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Volumn 93, Issue 6, 2007, Pages 1923-1937

Quantitative characterization of intrinsic disorder in polyglutamine: Insights from analysis based on polymer theories

Author keywords

[No Author keywords available]

Indexed keywords

INTRINSICALLY DISORDERED PROTEIN; MONOMER; POLYGLUTAMINE; POLYMER; SOLVENT; UNCLASSIFIED DRUG; WATER;

EID: 34548757409     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.110080     Document Type: Article
Times cited : (134)

References (98)
  • 1
    • 0036402827 scopus 로고    scopus 로고
    • Identification and functions of usefully disordered proteins
    • Dunker, A. K., C. J. Brown, and Z. Obradovic. 2002. Identification and functions of usefully disordered proteins. Adv. Protein Chem. 62:25-49.
    • (2002) Adv. Protein Chem , vol.62 , pp. 25-49
    • Dunker, A.K.1    Brown, C.J.2    Obradovic, Z.3
  • 3
    • 0036128797 scopus 로고    scopus 로고
    • Natively unfolded proteins: A point where biology waits for physics
    • Uversky, V. N. 2002. Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11:739-756.
    • (2002) Protein Sci , vol.11 , pp. 739-756
    • Uversky, V.N.1
  • 4
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson, H. J., and P. E. Wright. 2005. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6:197-208.
    • (2005) Nat. Rev. Mol. Cell Biol , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 5
    • 6344277430 scopus 로고    scopus 로고
    • Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein
    • Weathers, E. A., M. E. Paulaitis, T. B. Woolf, and J. H. Hoh. 2004. Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein. FEBS Lett. 576:348-352.
    • (2004) FEBS Lett , vol.576 , pp. 348-352
    • Weathers, E.A.1    Paulaitis, M.E.2    Woolf, T.B.3    Hoh, J.H.4
  • 7
    • 0035163689 scopus 로고    scopus 로고
    • Predicting properties of intrinsically unstructured proteins
    • Bright, J. N., T. B. Woolf, and J. H. Hoh. 2001. Predicting properties of intrinsically unstructured proteins. Prog. Biophys. Mol. Biol. 76:131-173.
    • (2001) Prog. Biophys. Mol. Biol , vol.76 , pp. 131-173
    • Bright, J.N.1    Woolf, T.B.2    Hoh, J.H.3
  • 9
    • 0003411482 scopus 로고
    • Cornell University Press, Ithaca, NY and London, UK
    • Flory, P. J. 1953. Principles of Polymer Chemistry. Cornell University Press, Ithaca, NY and London, UK.
    • (1953) Principles of Polymer Chemistry
    • Flory, P.J.1
  • 10
    • 0025906282 scopus 로고
    • Polymer principles in protein structure and stability
    • Chan, H. S., and K. A. Dill. 1991. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20:447-490.
    • (1991) Annu. Rev. Biophys. Biophys. Chem , vol.20 , pp. 447-490
    • Chan, H.S.1    Dill, K.A.2
  • 11
    • 0013373034 scopus 로고    scopus 로고
    • Oxford University Press, Oxford, UK and New York
    • Rubinstein, M., and R. H. Colby. 2003. Polymer Physics. Oxford University Press, Oxford, UK and New York.
    • (2003) Polymer Physics
    • Rubinstein, M.1    Colby, R.H.2
  • 13
    • 25844443895 scopus 로고    scopus 로고
    • History of genetic disease: The molecular genetics of Huntington disease - a history
    • Bates, G. P. 2005. History of genetic disease: the molecular genetics of Huntington disease - a history. Nat. Rev. Genet. 6:766-773.
    • (2005) Nat. Rev. Genet , vol.6 , pp. 766-773
    • Bates, G.P.1
  • 14
    • 0038701684 scopus 로고    scopus 로고
    • Huntingtin aggregation and toxicity in Huntington's disease
    • Bates, G. 2003. Huntingtin aggregation and toxicity in Huntington's disease. Lancet. 361:1642-1644.
    • (2003) Lancet , vol.361 , pp. 1642-1644
    • Bates, G.1
  • 15
    • 0034640011 scopus 로고    scopus 로고
    • Fourteen and counting: Unraveling trinucleotide repeat diseases
    • Cummings, C. J., and H. Y. Zoghbi. 2000. Fourteen and counting: unraveling trinucleotide repeat diseases. Hum. Mol. Genet. 9:909-916.
    • (2000) Hum. Mol. Genet , vol.9 , pp. 909-916
    • Cummings, C.J.1    Zoghbi, H.Y.2
  • 17
    • 0035504919 scopus 로고    scopus 로고
    • Polyglutamine expansion neurodegenerative disease
    • Fischbeck, K. H. 2001. Polyglutamine expansion neurodegenerative disease. Brain Res. Bull. 56:161-163.
    • (2001) Brain Res. Bull , vol.56 , pp. 161-163
    • Fischbeck, K.H.1
  • 18
    • 0141891215 scopus 로고    scopus 로고
    • Pathogenesis of polyglutamine disorders: Aggregation revisited
    • Michalik, A., and C. Van Broeckhoven. 2003. Pathogenesis of polyglutamine disorders: aggregation revisited. Hum. Mol. Genet. 12:R173-R186.
    • (2003) Hum. Mol. Genet , vol.12
    • Michalik, A.1    Van Broeckhoven, C.2
  • 19
    • 0033791230 scopus 로고    scopus 로고
    • Protein aggregation and pathogenesis of Huntington's disease: Mechanisms and correlations
    • Wanker, E. E. 2000. Protein aggregation and pathogenesis of Huntington's disease: mechanisms and correlations. Biol. Chem. 381:937-942.
    • (2000) Biol. Chem , vol.381 , pp. 937-942
    • Wanker, E.E.1
  • 20
    • 3142514201 scopus 로고    scopus 로고
    • Protein aggregation and neurodegenerative disease
    • Ross, C. A., and M. A. Poirier. 2004. Protein aggregation and neurodegenerative disease. Nat. Rev. Neurosci. 10:S10-S17.
    • (2004) Nat. Rev. Neurosci , vol.10
    • Ross, C.A.1    Poirier, M.A.2
  • 21
    • 1842766144 scopus 로고    scopus 로고
    • Eukaryotic proteasomes cannot digest polyglutamine sequences and release them during degradation of polyglutamine containing proteins
    • Venkataraman, P., R. Wetzel, M. Tanaka, N. Nukina, and A. L. Goldberg. 2004. Eukaryotic proteasomes cannot digest polyglutamine sequences and release them during degradation of polyglutamine containing proteins. Mol. Cell. 14:95-104.
    • (2004) Mol. Cell , vol.14 , pp. 95-104
    • Venkataraman, P.1    Wetzel, R.2    Tanaka, M.3    Nukina, N.4    Goldberg, A.L.5
  • 22
    • 32144436256 scopus 로고    scopus 로고
    • Proteolytic cleavage of polyglutamine-expanded ataxin-3 is critical for aggregation and sequestration of non-expanded ataxin-3
    • Haacke, A., S. A. Broadley, R. Boteva, N. Tzvetkov, F. U. Hartl, and P. Breuer. 2006. Proteolytic cleavage of polyglutamine-expanded ataxin-3 is critical for aggregation and sequestration of non-expanded ataxin-3. Hum. Mol. Genet. 15:555-568.
    • (2006) Hum. Mol. Genet , vol.15 , pp. 555-568
    • Haacke, A.1    Broadley, S.A.2    Boteva, R.3    Tzvetkov, N.4    Hartl, F.U.5    Breuer, P.6
  • 24
    • 0037461730 scopus 로고    scopus 로고
    • Pivotal role of oligomerization in expanded polyglutamine neurodegenerative disorders
    • Sanchez, I., C. Mahlke, and J. Y. Yuan. 2003. Pivotal role of oligomerization in expanded polyglutamine neurodegenerative disorders. Nature. 421:373-379.
    • (2003) Nature , vol.421 , pp. 373-379
    • Sanchez, I.1    Mahlke, C.2    Yuan, J.Y.3
  • 26
    • 0346220220 scopus 로고    scopus 로고
    • General transcriptional repression by polyglutamine disease proteins is not directly linked to the presence of inclusion bodies
    • Hoshino, M., K. Tagawa, T. Okuda, and H. Okazawa. 2004. General transcriptional repression by polyglutamine disease proteins is not directly linked to the presence of inclusion bodies. Biochem. Biophys. Res. Commun. 313:110-116.
    • (2004) Biochem. Biophys. Res. Commun , vol.313 , pp. 110-116
    • Hoshino, M.1    Tagawa, K.2    Okuda, T.3    Okazawa, H.4
  • 27
    • 7244236320 scopus 로고    scopus 로고
    • Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death
    • Arrasate, M., S. Mitra, E. S. Schweitzer, M. R. Segal, and S. Finkbeiner. 2004. Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death. Nature. 431:805-810.
    • (2004) Nature , vol.431 , pp. 805-810
    • Arrasate, M.1    Mitra, S.2    Schweitzer, E.S.3    Segal, M.R.4    Finkbeiner, S.5
  • 28
    • 0037181179 scopus 로고    scopus 로고
    • Solution structure of polyglutamine tracts in GST-polyglutamine fusion proteins
    • Masino, L., G. Kelly, K. Leonard, Y. Trottier, and A. Pastore. 2002. Solution structure of polyglutamine tracts in GST-polyglutamine fusion proteins. FEBS Lett. 513:267-272.
    • (2002) FEBS Lett , vol.513 , pp. 267-272
    • Masino, L.1    Kelly, G.2    Leonard, K.3    Trottier, Y.4    Pastore, A.5
  • 30
    • 0035800572 scopus 로고    scopus 로고
    • Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity
    • Chen, S., V. Berthelier, W. Yang, and R. Wetzel. 2001. Polyglutamine aggregation behavior in vitro supports a recruitment mechanism of cytotoxicity. J. Mol. Biol. 311:173-182.
    • (2001) J. Mol. Biol , vol.311 , pp. 173-182
    • Chen, S.1    Berthelier, V.2    Yang, W.3    Wetzel, R.4
  • 31
    • 33746376976 scopus 로고    scopus 로고
    • Evidence for polyproline II helical structure in short polyglutamine tracts
    • Chellgren, B. W., A. F. Miller, and T. P. Creamer. 2006. Evidence for polyproline II helical structure in short polyglutamine tracts. J. Mol. Biol. 361:362-371.
    • (2006) J. Mol. Biol , vol.361 , pp. 362-371
    • Chellgren, B.W.1    Miller, A.F.2    Creamer, T.P.3
  • 32
    • 33645281939 scopus 로고    scopus 로고
    • Characterizing the conformational ensemble of monomeric polyglutamine
    • Wang, X. L., A. Vitalis, M. A. Wyczalkowski, and R. V. Pappu. 2006. Characterizing the conformational ensemble of monomeric polyglutamine. Proteins. 63:297-311.
    • (2006) Proteins , vol.63 , pp. 297-311
    • Wang, X.L.1    Vitalis, A.2    Wyczalkowski, M.A.3    Pappu, R.V.4
  • 33
    • 0034338307 scopus 로고    scopus 로고
    • Heteropolymer freezing and design: Towards physical models of protein folding
    • Pande, V. S., A. Y. Grosberg, and T. Tanaka. 2000. Heteropolymer freezing and design: towards physical models of protein folding. Rev. Mod. Phys. 72:259-314.
    • (2000) Rev. Mod. Phys , vol.72 , pp. 259-314
    • Pande, V.S.1    Grosberg, A.Y.2    Tanaka, T.3
  • 34
    • 0028966781 scopus 로고    scopus 로고
    • Dill, K. A., and D. Stigter. 1995. Modeling protein stability as heteropolymer collapse. In Advances in Protein Chemistry, 46. editors. 59-104.
    • Dill, K. A., and D. Stigter. 1995. Modeling protein stability as heteropolymer collapse. In Advances in Protein Chemistry, Vol 46. editors. 59-104.
  • 35
    • 33750934185 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions
    • Crick, S. L., M. Jayaraman, C. Frieden, R. Wetzel, and R. V. Pappu. 2006. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc. Natl. Acad. Sci. USA. 103:16764-16769.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 16764-16769
    • Crick, S.L.1    Jayaraman, M.2    Frieden, C.3    Wetzel, R.4    Pappu, R.V.5
  • 36
    • 0026839336 scopus 로고
    • Quantitative theory of the globule-to-coil transition. 1. Link density distribution in a globule and its radius of gyration
    • Grosberg, A. Y., and D. V. Kuznetsov. 1992. Quantitative theory of the globule-to-coil transition. 1. Link density distribution in a globule and its radius of gyration. Macromolecules. 25:1970-1979.
    • (1992) Macromolecules , vol.25 , pp. 1970-1979
    • Grosberg, A.Y.1    Kuznetsov, D.V.2
  • 37
    • 0006803654 scopus 로고    scopus 로고
    • Distribution of the order parameter of the coil-globule transition
    • Imbert, J. B., A. Lesne, and J. M. Victor. 1997. Distribution of the order parameter of the coil-globule transition. Phys. Rev. E. 56:5630-5647.
    • (1997) Phys. Rev. E , vol.56 , pp. 5630-5647
    • Imbert, J.B.1    Lesne, A.2    Victor, J.M.3
  • 38
    • 33846137276 scopus 로고    scopus 로고
    • Implicit and explicit solvent models for the simulation of dilute polymer solutions
    • Reddy, G., and A. Yethiraj. 2006. Implicit and explicit solvent models for the simulation of dilute polymer solutions. Macromolecules. 39:8536-8542.
    • (2006) Macromolecules , vol.39 , pp. 8536-8542
    • Reddy, G.1    Yethiraj, A.2
  • 39
    • 22944444526 scopus 로고    scopus 로고
    • A molecular dynamics study on universal properties of polymer chains in different solvent qualities. Part I. A review of linear chain properties
    • Steinhauser, M. O. 2005. A molecular dynamics study on universal properties of polymer chains in different solvent qualities. Part I. A review of linear chain properties. J. Chem. Phys. 122:094901.
    • (2005) J. Chem. Phys , vol.122 , pp. 094901
    • Steinhauser, M.O.1
  • 40
    • 0013906079 scopus 로고
    • Synthetic polypeptides containing side-chain amide groups. water-soluble polymers
    • Krull, L. H., and J. S. Wall. 1966. Synthetic polypeptides containing side-chain amide groups. water-soluble polymers. Biochemistry. 5:1521-1527.
    • (1966) Biochemistry , vol.5 , pp. 1521-1527
    • Krull, L.H.1    Wall, J.S.2
  • 42
    • 0017855698 scopus 로고
    • Interaction of the peptide bond with solvent water: A vapor phase analysis
    • Wolfenden, R. 1978. Interaction of the peptide bond with solvent water: a vapor phase analysis. Biochemistry. 17:201-204.
    • (1978) Biochemistry , vol.17 , pp. 201-204
    • Wolfenden, R.1
  • 44
    • 0037015081 scopus 로고    scopus 로고
    • Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation
    • Chen, S. M., F. A. Ferrone, and R. Wetzel. 2002. Huntington's disease age-of-onset linked to polyglutamine aggregation nucleation. Proc. Natl. Acad. Sci. USA. 99:11884-11889.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11884-11889
    • Chen, S.M.1    Ferrone, F.A.2    Wetzel, R.3
  • 45
    • 0000780297 scopus 로고    scopus 로고
    • Topological repulsion between polymer globules
    • Chuang, J., A. Y. Grosberg, and T. Tanaka. 2000. Topological repulsion between polymer globules. J. Chem. Phys. 112:6434-6442.
    • (2000) J. Chem. Phys , vol.112 , pp. 6434-6442
    • Chuang, J.1    Grosberg, A.Y.2    Tanaka, T.3
  • 46
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein-folding: A synthesis
    • Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein-folding: a synthesis. Proteins. 21:167-195.
    • (1995) Proteins , vol.21 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 47
    • 33748454896 scopus 로고    scopus 로고
    • Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions
    • Tran, H. T., and R. V. Pappu. 2006. Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Biophys. J. 91:1868-1886.
    • (2006) Biophys. J , vol.91 , pp. 1868-1886
    • Tran, H.T.1    Pappu, R.V.2
  • 48
    • 23944453852 scopus 로고    scopus 로고
    • Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins
    • Tran, H. T., X. L. Wang, and R. V. Pappu. 2005. Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins. Biochemistry. 44:11369-11380.
    • (2005) Biochemistry , vol.44 , pp. 11369-11380
    • Tran, H.T.1    Wang, X.L.2    Pappu, R.V.3
  • 49
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski, G. A., R. A. Friesner, J. Tirado-Rives, and W. L. Jorgensen. 2001. Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B. 105:6474-6487.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 50
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
    • (2001) J. Mol. Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 53
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess, B., H. Bekker, H. J. C. Berendsen, and J. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472.
    • (1997) J. Comput. Chem , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.4
  • 54
    • 84986440341 scopus 로고
    • Settle: An analytical version of the shake and rattle algorithm for rigid water models
    • Miyamoto, S., and P. A. Kollman. 1992. Settle: an analytical version of the shake and rattle algorithm for rigid water models. J. Comput. Chem. 13:952-962.
    • (1992) J. Comput. Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 55
    • 0343791148 scopus 로고
    • Electric moments of molecules in liquids
    • Onsager, L. 1936. Electric moments of molecules in liquids. J. Am. Chem. Soc. 58:1486-1493.
    • (1936) J. Am. Chem. Soc , vol.58 , pp. 1486-1493
    • Onsager, L.1
  • 56
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W. L., D. S. Maxwell, and J. TiradoRives. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-11236.
    • (1996) J. Am. Chem. Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    TiradoRives, J.3
  • 57
    • 1842857771 scopus 로고    scopus 로고
    • Asymmetry in the shapes of folded and denatured states of proteins
    • Dima, R. I., and D. Thirumalai. 2004. Asymmetry in the shapes of folded and denatured states of proteins. J. Phys. Chem. B. 108:6564-6570.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 6564-6570
    • Dima, R.I.1    Thirumalai, D.2
  • 59
    • 21744448828 scopus 로고    scopus 로고
    • Scaling behavior and structure of denatured proteins
    • Ding, F., R. K. Jha, and N. V. Dokholyan. 2005. Scaling behavior and structure of denatured proteins. Structure. 13:1047-1054.
    • (2005) Structure , vol.13 , pp. 1047-1054
    • Ding, F.1    Jha, R.K.2    Dokholyan, N.V.3
  • 60
    • 0000778705 scopus 로고
    • Properties and origins of protein secondary structure
    • Socci, N. D., W. S. Bialek, and J. N. Onuchic. 1994. Properties and origins of protein secondary structure. Phys. Rev. E. 49:3440-3443.
    • (1994) Phys. Rev. E , vol.49 , pp. 3440-3443
    • Socci, N.D.1    Bialek, W.S.2    Onuchic, J.N.3
  • 61
    • 4644311920 scopus 로고    scopus 로고
    • Average protein density is a molecular-weight dependent function
    • Fischer H., I. Polikarpov, and A. F. Craievich. 2004. Average protein density is a molecular-weight dependent function. Protein Sci. 13:2825-2828.
    • (2004) Protein Sci , vol.13 , pp. 2825-2828
    • Fischer, H.1    Polikarpov, I.2    Craievich, A.F.3
  • 63
    • 33747623305 scopus 로고    scopus 로고
    • End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation
    • Moglich, A., K. Joder, and T. Kiefhaber. 2006. End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation. Proc. Natl. Acad. Sci. USA. 103:12394-12399.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 12394-12399
    • Moglich, A.1    Joder, K.2    Kiefhaber, T.3
  • 64
    • 26944481188 scopus 로고    scopus 로고
    • Interfaces and the driving force of hydrophobic assembly
    • Chandler, D. 2005. Interfaces and the driving force of hydrophobic assembly. Nature. 437:640-647.
    • (2005) Nature , vol.437 , pp. 640-647
    • Chandler, D.1
  • 67
    • 33846512404 scopus 로고    scopus 로고
    • Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water
    • Athawale, M. V., G. Goel, T. Ghosh, T. M. Truskett, and S. Garde. 2007. Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water. Proc. Natl. Acad. Sci. USA. 104:733-738.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 733-738
    • Athawale, M.V.1    Goel, G.2    Ghosh, T.3    Truskett, T.M.4    Garde, S.5
  • 68
    • 57249096918 scopus 로고    scopus 로고
    • Recent advances in the description of the structure of water, the hydrophobic effect, and the like-dissolves-like rule
    • Schmid, R. 2001. Recent advances in the description of the structure of water, the hydrophobic effect, and the like-dissolves-like rule. Monatsh. Chem. 132:1295-1326.
    • (2001) Monatsh. Chem , vol.132 , pp. 1295-1326
    • Schmid, R.1
  • 70
    • 0032508044 scopus 로고    scopus 로고
    • Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid
    • Sastry, S., P. G. Debenedetti, and F. H. Stillinger. 1998. Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid. Nature. 393:554-557.
    • (1998) Nature , vol.393 , pp. 554-557
    • Sastry, S.1    Debenedetti, P.G.2    Stillinger, F.H.3
  • 71
    • 2742612566 scopus 로고    scopus 로고
    • Stretched exponential relaxation in molecular and electronic glasses
    • Phillips, J. C. 1996. Stretched exponential relaxation in molecular and electronic glasses. Rep. Prog. Phys. 59:1133-1207.
    • (1996) Rep. Prog. Phys , vol.59 , pp. 1133-1207
    • Phillips, J.C.1
  • 72
    • 0000353328 scopus 로고
    • Activated dynamics, loss of ergodicity, and transport in supercooled liquids
    • Thirumalai, D., and R. D. Mountain. 1993. Activated dynamics, loss of ergodicity, and transport in supercooled liquids. Phys. Rev. E. 47:479-489.
    • (1993) Phys. Rev. E , vol.47 , pp. 479-489
    • Thirumalai, D.1    Mountain, R.D.2
  • 73
    • 0001759392 scopus 로고    scopus 로고
    • Macromolecular clusters in poor-solvent polymer solutions
    • Raos, G., and G. Allegra. 1997. Macromolecular clusters in poor-solvent polymer solutions. J. Chem. Phys. 107:6479-6490.
    • (1997) J. Chem. Phys , vol.107 , pp. 6479-6490
    • Raos, G.1    Allegra, G.2
  • 74
    • 0011683871 scopus 로고
    • Phase-separation of polymer-solutions and interactions of globules
    • Grosberg, A. Y., and D. V. Kuznetsov. 1992. Phase-separation of polymer-solutions and interactions of globules. Journal De Physique Ii. 2:1327-1339.
    • (1992) Journal De Physique Ii , vol.2 , pp. 1327-1339
    • Grosberg, A.Y.1    Kuznetsov, D.V.2
  • 75
    • 55449095000 scopus 로고    scopus 로고
    • Molecular origin of polyglutamine aggregation in neurodegenerative diseases
    • Khare, S. D., F. Ding, K. N. Gwanmesia, and N. V. Dokholyan. 2005. Molecular origin of polyglutamine aggregation in neurodegenerative diseases. Plos Computational Biology. 1:230-235.
    • (2005) Plos Computational Biology , vol.1 , pp. 230-235
    • Khare, S.D.1    Ding, F.2    Gwanmesia, K.N.3    Dokholyan, N.V.4
  • 76
    • 33646794342 scopus 로고    scopus 로고
    • Polyglutamine repeats and beta-helix structure: Molecular dynamics study
    • Merlino, A., L. Esposito, and L. Vitagliano. 2006. Polyglutamine repeats and beta-helix structure: molecular dynamics study. Proteins. 63:918-927.
    • (2006) Proteins , vol.63 , pp. 918-927
    • Merlino, A.1    Esposito, L.2    Vitagliano, L.3
  • 77
    • 84986497803 scopus 로고
    • Multidimensional free-energy calculations using the weighted histogram analysis method
    • Kumar, S., J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman. 1995. Multidimensional free-energy calculations using the weighted histogram analysis method. J. Comput. Chem. 16:1339-1350.
    • (1995) J. Comput. Chem , vol.16 , pp. 1339-1350
    • Kumar, S.1    Rosenberg, J.M.2    Bouzida, D.3    Swendsen, R.H.4    Kollman, P.A.5
  • 78
    • 0032080053 scopus 로고    scopus 로고
    • Calculations on folding of segment B1 of streptococcal protein G
    • Sheinerman, F. B., and C. L. Brooks. 1998. Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol. 278:439-456.
    • (1998) J. Mol. Biol , vol.278 , pp. 439-456
    • Sheinerman, F.B.1    Brooks, C.L.2
  • 79
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer-simulations
    • Roux, B. 1995. The calculation of the potential of mean force using computer-simulations. Comput. Phys. Commun. 91:275-282.
    • (1995) Comput. Phys. Commun , vol.91 , pp. 275-282
    • Roux, B.1
  • 80
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314:141-151.
    • (1999) Chem. Phys. Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 81
    • 1642546396 scopus 로고    scopus 로고
    • Atomic simulations of protein folding, using the replica exchange algorithm
    • Nymeyer, H., S. Gnanakaran, and A. E. Garcia. 2004. Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol. 383:119-149.
    • (2004) Methods Enzymol , vol.383 , pp. 119-149
    • Nymeyer, H.1    Gnanakaran, S.2    Garcia, A.E.3
  • 82
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin, E. J., and V. S. Pande. 2005. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 88:2472-2493.
    • (2005) Biophys. J , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 83
    • 85047692291 scopus 로고    scopus 로고
    • Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling
    • Sorin, E. J., and V. S. Pande. 2005. Empirical force-field assessment: the interplay between backbone torsions and noncovalent term scaling. J. Comput. Chem. 26:682-690.
    • (2005) J. Comput. Chem , vol.26 , pp. 682-690
    • Sorin, E.J.1    Pande, V.S.2
  • 84
    • 0037441479 scopus 로고    scopus 로고
    • Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
    • Hu, H., M. Elstner, and J. Hermans. 2003. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins. 50:451-463.
    • (2003) Proteins , vol.50 , pp. 451-463
    • Hu, H.1    Elstner, M.2    Hermans, J.3
  • 85
    • 33748488032 scopus 로고    scopus 로고
    • Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles
    • Zagrovic, B., and V. S. Pande. 2006. Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles. J. Am. Chem. Soc. 128:11742-11743.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 11742-11743
    • Zagrovic, B.1    Pande, V.S.2
  • 86
    • 18844361915 scopus 로고    scopus 로고
    • Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures
    • Gnanakaran, S., and A. E. Garcia. 2005. Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures. Proteins. 59:773-782.
    • (2005) Proteins , vol.59 , pp. 773-782
    • Gnanakaran, S.1    Garcia, A.E.2
  • 87
    • 0042701995 scopus 로고    scopus 로고
    • Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the flory isolated-pair hypothesis for peptides
    • Zaman, M. H., M. Y. Shen, R. S. Berry, K. F. Freed, and T. R. Sosnick. 2003. Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the flory isolated-pair hypothesis for peptides. J. Mol. Biol. 331:693-711.
    • (2003) J. Mol. Biol , vol.331 , pp. 693-711
    • Zaman, M.H.1    Shen, M.Y.2    Berry, R.S.3    Freed, K.F.4    Sosnick, T.R.5
  • 88
    • 26444534036 scopus 로고    scopus 로고
    • Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases
    • Armen, R. S., B. M. Bernard, R. Day, D. O. V. Alonso, and V. Daggett. 2005. Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases. Proc. Natl. Acad. Sci. USA. 102:13433-13438.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13433-13438
    • Armen, R.S.1    Bernard, B.M.2    Day, R.3    Alonso, D.O.V.4    Daggett, V.5
  • 89
    • 33645101164 scopus 로고    scopus 로고
    • Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices
    • Zanuy, D., K. Gunasekaran, A. M. Lesk, and R. Nussinov. 2006. Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices. J. Mol. Biol. 358:330-345.
    • (2006) J. Mol. Biol , vol.358 , pp. 330-345
    • Zanuy, D.1    Gunasekaran, K.2    Lesk, A.M.3    Nussinov, R.4
  • 90
    • 0033450855 scopus 로고    scopus 로고
    • Folding of oligoglutamines: A theoretical approach based upon thermodynamics and molecular mechanics
    • Starikov, E. B., H. Lehrach, and E. E. Wanker. 1999. Folding of oligoglutamines: a theoretical approach based upon thermodynamics and molecular mechanics. J. Biomol. Struct. Dyn. 17:409-427.
    • (1999) J. Biomol. Struct. Dyn , vol.17 , pp. 409-427
    • Starikov, E.B.1    Lehrach, H.2    Wanker, E.E.3
  • 91
    • 33845652619 scopus 로고    scopus 로고
    • Effects of chain length on the aggregation of model polyglutamine peptides: Molecular dynamics simulations
    • Marchut, A. J., and C. K. Hall. 2007. Effects of chain length on the aggregation of model polyglutamine peptides: molecular dynamics simulations. Proteins. 66:96-109.
    • (2007) Proteins , vol.66 , pp. 96-109
    • Marchut, A.J.1    Hall, C.K.2
  • 92
    • 33745727173 scopus 로고    scopus 로고
    • Interpreting the aggregation kinetics of amyloid peptides
    • Pellarin, R., and A. Caflisch. 2006. Interpreting the aggregation kinetics of amyloid peptides. J. Mol. Biol. 360:882-892.
    • (2006) J. Mol. Biol , vol.360 , pp. 882-892
    • Pellarin, R.1    Caflisch, A.2
  • 93
    • 33747032067 scopus 로고    scopus 로고
    • Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides
    • Marchut, A. J., and C. K. Hall. 2006. Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides. Comput. Biol. Chem. 30:215-218.
    • (2006) Comput. Biol. Chem , vol.30 , pp. 215-218
    • Marchut, A.J.1    Hall, C.K.2
  • 94
    • 33644821609 scopus 로고    scopus 로고
    • A molecular dynamics approach to the structural characterization of amyloid aggregation
    • Cecchini, M., R. Curcio, M. Pappalardo, R. Melki, and A. Caflisch. 2006. A molecular dynamics approach to the structural characterization of amyloid aggregation. J. Mol. Biol. 357:1306-1321.
    • (2006) J. Mol. Biol , vol.357 , pp. 1306-1321
    • Cecchini, M.1    Curcio, R.2    Pappalardo, M.3    Melki, R.4    Caflisch, A.5
  • 95
    • 32344442405 scopus 로고    scopus 로고
    • Studies of folding and misfolding using simplified models
    • Dokholyan, N. V. 2006. Studies of folding and misfolding using simplified models. Curr. Opin. Struct. Biol. 16:79-85.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 79-85
    • Dokholyan, N.V.1
  • 96
    • 9244260521 scopus 로고    scopus 로고
    • Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
    • Nguyen, H. D., and C. K. Hall. 2004. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. USA. 101:16180-16185.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 16180-16185
    • Nguyen, H.D.1    Hall, C.K.2
  • 97
    • 85036137644 scopus 로고    scopus 로고
    • Peng, S., F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz, H. E. Stanley, and N. V. Dokholyan. 2004. Discrete molecular dynamics simulations of peptide aggregation. Phys. Rev. E. 69.
    • Peng, S., F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz, H. E. Stanley, and N. V. Dokholyan. 2004. Discrete molecular dynamics simulations of peptide aggregation. Phys. Rev. E. 69.
  • 98
    • 0037627715 scopus 로고    scopus 로고
    • The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
    • Gsponer, J., U. Haberthur, and A. Caflisch. 2003. The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc. Natl. Acad. Sci. USA. 100:5154-5159.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5154-5159
    • Gsponer, J.1    Haberthur, U.2    Caflisch, A.3


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