메뉴 건너뛰기




Volumn 70, Issue 3, 2008, Pages 863-872

Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A

Author keywords

Aggregation; Amyloid formation; Fibrils; Folding misfolding; Molecular dynamics; Molecular recognition

Indexed keywords

AMYLOID; POLYGLUTAMINE; RIBONUCLEASE; RIBONUCLEASE A;

EID: 38549138415     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21648     Document Type: Article
Times cited : (18)

References (43)
  • 1
    • 0031825554 scopus 로고    scopus 로고
    • From the globular to the fibrous state: Protein structure and structural conversion in amyloid formation
    • Sunde M, Blake CCF. From the globular to the fibrous state: protein structure and structural conversion in amyloid formation. Quart Rev Biophys 1998;31:1-39.
    • (1998) Quart Rev Biophys , vol.31 , pp. 1-39
    • Sunde, M.1    Blake, C.C.F.2
  • 2
    • 0033977086 scopus 로고    scopus 로고
    • Rochet JC, Jr. PTL. Amyloid fibrillogenesis: themes and variations. Curr Opin Struct Biol 2000;10:60-68.
    • Rochet JC, Jr. PTL. Amyloid fibrillogenesis: themes and variations. Curr Opin Struct Biol 2000;10:60-68.
  • 3
    • 0034718157 scopus 로고    scopus 로고
    • Alzheimer's amyloid fibrils: Structure and assembly
    • Serpell LC. Alzheimer's amyloid fibrils: structure and assembly. Biochim Biophys Acta 2000;1502:16-30.
    • (2000) Biochim Biophys Acta , vol.1502 , pp. 16-30
    • Serpell, L.C.1
  • 4
    • 33746377894 scopus 로고    scopus 로고
    • Protein misfolding, functional amyloid, and human disease
    • Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006;75:333-366.
    • (2006) Annu Rev Biochem , vol.75 , pp. 333-366
    • Chiti, F.1    Dobson, C.M.2
  • 5
    • 0037102362 scopus 로고    scopus 로고
    • Protein misfolding diseases: Getting out of shape
    • Dobson CM. Protein misfolding diseases: getting out of shape. Nature 2002;418:729-730.
    • (2002) Nature , vol.418 , pp. 729-730
    • Dobson, C.M.1
  • 6
    • 0036527699 scopus 로고    scopus 로고
    • Therapeutic strategies for human amyloid diseases
    • Sacchettini JC, Kelly JW. Therapeutic strategies for human amyloid diseases. Nat Rev Drug Discov 2002;1:267-275.
    • (2002) Nat Rev Drug Discov , vol.1 , pp. 267-275
    • Sacchettini, J.C.1    Kelly, J.W.2
  • 7
    • 0036385453 scopus 로고    scopus 로고
    • Mechanistic studies of the process of amyloid fibrils formation by the use of peptide fragments and analogues: Implications for the design of fibrillization inhibitors
    • Gazit E. Mechanistic studies of the process of amyloid fibrils formation by the use of peptide fragments and analogues: implications for the design of fibrillization inhibitors. Curr Med Chem 2002;9:1725-1735.
    • (2002) Curr Med Chem , vol.9 , pp. 1725-1735
    • Gazit, E.1
  • 8
    • 0037643298 scopus 로고    scopus 로고
    • Completely different amyloidogenic potential of nearly identical peptide fragments
    • Porat Y, Stepensky A, Ding FX, Naider F, Gazit E. Completely different amyloidogenic potential of nearly identical peptide fragments. Bioplymers 2003;69:161-164.
    • (2003) Bioplymers , vol.69 , pp. 161-164
    • Porat, Y.1    Stepensky, A.2    Ding, F.X.3    Naider, F.4    Gazit, E.5
  • 9
    • 1542686314 scopus 로고    scopus 로고
    • Peptide sequence and amyloid formation: Molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs
    • Zanuy D, Porat Y, Gazit E, Nussinov R. Peptide sequence and amyloid formation: molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs. Structure 2004;12:439-455.
    • (2004) Structure , vol.12 , pp. 439-455
    • Zanuy, D.1    Porat, Y.2    Gazit, E.3    Nussinov, R.4
  • 10
    • 0035839035 scopus 로고    scopus 로고
    • Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain
    • Zurdo J, Guijarro JI, Jimenez JL, Saibil HR, Dobson CM. Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain. J Mol Biol 2001;311:325-340.
    • (2001) J Mol Biol , vol.311 , pp. 325-340
    • Zurdo, J.1    Guijarro, J.I.2    Jimenez, J.L.3    Saibil, H.R.4    Dobson, C.M.5
  • 11
  • 12
    • 33845958636 scopus 로고    scopus 로고
    • Encapsulation and NMR on an aggregating peptide before fibrillogenesis
    • Lazar KL, Kurutz JW, Tycko R, Meredith SC. Encapsulation and NMR on an aggregating peptide before fibrillogenesis. J Am Chem Soc 2006;128:16460-16461.
    • (2006) J Am Chem Soc , vol.128 , pp. 16460-16461
    • Lazar, K.L.1    Kurutz, J.W.2    Tycko, R.3    Meredith, S.C.4
  • 14
    • 0242490659 scopus 로고    scopus 로고
    • The organization and assembly of a β-sheet formed by a prion peptide in solution: An isotope-edited FTIR study
    • Silva RAGD, Barber-Armstrong W, Decatur SM. The organization and assembly of a β-sheet formed by a prion peptide in solution: An isotope-edited FTIR study. J Am Chem Soc 2003;125:13674-13675.
    • (2003) J Am Chem Soc , vol.125 , pp. 13674-13675
    • Silva, R.A.G.D.1    Barber-Armstrong, W.2    Decatur, S.M.3
  • 15
    • 25844493690 scopus 로고    scopus 로고
    • Experimental evidence for the reorganization of β-strands within aggregates of the aβ-(16-22) peptide
    • Petty SA, Decatur SM. Experimental evidence for the reorganization of β-strands within aggregates of the aβ-(16-22) peptide. J Am Chem Soc 2005;127:13488-13489.
    • (2005) J Am Chem Soc , vol.127 , pp. 13488-13489
    • Petty, S.A.1    Decatur, S.M.2
  • 16
    • 4744359865 scopus 로고    scopus 로고
    • Insights into amyloid structural formation and assembly through computational approaches
    • Zanuy D, Gunasekaran K, Ma BY, Tsai HH, Tsai CJ, Nussinov R. Insights into amyloid structural formation and assembly through computational approaches. Amyloid 2004;11:143-161.
    • (2004) Amyloid , vol.11 , pp. 143-161
    • Zanuy, D.1    Gunasekaran, K.2    Ma, B.Y.3    Tsai, H.H.4    Tsai, C.J.5    Nussinov, R.6
  • 19
    • 24644510813 scopus 로고    scopus 로고
    • Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native like structure
    • Sambashivan S, Liu Y, Sawaya MR, Gingery M, Eisenberg D. Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native like structure. Nature 2005;437:266-269.
    • (2005) Nature , vol.437 , pp. 266-269
    • Sambashivan, S.1    Liu, Y.2    Sawaya, M.R.3    Gingery, M.4    Eisenberg, D.5
  • 22
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
    • Miyamoto S, Kollman PA. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 1992;13:952-962.
    • (1992) J Comput Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 24
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J Mol Mod 2001;7:306-317.
    • (2001) J Mol Mod , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 28
    • 19644385843 scopus 로고    scopus 로고
    • Prion and water: Tight and dynamical hydration sites have a key role in structural stability
    • De Simone A, Dodson GG, Verma CS, Zagari A, Fraternali F. Prion and water: tight and dynamical hydration sites have a key role in structural stability. Proc Natl Acad Sci USA 2005;102:7535-7540.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7535-7540
    • De Simone, A.1    Dodson, G.G.2    Verma, C.S.3    Zagari, A.4    Fraternali, F.5
  • 29
    • 20444387408 scopus 로고    scopus 로고
    • Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A
    • Merlino A, Ceruso MA, Vitagliano L, Mazzarella L. Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A. Biophys J 2005;88:2003-2012.
    • (2005) Biophys J , vol.88 , pp. 2003-2012
    • Merlino, A.1    Ceruso, M.A.2    Vitagliano, L.3    Mazzarella, L.4
  • 30
    • 33746800825 scopus 로고    scopus 로고
    • Molecular dynamics analyses of cross-β-spine zipper models: β-sheet twisting and aggregation
    • Esposito L, Pedone C, Vitagliano L. Molecular dynamics analyses of cross-β-spine zipper models: β-sheet twisting and aggregation. Proc Natl Acad Sci USA 2006;103:11533-11538.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 11533-11538
    • Esposito, L.1    Pedone, C.2    Vitagliano, L.3
  • 32
    • 15444364664 scopus 로고    scopus 로고
    • Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations
    • Soto P, Cladera J, Mark AE, Daura X. Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations. Angew Chem Int Ed Engl 2005;44:1065-1067.
    • (2005) Angew Chem Int Ed Engl , vol.44 , pp. 1065-1067
    • Soto, P.1    Cladera, J.2    Mark, A.E.3    Daura, X.4
  • 33
    • 1942519384 scopus 로고    scopus 로고
    • Dynamic properties of the N-terminal swapped dimer of ribonuclease A
    • Merlino A, Vitagliano L, Ceruso MA, Mazzarella L. Dynamic properties of the N-terminal swapped dimer of ribonuclease A. Biophys J 2004;85:2383-2391.
    • (2004) Biophys J , vol.85 , pp. 2383-2391
    • Merlino, A.1    Vitagliano, L.2    Ceruso, M.A.3    Mazzarella, L.4
  • 35
    • 26844435756 scopus 로고    scopus 로고
    • Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments
    • Buchete NV, Tycko R, Hummer G. Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments. J Mol Biol 2005;353:804-821.
    • (2005) J Mol Biol , vol.353 , pp. 804-821
    • Buchete, N.V.1    Tycko, R.2    Hummer, G.3
  • 36
    • 0035127031 scopus 로고    scopus 로고
    • A domain-swapped RNase A dimer with implications for amyloid formation
    • Liu Y, Gotte G, Libonati M, Eisenberg D. A domain-swapped RNase A dimer with implications for amyloid formation. Nat Struct Biol 2001;8:211-214.
    • (2001) Nat Struct Biol , vol.8 , pp. 211-214
    • Liu, Y.1    Gotte, G.2    Libonati, M.3    Eisenberg, D.4
  • 37
    • 33644841204 scopus 로고    scopus 로고
    • Three-dimensional domain-swapped oligomers of ribonuclease A: Identification of a fifth tetramer, pentamers and hexamers, and detection of trace heptameric, octameric and nonameric species
    • Gotte G,Laurents, DV, Libonati M. Three-dimensional domain-swapped oligomers of ribonuclease A: identification of a fifth tetramer, pentamers and hexamers, and detection of trace heptameric, octameric and nonameric species. Biochim Biophys Acta 2006;1764:44-54.
    • (2006) Biochim Biophys Acta , vol.1764 , pp. 44-54
    • Gotte, G.1    Laurents, D.V.2    Libonati, M.3
  • 38
    • 0038446327 scopus 로고    scopus 로고
    • Chemical physics: How to keep dry in water
    • Ball P. Chemical physics: how to keep dry in water. Nature 2003;423:25-26.
    • (2003) Nature , vol.423 , pp. 25-26
    • Ball, P.1
  • 39
    • 24344448662 scopus 로고    scopus 로고
    • Observation of a dewetting transition in the collapse of the melittin tetramer
    • Liu P, Huang X, Zhou R, Berne BJ. Observation of a dewetting transition in the collapse of the melittin tetramer. Nature 2005;437:159-162.
    • (2005) Nature , vol.437 , pp. 159-162
    • Liu, P.1    Huang, X.2    Zhou, R.3    Berne, B.J.4
  • 40
    • 33750934185 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions
    • Crick SL, Jayaraman M, Frieden C, Wetzel R, Pappu RV. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc Natl Acad Sci USA 2006;103:1674-1679.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 1674-1679
    • Crick, S.L.1    Jayaraman, M.2    Frieden, C.3    Wetzel, R.4    Pappu, R.V.5
  • 41
    • 0021691817 scopus 로고
    • Analysis of membrane and surface protein sequences with the hydrophobic moment plot
    • Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 1984;179:125-142.
    • (1984) J Mol Biol , vol.179 , pp. 125-142
    • Eisenberg, D.1    Schwarz, E.2    Komaromy, M.3    Wall, R.4
  • 42
    • 0018784438 scopus 로고
    • Surface and inside volumes in globular proteins
    • Janin J. Surface and inside volumes in globular proteins. Nature 1979;157:491-492.
    • (1979) Nature , vol.157 , pp. 491-492
    • Janin, J.1
  • 43
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.