메뉴 건너뛰기




Volumn 10, Issue 11, 2015, Pages

Dancing through life: Molecular dynamics simulations and network-centric modeling of allosteric mechanisms in Hsp70 and Hsp110 chaperone proteins

Author keywords

[No Author keywords available]

Indexed keywords

HEAT SHOCK PROTEIN 110; HEAT SHOCK PROTEIN 70; PROTEIN DNAK; PEPTIDE;

EID: 84957539705     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0143752     Document Type: Article
Times cited : (40)

References (168)
  • 2
    • 79960652801 scopus 로고    scopus 로고
    • Molecular chaperones in protein folding and proteostasis
    • PMID: 21776078
    • Hartl FU, Bracher A, Hayer-Hartl M. Molecular chaperones in protein folding and proteostasis. Nature. 2011; 475: 324-332. doi: 10.1038/nature10317 PMID: 21776078
    • (2011) Nature , vol.475 , pp. 324-332
    • Hartl, F.U.1    Bracher, A.2    Hayer-Hartl, M.3
  • 3
    • 84878948560 scopus 로고    scopus 로고
    • Molecular chaperone functions in protein folding and proteostasis
    • PMID: 23746257
    • Kim YE, Hipp MS, Bracher A, Hayer-Hartl M, Hartl FU. Molecular chaperone functions in protein folding and proteostasis. Annu Rev Biochem. 2013; 82: 323-355. doi: 10.1146/annurev-biochem- 060208-092442 PMID: 23746257
    • (2013) Annu Rev Biochem , vol.82 , pp. 323-355
    • Kim, Y.E.1    Hipp, M.S.2    Bracher, A.3    Hayer-Hartl, M.4    Hartl, F.U.5
  • 4
    • 84886412961 scopus 로고    scopus 로고
    • Chaperone machines for protein folding, unfolding and disaggregation
    • PMID: 24026055
    • Saibil H.Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol. 2013; 14: 630-642. doi: 10.1038/nrm3658 PMID: 24026055
    • (2013) Nat Rev Mol Cell Biol , vol.14 , pp. 630-642
    • Saibil, H.1
  • 5
    • 17044387386 scopus 로고    scopus 로고
    • Hsp70 chaperones: Cellular functions and molecular mechanism
    • PMID: 15770419
    • Mayer MP, Bukau B. Hsp70 chaperones: Cellular functions and molecular mechanism. Cell Mol Life Sci. 2005; 62: 670-684. PMID: 15770419
    • (2005) Cell Mol Life Sci , vol.62 , pp. 670-684
    • Mayer, M.P.1    Bukau, B.2
  • 6
    • 84884589727 scopus 로고    scopus 로고
    • Hsp70 chaperone dynamics and molecular mechanism
    • PMID: 24012426
    • Mayer MP. Hsp70 chaperone dynamics and molecular mechanism. Trends Biochem Sci. 2013; 38: 507-514. doi: 10.1016/j.tibs.2013.08.001 PMID: 24012426
    • (2013) Trends Biochem Sci , vol.38 , pp. 507-514
    • Mayer, M.P.1
  • 8
    • 84930205629 scopus 로고    scopus 로고
    • The role of HSP70 and its co-chaperones in protein misfolding, aggregation and disease
    • PMID: 25487025
    • Duncan EJ, Cheetham ME, Chapple JP, van der Spuy J. The role of HSP70 and its co-chaperones in protein misfolding, aggregation and disease. Subcell Biochem. 2015; 78: 243-273. doi: 10.1007/978- 3-319-11731-7-12 PMID: 25487025
    • (2015) Subcell Biochem , vol.78 , pp. 243-273
    • Duncan, E.J.1    Cheetham, M.E.2    Chapple, J.P.3    Van Der Spuy, J.4
  • 9
    • 33746330168 scopus 로고    scopus 로고
    • Hsp70 molecular chaperones: Emerging roles in human disease and identification of small molecule modulators
    • PMID: 16842158
    • Brodsky JL, Chiosis G. Hsp70 molecular chaperones: Emerging roles in human disease and identification of small molecule modulators. Curr Top Med Chem. 2006; 6: 1215-1225. PMID: 16842158
    • (2006) Curr Top Med Chem , vol.6 , pp. 1215-1225
    • Brodsky, J.L.1    Chiosis, G.2
  • 10
    • 77953734857 scopus 로고    scopus 로고
    • Heat shock protein 70 (hsp70) as an emerging drug target
    • PMID: 20334364
    • Evans CG, Chang L, Gestwicki JE. Heat shock protein 70 (hsp70) as an emerging drug target. J Med Chem. 2010; 53: 4585-4602. doi: 10.1021/jm100054f PMID: 20334364
    • (2010) J Med Chem , vol.53 , pp. 4585-4602
    • Evans, C.G.1    Chang, L.2    Gestwicki, J.E.3
  • 11
    • 84890860170 scopus 로고    scopus 로고
    • Identification of an allosteric pocket on human hsp70 reveals a mode of inhibition of this therapeutically important protein
    • PMID: 24239008
    • Rodina A, Patel PD, Kang Y, Patel Y, Baaklini I, Wong MJ, et al. Identification of an allosteric pocket on human hsp70 reveals a mode of inhibition of this therapeutically important protein. Chem Biol. 2013; 20: 1469-1480. doi: 10.1016/j.chembiol.2013.10.008 PMID: 24239008
    • (2013) Chem Biol , vol.20 , pp. 1469-1480
    • Rodina, A.1    Patel, P.D.2    Kang, Y.3    Patel, Y.4    Baaklini, I.5    Wong, M.J.6
  • 14
    • 82755187767 scopus 로고    scopus 로고
    • Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface
    • PMID: 22065753
    • Ahmad A, Bhattacharya A, McDonald RA, Cordes M, Ellington B, Bertelsen EB, et al. Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface. Proc Natl Acad Sci U S A. 2011; 108: 18966-18971. doi: 10.1073/pnas.1111220108 PMID: 22065753
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 18966-18971
    • Ahmad, A.1    Bhattacharya, A.2    McDonald, R.A.3    Cordes, M.4    Ellington, B.5    Bertelsen, E.B.6
  • 15
    • 80054740161 scopus 로고    scopus 로고
    • Nucleotide exchange factors for Hsp70 chaperones
    • PMID: 21898229
    • Rampelt H, Mayer MP, Bukau B. Nucleotide exchange factors for Hsp70 chaperones. Methods Mol Biol. 2011; 787: 83-91. doi: 10.1007/978-1-61779-295-3-7 PMID: 21898229
    • (2011) Methods Mol Biol , vol.787 , pp. 83-91
    • Rampelt, H.1    Mayer, M.P.2    Bukau, B.3
  • 16
    • 84924187480 scopus 로고    scopus 로고
    • GrpE, Hsp110/Grp170, HspBP1/Sil1 and BAG domain proteins: Nucleotide exchange factors for Hsp70 molecular chaperones
    • PMID: 25487014
    • Bracher A, Verghese J. GrpE, Hsp110/Grp170, HspBP1/Sil1 and BAG domain proteins: Nucleotide exchange factors for Hsp70 molecular chaperones. Subcell Biochem. 2015; 78: 1-33. doi: 10.1007/ 978-3-319-11731-7-1 PMID: 25487014
    • (2015) Subcell Biochem , vol.78 , pp. 1-33
    • Bracher, A.1    Verghese, J.2
  • 17
    • 0028240468 scopus 로고
    • Structural basis of the 70-kilodalton heat shock cognate protein ATP hydrolytic activity. II. Structure of the active site with ADP or ATP bound to wild type and mutant ATPase fragment
    • PMID: 8175707
    • Flaherty KM, Wilbanks SM, DeLuca-Flaherty C, McKay DB. Structural basis of the 70-kilodalton heat shock cognate protein ATP hydrolytic activity. II. Structure of the active site with ADP or ATP bound to wild type and mutant ATPase fragment. J Biol Chem. 1994; 269: 12899-12907. PMID: 8175707
    • (1994) J Biol Chem , vol.269 , pp. 12899-12907
    • Flaherty, K.M.1    Wilbanks, S.M.2    DeLuca-Flaherty, C.3    McKay, D.B.4
  • 18
    • 0030936995 scopus 로고    scopus 로고
    • Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK
    • PMID: 9103205
    • Harrison CJ, Hayer-Hartl M, Di Liberto M, Hartl F, Kuriyan J. Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK. Science. 1997; 276: 431-435. PMID: 9103205
    • (1997) Science , vol.276 , pp. 431-435
    • Harrison, C.J.1    Hayer-Hartl, M.2    Di Liberto, M.3    Hartl, F.4    Kuriyan, J.5
  • 19
    • 0029937037 scopus 로고    scopus 로고
    • Structural analysis of substrate binding by the molecular chaperone DnaK
    • PMID: 8658133
    • Zhu XT, Zhao X, Burkholder WF, Gragerov A, Ogata CM, Gottesman ME, et al. Structural analysis of substrate binding by the molecular chaperone DnaK. Science. 1996; 272: 1606-1614. PMID: 8658133
    • (1996) Science , vol.272 , pp. 1606-1614
    • Zhu, X.T.1    Zhao, X.2    Burkholder, W.F.3    Gragerov, A.4    Ogata, C.M.5    Gottesman, M.E.6
  • 20
    • 0033603631 scopus 로고    scopus 로고
    • High-resolution solution structure of the 18 kDa substrate-binding domain of the mammalian chaperone protein Hsc70
    • PMID: 10373374
    • Morshauser RC, Hu W, Wang H, Pang Y, Flynn GC, Zuiderweg ER. High-resolution solution structure of the 18 kDa substrate-binding domain of the mammalian chaperone protein Hsc70. J Mol Biol. 1999; 289: 1387-1403. PMID: 10373374
    • (1999) J Mol Biol , vol.289 , pp. 1387-1403
    • Morshauser, R.C.1    Hu, W.2    Wang, H.3    Pang, Y.4    Flynn, G.C.5    Zuiderweg, E.R.6
  • 22
    • 0142148040 scopus 로고    scopus 로고
    • The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG
    • PMID: 14573869
    • Stevens SY, Cai S, Pellecchia M, Zuiderweg ER. The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG. Protein Sci. 2003; 12: 2588-2596. PMID: 14573869
    • (2003) Protein Sci , vol.12 , pp. 2588-2596
    • Stevens, S.Y.1    Cai, S.2    Pellecchia, M.3    Zuiderweg, E.R.4
  • 23
    • 18144374138 scopus 로고    scopus 로고
    • NMR investigations of allosteric processes in a two-domain Thermus thermophilus Hsp70 molecular chaperone
    • PMID: 15876376
    • Revington M, Zhang Y, Yip GN, Kurochkin AV, Zuiderweg ER. NMR investigations of allosteric processes in a two-domain Thermus thermophilus Hsp70 molecular chaperone. J Mol Biol. 2005; 349: 163-183. PMID: 15876376
    • (2005) J Mol Biol , vol.349 , pp. 163-183
    • Revington, M.1    Zhang, Y.2    Yip, G.N.3    Kurochkin, A.V.4    Zuiderweg, E.R.5
  • 24
    • 27944436648 scopus 로고    scopus 로고
    • Structural basis of interdomain communication in the Hsc70 chaperone
    • PMID: 16307916
    • Jiang J, Prasad K, Lafer EM, Sousa R. Structural basis of interdomain communication in the Hsc70 chaperone. Mol Cell. 2005; 20: 513-524. PMID: 16307916
    • (2005) Mol Cell , vol.20 , pp. 513-524
    • Jiang, J.1    Prasad, K.2    Lafer, E.M.3    Sousa, R.4
  • 25
    • 44649169371 scopus 로고    scopus 로고
    • Crystal structures of the 70-kDa heat shock proteins in domain disjoining conformation
    • PMID: 18400763
    • Chang YW, Sun YJ, Wang C, Hsiao CD. Crystal structures of the 70-kDa heat shock proteins in domain disjoining conformation. J Biol Chem. 2008; 283: 15502-15511. doi: 10.1074/jbc. M708992200 PMID: 18400763
    • (2008) J Biol Chem , vol.283 , pp. 15502-15511
    • Chang, Y.W.1    Sun, Y.J.2    Wang, C.3    Hsiao, C.D.4
  • 26
    • 33644990203 scopus 로고    scopus 로고
    • Direct comparison of a stable isolated Hsp70 substrate-binding domain in the empty and substrate-bound states
    • PMID: 16275641
    • Swain JF, Schulz EG, Gierasch LM. Direct comparison of a stable isolated Hsp70 substrate-binding domain in the empty and substrate-bound states. J Biol Chem. 2006; 281: 1605-1611. PMID: 16275641
    • (2006) J Biol Chem , vol.281 , pp. 1605-1611
    • Swain, J.F.1    Schulz, E.G.2    Gierasch, L.M.3
  • 27
    • 34047268015 scopus 로고    scopus 로고
    • Hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker
    • PMID: 17434124
    • Swain JF, Dinler G, Sivendran R, Montgomery DL, Stotz M, Gierasch LM. Hsp70 chaperone ligands control domain association via an allosteric mechanism mediated by the interdomain linker. Mol Cell. 2007; 26: 27-39. PMID: 17434124
    • (2007) Mol Cell , vol.26 , pp. 27-39
    • Swain, J.F.1    Dinler, G.2    Sivendran, R.3    Montgomery, D.L.4    Stotz, M.5    Gierasch, L.M.6
  • 28
    • 33745183353 scopus 로고    scopus 로고
    • Amide hydrogen exchange reveals conformational in hsp70 chaperones important for allosteric regulation
    • PMID: 16613854
    • Rist W, Graf C, Bukau B, Mayer MP. Amide hydrogen exchange reveals conformational in hsp70 chaperones important for allosteric regulation. J Biol Chem. 2006; 281: 16493-16501. PMID: 16613854
    • (2006) J Biol Chem , vol.281 , pp. 16493-16501
    • Rist, W.1    Graf, C.2    Bukau, B.3    Mayer, M.P.4
  • 29
    • 0029037015 scopus 로고
    • Nucleotideinduced conformational changes in the ATPase and substrate binding domains of the DnaK chaperone provide evidence for interdomain communication
    • PMID: 7622507
    • Buchberger A, Theyssen H, Schröder H, McCarty JS, Virgallita G, Milkereit P, et al. Nucleotideinduced conformational changes in the ATPase and substrate binding domains of the DnaK chaperone provide evidence for interdomain communication. J Biol Chem. 1995; 270: 16903-16910. PMID: 7622507
    • (1995) J Biol Chem , vol.270 , pp. 16903-16910
    • Buchberger, A.1    Theyssen, H.2    Schröder, H.3    McCarty, J.S.4    Virgallita, G.5    Milkereit, P.6
  • 30
    • 31344456740 scopus 로고    scopus 로고
    • The allosteric transition in DnaK probed by infrared difference spectroscopy. Concerted ATP-induced rearrangement of the substrate binding domain
    • PMID: 16384998
    • Moro F, Fernández-Sáiz V, Muga A.The allosteric transition in DnaK probed by infrared difference spectroscopy. Concerted ATP-induced rearrangement of the substrate binding domain. Protein Sci. 2006; 15: 223-233. PMID: 16384998
    • (2006) Protein Sci , vol.15 , pp. 223-233
    • Moro, F.1    Fernández-Sáiz, V.2    Muga, A.3
  • 31
    • 64649094781 scopus 로고    scopus 로고
    • Solution conformation of wild-type E. Coli Hsp70 (DnaK) chaperone complexed with ADP and substrate
    • PMID: 19439666
    • Bertelsen EB, Chang L, Gestwicki JE, Zuiderweg ER. Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate. Proc Natl Acad Sci U S A. 2009; 106: 8471-8476. doi: 10.1073/pnas.0903503106 PMID: 19439666
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 8471-8476
    • Bertelsen, E.B.1    Chang, L.2    Gestwicki, J.E.3    Zuiderweg, E.R.4
  • 32
    • 79955565642 scopus 로고    scopus 로고
    • Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones
    • PMID: 21482798
    • Zhuravleva A, Gierasch LM. Allosteric signal transmission in the nucleotide-binding domain of 70-kDa heat shock protein (Hsp70) molecular chaperones. Proc Natl Acad Sci USA. 2011; 108: 6987-6992. doi: 10.1073/pnas.1014448108 PMID: 21482798
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 6987-6992
    • Zhuravleva, A.1    Gierasch, L.M.2
  • 34
    • 84871689599 scopus 로고    scopus 로고
    • Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones
    • PMID: 23123194
    • Kityk R, Kopp J, Sinning I, Mayer MP. Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. Mol Cell. 2012; 48: 863-874. doi: 10.1016/j.molcel.2012.09.023 PMID: 23123194
    • (2012) Mol Cell , vol.48 , pp. 863-874
    • Kityk, R.1    Kopp, J.2    Sinning, I.3    Mayer, M.P.4
  • 35
    • 84880167772 scopus 로고    scopus 로고
    • Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP
    • PMID: 23708608
    • Qi R, Sarbeng EB, Liu Q, Le KQ, Xu X, Xu H, et al. Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP. Nat Struct Mol Biol. 2013; 20: 900-907. doi: 10.1038/nsmb.2583 PMID: 23708608
    • (2013) Nat Struct Mol Biol , vol.20 , pp. 900-907
    • Qi, R.1    Sarbeng, E.B.2    Liu, Q.3    Le, K.Q.4    Xu, X.5    Xu, H.6
  • 36
    • 84870916379 scopus 로고    scopus 로고
    • An interdomain energetic tug-of-war creates the allosterically active state in Hsp70 molecular chaperones
    • PMID: 23217711
    • Zhuravleva A, Clerico EM, Gierasch LM. An interdomain energetic tug-of-war creates the allosterically active state in Hsp70 molecular chaperones. Cell. 2012; 151: 1296-1307. doi: 10.1016/j.cell.2012. 11.002 PMID: 23217711
    • (2012) Cell , vol.151 , pp. 1296-1307
    • Zhuravleva, A.1    Clerico, E.M.2    Gierasch, L.M.3
  • 37
    • 84930939681 scopus 로고    scopus 로고
    • Substrate-binding domain conformational dynamics mediate Hsp70 allostery
    • PMID: 26038563
    • Zhuravleva A, Gierasch LM. Substrate-binding domain conformational dynamics mediate Hsp70 allostery. Proc Natl Acad Sci U S A. 2015; 112: E2865-E2873. doi: 10.1073/pnas.1506692112 PMID: 26038563
    • (2015) Proc Natl Acad Sci U S A , vol.112 , pp. E2865-E2873
    • Zhuravleva, A.1    Gierasch, L.M.2
  • 38
    • 0033936317 scopus 로고    scopus 로고
    • Multistep mechanism of substrate binding determines chaperone activity of Hsp70
    • PMID: 10876246
    • Mayer MP, Schröder H, Rüdiger S, Paal K, Laufen T, Bukau B. Multistep mechanism of substrate binding determines chaperone activity of Hsp70. Nat Struct Biol. 2000; 7: 586-593. PMID: 10876246
    • (2000) Nat Struct Biol , vol.7 , pp. 586-593
    • Mayer, M.P.1    Schröder, H.2    Rüdiger, S.3    Paal, K.4    Laufen, T.5    Bukau, B.6
  • 39
    • 0033783190 scopus 로고    scopus 로고
    • Molecular basis for interactions of the DnaK chaperone with substrates
    • PMID: 11076019
    • Mayer MP, Rüdiger S, Bukau B. Molecular basis for interactions of the DnaK chaperone with substrates. Biol Chem. 2000; 381: 877-885. PMID: 11076019
    • (2000) Biol Chem , vol.381 , pp. 877-885
    • Mayer, M.P.1    Rüdiger, S.2    Bukau, B.3
  • 40
    • 79952364237 scopus 로고    scopus 로고
    • Mechanics of Hsp70 chaperones enables differential interaction with client proteins
    • PMID: 21278757
    • Schlecht R, Erbse AH, Bukau B, Mayer MP. Mechanics of Hsp70 chaperones enables differential interaction with client proteins. Nat Struct Mol Biol. 2011; 18: 345-351. doi: 10.1038/nsmb.2006 PMID: 21278757
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 345-351
    • Schlecht, R.1    Erbse, A.H.2    Bukau, B.3    Mayer, M.P.4
  • 41
    • 77950431096 scopus 로고    scopus 로고
    • The conformational dynamics of the mitochondrial Hsp70 chaperone
    • PMID: 20385092
    • Mapa K, Sikor M, Kudryavtsev V, Waegemann K, Kalinin S, Seidel CA, et al. The conformational dynamics of the mitochondrial Hsp70 chaperone. Mol Cell. 2010; 38: 89-100. doi: 10.1016/j.molcel. 2010.03.010 PMID: 20385092
    • (2010) Mol Cell , vol.38 , pp. 89-100
    • Mapa, K.1    Sikor, M.2    Kudryavtsev, V.3    Waegemann, K.4    Kalinin, S.5    Seidel, C.A.6
  • 42
    • 79551632223 scopus 로고    scopus 로고
    • Substrate discrimination of the chaperone BiP by autonomous and cochaperone-regulated conformational transitions
    • PMID: 21217698
    • Marcinowski M, Höller M, Feige MJ, Baerend D, Lamb DC, Buchner J. Substrate discrimination of the chaperone BiP by autonomous and cochaperone-regulated conformational transitions. Nat Struct Mol Biol. 2011; 18: 150-158. doi: 10.1038/nsmb.1970 PMID: 21217698
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 150-158
    • Marcinowski, M.1    Höller, M.2    Feige, M.J.3    Baerend, D.4    Lamb, D.C.5    Buchner, J.6
  • 43
    • 84878617377 scopus 로고    scopus 로고
    • Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET
    • PMID: 23624933
    • Sikor M, Mapa K, von Voithenberg LV, Mokranjac D, Lamb DC. Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET. EMBO J. 2013; 32: 1639-1649. doi: 10.1038/ emboj.2013.89 PMID: 23624933
    • (2013) EMBO J , vol.32 , pp. 1639-1649
    • Sikor, M.1    Mapa, K.2    Von Voithenberg, L.V.3    Mokranjac, D.4    Lamb, D.C.5
  • 44
    • 76749141462 scopus 로고    scopus 로고
    • Energetics of nucleotide-induced DnaK conformational states
    • PMID: 20078127
    • Taneva SG, Moro F, Velázquez-Campoy A, Muga A. Energetics of nucleotide-induced DnaK conformational states. Biochemistry. 2010; 49: 1338-1345. doi: 10.1021/bi901847q PMID: 20078127
    • (2010) Biochemistry , vol.49 , pp. 1338-1345
    • Taneva, S.G.1    Moro, F.2    Velázquez-Campoy, A.3    Muga, A.4
  • 47
    • 0033605086 scopus 로고    scopus 로고
    • Mutations in the substrate binding domain of the Escherichia coli 70 kDa molecular chaperone, DnaK, which alter substrate affinity or interdomain coupling
    • PMID: 10024459
    • Montgomery DL, Morimoto RI, Gierasch LM. Mutations in the substrate binding domain of the Escherichia coli 70 kDa molecular chaperone, DnaK, which alter substrate affinity or interdomain coupling. J Mol Biol. 1999; 286: 915-932. PMID: 10024459
    • (1999) J Mol Biol , vol.286 , pp. 915-932
    • Montgomery, D.L.1    Morimoto, R.I.2    Gierasch, L.M.3
  • 48
    • 0035907104 scopus 로고    scopus 로고
    • Mutations in the interdomain linker region of DnaK abolish the chaperone action of the DnaK/DnaJ/GrpE system
    • PMID: 11376662
    • Han W, Christen P. Mutations in the interdomain linker region of DnaK abolish the chaperone action of the DnaK/DnaJ/GrpE system. FEBS letters. 2001; 497: 55-58. PMID: 11376662
    • (2001) FEBS letters , vol.497 , pp. 55-58
    • Han, W.1    Christen, P.2
  • 49
    • 31544442176 scopus 로고    scopus 로고
    • Allosteric regulation of Hsp70 chaperones by a proline switch
    • PMID: 16455491
    • Vogel M, Bukau B, Mayer MP. Allosteric regulation of Hsp70 chaperones by a proline switch. Mol Cell. 2006; 21: 359-367. PMID: 16455491
    • (2006) Mol Cell , vol.21 , pp. 359-367
    • Vogel, M.1    Bukau, B.2    Mayer, M.P.3
  • 50
    • 33846020582 scopus 로고    scopus 로고
    • Allosteric regulation of Hsp70 chaperones involves a conserved interdomain linker
    • PMID: 17052976
    • Vogel M, Mayer MP, Bukau B. Allosteric regulation of Hsp70 chaperones involves a conserved interdomain linker. J Biol Chem. 2006; 281: 38705-38711. PMID: 17052976
    • (2006) J Biol Chem , vol.281 , pp. 38705-38711
    • Vogel, M.1    Mayer, M.P.2    Bukau, B.3
  • 51
    • 77957274298 scopus 로고    scopus 로고
    • An interdomain sector mediating allostery in Hsp70 molecular chaperones
    • PMID: 20865007
    • Smock RG, Rivoire O, Russ WP, Swain JF, Leibler S, Ranganathan R, et al. An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol. 2010; 6: 414. doi: 10.1038/msb. 2010.65 PMID: 20865007
    • (2010) Mol Syst Biol , vol.6 , pp. 414
    • Smock, R.G.1    Rivoire, O.2    Russ, W.P.3    Swain, J.F.4    Leibler, S.5    Ranganathan, R.6
  • 52
    • 84942019140 scopus 로고    scopus 로고
    • Pathways of allosteric regulation in Hsp70 chaperones
    • PMID: 26383706
    • Kityk R, Vogel M, Schlecht R, Bukau B, Mayer MP. Pathways of allosteric regulation in Hsp70 chaperones. Nat Commun. 2015; 6: 8308. doi: 10.1038/ncomms9308 PMID: 26383706
    • (2015) Nat Commun , vol.6 , pp. 8308
    • Kityk, R.1    Vogel, M.2    Schlecht, R.3    Bukau, B.4    Mayer, M.P.5
  • 53
    • 34848869936 scopus 로고    scopus 로고
    • Insights into Hsp70 chaperone activity from a crystal structure of the yeast Hsp110 Sse1
    • PMID: 17923091
    • Liu Q, Hendrickson WA. Insights into Hsp70 chaperone activity from a crystal structure of the yeast Hsp110 Sse1. Cell. 2007; 131: 106-120. PMID: 17923091
    • (2007) Cell , vol.131 , pp. 106-120
    • Liu, Q.1    Hendrickson, W.A.2
  • 54
    • 44049083594 scopus 로고    scopus 로고
    • Hsp110 is a nucleotide-activated exchange factor for Hsp70
    • PMID: 18218635
    • Andréasson C, Fiaux J, Rampelt H, Mayer MP, Bukau B. Hsp110 is a nucleotide-activated exchange factor for Hsp70. J Biol Chem. 2008; 283: 8877-8884. doi: 10.1074/jbc.M710063200 PMID: 18218635
    • (2008) J Biol Chem , vol.283 , pp. 8877-8884
    • Andréasson, C.1    Fiaux, J.2    Rampelt, H.3    Mayer, M.P.4    Bukau, B.5
  • 55
    • 55949092734 scopus 로고    scopus 로고
    • Insights into the structural dynamics of the Hsp110-Hsp70 interaction reveal the mechanism for nucleotide exchange activity
    • PMID: 18948593
    • Andréasson C, Fiaux J, Rampelt H, Druffel-Augustin S, Bukau B. Insights into the structural dynamics of the Hsp110-Hsp70 interaction reveal the mechanism for nucleotide exchange activity. Proc Natl Acad Sci U S A. 2008; 105: 16519-16524. doi: 10.1073/pnas.0804187105 PMID: 18948593
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 16519-16524
    • Andréasson, C.1    Fiaux, J.2    Rampelt, H.3    Druffel-Augustin, S.4    Bukau, B.5
  • 56
    • 44649110104 scopus 로고    scopus 로고
    • Structural basis for the cooperation of Hsp70 and Hsp110 chaperones in protein folding
    • PMID: 18555782
    • Polier S, Dragovic Z, Hartl FU, Bracher A. Structural basis for the cooperation of Hsp70 and Hsp110 chaperones in protein folding. Cell. 2008; 133: 1068-10679. doi: 10.1016/j.cell.2008.05.022 PMID: 18555782
    • (2008) Cell , vol.133 , pp. 1068-10679
    • Polier, S.1    Dragovic, Z.2    Hartl, F.U.3    Bracher, A.4
  • 57
    • 84863155446 scopus 로고    scopus 로고
    • Unique peptide substrate binding properties of 110-kDa heat-shock protein (Hsp110) determine its distinct chaperone activity
    • PMID: 22157767
    • Xu X, Sarbeng EB, Vorvis C, Kumar DP, Zhou L, Liu Q. Unique peptide substrate binding properties of 110-kDa heat-shock protein (Hsp110) determine its distinct chaperone activity. J Biol Chem. 2012; 287: 5661-5672. doi: 10.1074/jbc.M111.275057 PMID: 22157767
    • (2012) J Biol Chem , vol.287 , pp. 5661-5672
    • Xu, X.1    Sarbeng, E.B.2    Vorvis, C.3    Kumar, D.P.4    Zhou, L.5    Liu, Q.6
  • 58
    • 84883235332 scopus 로고    scopus 로고
    • Mutational analysis of Sse1 (Hsp110) suggests an integral role for this chaperone in yeast prion propagation in vivo
    • Moran C, Kinsella GK, Zhang ZR, Perrett S, Jones GW. Mutational analysis of Sse1 (Hsp110) suggests an integral role for this chaperone in yeast prion propagation in vivo. G3 (Bethesda). 2013; 3: 1409-1418.
    • (2013) G3 (Bethesda , vol.3 , pp. 1409-1418
    • Moran, C.1    Kinsella, G.K.2    Zhang, Z.R.3    Perrett, S.4    Jones, G.W.5
  • 59
    • 73149114876 scopus 로고    scopus 로고
    • ATP-induced conformational changes in Hsp70: Molecular dynamics and experimental validation of an in silico predicted conformation
    • PMID: 19883127
    • Woo HJ, Jiang J, Lafer EM, Sousa R. ATP-induced conformational changes in Hsp70: Molecular dynamics and experimental validation of an in silico predicted conformation. Biochemistry. 2009; 48: 11470-11477. doi: 10.1021/bi901256y PMID: 19883127
    • (2009) Biochemistry , vol.48 , pp. 11470-11477
    • Woo, H.J.1    Jiang, J.2    Lafer, E.M.3    Sousa, R.4
  • 60
    • 78049433050 scopus 로고    scopus 로고
    • Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs
    • PMID: 20862304
    • Liu Y, Gierasch LM, Bahar I. Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PLoS Comput Biol. 2010; 6: E1000931. doi: 10. 1371/journal.pcbi.1000931 PMID: 20862304
    • (2010) PLoS Comput Biol , vol.6 , pp. e1000931
    • Liu, Y.1    Gierasch, L.M.2    Bahar, I.3
  • 61
    • 84872012970 scopus 로고    scopus 로고
    • Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations
    • PMID: 23300424
    • Chiappori F, Merelli I, Colombo G, Milanesi L, Morra G. Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations. PLoS Comput Biol. 2012; 8: E1002844. doi: 10.1371/journal.pcbi.1002844 PMID: 23300424
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002844
    • Chiappori, F.1    Merelli, I.2    Colombo, G.3    Milanesi, L.4    Morra, G.5
  • 62
    • 84860723030 scopus 로고    scopus 로고
    • Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics
    • PMID: 22737044
    • Golas E, Maisuradze GG, Senet P, Oldziej S, Czaplewski C, Scheraga HA, et al. Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics. J Chem Theory Comput. 2012; 8: 1750-1764. PMID: 22737044
    • (2012) J Chem Theory Comput , vol.8 , pp. 1750-1764
    • Golas, E.1    Maisuradze, G.G.2    Senet, P.3    Oldziej, S.4    Czaplewski, C.5    Scheraga, H.A.6
  • 63
    • 84884546232 scopus 로고    scopus 로고
    • Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent
    • PMID: 23075261
    • Nicolaï A, Delarue P, Senet P. Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent. J Biomol Struct Dyn. 2013; 31: 1111-1126. doi: 10.1080/07391102.2012.726190 PMID: 23075261
    • (2013) J Biomol Struct Dyn , vol.31 , pp. 1111-1126
    • Nicolaï, A.1    Delarue, P.2    Senet, P.3
  • 64
    • 84892702922 scopus 로고    scopus 로고
    • Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70
    • PMID: 24348227
    • Nicolaï A, Delarue P, Senet P. Decipher the mechanisms of protein conformational changes induced by nucleotide binding through free-energy landscape analysis: ATP binding to Hsp70. PLoS Comput Biol. 2013; 9: E1003379. doi: 10.1371/journal.pcbi.1003379 PMID: 24348227
    • (2013) PLoS Comput Biol , vol.9 , pp. e1003379
    • Nicolaï, A.1    Delarue, P.2    Senet, P.3
  • 65
    • 84888245316 scopus 로고    scopus 로고
    • Identification of key hinge residues important for nucleotide-dependent allostery in E. Coli Hsp70/DnaK
    • PMID: 24277995
    • Ung PM, Thompson AD, Chang L, Gestwicki JE, Carlson HA. Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK. PLoS Comput Biol. 2013; 9: E1003279. doi: 10.1371/journal.pcbi.1003279 PMID: 24277995
    • (2013) PLoS Comput Biol , vol.9 , pp. e1003279
    • Ung, P.M.1    Thompson, A.D.2    Chang, L.3    Gestwicki, J.E.4    Carlson, H.A.5
  • 66
    • 84901650125 scopus 로고    scopus 로고
    • ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones
    • PMID: 24831085
    • General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I. ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. PLoS Comput Biol. 2014; 10: E1003624. doi: 10.1371/journal.pcbi.1003624 PMID: 24831085
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003624
    • General, I.J.1    Liu, Y.2    Blackburn, M.E.3    Mao, W.4    Gierasch, L.M.5    Bahar, I.6
  • 67
    • 0021658956 scopus 로고
    • Allostery without conformational change. A plausible model
    • PMID: 6544679
    • Cooper A, Dryden DT. Allostery without conformational change. A plausible model. Eur Biophys J. 1984; 11: 103-109. PMID: 6544679
    • (1984) Eur Biophys J , vol.11 , pp. 103-109
    • Cooper, A.1    Dryden, D.T.2
  • 69
    • 79551689721 scopus 로고    scopus 로고
    • Protein dynamics and allostery: An NMR view
    • PMID: 21109422
    • Tzeng SR, Kalodimos CG. Protein dynamics and allostery: An NMR view. Curr Opin Struct Biol. 2011; 21: 62-67. doi: 10.1016/j.sbi.2010.10.007 PMID: 21109422
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 62-67
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 70
    • 84864065499 scopus 로고    scopus 로고
    • Protein function and allostery: A dynamic relationship
    • PMID: 22256894
    • Kalodimos CG. Protein function and allostery: A dynamic relationship. Ann N Y Acad Sci. 2012; 1260: 81-86. doi: 10.1111/j.1749-6632.2011.06319.x PMID: 22256894
    • (2012) Ann N Y Acad Sci , vol.1260 , pp. 81-86
    • Kalodimos, C.G.1
  • 71
    • 84864651001 scopus 로고    scopus 로고
    • Protein activity regulation by conformational entropy
    • PMID: 22801505
    • Tzeng SR, Kalodimos CG. Protein activity regulation by conformational entropy. Nature. 2012; 488: 236-240. doi: 10.1038/nature11271 PMID: 22801505
    • (2012) Nature , vol.488 , pp. 236-240
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 72
    • 84895745240 scopus 로고    scopus 로고
    • A unified view of "how allostery works"
    • PMID: 24516370
    • Tsai CJ, Nussinov R. A unified view of "how allostery works". PLoS Comput Biol. 2014; 10: E1003394. doi: 10.1371/journal.pcbi.1003394 PMID: 24516370
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003394
    • Tsai, C.J.1    Nussinov, R.2
  • 74
    • 84893847867 scopus 로고    scopus 로고
    • Molecular dynamics simulation studies on the positive cooperativity of the Kemptide substrate with protein kinase A induced by the ATP ligand
    • PMID: 24456306
    • Li C, Ma N, Wang Y, Wang Y, Chen G. Molecular dynamics simulation studies on the positive cooperativity of the Kemptide substrate with protein kinase A induced by the ATP ligand. J Phys Chem B. 2014; 118: 1273-1287. doi: 10.1021/jp411111g PMID: 24456306
    • (2014) J Phys Chem B , vol.118 , pp. 1273-1287
    • Li, C.1    Ma, N.2    Wang, Y.3    Wang, Y.4    Chen, G.5
  • 75
    • 0037192145 scopus 로고    scopus 로고
    • Negative cooperativity associated with binding of multivalent carbohydrates to lectins. Thermodynamic analysis of the "multivalency effect"
    • PMID: 11802737
    • Dam TK, Roy R, Pagé D, Brewer CF. Negative cooperativity associated with binding of multivalent carbohydrates to lectins. Thermodynamic analysis of the "multivalency effect". Biochemistry. 2002; 41: 1351-1358. PMID: 11802737
    • (2002) Biochemistry , vol.41 , pp. 1351-1358
    • Dam, T.K.1    Roy, R.2    Pagé, D.3    Brewer, C.F.4
  • 76
    • 0034765285 scopus 로고    scopus 로고
    • Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity
    • PMID: 11685240
    • Stevens SY, Sanker S, Kent C, Zuiderweg ER. Delineation of the allosteric mechanism of a cytidylyltransferase exhibiting negative cooperativity. Nat Struct Biol. 2001; 8: 947-952. PMID: 11685240
    • (2001) Nat Struct Biol , vol.8 , pp. 947-952
    • Stevens, S.Y.1    Sanker, S.2    Kent, C.3    Zuiderweg, E.R.4
  • 77
    • 77950521526 scopus 로고    scopus 로고
    • Lactose binding to galectin-1 modulates structural dynamics, increases conformational entropy, and occurs with apparent negative cooperativity
    • PMID: 20184898
    • Nesmelova IV, Ermakova E, Daragan VA, Pang M, Menéndez M, Lagartera L, et al. Lactose binding to galectin-1 modulates structural dynamics, increases conformational entropy, and occurs with apparent negative cooperativity. J Mol Biol. 2010; 397: 1209-1230. doi: 10.1016/j.jmb.2010.02.033 PMID: 20184898
    • (2010) J Mol Biol , vol.397 , pp. 1209-1230
    • Nesmelova, I.V.1    Ermakova, E.2    Daragan, V.A.3    Pang, M.4    Menéndez, M.5    Lagartera, L.6
  • 78
    • 41149104308 scopus 로고    scopus 로고
    • Allostery: Absence of a change in shape does not imply that allostery is not at play
    • PMID: 18353365
    • Tsai CJ, Sol AD, Nussinov R. Allostery: Absence of a change in shape does not imply that allostery is not at play. J Mol Biol. 2008; 378: 1-11. doi: 10.1016/j.jmb.2008.02.034 PMID: 18353365
    • (2008) J Mol Biol , vol.378 , pp. 1-11
    • Tsai, C.J.1    Sol, A.D.2    Nussinov, R.3
  • 79
    • 68149157248 scopus 로고    scopus 로고
    • The origin of allosteric functional modulation: Multiple pre-existing pathways
    • PMID: 19679084
    • Sol AD, Tsai CJ, Ma B, Nussinov R. The origin of allosteric functional modulation: Multiple pre-existing pathways. Structure. 2009; 17: 1042-1050. doi: 10.1016/j.str.2009.06.008 PMID: 19679084
    • (2009) Structure , vol.17 , pp. 1042-1050
    • Sol, A.D.1    Tsai, C.J.2    Ma, B.3    Nussinov, R.4
  • 80
    • 60649109828 scopus 로고    scopus 로고
    • Protein allostery, signal transmission and dynamics: A classification scheme of allosteric mechanisms
    • PMID: 19225609
    • Tsai CJ, Sol AD, Nussinov R. Protein allostery, signal transmission and dynamics: A classification scheme of allosteric mechanisms. Mol Biosyst. 2009; 5: 207-216. doi: 10.1039/b819720b PMID: 19225609
    • (2009) Mol Biosyst , vol.5 , pp. 207-216
    • Tsai, C.J.1    Sol, A.D.2    Nussinov, R.3
  • 81
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: An extended view of binding events
    • PMID: 20541943
    • Csermely P, Palotai R, Nussinov R. Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends Biochem Sci. 2010; 35: 539-546. doi: 10. 1016/j.tibs.2010.04.009 PMID: 20541943
    • (2010) Trends Biochem Sci , vol.35 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 82
    • 79960189344 scopus 로고    scopus 로고
    • Dynamic allostery: Linkers are not merely flexible
    • PMID: 21742258
    • Ma B, Tsai CJ, Haliloglu T, Nussinov R. Dynamic allostery: Linkers are not merely flexible. Structure. 2011; 19: 907-917. doi: 10.1016/j.str.2011.06.002 PMID: 21742258
    • (2011) Structure , vol.19 , pp. 907-917
    • Ma, B.1    Tsai, C.J.2    Haliloglu, T.3    Nussinov, R.4
  • 83
    • 84861219631 scopus 로고    scopus 로고
    • Allostery and the Monod-Wyman-Changeux model after 50 years
    • PMID: 22224598
    • Changeux JP. Allostery and the Monod-Wyman-Changeux model after 50 years. Annu Rev Biophys. 2012; 41: 103-133. doi: 10.1146/annurev-biophys-050511-102222 PMID: 22224598
    • (2012) Annu Rev Biophys , vol.41 , pp. 103-133
    • Changeux, J.P.1
  • 84
    • 82655179921 scopus 로고    scopus 로고
    • How do dynamic cellular signals travel long distances?
    • PMID: 21766126
    • Nussinov R. How do dynamic cellular signals travel long distances? Mol Biosyst. 2012; 8: 22-26. doi: 10.1039/c1mb05205e PMID: 21766126
    • (2012) Mol Biosyst , vol.8 , pp. 22-26
    • Nussinov, R.1
  • 85
    • 84876275408 scopus 로고    scopus 로고
    • The underappreciated role of allostery in the cellular network
    • PMID: 23451894
    • Nussinov R, Tsai CJ, Ma B. The underappreciated role of allostery in the cellular network. Annu Rev Biophys. 2013; 42: 169-189. doi: 10.1146/annurev-biophys-083012-130257 PMID: 23451894
    • (2013) Annu Rev Biophys , vol.42 , pp. 169-189
    • Nussinov, R.1    Tsai, C.J.2    Ma, B.3
  • 86
    • 84876266689 scopus 로고    scopus 로고
    • Allostery in disease and in drug discovery
    • PMID: 23582321
    • Nussinov R, Tsai CJ. Allostery in disease and in drug discovery. Cell. 2013; 153: 293-305. doi: 10. 1016/j.cell.2013.03.034 PMID: 23582321
    • (2013) Cell , vol.153 , pp. 293-305
    • Nussinov, R.1    Tsai, C.J.2
  • 87
    • 84883480131 scopus 로고    scopus 로고
    • Allosteric conformational barcodes direct signaling in the cell
    • PMID: 24010710
    • Nussinov R, Ma B, Tsai CJ, Csermely P. Allosteric conformational barcodes direct signaling in the cell. Structure. 2013; 21: 1509-1521. doi: 10.1016/j.str.2013.06.002 PMID: 24010710
    • (2013) Structure , vol.21 , pp. 1509-1521
    • Nussinov, R.1    Ma, B.2    Tsai, C.J.3    Csermely, P.4
  • 88
    • 84857131975 scopus 로고    scopus 로고
    • Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: Hypotheses and a comprehensive review
    • PMID: 22044146
    • Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJ, Miozzo F, et al. Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: Hypotheses and a comprehensive review. Curr Protein Pept Sci. 2012; 13: 19-33. PMID: 22044146
    • (2012) Curr Protein Pept Sci , vol.13 , pp. 19-33
    • Csermely, P.1    Sandhu, K.S.2    Hazai, E.3    Hoksza, Z.4    Kiss, H.J.5    Miozzo, F.6
  • 89
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
    • PMID: 23384594
    • Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R. Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review. Pharmacol Ther. 2013; 138: 333-408. doi: 10.1016/j.pharmthera.2013.01.016 PMID: 23384594
    • (2013) Pharmacol Ther , vol.138 , pp. 333-408
    • Csermely, P.1    Korcsmáros, T.2    Kiss, H.J.3    London, G.4    Nussinov, R.5
  • 90
    • 84876709135 scopus 로고    scopus 로고
    • Allo-network drugs: Extension of the allosteric drug concept to protein- protein interaction and signaling networks
    • PMID: 23409766
    • Szilágyi A, Nussinov R, Csermely P. Allo-network drugs: Extension of the allosteric drug concept to protein- protein interaction and signaling networks. Curr Top Med Chem. 2013; 13: 64-77. PMID: 23409766
    • (2013) Curr Top Med Chem , vol.13 , pp. 64-77
    • Szilágyi, A.1    Nussinov, R.2    Csermely, P.3
  • 92
    • 0346057951 scopus 로고    scopus 로고
    • Small-world communication of residues and significance for protein dynamics
    • PMID: 14695252
    • Atilgan AR, Akan P, Baysal C. Small-world communication of residues and significance for protein dynamics. Biophys J. 2004; 86: 85-91. PMID: 14695252
    • (2004) Biophys J , vol.86 , pp. 85-91
    • Atilgan, A.R.1    Akan, P.2    Baysal, C.3
  • 93
    • 28444453011 scopus 로고    scopus 로고
    • A network representation of protein structures: Implications for protein stability
    • PMID: 16150969
    • Brinda KV, Vishveshwara S. A network representation of protein structures: Implications for protein stability. Biophys J. 2005; 89: 4159-4170. PMID: 16150969
    • (2005) Biophys J , vol.89 , pp. 4159-4170
    • Brinda, K.V.1    Vishveshwara, S.2
  • 94
    • 78649883885 scopus 로고    scopus 로고
    • Vishveshwara S Interaction energy based protein structure networks
    • PMID: 21112295
    • Vijayabaskar MS, Vishveshwara S Interaction energy based protein structure networks. Biophys J. 2010; 99: 3704-3715. doi: 10.1016/j.bpj.2010.08.079 PMID: 21112295
    • (2010) Biophys J , vol.99 , pp. 3704-3715
    • Vijayabaskar, M.S.1
  • 95
    • 12944331889 scopus 로고    scopus 로고
    • Small-world network approach to identify key residues in protein-protein interaction
    • PMID: 15617065
    • del Sol A, O'Meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins. 2005; 58: 672-682. PMID: 15617065
    • (2005) Proteins , vol.58 , pp. 672-682
    • Del Sol, A.1    O'Meara, P.2
  • 96
    • 17444396776 scopus 로고    scopus 로고
    • Topology of small-world networks of protein-protein complex structures
    • PMID: 15659419
    • del Sol A, Fujihashi H, O'Meara P. Topology of small-world networks of protein-protein complex structures. Bioinformatics. 2005; 21: 1311-1315. PMID: 15659419
    • (2005) Bioinformatics , vol.21 , pp. 1311-1315
    • Del Sol, A.1    Fujihashi, H.2    O'Meara, P.3
  • 97
    • 8544221118 scopus 로고    scopus 로고
    • Network analysis of protein structures identifies functional residues
    • PMID: 15544817
    • Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, et al. Network analysis of protein structures identifies functional residues. J Mol Biol. 2004; 344: 1135-1146. PMID: 15544817
    • (2004) J Mol Biol , vol.344 , pp. 1135-1146
    • Amitai, G.1    Shemesh, A.2    Sitbon, E.3    Shklar, M.4    Netanely, D.5    Venger, I.6
  • 98
    • 34347326305 scopus 로고    scopus 로고
    • Ligand binding and circular permutation modify residue interaction network in DHFR
    • PMID: 17571919
    • Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, et al. Ligand binding and circular permutation modify residue interaction network in DHFR. PLoS Comput Biol. 2007; 3: E117. PMID: 17571919
    • (2007) PLoS Comput Biol , vol.3 , pp. e117
    • Hu, Z.1    Bowen, D.2    Southerland, W.M.3    Del Sol, A.4    Pan, Y.5    Nussinov, R.6
  • 99
    • 33748207211 scopus 로고    scopus 로고
    • Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families
    • PMID: 16882992
    • del Sol A, Fujihashi H, Amoros D, Nussinov R. Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families. Protein Sci. 2006; 15: 2120-2128. PMID: 16882992
    • (2006) Protein Sci , vol.15 , pp. 2120-2128
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 100
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • PMID: 16738564
    • del Sol A, Fujihashi H, Amoros D, Nussinov R. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol. 2006; 2: 2006.0019. PMID: 16738564
    • (2006) Mol Syst Biol , vol.2 , Issue.2006 , pp. 0019
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 101
    • 4444251032 scopus 로고    scopus 로고
    • Probing protein mechanics: Residue-level properties and their use in defining domains
    • PMID: 15345525
    • Navizet I, Cailliez F, Lavery R. Probing protein mechanics: Residue-level properties and their use in defining domains. Biophys J. 2004; 87: 1426-1435. PMID: 15345525
    • (2004) Biophys J , vol.87 , pp. 1426-1435
    • Navizet, I.1    Cailliez, F.2    Lavery, R.3
  • 102
    • 33646200456 scopus 로고    scopus 로고
    • Investigating the local flexibility of functional residues in hemoproteins
    • PMID: 16428284
    • Sacquin-Mora S, Lavery R. Investigating the local flexibility of functional residues in hemoproteins. Biophys J. 2006; 90: 2706-2717. PMID: 16428284
    • (2006) Biophys J , vol.90 , pp. 2706-2717
    • Sacquin-Mora, S.1    Lavery, R.2
  • 103
    • 84911453369 scopus 로고    scopus 로고
    • Quantitative method for the assignment of hinge and shear mechanism in protein domain movements
    • PMID: 25078396
    • Taylor D, Cawley G, Hayward S. Quantitative method for the assignment of hinge and shear mechanism in protein domain movements. Bioinformatics. 2014; 30: 3189-3196. doi: 10.1093/ bioinformatics/btu506 PMID: 25078396
    • (2014) Bioinformatics , vol.30 , pp. 3189-3196
    • Taylor, D.1    Cawley, G.2    Hayward, S.3
  • 104
    • 0034710950 scopus 로고    scopus 로고
    • Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble
    • PMID: 11035796
    • Pan H, Lee JC, Hilser VJ. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Proc Natl Acad Sci U S A. 2000; 97: 12020-12025. PMID: 11035796
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 12020-12025
    • Pan, H.1    Lee, J.C.2    Hilser, V.J.3
  • 105
    • 84861371612 scopus 로고    scopus 로고
    • Structural and energetic basis of allostery
    • PMID: 22577828
    • Hilser VJ, Wrabl JO, Motlagh HN. Structural and energetic basis of allostery. Annu Rev Biophys. 2012; 41: 585-609. doi: 10.1146/annurev-biophys-050511-102319 PMID: 22577828
    • (2012) Annu Rev Biophys , vol.41 , pp. 585-609
    • Hilser, V.J.1    Wrabl, J.O.2    Motlagh, H.N.3
  • 106
    • 84898993517 scopus 로고    scopus 로고
    • The ensemble nature of allostery
    • PMID: 24740064
    • Motlagh HN, Wrabl JO, Li J, Hilser VJ. The ensemble nature of allostery. Nature. 2014; 508: 331-339. doi: 10.1038/nature13001 PMID: 24740064
    • (2014) Nature , vol.508 , pp. 331-339
    • Motlagh, H.N.1    Wrabl, J.O.2    Li, J.3    Hilser, V.J.4
  • 107
    • 84858234186 scopus 로고    scopus 로고
    • Agonism/antagonism switching in allosteric ensembles
    • PMID: 22388747
    • Motlagh HN, Hilser VJ. Agonism/antagonism switching in allosteric ensembles. Proc Natl Acad Sci U S A. 2012; 109: 4134-4139. doi: 10.1073/pnas.1120519109 PMID: 22388747
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 4134-4139
    • Motlagh, H.N.1    Hilser, V.J.2
  • 108
    • 6344223617 scopus 로고    scopus 로고
    • A flexible approach for understanding protein stability
    • PMID: 15498582
    • Livesay DR, Dallakyan S, Wood GG, Jacobs DJ. A flexible approach for understanding protein stability. FEBS Lett. 2004; 576: 468-476. PMID: 15498582
    • (2004) FEBS Lett , vol.576 , pp. 468-476
    • Livesay, D.R.1    Dallakyan, S.2    Wood, G.G.3    Jacobs, D.J.4
  • 109
    • 82455220946 scopus 로고    scopus 로고
    • Ensemble properties of network rigidity reveal allosteric mechanisms
    • PMID: 22052496
    • Jacobs DJ, Livesay DR, Mottonen JM, Vorov OK, Istomin AY, Verma D. Ensemble properties of network rigidity reveal allosteric mechanisms. Methods Mol Biol. 2012; 796: 279-304. doi: 10.1007/978- 1-61779-334-9-15 PMID: 22052496
    • (2012) Methods Mol Biol , vol.796 , pp. 279-304
    • Jacobs, D.J.1    Livesay, D.R.2    Mottonen, J.M.3    Vorov, O.K.4    Istomin, A.Y.5    Verma, D.6
  • 110
    • 84944259026 scopus 로고    scopus 로고
    • Rigidity versus flexibility: The dilemma of understanding protein thermal stability
    • PMID: 26074325
    • Karshikoff A, Nilsson L, Ladenstein R. Rigidity versus flexibility: The dilemma of understanding protein thermal stability. FEBS J. 2015; 282: 3899-3917. doi: 10.1111/febs.13343 PMID: 26074325
    • (2015) FEBS J , vol.282 , pp. 3899-3917
    • Karshikoff, A.1    Nilsson, L.2    Ladenstein, R.3
  • 111
    • 4043116913 scopus 로고    scopus 로고
    • Predictions of protein flexibility: First-order measures
    • PMID: 15281119
    • Kovacs JA, Chacón P, Abagyan R. Predictions of protein flexibility: First-order measures. Proteins. 2004; 56: 661-668. PMID: 15281119
    • (2004) Proteins , vol.56 , pp. 661-668
    • Kovacs, J.A.1    Chacón, P.2    Abagyan, R.3
  • 112
    • 34248523175 scopus 로고    scopus 로고
    • DFprot: A webtool for predicting local chain deformability
    • PMID: 17277334
    • Garzón JI, Kovacs J, Abagyan R, Chacón P. DFprot: A webtool for predicting local chain deformability. Bioinformatics. 2007; 23: 901-902. PMID: 17277334
    • (2007) Bioinformatics , vol.23 , pp. 901-902
    • Garzón, J.I.1    Kovacs, J.2    Abagyan, R.3    Chacón, P.4
  • 114
    • 84924301769 scopus 로고    scopus 로고
    • Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution
    • PMID: 25646698
    • Ma W, Schulten K. Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. J Am Chem Soc. 2015; 137: 3031-3040. doi: 10.1021/ja512605w PMID: 25646698
    • (2015) J Am Chem Soc , vol.137 , pp. 3031-3040
    • Ma, W.1    Schulten, K.2
  • 115
    • 45949108535 scopus 로고    scopus 로고
    • Finding transition pathways using the string method with swarms of trajectories
    • PMID: 18290641
    • Pan AC, Sezer D, Roux B. Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B. 2008; 112: 3432-3440. doi: 10.1021/jp0777059 PMID: 18290641
    • (2008) J Phys Chem B , vol.112 , pp. 3432-3440
    • Pan, A.C.1    Sezer, D.2    Roux, B.3
  • 116
    • 84919832780 scopus 로고    scopus 로고
    • Activation pathway of Src kinase reveals intermediate states as targets for drug design
    • PMID: 24584478
    • Shukla D, Meng Y, Roux B, Pande VS. Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nat Commun. 2014; 5: 3397. doi: 10.1038/ncomms4397 PMID: 24584478
    • (2014) Nat Commun , vol.5 , pp. 3397
    • Shukla, D.1    Meng, Y.2    Roux, B.3    Pande, V.S.4
  • 117
    • 84924043002 scopus 로고    scopus 로고
    • Exact milestoning
    • PMID: 25747056
    • Bello-Rivas JM, Elber R. Exact milestoning. J Chem Phys. 2015; 142: 094102. doi: 10.1063/1. 4913399 PMID: 25747056
    • (2015) J Chem Phys , vol.142 , pp. 094102
    • Bello-Rivas, J.M.1    Elber, R.2
  • 118
    • 84901376917 scopus 로고    scopus 로고
    • Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model
    • PMID: 24699246
    • Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLoS Comput Biol. 2014; 10: E1003521. doi: 10.1371/journal.pcbi.1003521 PMID: 24699246
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003521
    • Das, A.1    Gur, M.2    Cheng, M.H.3    Jo, S.4    Bahar, I.5    Roux, B.6
  • 119
    • 77951294588 scopus 로고    scopus 로고
    • Targeting biomolecular flexibility with metadynamics
    • PMID: 20171876
    • Leone V, Marinelli F, Carloni P, Parrinello M. Targeting biomolecular flexibility with metadynamics. Curr Opin Struct Biol. 2010; 20: 148-154. doi: 10.1016/j.sbi.2010.01.011 PMID: 20171876
    • (2010) Curr Opin Struct Biol , vol.20 , pp. 148-154
    • Leone, V.1    Marinelli, F.2    Carloni, P.3    Parrinello, M.4
  • 120
    • 84855961734 scopus 로고    scopus 로고
    • Using metadynamics and path collective variables to study ligand binding and induced conformational transitions
    • PMID: 22183554
    • Bešker N, Gervasio FL. Using metadynamics and path collective variables to study ligand binding and induced conformational transitions. Methods Mol Biol. 2012; 819: 501-513. doi: 10.1007/978-1- 61779-465-0-29 PMID: 22183554
    • (2012) Methods Mol Biol , vol.819 , pp. 501-513
    • Bešker, N.1    Gervasio, F.L.2
  • 121
    • 84879510153 scopus 로고    scopus 로고
    • Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase
    • PMID: 23754386
    • Sutto L, Gervasio FL. Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase. Proc Natl Acad Sci U S A. 2013; 110: 10616-10621. doi: 10.1073/pnas.1221953110 PMID: 23754386
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 10616-10621
    • Sutto, L.1    Gervasio, F.L.2
  • 122
    • 84923072401 scopus 로고    scopus 로고
    • Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms
    • PMID: 25496113
    • Cavalli A, Spitaleri A, Saladino G, Gervasio FL. Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms. Acc Chem Res. 2015; 48: 277-285. doi: 10. 1021/ar500356n PMID: 25496113
    • (2015) Acc Chem Res , vol.48 , pp. 277-285
    • Cavalli, A.1    Spitaleri, A.2    Saladino, G.3    Gervasio, F.L.4
  • 123
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • PMID: 12079393
    • Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J Mol Biol. 2002; 320: 369-87. PMID: 12079393
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 124
    • 34248674895 scopus 로고    scopus 로고
    • The stability effects of protein mutations appear to be universally distributed
    • PMID: 17482644
    • Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS. The stability effects of protein mutations appear to be universally distributed. J Mol Biol. 2007; 369: 1318-1332. PMID: 17482644
    • (2007) J Mol Biol , vol.369 , pp. 1318-1332
    • Tokuriki, N.1    Stricher, F.2    Schymkowitz, J.3    Serrano, L.4    Tawfik, D.S.5
  • 127
    • 84870051131 scopus 로고    scopus 로고
    • Accurate stabilities of laccase mutants predicted with a modified FoldX protocol
    • PMID: 23102044
    • Christensen NJ, Kepp KP. Accurate stabilities of laccase mutants predicted with a modified FoldX protocol. J Chem Inf Model. 2012; 52: 3028-3042. doi: 10.1021/ci300398z PMID: 23102044
    • (2012) J Chem Inf Model , vol.52 , pp. 3028-3042
    • Christensen, N.J.1    Kepp, K.P.2
  • 128
    • 84880023622 scopus 로고    scopus 로고
    • Stability mechanisms of laccase isoforms using a modified FoldX Pprotocol applicable to widely different proteins
    • Christensen NJ, Kepp KP. Stability mechanisms of laccase isoforms using a modified FoldX Pprotocol applicable to widely different proteins. J. Chem. Theory Comput. 2013; 9: 3210-3223.
    • (2013) J. Chem. Theory Comput , vol.9 , pp. 3210-3223
    • Christensen, N.J.1    Kepp, K.P.2
  • 129
    • 84904803708 scopus 로고    scopus 로고
    • DUET: A server for predicting effects of mutations on protein stability using an integrated computational approach
    • PMID: 24829462
    • Pires DE, Ascher DB, Blundell TL. DUET: A server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res. 2014; 42: W314-W319. doi: 10. 1093/nar/gku411 PMID: 24829462
    • (2014) Nucleic Acids Res , vol.42 , pp. W314-W319
    • Pires, D.E.1    Ascher, D.B.2    Blundell, T.L.3
  • 130
    • 84893298981 scopus 로고    scopus 로고
    • MCSM: Predicting the effects of mutations in proteins using graphbased signatures
    • PMID: 24281696
    • Pires DE, Ascher DB, Blundell TL. mCSM: Predicting the effects of mutations in proteins using graphbased signatures. Bioinformatics. 2014; 30: 335-342. doi: 10.1093/bioinformatics/btt691 PMID: 24281696
    • (2014) Bioinformatics , vol.30 , pp. 335-342
    • Pires, D.E.1    Ascher, D.B.2    Blundell, T.L.3
  • 131
    • 79959942908 scopus 로고    scopus 로고
    • SDM-A server for predicting effects of mutations on protein stability and malfunction
    • PMID: 21593128
    • Worth CL, Preissner R, Blundell TL. SDM-A server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res. 2011; 39: W215-W222. doi: 10.1093/nar/gkr363 PMID: 21593128
    • (2011) Nucleic Acids Res , vol.39 , pp. W215-W222
    • Worth, C.L.1    Preissner, R.2    Blundell, T.L.3
  • 132
    • 0033568644 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J Am Chem Soc. 1999; 121: 8133-8143.
    • (1999) J Am Chem Soc , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 133
    • 0037079570 scopus 로고    scopus 로고
    • Computational alanine scanning of the 1: 1 human growth hormonereceptor complex
    • PMID: 11913381
    • Huo S, Massova I, Kollman PA. Computational alanine scanning of the 1: 1 human growth hormonereceptor complex. J Comput Chem. 2002; 23: 15-27. PMID: 11913381
    • (2002) J Comput Chem , vol.23 , pp. 15-27
    • Huo, S.1    Massova, I.2    Kollman, P.A.3
  • 134
    • 2942532422 scopus 로고    scopus 로고
    • Development and testing of a general amber force field
    • PMID: 15116359
    • Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general amber force field. J Comput Chem. 2004; 25: 1157-1174. PMID: 15116359
    • (2004) J Comput Chem , vol.25 , pp. 1157-1174
    • Wang, J.1    Wolf, R.M.2    Caldwell, J.W.3    Kollman, P.A.4    Case, D.A.5
  • 135
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices
    • Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J Am Chem Soc 1998; 120: 9401-9409.
    • (1998) J Am Chem Soc , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 136
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • PMID: 11123888
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, et al. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res. 2000; 33: 889-897. PMID: 11123888
    • (2000) Acc Chem Res , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6
  • 137
    • 0033565815 scopus 로고    scopus 로고
    • Residue depth: A novel parameter for the analysis of protein structure and stability
    • PMID: 10425675
    • Chakravarty S, Varadarajan R. Residue depth: A novel parameter for the analysis of protein structure and stability. Structure. 1999; 7: 723-72. PMID: 10425675
    • (1999) Structure , vol.7 , pp. 723-772
    • Chakravarty, S.1    Varadarajan, R.2
  • 138
    • 84883592483 scopus 로고    scopus 로고
    • Depth: A web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins
    • PMID: 23766289
    • Tan KP, Nguyen TB, Patel S, Varadarajan R, Madhusudhan MS. Depth: A web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. Nucleic Acids Res. 2013; 41: W314-W321. doi: 10.1093/nar/gkt503 PMID: 23766289
    • (2013) Nucleic Acids Res , vol.41 , pp. W314-W321
    • Tan, K.P.1    Nguyen, T.B.2    Patel, S.3    Varadarajan, R.4    Madhusudhan, M.S.5
  • 139
    • 70349392341 scopus 로고    scopus 로고
    • Prodepth: Predict residue depth by support vector regression approach from protein sequences only
    • PMID: 19759917
    • Song J, Tan H, Mahmood K, Law RH, Buckle AM, Webb GI, et al. Prodepth: Predict residue depth by support vector regression approach from protein sequences only. PLoS One. 2009; 4: E7072. doi: 10. 1371/journal.pone.0007072 PMID: 19759917
    • (2009) PLoS One , vol.4 , pp. e7072
    • Song, J.1    Tan, H.2    Mahmood, K.3    Law, R.H.4    Buckle, A.M.5    Webb, G.I.6
  • 140
    • 0032570266 scopus 로고    scopus 로고
    • Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model
    • PMID: 9454598
    • Bahar I, Wallqvist A, Covell DG, Jernigan RL. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry. 1998; 37: 1067-1075. PMID: 9454598
    • (1998) Biochemistry , vol.37 , pp. 1067-1075
    • Bahar, I.1    Wallqvist, A.2    Covell, D.G.3    Jernigan, R.L.4
  • 141
    • 1542606700 scopus 로고    scopus 로고
    • Atom depth in protein structure and function
    • PMID: 14607089
    • Pintar A, Carugo O, Pongor S. Atom depth in protein structure and function. Trends Biochem Sci. 2003; 28: 593-597. PMID: 14607089
    • (2003) Trends Biochem Sci , vol.28 , pp. 593-597
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 142
    • 37849034569 scopus 로고    scopus 로고
    • Quantifying the relationship of protein burying depth and sequence
    • PMID: 17705271
    • Yuan Z, Wang ZX. Quantifying the relationship of protein burying depth and sequence. Proteins. 2008; 70: 509-516. PMID: 17705271
    • (2008) Proteins , vol.70 , pp. 509-516
    • Yuan, Z.1    Wang, Z.X.2
  • 143
    • 84870328990 scopus 로고    scopus 로고
    • Rigidity and flexibility of biological networks
    • PMID: 23165349
    • Gáspár ME, Csermely P. Rigidity and flexibility of biological networks. Brief Funct Genomics. 2012; 11: 443-456. doi: 10.1093/bfgp/els023 PMID: 23165349
    • (2012) Brief Funct Genomics , vol.11 , pp. 443-456
    • Gáspár, M.E.1    Csermely, P.2
  • 144
    • 84899890103 scopus 로고    scopus 로고
    • Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle
    • PMID: 24671209
    • Li T, Tracka MB, Uddin S, Casas-Finet J, Jacobs DJ, Livesay DR. Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle. PLoS One. 2014; 9: E92870. doi: 10. 1371/journal.pone.0092870 PMID: 24671209
    • (2014) PLoS One , vol.9 , pp. e92870
    • Li, T.1    Tracka, M.B.2    Uddin, S.3    Casas-Finet, J.4    Jacobs, D.J.5    Livesay, D.R.6
  • 145
    • 84870579518 scopus 로고    scopus 로고
    • Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding
    • PMID: 23150595
    • Fenley AT, Muddana HS, Gilson MK. Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad Sci U S A. 2012; 109: 20006-20011. doi: 10.1073/pnas.1213180109 PMID: 23150595
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 20006-20011
    • Fenley, A.T.1    Muddana, H.S.2    Gilson, M.K.3
  • 146
    • 77955559261 scopus 로고    scopus 로고
    • Interaction of the Hsp110 molecular chaperones from S. Cerevisiae with substrate protein
    • PMID: 20624400
    • Polier S, Hartl FU, Bracher A. Interaction of the Hsp110 molecular chaperones from S. cerevisiae with substrate protein. J Mol Biol. 2010; 401: 696-707. doi: 10.1016/j.jmb.2010.07.004 PMID: 20624400
    • (2010) J Mol Biol , vol.401 , pp. 696-707
    • Polier, S.1    Hartl, F.U.2    Bracher, A.3
  • 147
    • 61449101487 scopus 로고    scopus 로고
    • Allosteric communication occurs via networks of tertiary and quaternary motions in proteins
    • PMID: 19229311
    • Daily MD, Gray JJ. Allosteric communication occurs via networks of tertiary and quaternary motions in proteins. PLoS Comput Biol. 2009; 5: E1000293. doi: 10.1371/journal.pcbi.1000293 PMID: 19229311
    • (2009) PLoS Comput Biol , vol.5 , pp. e1000293
    • Daily, M.D.1    Gray, J.J.2
  • 148
    • 78751665063 scopus 로고    scopus 로고
    • Correlating allostery with rigidity
    • PMID: 21060909
    • Rader AJ, Brown SM. Correlating allostery with rigidity. Mol Biosyst. 2011; 7: 464-471. doi: 10.1039/ c0mb00054j PMID: 21060909
    • (2011) Mol Biosyst , vol.7 , pp. 464-471
    • Rader, A.J.1    Brown, S.M.2
  • 149
    • 84859455527 scopus 로고    scopus 로고
    • Structure-based model of allostery predicts coupling between distant sites
    • PMID: 22403063
    • Weinkam P, Pons J, Sali A. Structure-based model of allostery predicts coupling between distant sites. Proc Natl Acad Sci U S A. 2012; 109: 4875-4880. doi: 10.1073/pnas.1116274109 PMID: 22403063
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 4875-4880
    • Weinkam, P.1    Pons, J.2    Sali, A.3
  • 150
    • 51649113464 scopus 로고    scopus 로고
    • Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
    • PMID: 18487297
    • Emperador A, Carrillo O, Rueda M, Orozco M. Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. Biophys J. 2008; 95: 2127-2138. doi: 10.1529/biophysj. 107.119115 PMID: 18487297
    • (2008) Biophys J , vol.95 , pp. 2127-2138
    • Emperador, A.1    Carrillo, O.2    Rueda, M.3    Orozco, M.4
  • 151
    • 77949346997 scopus 로고    scopus 로고
    • Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials
    • PMID: 19816993
    • Emperador A, Meyer T, Orozco M. Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials. Proteins. 2010; 78: 83-94. doi: 10.1002/prot.22563 PMID: 19816993
    • (2010) Proteins , vol.78 , pp. 83-94
    • Emperador, A.1    Meyer, T.2    Orozco, M.3
  • 153
    • 84880986455 scopus 로고    scopus 로고
    • Exploration of conformational transition pathways from coarse-grained simulations
    • PMID: 23740746
    • Sfriso P, Hospital A, Emperador A, Orozco M. Exploration of conformational transition pathways from coarse-grained simulations. Bioinformatics. 2013; 29: 1980-1986. doi: 10.1093/bioinformatics/btt324 PMID: 23740746
    • (2013) Bioinformatics , vol.29 , pp. 1980-1986
    • Sfriso, P.1    Hospital, A.2    Emperador, A.3    Orozco, M.4
  • 156
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • PMID: 11045621
    • Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Protein Sci. 2000; 9: 1753-1773. PMID: 11045621
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 157
    • 33747863016 scopus 로고    scopus 로고
    • ArchPRED: A template based loop structure prediction server
    • PMID: 16844985
    • Fernandez-Fuentes N, Zhai J, Fiser A. ArchPRED: A template based loop structure prediction server. Nucleic Acids Res. 2006; 34: W173-W176. PMID: 16844985
    • (2006) Nucleic Acids Res , vol.34 , pp. W173-W176
    • Fernandez-Fuentes, N.1    Zhai, J.2    Fiser, A.3
  • 159
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • PMID: 24889800
    • MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998; 102: 3586-3616. doi: 10.1021/jp973084f PMID: 24889800
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1    Bashford, D.2    Bellott, M.3    Dunbrack, R.L.4    Evanseck, J.D.5    Field, M.J.6
  • 160
    • 84862098170 scopus 로고    scopus 로고
    • Probing molecular mechanisms of the Hsp90 chaperone: Biophysical modeling identifies key regulators of functional dynamics
    • PMID: 22624053
    • Dixit A, Verkhivker GM. Probing molecular mechanisms of the Hsp90 chaperone: Biophysical modeling identifies key regulators of functional dynamics. PLoS One. 2012; 7: E37605. doi: 10.1371/journal. pone.0037605 PMID: 22624053
    • (2012) PLoS One , vol.7 , pp. e37605
    • Dixit, A.1    Verkhivker, G.M.2
  • 161
    • 84888606976 scopus 로고    scopus 로고
    • Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: A computational study
    • PMID: 23977182
    • Blacklock K, Verkhivker G. Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: A computational study. PLoS One. 2013; 8: E71936. doi: 10.1371/journal.pone.0071936 PMID: 23977182
    • (2013) PLoS One , vol.8 , pp. e71936
    • Blacklock, K.1    Verkhivker, G.2
  • 162
    • 84903398935 scopus 로고    scopus 로고
    • Computational modeling of allosteric regulation in the hsp90 chaperones: A statistical ensemble analysis of protein structure networks and allosteric communications
    • PMID: 24922508
    • Blacklock K, Verkhivker GM. Computational modeling of allosteric regulation in the hsp90 chaperones: A statistical ensemble analysis of protein structure networks and allosteric communications. PLoS Comput Biol. 2014; 10: E1003679. doi: 10.1371/journal.pcbi.1003679 PMID: 24922508
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003679
    • Blacklock, K.1    Verkhivker, G.M.2
  • 163
    • 84883743019 scopus 로고    scopus 로고
    • Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories
    • PMID: 24159629
    • Koukos PI, Glykos NM. Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories. J Comput Chem. 2013; 34: 2310-2312. PMID: 24159629
    • (2013) J Comput Chem , vol.34 , pp. 2310-2312
    • Koukos, P.I.1    Glykos, N.M.2
  • 164
    • 33750407288 scopus 로고    scopus 로고
    • Anisotropic network model: Systematic evaluation and a new web interface
    • Eyal E, Yang LW, Bahar I. Anisotropic network model: Systematic evaluation and a new web interface, Bioinformatics. 2006; 22: 2619-2627.
    • (2006) Bioinformatics , vol.22 , pp. 2619-2627
    • Eyal, E.1    Yang, L.W.2    Bahar, I.3
  • 165
    • 66149086947 scopus 로고    scopus 로고
    • Dynamical networks in tRNA: Protein complexes
    • PMID: 19351898
    • Sethi A, Eargle J, Black AA, Luthey-Schulten Z. Dynamical networks in tRNA: Protein complexes. Proc Natl Acad Sci USA. 2009; 106: 6620-6625. doi: 10.1073/pnas.0810961106 PMID: 19351898
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 6620-6625
    • Sethi, A.1    Eargle, J.2    Black, A.A.3    Luthey-Schulten, Z.4
  • 167
    • 20444504323 scopus 로고    scopus 로고
    • Uncovering the overlapping community structure of complex networks in nature and society
    • PMID: 15944704
    • Palla G, Derényi I, Farkas I, Vicsek T. Uncovering the overlapping community structure of complex networks in nature and society. Nature. 2005; 435: 814-818. PMID: 15944704
    • (2005) Nature , vol.435 , pp. 814-818
    • Palla, G.1    Derényi, I.2    Farkas, I.3    Vicsek, T.4
  • 168
    • 33645830948 scopus 로고    scopus 로고
    • Finder: Locating cliques and overlapping modules in biological networks
    • PMID: 16473872
    • Adamcsek B, Palla G, Farkas IJ, Derényi I, Vicsek T. CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics. 2006; 22: 1021-1023. PMID: 16473872
    • (2006) Bioinformatics , vol.22 , pp. 1021-1023
    • Adamcsek, B.1    Palla, G.2    Farkas, I.J.3    Derényi, I.4    Vicsek, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.