References
- Vidal M, Cusick ME & Barabási A‐L (2011) Interactome networks and
human disease. Cell 144 , 986– 998
- Von Eichborn J, Günther S & Preissner R (2010) Structural features
and evolution of protein–protein interactions. Genome
Inform 22 , 1– 10.
- Kolodny R, Pereyaslavets L, Samson AO & Levitt M (2013) On the
universe of protein folds. Annu Rev
Biophys 42 , 559– 582.
- Schlick T, Portillo-Ledesma S, Myers CG, Beljak L, Chen J, Dakhel S,
Darling D, Ghosh S, Hall J, Jan M, Liang E, Saju S, Vohr M, Wu C, Xu
Y, Xue E. Biomolecular Modeling and Simulation: A Prospering
Multidisciplinary Field. Annu Rev Biophys. 2021 May 6;50:267-301. doi:
10.1146/annurev-biophys-091720-102019. Epub 2021 Feb 19. PMID:
33606945; PMCID: PMC8105287.
- Rodrigues JP, Bonvin AM. Integrative computational modeling of protein
interactions. FEBS J. 2014 Apr;281(8):1988-2003. doi:
10.1111/febs.12771. Epub 2014 Mar 26. PMID: 24588898.
- Klare K, Weir JR, Basilico F, Zimniak T, Massimiliano L, Ludwigs N,
Herzog F, Musacchio A. CENP-C is a blueprint for constitutive
centromere-associated network assembly within human kinetochores. J
Cell Biol. 2015 Jul 6;210(1):11-22. doi: 10.1083/jcb.201412028. Epub
2015 Jun 29. PMID: 26124289; PMCID: PMC4494010.
- Cheerambathur D.K., and Desai A.. 2014. Linked in: formation and
regulation of microtubule attachments during chromosome
segregation. Curr. Opin. Cell Biol. 26:113–122.
10.1016/j.ceb.2013.12.005.
- Fukagawa T., and Earnshaw W.C.. 2014. The centromere: chromatin
foundation for the kinetochore machinery. Dev.
Cell. 30:496–508. 10.1016/j.devcel.2014.08.016.
- Cheeseman I.M. 2014. The kinetochore. Cold Spring Harb.
Perspect. Biol. 6:a015826 10.1101/cshperspect.a015826.
- Cheeseman I.M., Chappie J.S., Wilson-Kubalek E.M., and Desai A..
2006. The conserved KMN network constitutes the core
microtubule-binding site of the
kinetochore. Cell. 127:983–997. 10.1016/j.cell.2006.09.039.
- DeLuca J.G., Gall W.E., Ciferri C., Cimini D., Musacchio A., and
Salmon E.D.. 2006. Kinetochore microtubule dynamics and attachment
stability are regulated by Hec1. Cell. 127:969–982.
10.1016/j.cell.2006.09.047.
- Izuta H., Ikeno M., Suzuki N., Tomonaga T., Nozaki N., Obuse C., Kisu
Y., Goshima N., Nomura F., Nomura N., and Yoda K.. 2006. Comprehensive
analysis of the ICEN (Interphase Centromere Complex) components
enriched in the CENP-A chromatin of human cells. Genes
Cells. 11:673–684. 10.1111/j.1365-2443.2006.00969.x
- Okada M., Cheeseman I.M., Hori T., Okawa K., McLeod I.X., Yates J.R.
III, Desai A., and Fukagawa T.. 2006. The CENP-H-I complex is required
for the efficient incorporation of newly synthesized CENP-A into
centromeres. Nat. Cell Biol. 8:446–457. 10.1038/ncb1396.
- Hu, L., Huang, H., Hei, M., Yang, Y., Li, S., Liu, Y., Dou, Z., Wu,
M., Li, J., Wang, G. Z., Yao, X., Liu, H., He, X., & Tian, W. (2019).
Structural analysis of fungal CENP-H/I/K homologs reveals a conserved
assembly mechanism underlying proper chromosome
alignment. Nucleic acids research , 47 (1), 468–479.
https://doi.org/10.1093/nar/gky1108.
- Foltz D.R., Jansen L.E.T., Black B.E., Bailey A.O., Yates J.R.r.,
Cleveland D.W.. The human CENP-A centromeric nucleosome-associated
complex. Nat. Cell Biol. 2006; 8 :458–469.
- Westermann S., Schleiffer A.. Family matters: structural and
functional conservation of centromere-associated proteins from yeast
to humans. Trends Cell Biol. 2013; 23 :260–269.
- Amano M., Suzuki A., Hori T., Backer C., Okawa K., Cheeseman I.M.,
Fukagawa T.. The CENP-S complex is essential for the stable assembly
of outer kinetochore structure. J. Cell
Biol. 2009; 186 :173–182.
- Black B.E., Brock M.A., Bedard S., Woods V.L., Cleveland D.W.. An
epigenetic mark generated by the incorporation of CENP-A into
centromeric nucleosomes. Proc. Natl. Acad. Sci.
U.S.A. 2007; 104 :5008–5013.
- Chittori S., Hong J., Saunders H., Feng H., Ghirlando R., Kelly A.E.,
Bai Y., Subramaniam S.. Structural mechanisms of centromeric
nucleosome recognition by the kinetochore protein
CENP-N. Science . 2018; 359 :339–343.
- Falk S.J., Guo L.Y., Sekulic N., Smoak E.M., Mani T., Logsdon G.A.,
Gupta K., Jansen L.E.T., Van Duyne G.D., Vinogradov S.A. et al.
. Chromosomes. CENP-C reshapes and stabilizes CENP-A nucleosomes at
the centromere. Science . 2015; 348 :699–703.
- Musacchio A., Desai A.. A molecular view of kinetochore assembly and
function. Biology (Basel) . 2017; 6 :5.
- McKinley K.L., Cheeseman I.M.. The molecular basis for centromere
identity and function. Nat. Rev. Mol. Cell
Biol. 2016; 17 :16–29.
- Huis In ’t Veld P.J., Jeganathan S., Petrovic A., Singh P., John J.,
Krenn V., Weissmann F., Bange T., Musacchio A.. Molecular basis of
outer kinetochore assembly on CENP-T. Elife .
2016; 5 :e21007.
- Petrovic A., Keller J., Liu Y.H., Overlack K., John J., Dimitrova
Y.N., Jenni S., van Gerwen S., Stege P., Wohlgemuth S. et al.
. Structure of the MIS12 complex and molecular basis of its
interaction with CENP-C at human kinetochores. Cell .
2016; 167 :1028–1040.
- Hara M., Fukagawa T.. Kinetochore assembly and disassembly during
mitotic entry and exit. Curr. Opin. Cell
Biol. 2018; 52 :73–81.
- Tian T., Li X.R., Liu Y.Y., Wang C.L., Liu X., Bi G.Q., Zhang X., Yao
X.B., Zhou Z.H., Zang J.Y.. Molecular basis for CENP-N recognition of
CENP-A nucleosome on the human kinetochore. Cell
Res. 2018; 28 :374–378.
- Pentakota S., Zhou K., Smith C., Maffini S., Petrovic A., Morgan G.P.,
Weir J.R., Vetter I.R., Musacchio A., Luger K.. Decoding the
centromeric nucleosome through CENP-N. Elife .
2017; 6 :e33442.
- Kim S., Yu H.T.. Multiple assembly mechanisms anchor the KMN spindle
checkpoint platform at human mitotic kinetochores. J. Cell
Biol. 2015; 208 :181–196.
- McKinley K.L., Sekulic N., Guo L.Y., Tsinman T., Black B.E.,
Cheeseman I.M.. The CENP-L-N complex forms a critical node in an
integrated meshwork of interactions at the Centromere-Kinetochore
interface. Mol. Cell . 2015; 60 :886–898.
- National Center for Biotechnology Information (NCBI)[Internet].
Bethesda (MD): National Library of Medicine (US), National Center for
Biotechnology Information; [1988] – [cited 2021 Feb 07].
Available from: https://www.ncbi.nlm.nih.gov/
- The Protein Data Bank H.M. Berman, J. Westbrook, Z. Feng, G.
Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne
(2000) Nucleic Acids Research , 28 : 235-242.
doi:10.1093/nar/28.1.235.
- Wang S, Sun S, Li Z, Zhang R, Xu J. Accurate De Novo Prediction of
Protein Contact Map by Ultra-Deep Learning Model. PLoS Comput Biol.
2017 Jan 5;13(1):e1005324. doi: 10.1371/journal.pcbi.1005324. PMID:
28056090; PMCID: PMC5249242.
- Heo, L., Park, H., & Seok, C. (2013). GalaxyRefine: Protein structure
refinement driven by side-chain repacking. Nucleic acids
research , 41 (Web Server issue), W384–W388.
https://doi.org/10.1093/nar/gkt458
- Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: interactive web
service for the recognition of errors in three-dimensional structures
of proteins. Nucleic acids research , 35 (Web Server
issue), W407–W410. https://doi.org/10.1093/nar/gkm290
- Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM. AQUA
and PROCHECK-NMR: programs for checking the quality of protein
structures solved by NMR. J Biomol NMR. 1996 Dec;8(4):477-86. doi:
10.1007/BF00228148. PMID: 9008363.
- Yuan, S., Chan, H. C. S., & Hu, Z. (2017). Using PyMOL as a
platform for computational drug design. Wiley Interdisciplinary
Reviews: Computational Molecular Science, 7(2),
e1298. doi:10.1002/wcms.1298
- Basilico, F., Maffini, S., Weir, J. R., Prumbaum, D., Rojas, A. M.,
Zimniak, T., De Antoni, A., Jeganathan, S., Voss, B., van Gerwen, S.,
Krenn, V., Massimiliano, L., Valencia, A., Vetter, I. R., Herzog, F.,
Raunser, S., Pasqualato, S., & Musacchio, A. (2014). The pseudo
GTPase CENP-M drives human kinetochore
assembly. eLife , 3 , e02978.
https://doi.org/10.7554/eLife.02978
- Ashkenazy H., Abadi S., Martz E., Chay O., Mayrose I., Pupko T., and
Ben-Tal N. 2016 ConSurf 2016: an improved methodology to estimate and
visualize evolutionary conservation in macromolecules. Nucl.
Acids Res. 2016; DOI: 10.1093/nar/gkw408; PMID: 27166375
- Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D,
Vajda S. The ClusPro web server for protein-protein
docking. Nature Protocols. 2017 Feb;12(2):255-278.
- Lopéz-Blanco JR, Garzón JI, Chacón P. iMod: multipurpose normal mode
analysis in internal coordinates. Bioinformatics. 2011 Oct
15;27(20):2843-50. doi: 10.1093/bioinformatics/btr497. Epub 2011 Aug
27. PMID: 21873636.
- Carlos HM Rodrigues, Douglas EV Pires, David B Ascher, DynaMut:
predicting the impact of mutations on protein conformation,
flexibility and stability, Nucleic Acids Research , Volume 46,
Issue W1, 2 July 2018, Pages
W350–W355, https://doi.org/10.1093/nar/gky300
- Shapovalov MV, Dunbrack RL Jr. A smoothed backbone-dependent rotamer
library for proteins derived from adaptive kernel density estimates
and regressions. Structure. 2011 Jun 8;19(6):844-58. doi:
10.1016/j.str.2011.03.019. PMID: 21645855; PMCID: PMC3118414.
- Dehouck, Y., Kwasigroch, J. M., Rooman, M., & Gilis, D. (2013).
BeAtMuSiC: Prediction of changes in protein-protein binding affinity
on mutations. Nucleic acids research , 41 (Web Server
issue), W333–W339. https://doi.org/10.1093/nar/gkt450.
- Carlos H M Rodrigues, Yoochan Myung, Douglas E V Pires, David B
Ascher, mCSM-PPI2: predicting the effects of mutations on
protein–protein interactions, Nucleic Acids Research , Volume
47, Issue W1, 02 July 2019, Pages
W338–W344, https://doi.org/10.1093/nar/gkz383
- Rodrigues CHM, Pires DEV, Ascher DB. mmCSM-PPI: predicting the effects
of multiple point mutations on protein-protein interactions. Nucleic
Acids Res. 2021 Apr 24:gkab273. doi: 10.1093/nar/gkab273. Epub ahead
of print. PMID: 33893812.
- Li, M., Simonetti, F.L., Goncearenco, A. and Panchenko, A.R. (2016)
MutaBind estimates and interprets the effects of sequence variants on
protein-protein interactions. Nucleic Acids Res, 44, W494-501.
- Weng GQ, Wang EC, Wang Z, Liu H, Li D, Zhu F, Hou TJ. HawkDock: a web
server to predict and analyze the structures of protein-protein
complexes based on computational docking and MM/GBSA. Nucleic
Acids Research , 2019, 47(W1): W322-W330.
- Jubb, H. C., Higueruelo, A. P., Ochoa-Montaño, B., Pitt, W. R.,
Ascher, D. B., & Blundell, T. L. (2017). Arpeggio: A Web Server for
Calculating and Visualising Interatomic Interactions in Protein
Structures. Journal of molecular biology , 429 (3),
365–371. https://doi.org/10.1016/j.jmb.2016.12.004
- Jayashree, S., Murugavel, P., Sowdhamini, R. et al. Interface
residues of transient protein-protein complexes have extensive
intra-protein interactions apart from inter-protein
interactions. Biol Direct 14, 1 (2019).
https://doi.org/10.1186/s13062-019-0232-2
- Mosca R, Céol A & Aloy P (2013) Interactome3D: adding structural
details to protein networks. Nat Method 10 , 47– 53.
- Vangone A, Cavallo L & Oliva R (2013) Using a consensus approach
based on the conservation of inter-residue contacts to rank CAPRI
models. Proteins 81 , 2210– 2220.
- Karaca E, Bonvin AM. Advances in integrative modeling of biomolecular
complexes. Methods. 2013 Mar;59(3):372-81. doi:
10.1016/j.ymeth.2012.12.004. Epub 2012 Dec 23. PMID: 23267861.
- Hori T., Amano M., Suzuki A., Backer C.B., Welburn J.P., Dong Y.,
McEwen B.F., Shang W.H., Suzuki E., Okawa K. et al. . CCAN makes
multiple contacts with centromeric DNA to provide distinct pathways to
the outer kinetochore. Cell . 2008; 135 :1039–1052.
- Carroll C.W., Milks K.J., Straight A.F.. Dual recognition of CENP-A
nucleosomes is required for centromere assembly. J. Cell
Biol. 2010; 189 :1143–1155.
- Gascoigne K.E., Takeuchi K., Suzuki A., Hori T., Fukagawa T.,
Cheeseman I.M.. Induced ectopic kinetochore assembly bypasses the
requirement for CENP-A nucleosomes. Cell .
2011; 145 :410–422.
- Nishino T., Takeuchi K., Gascoigne K.E., Suzuki A., Hori T., Oyama T.,
Morikawa K., Cheeseman I.M., Fukagawa T.. CENP-T-W-S-X forms a unique
centromeric chromatin structure with a Histone-like fold. Cell .
2012; 148 :487–501.
- Petrovic A., Keller J., Liu Y.H., Overlack K., John J., Dimitrova
Y.N., Jenni S., van Gerwen S., Stege P., Wohlgemuth S. et al.
. Structure of the MIS12 complex and molecular basis of its
interaction with CENP-C at human kinetochores. Cell .
2016; 167 :1028–1040.
- Cingolani G, Petosa C, Weis K, Müller CW. 1999. Structure of
importin-beta bound to the IBB domain of
importin-alpha. Nature 399:221–229. doi: 10.1038/20367.
- Vetter IR, Arndt A, Kutay U, Görlich D, Wittinghofer A.
1999. Structural view of the Ran-Importin beta interaction at 2.3 A
resolution. Cell 97:635–646. doi:
10.1016/S0092-8674(00)80774-6.
- Measday V, Hailey DW, Pot I, Givan SA, Hyland KM, Cagney G, Fields S,
Davis TN, Hieter P. 2002. Ctf3p, the Mis6 budding yeast homolog,
interacts with Mcm22p and Mcm16p at the yeast outer
kinetochore. Genes & Development 16:101–113. doi:
10.1101/gad.949302.
- McPherson A, Gavira JA. Introduction to protein crystallization. Acta
Crystallogr F Struct Biol Commun. 2014 Jan;70(Pt 1):2-20. doi:
10.1107/S2053230X13033141. Epub 2013 Dec 24. PMID: 24419610; PMCID:
PMC3943105.
- Kim DE, DiMaio F, Yu‐Ruei Wang R, Song Y, Baker D. One contact for
every twelve residues allows robust and accurate topology‐level
protein structure modeling. Proteins: Structure, Function, and
Bioinformatics. 2014;82(S2):208–18.
- de Juan D, Pazos F, Valencia A. Emerging methods in protein
co-evolution. Nature Reviews Genetics. 2013;14(4):249–61.
pmid:23458856.
- Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of
direct residue contacts in protein-protein interaction by message
passing. P Natl Acad Sci USA. 2009;106(1):67–72.
- Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A
comprehensive two-hybrid analysis to explore the yeast protein
interactome. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74. doi:
10.1073/pnas.061034498. Epub 2001 Mar 13. PMID: 11283351; PMCID:
PMC31875.
- Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A,
Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I,
Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B,
Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H,
Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH,
Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V,
Sørensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran
MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M. Systematic
identification of protein complexes in Saccharomyces cerevisiae by
mass spectrometry. Nature. 2002 Jan 10;415(6868):180-3. doi:
10.1038/415180a. PMID: 11805837.
- Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S,
McBroom-Cerajewski L, Robinson MD, O’Connor L, Li M, Taylor R, Dharsee
M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier
M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart
II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams
SL, Moran MF, Morin GB, Topaloglou T, Figeys D. Large-scale mapping of
human protein-protein interactions by mass spectrometry. Mol Syst
Biol. 2007;3:89. doi: 10.1038/msb4100134. Epub 2007 Mar 13. PMID:
17353931; PMCID: PMC1847948.
- Smith GR, Sternberg MJ. Prediction of protein-protein interactions by
docking methods. Curr Opin Struct Biol. 2002 Feb;12(1):28-35. doi:
10.1016/s0959-440x(02)00285-3. PMID: 11839486.
- Ritchie DW. Recent progress and future directions in protein-protein
docking. Curr Protein Pept Sci. 2008 Feb;9(1):1-15. doi:
10.2174/138920308783565741. PMID: 18336319.
- López-Blanco, J. R., Aliaga, J. I., Quintana-Ortí, E. S., & Chacón,
P. (2014). iMODS: internal coordinates normal mode analysis
server. Nucleic acids research , 42 (Web Server issue),
W271–W276. https://doi.org/10.1093/nar/gku339
- Mahajan S, Sanejouand YH. On the relationship between low-frequency
normal modes and the large-scale conformational changes of proteins.
Arch Biochem Biophys. 2015 Feb 1;567:59-65. doi:
10.1016/j.abb.2014.12.020. Epub 2015 Jan 3. PMID: 25562404.
- Bauer JA, Pavlović J, Bauerová-Hlinková V. Normal Mode Analysis as a
Routine Part of a Structural Investigation. Molecules. 2019 Sep
10;24(18):3293. doi: 10.3390/molecules24183293. PMID: 31510014; PMCID:
PMC6767145.
- Stefl S., Nishi H., Petukh M., Panchenko A.R., Alexov E. Molecular
mechanisms of disease-causing missense mutations. J. Mol.
Biol. 2013;425 :3919–3936.
- Wainreb G., Wolf L., Ashkenazy H., Dehouck Y., Ben-Tal N. Protein
stability: a single recorded mutation aids in predicting the effects
of other mutations in the same amino acid
site. Bioinformatics. 2011;27 :3286–3292.