATP hydrolysis. Biochim Biophys Acta 1866(8):899–912
22. Tirion MM (1996) Large amplitude elastic
motions in proteins from a single-parameter,
atomic analysis. Phys Rev Lett 77
(9):1905–1908
23. Li H et al (2016) iGNM 2.0: the Gaussian
network model database for biomolecular
structural dynamics. Nucleic Acids Res 44
(D1):D415–D422
24. Eyal E, Lum G, Bahar I (2015) The anisotropic
network model web server at 2015 (ANM 2.0).
Bioinformatics 31(9):1487–1489
25. Ming D, Wall ME (2005) Quantifying allosteric effects in proteins. Proteins 59(4):697–707
26. Atilgan C, Atilgan AR (2009) Perturbationresponse scanning reveals ligand entry-exit
mechanisms of ferric binding protein. PLoS
Comput Biol 5(10):e1000544
27. Zheng W, Brooks BR, Thirumalai D (2009)
Allosteric transitions in biological nanomachines are described by robust normal modes
34
Guang Hu