메뉴 건너뛰기




Volumn 10, Issue 8, 2014, Pages 3550-3562

Hamiltonian Switch Metropolis Monte Carlo simulations for improved conformational sampling of intrinsically disordered regions tethered to ordered domains of proteins

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84906277469     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct5002297     Document Type: Article
Times cited : (31)

References (125)
  • 2
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson, H. J.; Wright, P. E. Intrinsically unstructured proteins and their functions Nature Rev. Cell. Mol. Biol. 2005, 6, 197-208
    • (2005) Nature Rev. Cell. Mol. Biol. , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 3
    • 0036468397 scopus 로고    scopus 로고
    • Coupling of folding and binding for unstructured proteins
    • Dyson, H. J.; Wright, P. E. Coupling of folding and binding for unstructured proteins Curr. Opin. Struct. Biol. 2002, 12 (1) 54-60
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , Issue.1 , pp. 54-60
    • Dyson, H.J.1    Wright, P.E.2
  • 4
    • 0032559232 scopus 로고    scopus 로고
    • Induced folding in RNA-protein recognition: More than a simple molecular handshake
    • Frankel, A. D.; Smith, C. A. Induced folding in RNA-protein recognition: More than a simple molecular handshake Cell 1998, 92 (2) 149-151
    • (1998) Cell , vol.92 , Issue.2 , pp. 149-151
    • Frankel, A.D.1    Smith, C.A.2
  • 5
    • 0141634346 scopus 로고    scopus 로고
    • Binding-induced folding transitions in calpastatin subdomains A and C
    • Mucsi, Z.; Hudecz, F.; Hollosi, M.; Tompa, P.; Friedrich, P. Binding-induced folding transitions in calpastatin subdomains A and C Protein Sci. 2003, 12 (10) 2327-2336
    • (2003) Protein Sci. , vol.12 , Issue.10 , pp. 2327-2336
    • Mucsi, Z.1    Hudecz, F.2    Hollosi, M.3    Tompa, P.4    Friedrich, P.5
  • 8
    • 84865689638 scopus 로고    scopus 로고
    • Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins
    • Ganguly, D.; Otieno, S.; Waddell, B.; Iconaru, L.; Kriwacki, R. W.; Chen, J. Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins J. Mol. Biol. 2012, 422 (5) 674-684
    • (2012) J. Mol. Biol. , vol.422 , Issue.5 , pp. 674-684
    • Ganguly, D.1    Otieno, S.2    Waddell, B.3    Iconaru, L.4    Kriwacki, R.W.5    Chen, J.6
  • 9
    • 0029662315 scopus 로고    scopus 로고
    • Structural studies of p21(Waf1/Cip1/Sdi1) in the free and Cdk2-bound state: Conformational disorder mediates binding diversity
    • Kriwacki, R. W.; Hengst, L.; Tennant, L.; Reed, S. I.; Wright, P. E. Structural studies of p21(Waf1/Cip1/Sdi1) in the free and Cdk2-bound state: Conformational disorder mediates binding diversity Proc. Natl. Acad. Sci. U.S.A. 1996, 93 (21) 11504-11509
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , Issue.21 , pp. 11504-11509
    • Kriwacki, R.W.1    Hengst, L.2    Tennant, L.3    Reed, S.I.4    Wright, P.E.5
  • 11
    • 84860863700 scopus 로고    scopus 로고
    • Cell-free formation of RNA granules: Bound RNAs identify features and components of cellular assemblies
    • Han, T. W.; Kato, M.; Xie, S.; Wu, L. C.; Mirzaei, H.; Pei, J.; Chen, M.; Xie, Y.; Allen, J.; Xiao, G.; McKnight, S. L. Cell-free formation of RNA granules: Bound RNAs identify features and components of cellular assemblies Cell 2012, 149 (4) 768-779
    • (2012) Cell , vol.149 , Issue.4 , pp. 768-779
    • Han, T.W.1    Kato, M.2    Xie, S.3    Wu, L.C.4    Mirzaei, H.5    Pei, J.6    Chen, M.7    Xie, Y.8    Allen, J.9    Xiao, G.10    McKnight, S.L.11
  • 13
    • 84888440451 scopus 로고    scopus 로고
    • Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains
    • Kwon, I.; Kato, M.; Xiang, S.; Wu, L.; Theodoropoulos, P.; Mirzaei, H.; Han, T.; Xie, S.; Corden, J. L.; McKnight, S. L. Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains Cell 2013, 155 (5) 1049-1060
    • (2013) Cell , vol.155 , Issue.5 , pp. 1049-1060
    • Kwon, I.1    Kato, M.2    Xiang, S.3    Wu, L.4    Theodoropoulos, P.5    Mirzaei, H.6    Han, T.7    Xie, S.8    Corden, J.L.9    McKnight, S.L.10
  • 14
    • 84892696339 scopus 로고    scopus 로고
    • Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains (vol 155, pg 1049, 2013)
    • Kwon, I.; Kato, M.; Xiang, S.; Wu, L.; Theodoropoulos, P.; Mirzaei, H.; Han, T.; Xie, S.; Corden, J. L.; McKnight, S. L. Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains (vol 155, pg 1049, 2013) Cell 2014, 156 (1-2) 374-374
    • (2014) Cell , vol.156 , Issue.12 , pp. 374-374
    • Kwon, I.1    Kato, M.2    Xiang, S.3    Wu, L.4    Theodoropoulos, P.5    Mirzaei, H.6    Han, T.7    Xie, S.8    Corden, J.L.9    McKnight, S.L.10
  • 15
    • 80053353760 scopus 로고    scopus 로고
    • Single molecule study of the intrinsically disordered FG-repeat nucleoporin 153
    • Milles, S.; Lemke, E. A. Single molecule study of the intrinsically disordered FG-repeat nucleoporin 153 Biophys. J. 2011, 101 (7) 1710-1719
    • (2011) Biophys. J. , vol.101 , Issue.7 , pp. 1710-1719
    • Milles, S.1    Lemke, E.A.2
  • 16
    • 77958056909 scopus 로고    scopus 로고
    • Structural classification of proteins and structural genomics: New insights into protein folding and evolution
    • Andreeva, A.; Murzin, A. G. Structural classification of proteins and structural genomics: New insights into protein folding and evolution Acta Crystall. F-Struct. Biol. Crystall. Commun. 2010, 66, 1190-1197
    • (2010) Acta Crystall. F-Struct. Biol. Crystall. Commun. , vol.66 , pp. 1190-1197
    • Andreeva, A.1    Murzin, A.G.2
  • 18
    • 0036384350 scopus 로고    scopus 로고
    • One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures, and functions
    • Nagano, N.; Orengo, C. A.; Thornton, J. M. One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures, and functions J. Mol. Biol. 2002, 321 (5) 741-765
    • (2002) J. Mol. Biol. , vol.321 , Issue.5 , pp. 741-765
    • Nagano, N.1    Orengo, C.A.2    Thornton, J.M.3
  • 20
    • 70350321301 scopus 로고    scopus 로고
    • Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding
    • Toth-Petroczy, A.; Simon, I.; Fuxreiter, M.; Levy, Y. Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding J. Am. Chem. Soc. 2009, 131 (42) 15084-15085
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.42 , pp. 15084-15085
    • Toth-Petroczy, A.1    Simon, I.2    Fuxreiter, M.3    Levy, Y.4
  • 21
    • 78650453629 scopus 로고    scopus 로고
    • DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail
    • Vuzman, D.; Levy, Y. DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail Proc. Natl. Acad. Sci. U.S.A. 2010, 107 (49) 21004-21009
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , Issue.49 , pp. 21004-21009
    • Vuzman, D.1    Levy, Y.2
  • 22
    • 79953695332 scopus 로고    scopus 로고
    • Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains
    • Khazanov, N.; Levy, Y. Sliding of p53 along DNA can be modulated by its oligomeric state and by cross-talks between its constituent domains J. Mol. Biol. 2011, 408 (2) 335-355
    • (2011) J. Mol. Biol. , vol.408 , Issue.2 , pp. 335-355
    • Khazanov, N.1    Levy, Y.2
  • 23
    • 82655179905 scopus 로고    scopus 로고
    • Intrinsically disordered regions as affinity tuners in protein-DNA interactions
    • Vuzman, D.; Levy, Y. Intrinsically disordered regions as affinity tuners in protein-DNA interactions Mol. BioSys. 2012, 8 (1) 47-57
    • (2012) Mol. BioSys. , vol.8 , Issue.1 , pp. 47-57
    • Vuzman, D.1    Levy, Y.2
  • 24
    • 82655179907 scopus 로고    scopus 로고
    • Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: Association of HIF1 α with CBP
    • De Sancho, D.; Best, R. B. Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: Association of HIF1 α with CBP Mol. BioSys. 2012, 8 (1) 256-267
    • (2012) Mol. BioSys. , vol.8 , Issue.1 , pp. 256-267
    • De Sancho, D.1    Best, R.B.2
  • 25
    • 84864581257 scopus 로고    scopus 로고
    • A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: Evidence from molecular simulations
    • Knott, M.; Best, R. B. A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: Evidence from molecular simulations PLos Comput. Biol. 2012, 8 (7) e1002605(1-10)
    • (2012) PLos Comput. Biol. , vol.8 , Issue.7 , pp. 10026051-10026110
    • Knott, M.1    Best, R.B.2
  • 26
    • 44949262123 scopus 로고    scopus 로고
    • Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins
    • Tran, H. T.; Mao, A.; Pappu, R. V. Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins J. Am. Chem. Soc. 2008, 130 (23) 7380-7392
    • (2008) J. Am. Chem. Soc. , vol.130 , Issue.23 , pp. 7380-7392
    • Tran, H.T.1    Mao, A.2    Pappu, R.V.3
  • 27
    • 84873441997 scopus 로고    scopus 로고
    • Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure
    • Meng, W. L.; Lyle, N.; Luan, B. W.; Raleigh, D. P.; Pappu, R. V. Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure Proc. Natl. Acad. Sci. U.S.A. 2013, 110 (6) 2123-2128
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , Issue.6 , pp. 2123-2128
    • Meng, W.L.1    Lyle, N.2    Luan, B.W.3    Raleigh, D.P.4    Pappu, R.V.5
  • 28
    • 84882364963 scopus 로고    scopus 로고
    • Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
    • Das, R. K.; Pappu, R. V. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues Proc. Natl. Acad. Sci. U.S.A. 2013, 110 (33) 13392-13397
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , Issue.33 , pp. 13392-13397
    • Das, R.K.1    Pappu, R.V.2
  • 29
    • 84856434005 scopus 로고    scopus 로고
    • N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins
    • Das, R. K.; Crick, S. L.; Pappu, R. V. N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins J. Mol. Biol. 2012, 416 (2) 287-99
    • (2012) J. Mol. Biol. , vol.416 , Issue.2 , pp. 287-299
    • Das, R.K.1    Crick, S.L.2    Pappu, R.V.3
  • 30
    • 77952335311 scopus 로고    scopus 로고
    • Net charge per residue modulates conformational ensembles of intrinsically disordered proteins
    • Mao, A. H.; Crick, S. L.; Vitalis, A.; Chicoine, C. L.; Pappu, R. V. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins Proc. Natl. Acad. Sci. U.S.A. 2010, 107 (18) 8183-8188
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , Issue.18 , pp. 8183-8188
    • Mao, A.H.1    Crick, S.L.2    Vitalis, A.3    Chicoine, C.L.4    Pappu, R.V.5
  • 31
    • 84857492391 scopus 로고    scopus 로고
    • Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins
    • (1-15).
    • Zhang, W. H.; Ganguly, D.; Chen, J. H. Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins PLos Comput. Biol. 2012, 8 (1) e1002353 (1-15).
    • (2012) PLos Comput. Biol. , vol.8 , Issue.1 , pp. 1002353
    • Zhang, W.H.1    Ganguly, D.2    Chen, J.H.3
  • 33
    • 84865333057 scopus 로고    scopus 로고
    • Application of confocal single-molecule FRET to intrinsically disordered proteins
    • Schuler, B.; Muller-Spath, S.; Soranno, A.; Nettels, D. Application of confocal single-molecule FRET to intrinsically disordered proteins Methods Mol. Biol. 2012, 896, 21-45
    • (2012) Methods Mol. Biol. , vol.896 , pp. 21-45
    • Schuler, B.1    Muller-Spath, S.2    Soranno, A.3    Nettels, D.4
  • 34
    • 84867048390 scopus 로고    scopus 로고
    • Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
    • Hofmann, H.; Soranno, A.; Borgia, A.; Gast, K.; Nettels, D.; Schuler, B. Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy Proc. Natl. Acad. Sci. U.S.A. 2012, 109 (40) 16155-16160
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , Issue.40 , pp. 16155-16160
    • Hofmann, H.1    Soranno, A.2    Borgia, A.3    Gast, K.4    Nettels, D.5    Schuler, B.6
  • 36
    • 65249185574 scopus 로고    scopus 로고
    • Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence
    • Ferreon, A. C. M.; Gambin, Y.; Lemke, E. A.; Deniz, A. A. Interplay of α-synuclein binding and conformational switching probed by single-molecule fluorescence Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (14) 5645-5650
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , Issue.14 , pp. 5645-5650
    • Ferreon, A.C.M.1    Gambin, Y.2    Lemke, E.A.3    Deniz, A.A.4
  • 37
    • 33847324863 scopus 로고    scopus 로고
    • A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures
    • Mukhopadhyay, S.; Krishnan, R.; Lemke, E. A.; Lindquist, S.; Deniz, A. A. A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (8) 2649-2654
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , Issue.8 , pp. 2649-2654
    • Mukhopadhyay, S.1    Krishnan, R.2    Lemke, E.A.3    Lindquist, S.4    Deniz, A.A.5
  • 38
    • 84879327823 scopus 로고    scopus 로고
    • Modulation of allostery by protein intrinsic disorder
    • Ferreon, A. C. M.; Ferreon, J. C.; Wright, P. E.; Deniz, A. A. Modulation of allostery by protein intrinsic disorder Nature 2013, 498 (7454) 390-396
    • (2013) Nature , vol.498 , Issue.7454 , pp. 390-396
    • Ferreon, A.C.M.1    Ferreon, J.C.2    Wright, P.E.3    Deniz, A.A.4
  • 39
    • 84868091323 scopus 로고    scopus 로고
    • Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape
    • Ferreon, A. C. M.; Moosa, M. M.; Gambin, Y.; Deniz, A. A. Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape Proc. Natl. Acad. Sci. U.S.A. 2012, 109 (44) 17826-17831
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , Issue.44 , pp. 17826-17831
    • Ferreon, A.C.M.1    Moosa, M.M.2    Gambin, Y.3    Deniz, A.A.4
  • 40
    • 77957037991 scopus 로고    scopus 로고
    • Single-molecule fluorescence studies of intrinsically disordered proteins
    • Ferreon, A. C. M.; Moran, C. R.; Gambin, Y.; Deniz, A. A. Single-molecule fluorescence studies of intrinsically disordered proteins Methods Enzymol. 2010, 472, 179-204
    • (2010) Methods Enzymol. , vol.472 , pp. 179-204
    • Ferreon, A.C.M.1    Moran, C.R.2    Gambin, Y.3    Deniz, A.A.4
  • 41
    • 68849085159 scopus 로고    scopus 로고
    • High-resolution temperature-concentration diagram of α-synuclein conformation obtained from a single forster resonance energy transfer image in a microfluidic device
    • Vandelinder, V.; Ferreon, A. C. M.; Gambin, Y.; Deniz, A. A.; Groisman, A. High-resolution temperature-concentration diagram of α-synuclein conformation obtained from a single forster resonance energy transfer image in a microfluidic device Analyt. Chem. 2009, 81 (16) 6929-6935
    • (2009) Analyt. Chem. , vol.81 , Issue.16 , pp. 6929-6935
    • Vandelinder, V.1    Ferreon, A.C.M.2    Gambin, Y.3    Deniz, A.A.4    Groisman, A.5
  • 42
    • 79953838275 scopus 로고    scopus 로고
    • Beyond the random coil: Stochastic conformational switching in intrinsically disordered proteins
    • Choi, U. B.; McCann, J. J.; Weninger, K. R.; Bowen, M. E. Beyond the random coil: Stochastic conformational switching in intrinsically disordered proteins Structure 2011, 19 (4) 566-576
    • (2011) Structure , vol.19 , Issue.4 , pp. 566-576
    • Choi, U.B.1    McCann, J.J.2    Weninger, K.R.3    Bowen, M.E.4
  • 43
    • 84857698871 scopus 로고    scopus 로고
    • Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase
    • Tang, X. J.; Orlicky, S.; Mittag, T.; Csizmok, V.; Pawson, T.; Forman-Kay, J. D.; Sicheri, F.; Tyers, M. Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase Proc. Natl. Acad. Sci. U.S.A. 2012, 109 (9) 3287-3292
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , Issue.9 , pp. 3287-3292
    • Tang, X.J.1    Orlicky, S.2    Mittag, T.3    Csizmok, V.4    Pawson, T.5    Forman-Kay, J.D.6    Sicheri, F.7    Tyers, M.8
  • 45
    • 84860168892 scopus 로고    scopus 로고
    • Mechanism of Cell Cycle. Entry Mediated by the Intrinsically Disordered Protein p27(Kip1)
    • Ou, L.; Waddell, M. B.; Kriwacki, R. W. Mechanism of Cell Cycle. Entry Mediated by the Intrinsically Disordered Protein p27(Kip1) ACS Chem. Biol. 2012, 7 (4) 678-682
    • (2012) ACS Chem. Biol. , vol.7 , Issue.4 , pp. 678-682
    • Ou, L.1    Waddell, M.B.2    Kriwacki, R.W.3
  • 48
    • 65449119145 scopus 로고    scopus 로고
    • Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains
    • Wojciak, J. M.; Martinez-Yamout, M. A.; Dyson, H. J.; Wright, P. E. Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains EMBO J. 2009, 28 (7) 948-958
    • (2009) EMBO J. , vol.28 , Issue.7 , pp. 948-958
    • Wojciak, J.M.1    Martinez-Yamout, M.A.2    Dyson, H.J.3    Wright, P.E.4
  • 49
    • 33750934185 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions
    • Crick, S. L.; Jayaraman, M.; Frieden, C.; Wetzel, R.; Pappu, R. V. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (45) 16764-16769
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , Issue.45 , pp. 16764-16769
    • Crick, S.L.1    Jayaraman, M.2    Frieden, C.3    Wetzel, R.4    Pappu, R.V.5
  • 50
    • 77951645923 scopus 로고    scopus 로고
    • Sequence determinants of compaction in intrinsically disordered proteins
    • Marsh, J. A.; Forman-Kay, J. D. Sequence determinants of compaction in intrinsically disordered proteins Biophys. J. 2010, 98 (10) 2383-2390
    • (2010) Biophys. J. , vol.98 , Issue.10 , pp. 2383-2390
    • Marsh, J.A.1    Forman-Kay, J.D.2
  • 51
    • 84871427941 scopus 로고    scopus 로고
    • Describing sequence-ensemble relationships for intrinsically disordered proteins
    • Mao, A. H.; Lyle, N.; Pappu, R. V. Describing sequence-ensemble relationships for intrinsically disordered proteins Biochem. J. 2013, 449, 307-318
    • (2013) Biochem. J. , vol.449 , pp. 307-318
    • Mao, A.H.1    Lyle, N.2    Pappu, R.V.3
  • 52
    • 84885449854 scopus 로고    scopus 로고
    • A quantitative measure for protein conformational heterogeneity
    • Lyle, N.; Das, R. K.; Pappu, R. V. A quantitative measure for protein conformational heterogeneity J. Chem. Phys. 2013, 139 (12) 121907(1-12)
    • (2013) J. Chem. Phys. , vol.139 , Issue.12 , pp. 1219071-1219112
    • Lyle, N.1    Das, R.K.2    Pappu, R.V.3
  • 53
    • 84875885473 scopus 로고    scopus 로고
    • Comparative studies of disordered proteins with similar sequences: Application to A β-40 and A β-42
    • Fisher, C. K.; Ullman, O.; Stultz, C. M. Comparative studies of disordered proteins with similar sequences: Application to A β-40 and A β-42 Biophys. J. 2013, 104 (7) 1546-1555
    • (2013) Biophys. J. , vol.104 , Issue.7 , pp. 1546-1555
    • Fisher, C.K.1    Ullman, O.2    Stultz, C.M.3
  • 54
    • 79958037883 scopus 로고    scopus 로고
    • Constructing ensembles for intrinsically disordered proteins
    • Fisher, C. K.; Stultz, C. M. Constructing ensembles for intrinsically disordered proteins Curr. Opin. Struct. Biol. 2011, 21 (3) 426-431
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , Issue.3 , pp. 426-431
    • Fisher, C.K.1    Stultz, C.M.2
  • 55
    • 79959903065 scopus 로고    scopus 로고
    • Protein structure along the order-disorder continuum
    • Fisher, C. K.; Stultz, C. M. Protein structure along the order-disorder continuum J. Am. Chem. Soc. 2011, 133 (26) 10022-10025
    • (2011) J. Am. Chem. Soc. , vol.133 , Issue.26 , pp. 10022-10025
    • Fisher, C.K.1    Stultz, C.M.2
  • 56
    • 77958510026 scopus 로고    scopus 로고
    • Modeling intrinsically disordered proteins with Bayesian statistics
    • Fisher, C. K.; Huang, A.; Stultz, C. M. Modeling intrinsically disordered proteins with Bayesian statistics J. Am. Chem. Soc. 2010, 132 (42) 14919-14927
    • (2010) J. Am. Chem. Soc. , vol.132 , Issue.42 , pp. 14919-14927
    • Fisher, C.K.1    Huang, A.2    Stultz, C.M.3
  • 57
    • 84866463338 scopus 로고    scopus 로고
    • Versatility from protein disorder
    • Babu, M. M.; Kriwacki, R. W.; Pappu, R. V. Versatility from protein disorder Science 2012, 337, 1460-1461
    • (2012) Science , vol.337 , pp. 1460-1461
    • Babu, M.M.1    Kriwacki, R.W.2    Pappu, R.V.3
  • 58
    • 0035163689 scopus 로고    scopus 로고
    • Predicting properties of intrinsically unstructured proteins
    • Bright, J. N.; Woolf, T. B.; Hoh, J. H. Predicting properties of intrinsically unstructured proteins Prog. Biophys. Mol. Biol. 2001, 76 (3) 131-173
    • (2001) Prog. Biophys. Mol. Biol. , vol.76 , Issue.3 , pp. 131-173
    • Bright, J.N.1    Woolf, T.B.2    Hoh, J.H.3
  • 59
    • 55749083564 scopus 로고    scopus 로고
    • Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm
    • Papoian, G. A. Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (38) 14237-14238
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , Issue.38 , pp. 14237-14238
    • Papoian, G.A.1
  • 60
    • 69449096819 scopus 로고    scopus 로고
    • Methods for Monte Carlo simulations of biomacromolecules
    • Vitalis, A.; Pappu, R. V. Methods for Monte Carlo simulations of biomacromolecules Annu. Rep. Comput. Chem. 2009, 5, 49-76
    • (2009) Annu. Rep. Comput. Chem. , vol.5 , pp. 49-76
    • Vitalis, A.1    Pappu, R.V.2
  • 62
    • 64549131279 scopus 로고    scopus 로고
    • ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions
    • Vitalis, A.; Pappu, R. V. ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions J. Comput. Chem. 2009, 30 (5) 673-699
    • (2009) J. Comput. Chem. , vol.30 , Issue.5 , pp. 673-699
    • Vitalis, A.1    Pappu, R.V.2
  • 63
    • 84862278772 scopus 로고    scopus 로고
    • Improved atomistic Monte Carlo simulations demonstrate that poly- l -proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks
    • Radhakrishnan, A.; Vitalis, A.; Mao, A. H.; Steffen, A. T.; Pappu, R. V. Improved atomistic Monte Carlo simulations demonstrate that poly- l -proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks J. Phys. Chem. B 2012, 116 (23) 6862-6871
    • (2012) J. Phys. Chem. B , vol.116 , Issue.23 , pp. 6862-6871
    • Radhakrishnan, A.1    Vitalis, A.2    Mao, A.H.3    Steffen, A.T.4    Pappu, R.V.5
  • 64
    • 84865165611 scopus 로고    scopus 로고
    • Crystal lattice properties fully determine short-range interaction parameters for alkali and halide ions
    • Mao, A. H.; Pappu, R. V. Crystal lattice properties fully determine short-range interaction parameters for alkali and halide ions J. Chem. Phys. 2012, 137 (6) 064104(1-9)
    • (2012) J. Chem. Phys. , vol.137 , Issue.6 , pp. 0641041-0641049
    • Mao, A.H.1    Pappu, R.V.2
  • 65
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314 (1-2) 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , Issue.12 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 66
    • 0034864528 scopus 로고    scopus 로고
    • Generalized-ensemble algorithms for molecular simulations of biopolymers
    • Mitsutake, A.; Sugita, Y.; Okamoto, Y. Generalized-ensemble algorithms for molecular simulations of biopolymers Biopolymers 2001, 60 (2) 96-123
    • (2001) Biopolymers , vol.60 , Issue.2 , pp. 96-123
    • Mitsutake, A.1    Sugita, Y.2    Okamoto, Y.3
  • 67
    • 77957256708 scopus 로고    scopus 로고
    • Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for a β aggregation
    • Vitalis, A.; Caflisch, A. Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for a β aggregation J. Mol. Biol. 2010, 403 (1) 148-165
    • (2010) J. Mol. Biol. , vol.403 , Issue.1 , pp. 148-165
    • Vitalis, A.1    Caflisch, A.2
  • 68
    • 68949127591 scopus 로고    scopus 로고
    • Thermodynamics of β-sheet formation in polyglutamine
    • Vitalis, A.; Lyle, N.; Pappu, R. V. Thermodynamics of β-sheet formation in polyglutamine Biophys. J. 2009, 97 (1) 303-311
    • (2009) Biophys. J. , vol.97 , Issue.1 , pp. 303-311
    • Vitalis, A.1    Lyle, N.2    Pappu, R.V.3
  • 69
    • 17444366185 scopus 로고    scopus 로고
    • Temperature weighted histogram analysis method, replica exchange, and transition paths
    • Gallicchio, E.; Andrec, M.; Felts, A. K.; Levy, R. M. Temperature weighted histogram analysis method, replica exchange, and transition paths J. Phys. Chem. B 2005, 109 (14) 6722-6731
    • (2005) J. Phys. Chem. B , vol.109 , Issue.14 , pp. 6722-6731
    • Gallicchio, E.1    Andrec, M.2    Felts, A.K.3    Levy, R.M.4
  • 70
    • 79960157219 scopus 로고    scopus 로고
    • Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures
    • Chodera, J. D.; Swope, W. C.; Noe, F.; Prinz, J. H.; Shirts, M. R.; Pande, V. S. Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures J. Chem. Phys. 2011, 134 (24) 244107(1-15)
    • (2011) J. Chem. Phys. , vol.134 , Issue.24 , pp. 2441071-2441115
    • Chodera, J.D.1    Swope, W.C.2    Noe, F.3    Prinz, J.H.4    Shirts, M.R.5    Pande, V.S.6
  • 71
    • 84879107473 scopus 로고    scopus 로고
    • Efficiency of adaptive temperature-based replica exchange for sampling large-scale protein conformational transitions
    • Zhang, W.; Chen, J. H. Efficiency of adaptive temperature-based replica exchange for sampling large-scale protein conformational transitions J. Chem. Theory Comput. 2013, 9 (6) 2849-2856
    • (2013) J. Chem. Theory Comput. , vol.9 , Issue.6 , pp. 2849-2856
    • Zhang, W.1    Chen, J.H.2
  • 72
    • 0037961507 scopus 로고    scopus 로고
    • Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test
    • Mitsutake, A.; Sugita, Y.; Okamoto, Y. Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test J. Chem. Phys. 2003, 118 (14) 6664-6675
    • (2003) J. Chem. Phys. , vol.118 , Issue.14 , pp. 6664-6675
    • Mitsutake, A.1    Sugita, Y.2    Okamoto, Y.3
  • 73
    • 0034294024 scopus 로고    scopus 로고
    • Multidimensional replica-exchange method for free-energy calculations
    • Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional replica-exchange method for free-energy calculations J. Chem. Phys. 2000, 113 (15) 6042-6051
    • (2000) J. Chem. Phys. , vol.113 , Issue.15 , pp. 6042-6051
    • Sugita, Y.1    Kitao, A.2    Okamoto, Y.3
  • 74
    • 0038515446 scopus 로고    scopus 로고
    • Monte Carlo simulations using sampling from an approximate potential
    • Gelb, L. D. Monte Carlo simulations using sampling from an approximate potential J. Chem. Phys. 2003, 118 (17) 7747-7750
    • (2003) J. Chem. Phys. , vol.118 , Issue.17 , pp. 7747-7750
    • Gelb, L.D.1
  • 75
    • 84872302071 scopus 로고    scopus 로고
    • Increasing the efficiency of Monte Carlo simulation with sampling from an approximate potential
    • Bandyopadhyay, P. Increasing the efficiency of Monte Carlo simulation with sampling from an approximate potential Chem. Phys. Lett. 2013, 556, 341-345
    • (2013) Chem. Phys. Lett. , vol.556 , pp. 341-345
    • Bandyopadhyay, P.1
  • 76
    • 77958028868 scopus 로고    scopus 로고
    • Efficiency of nested Markov chain Monte Carlo for polarizable potentials and perturbed Hamiltonians
    • Calvo, F. Efficiency of nested Markov chain Monte Carlo for polarizable potentials and perturbed Hamiltonians Int. J. Quantum Chem. 2010, 110 (13) 2347-2354
    • (2010) Int. J. Quantum Chem. , vol.110 , Issue.13 , pp. 2347-2354
    • Calvo, F.1
  • 77
    • 69249176059 scopus 로고    scopus 로고
    • Nested Markov chain Monte Carlo sampling of a density functional theory potential: Equilibrium thermodynamics of dense fluid nitrogen
    • Coe, J. D.; Sewell, T. D.; Shaw, M. S. Nested Markov chain Monte Carlo sampling of a density functional theory potential: Equilibrium thermodynamics of dense fluid nitrogen J. Chem. Phys. 2009, 131 (7) 074105
    • (2009) J. Chem. Phys. , vol.131 , Issue.7 , pp. 074105
    • Coe, J.D.1    Sewell, T.D.2    Shaw, M.S.3
  • 78
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105 (28) 6474-6487
    • (2001) J. Phys. Chem. B , vol.105 , Issue.28 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 79
    • 0000275936 scopus 로고
    • Preferential sampling near solutes in Monte Carlo calculations on dilute solutions
    • Owicki, J. C.; Scheraga, H. A. Preferential sampling near solutes in Monte Carlo calculations on dilute solutions Chem. Phys. Lett. 1977, 47 (3) 600-602
    • (1977) Chem. Phys. Lett. , vol.47 , Issue.3 , pp. 600-602
    • Owicki, J.C.1    Scheraga, H.A.2
  • 80
    • 0000967315 scopus 로고
    • Sampling methods for Monte-Carlo simulations of normal-butane in dilute-solution
    • Bigot, B.; Jorgensen, W. L. Sampling methods for Monte-Carlo simulations of normal-butane in dilute-solution J. Chem. Phys. 1981, 75 (4) 1944-1952
    • (1981) J. Chem. Phys. , vol.75 , Issue.4 , pp. 1944-1952
    • Bigot, B.1    Jorgensen, W.L.2
  • 81
    • 0000793569 scopus 로고
    • Convergence acceleration in Monte-Carlo computer-simulation on water and aqueous solutions
    • Mehrotra, P. K.; Mezei, M.; Beveridge, D. L. Convergence acceleration in Monte-Carlo computer-simulation on water and aqueous solutions J. Chem. Phys. 1983, 78 (6) 3156-3166
    • (1983) J. Chem. Phys. , vol.78 , Issue.6 , pp. 3156-3166
    • Mehrotra, P.K.1    Mezei, M.2    Beveridge, D.L.3
  • 82
    • 0001454111 scopus 로고
    • Monte Carlo methodologies for enhanced configurational sampling of dense systems-Motion of a spherical solute in a polymer melt as a model problem
    • Leontidis, E.; Suter, U. W. Monte Carlo methodologies for enhanced configurational sampling of dense systems-Motion of a spherical solute in a polymer melt as a model problem Mol. Phys. 1994, 83 (3) 489-518
    • (1994) Mol. Phys. , vol.83 , Issue.3 , pp. 489-518
    • Leontidis, E.1    Suter, U.W.2
  • 83
    • 0037304363 scopus 로고    scopus 로고
    • MC-PHS: A Monte Carlo implementation of the primary hydration shell for protein folding and design
    • Kentsis, A.; Mezei, M.; Osman, R. MC-PHS: A Monte Carlo implementation of the primary hydration shell for protein folding and design Biophys. J. 2003, 84 (2) 805-815
    • (2003) Biophys. J. , vol.84 , Issue.2 , pp. 805-815
    • Kentsis, A.1    Mezei, M.2    Osman, R.3
  • 86
    • 40549083345 scopus 로고    scopus 로고
    • Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange
    • Wyczalkowski, M. A.; Pappu, R. V. Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange Phys. Rev. E 2008, 77 (2) 026104(1-12)
    • (2008) Phys. Rev. e , vol.77 , Issue.2 , pp. 0261041-0261112
    • Wyczalkowski, M.A.1    Pappu, R.V.2
  • 87
    • 0020621373 scopus 로고
    • Van der Waals picture of liquids, solids, and phase transformations
    • Chandler, D.; Weeks, J. D.; Andersen, H. C. Van der Waals picture of liquids, solids, and phase transformations Science 1983, 220 (4599) 787-794
    • (1983) Science , vol.220 , Issue.4599 , pp. 787-794
    • Chandler, D.1    Weeks, J.D.2    Andersen, H.C.3
  • 88
    • 36849114698 scopus 로고
    • Thermodynamic properties of the fluid and solid phases for inverse power potentials
    • Hoover, W. G.; Gray, S. G.; Johnson, K. W. Thermodynamic properties of the fluid and solid phases for inverse power potentials J. Chem. Phys. 1971, 55, 1128-1136
    • (1971) J. Chem. Phys. , vol.55 , pp. 1128-1136
    • Hoover, W.G.1    Gray, S.G.2    Johnson, K.W.3
  • 89
    • 23944453852 scopus 로고    scopus 로고
    • Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins
    • Tran, H. T.; Wang, X.; Pappu, R. V. Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins Biochemistry 2005, 44 (34) 11369-80
    • (2005) Biochemistry , vol.44 , Issue.34 , pp. 11369-11380
    • Tran, H.T.1    Wang, X.2    Pappu, R.V.3
  • 90
    • 84864236589 scopus 로고    scopus 로고
    • Exploring the solid-liquid phase change of an adapted Dzugutov model using generalized replica exchange method
    • Lu, Q.; Kim, J.; Straub, J. E. Exploring the solid-liquid phase change of an adapted Dzugutov model using generalized replica exchange method J. Phys. Chem. B 2012, 116 (29) 8654-8661
    • (2012) J. Phys. Chem. B , vol.116 , Issue.29 , pp. 8654-8661
    • Lu, Q.1    Kim, J.2    Straub, J.E.3
  • 91
    • 0027972206 scopus 로고
    • Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease-A
    • Straub, J. E.; Rashkin, A. B.; Thirumalai, D. Dynamics in rugged energy landscapes with applications to the S-peptide and ribonuclease-A J. Am. Chem. Soc. 1994, 116 (5) 2049-2063
    • (1994) J. Am. Chem. Soc. , vol.116 , Issue.5 , pp. 2049-2063
    • Straub, J.E.1    Rashkin, A.B.2    Thirumalai, D.3
  • 93
    • 84859976535 scopus 로고    scopus 로고
    • Unmasking functional motifs within disordered regions of proteins
    • Das, R. K.; Mao, A. H.; Pappu, R. V. Unmasking functional motifs within disordered regions of proteins Sci. Signal. 2012, 5 (220) pe17
    • (2012) Sci. Signal. , vol.5 , Issue.220 , pp. 17
    • Das, R.K.1    Mao, A.H.2    Pappu, R.V.3
  • 94
    • 0002057815 scopus 로고    scopus 로고
    • Computational studies of clusters: Methods and results
    • Freeman, D. L.; Doll, J. D. Computational studies of clusters: Methods and results Annu. Rev. Phys. Chem. 1996, 47, 43-80
    • (1996) Annu. Rev. Phys. Chem. , vol.47 , pp. 43-80
    • Freeman, D.L.1    Doll, J.D.2
  • 95
    • 0000260836 scopus 로고    scopus 로고
    • Study of the solid-liquid transition for Ar-55 using the J-walking Monte Carlo method
    • Lopez, G. E. Study of the solid-liquid transition for Ar-55 using the J-walking Monte Carlo method J. Chem. Phys. 1996, 104 (17) 6650-6653
    • (1996) J. Chem. Phys. , vol.104 , Issue.17 , pp. 6650-6653
    • Lopez, G.E.1
  • 96
    • 0000666868 scopus 로고    scopus 로고
    • Smart walking: A new method for Boltzmann sampling of protein conformations
    • Zhou, R. H.; Berne, B. J. Smart walking: A new method for Boltzmann sampling of protein conformations J. Chem. Phys. 1997, 107 (21) 9185-9196
    • (1997) J. Chem. Phys. , vol.107 , Issue.21 , pp. 9185-9196
    • Zhou, R.H.1    Berne, B.J.2
  • 97
    • 0034318664 scopus 로고    scopus 로고
    • Approach to ergodicity in Monte Carlo simulations
    • Neirotti, J. P.; Freeman, D. L.; Doll, J. D. Approach to ergodicity in Monte Carlo simulations Phys. Rev. E 2000, 62 (5) 7445-7461
    • (2000) Phys. Rev. e , vol.62 , Issue.5 , pp. 7445-7461
    • Neirotti, J.P.1    Freeman, D.L.2    Doll, J.D.3
  • 98
    • 21244487831 scopus 로고    scopus 로고
    • Stochastic potential switching algorithm for Monte Carlo simulations of complex systems
    • Mak, C. H. Stochastic potential switching algorithm for Monte Carlo simulations of complex systems J. Chem. Phys. 2005, 122 (21) 214110
    • (2005) J. Chem. Phys. , vol.122 , Issue.21 , pp. 214110
    • Mak, C.H.1
  • 99
    • 18644366819 scopus 로고    scopus 로고
    • Combining smart darting with parallel tempering using Eckart space: Application to Lennard-Jones clusters
    • Nigra, P.; Freeman, D. L.; Doll, J. D. Combining smart darting with parallel tempering using Eckart space: Application to Lennard-Jones clusters J. Chem. Phys. 2005, 122 (11) 114113
    • (2005) J. Chem. Phys. , vol.122 , Issue.11 , pp. 114113
    • Nigra, P.1    Freeman, D.L.2    Doll, J.D.3
  • 101
    • 81855228612 scopus 로고    scopus 로고
    • Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
    • Chodera, J. D.; Shirts, M. R. Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing J. Chem. Phys. 2011, 135 (19) 194110
    • (2011) J. Chem. Phys. , vol.135 , Issue.19 , pp. 194110
    • Chodera, J.D.1    Shirts, M.R.2
  • 102
    • 33749997738 scopus 로고    scopus 로고
    • Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces
    • Li, H. Z.; Li, G. H.; Berg, B. A.; Yang, W. Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces J. Chem. Phys. 2006, 125 (14) 144902
    • (2006) J. Chem. Phys. , vol.125 , Issue.14 , pp. 144902
    • Li, H.Z.1    Li, G.H.2    Berg, B.A.3    Yang, W.4
  • 103
    • 34047256709 scopus 로고    scopus 로고
    • Coupling of replica exchange simulations to a non-Boltzmann structure reservoir
    • Roitberg, A. E.; Okur, A.; Simmerling, C. Coupling of replica exchange simulations to a non-Boltzmann structure reservoir J. Phys. Chem. B 2007, 111 (10) 2415-2418
    • (2007) J. Phys. Chem. B , vol.111 , Issue.10 , pp. 2415-2418
    • Roitberg, A.E.1    Okur, A.2    Simmerling, C.3
  • 104
    • 75649134635 scopus 로고    scopus 로고
    • How Hot? Systematic convergence of the replica exchange method using multiple reservoirs
    • Ruscio, J. Z.; Fawzi, N. L.; Head-Gordon, T. How Hot? Systematic convergence of the replica exchange method using multiple reservoirs J. Comput. Chem. 2010, 31 (3) 620-627
    • (2010) J. Comput. Chem. , vol.31 , Issue.3 , pp. 620-627
    • Ruscio, J.Z.1    Fawzi, N.L.2    Head-Gordon, T.3
  • 105
    • 84906245539 scopus 로고    scopus 로고
    • Extending fragment based free energy calculations with library based Monte Carlo simulation: Annealing in interaction space
    • Lettieri, S.; Mamonov, A. B.; Zuckerman, D. M. Extending fragment based free energy calculations with library based Monte Carlo simulation: Annealing in interaction space Biophys. J. 2011, 100 (3) 154-154
    • (2011) Biophys. J. , vol.100 , Issue.3 , pp. 154-154
    • Lettieri, S.1    Mamonov, A.B.2    Zuckerman, D.M.3
  • 106
    • 68149131990 scopus 로고    scopus 로고
    • General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models
    • Mamonov, A. B.; Bhatt, D.; Cashman, D. J.; Ding, Y.; Zuckerman, D. M. General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models J. Phys. Chem. B 2009, 113 (31) 10891-10904
    • (2009) J. Phys. Chem. B , vol.113 , Issue.31 , pp. 10891-10904
    • Mamonov, A.B.1    Bhatt, D.2    Cashman, D.J.3    Ding, Y.4    Zuckerman, D.M.5
  • 109
    • 33846204007 scopus 로고    scopus 로고
    • Resolution exchange simulation with incremental coarsening
    • Lyman, E.; Zuckerman, D. M. Resolution exchange simulation with incremental coarsening J. Chem. Theory Comput. 2006, 2 (3) 656-666
    • (2006) J. Chem. Theory Comput. , vol.2 , Issue.3 , pp. 656-666
    • Lyman, E.1    Zuckerman, D.M.2
  • 110
    • 65249178937 scopus 로고    scopus 로고
    • Optimal replica exchange method combined with Tsallis weight sampling
    • Kim, J.; Straub, J. E. Optimal replica exchange method combined with Tsallis weight sampling J. Chem. Phys. 2009, 130 (14) 144114
    • (2009) J. Chem. Phys. , vol.130 , Issue.14 , pp. 144114
    • Kim, J.1    Straub, J.E.2
  • 111
    • 78049317315 scopus 로고    scopus 로고
    • Generalized simulated tempering for exploring strong phase transitions
    • Kim, J.; Straub, J. E. Generalized simulated tempering for exploring strong phase transitions J. Chem. Phys. 2010, 133 (15) 154101
    • (2010) J. Chem. Phys. , vol.133 , Issue.15 , pp. 154101
    • Kim, J.1    Straub, J.E.2
  • 113
    • 84873526912 scopus 로고    scopus 로고
    • To milliseconds and beyond: Challenges in the simulation of protein folding
    • Lane, T. J.; Shukla, D.; Beauchamp, K. A.; Pande, V. S. To milliseconds and beyond: Challenges in the simulation of protein folding Curr. Opin. Struct. Biol. 2013, 23 (1) 58-65
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , Issue.1 , pp. 58-65
    • Lane, T.J.1    Shukla, D.2    Beauchamp, K.A.3    Pande, V.S.4
  • 114
    • 77649271684 scopus 로고    scopus 로고
    • Modulation of polyglutamine conformations and dimer formation by the N-terminus of huntingtin
    • Williamson, T. E.; Vitalis, A.; Crick, S. L.; Pappu, R. V. Modulation of polyglutamine conformations and dimer formation by the N-terminus of huntingtin J. Mol. Biol. 2010, 396 (5) 1295-1309
    • (2010) J. Mol. Biol. , vol.396 , Issue.5 , pp. 1295-1309
    • Williamson, T.E.1    Vitalis, A.2    Crick, S.L.3    Pappu, R.V.4
  • 115
    • 84876030863 scopus 로고    scopus 로고
    • Regulated unfolding of proteins in signaling
    • Mitrea, D. M.; Kriwacki, R. W. Regulated unfolding of proteins in signaling FEBS Lett. 2013, 587 (8) 1081-1088
    • (2013) FEBS Lett. , vol.587 , Issue.8 , pp. 1081-1088
    • Mitrea, D.M.1    Kriwacki, R.W.2
  • 117
    • 84872064426 scopus 로고    scopus 로고
    • Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation
    • Joonseong, L.; Seonghoon, K.; Rakwoo, C.; Jayanthi, L.; Gebremichael, Y. Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation J. Chem. Phys. 2013, 138 (1) 015103
    • (2013) J. Chem. Phys. , vol.138 , Issue.1 , pp. 015103
    • Joonseong, L.1    Seonghoon, K.2    Rakwoo, C.3    Jayanthi, L.4    Gebremichael, Y.5
  • 118
    • 0036226094 scopus 로고    scopus 로고
    • Relating interactions between neurofilaments to the structure of axonal neurofilament distributions through polymer brush models
    • Kumar, S.; Yin, X. H.; Trapp, B. D.; Hoh, J. H.; Paulaitis, M. E. Relating interactions between neurofilaments to the structure of axonal neurofilament distributions through polymer brush models Biophys. J. 2002, 82 (5) 2360-2372
    • (2002) Biophys. J. , vol.82 , Issue.5 , pp. 2360-2372
    • Kumar, S.1    Yin, X.H.2    Trapp, B.D.3    Hoh, J.H.4    Paulaitis, M.E.5
  • 119
    • 84863774430 scopus 로고    scopus 로고
    • The chemical complexity of cellular microtubules: Tubulin post-translational modification enzymes and their roles in tuning microtubule functions
    • Garnham, C. P.; Roll-Mecak, A. The chemical complexity of cellular microtubules: Tubulin post-translational modification enzymes and their roles in tuning microtubule functions Cytoskeleton 2012, 69 (7) 442-463
    • (2012) Cytoskeleton , vol.69 , Issue.7 , pp. 442-463
    • Garnham, C.P.1    Roll-Mecak, A.2
  • 120
    • 84855221276 scopus 로고    scopus 로고
    • Single-molecule studies of nucleocytoplasmic transport: From one dimension to three dimensions
    • Goryaynov, A.; Ma, J.; Yang, W. Single-molecule studies of nucleocytoplasmic transport: From one dimension to three dimensions Integ. Biol. 2012, 4 (1) 10-21
    • (2012) Integ. Biol. , vol.4 , Issue.1 , pp. 10-21
    • Goryaynov, A.1    Ma, J.2    Yang, W.3
  • 121
    • 84872847336 scopus 로고    scopus 로고
    • Systematic analysis of barrier-forming FG hydrogels from Xenopus nuclear pore complexes
    • Labokha, A. A.; Gradmann, S.; Frey, S.; Huelsmann, B. B.; Urlaub, H.; Baldus, M.; Goerlich, D. Systematic analysis of barrier-forming FG hydrogels from Xenopus nuclear pore complexes EMBO J. 2013, 32 (2) 204-218
    • (2013) EMBO J. , vol.32 , Issue.2 , pp. 204-218
    • Labokha, A.A.1    Gradmann, S.2    Frey, S.3    Huelsmann, B.B.4    Urlaub, H.5    Baldus, M.6    Goerlich, D.7
  • 122
    • 73349134975 scopus 로고    scopus 로고
    • Flexible Gates: Dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic Transport
    • Terry, L. J.; Wente, S. R. Flexible Gates: Dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic Transport Eukaryotic Cell 2009, 8 (12) 1814-1827
    • (2009) Eukaryotic Cell , vol.8 , Issue.12 , pp. 1814-1827
    • Terry, L.J.1    Wente, S.R.2
  • 124
    • 0035964342 scopus 로고    scopus 로고
    • Electrostatics of nanosystems: Application to microtubules and the ribosome
    • Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Electrostatics of nanosystems: Application to microtubules and the ribosome Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (18) 10037-10041
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , Issue.18 , pp. 10037-10041
    • Baker, N.A.1    Sept, D.2    Joseph, S.3    Holst, M.J.4    McCammon, J.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.