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Volumn 156, Issue 1, 2011, Pages 43-50

Comparing the structural properties of human and rat islet amyloid polypeptide by MD computer simulations

Author keywords

Disulfide bond; hIAPP; MD simulation; Proline; rIAPP

Indexed keywords

AMYLIN; CYSTEINE; CYSTINE;

EID: 79955954237     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2010.12.007     Document Type: Article
Times cited : (51)

References (58)
  • 1
    • 0035551830 scopus 로고    scopus 로고
    • Amyloidogenicity and cytotoxicity of islet amyloid polypeptide
    • DOI 10.1002/1097-0282(2001)60:6<438::AID-BIP10182>3.0.CO;2-A
    • A. Kapurniotu, Amyloidogenicity and cytotoxicity of islet amyloid polypeptide, Biopolymers 60 (2001) 438-459. (Pubitemid 35000911)
    • (2001) Biopolymers - Peptide Science Section , vol.60 , Issue.6 , pp. 438-459
    • Kapurniotu, A.1
  • 2
    • 36049013172 scopus 로고    scopus 로고
    • Mechanism of islet amyloid polypeptide fibrillation at lipid interfaces studied by infrared reflection absorption spectroscopy
    • DOI 10.1529/biophysj.107.110635
    • D.H.J. Lopes, A. Meister, A. Gohlke, A. Hauser, A. Blume, R. Winter, Mechanism of islet amyloid polypeptide fibrillation at lipid interfaces studied by infrared reflection absorption spectroscopy, Biophys. J. 93 (2007) 3132-3141. (Pubitemid 350097104)
    • (2007) Biophysical Journal , vol.93 , Issue.9 , pp. 3132-3141
    • Lopes, D.H.J.1    Meister, A.2    Gohlke, A.3    Hauser, A.4    Blume, A.5    Winter, R.6
  • 3
    • 67349227494 scopus 로고    scopus 로고
    • Amyloidogenic propensities and conformational properties of proIAPP and IAPP in the presence of lipid bilayer membranes
    • S. Jha, D. Sellin, R. Seidel, R. Winter, Amyloidogenic propensities and conformational properties of proIAPP and IAPP in the presence of lipid bilayer membranes, J. Mol. Biol. 389 (2009) 907-920.
    • (2009) J. Mol. Biol. , vol.389 , pp. 907-920
    • Jha, S.1    Sellin, D.2    Seidel, R.3    Winter, R.4
  • 4
    • 77953710075 scopus 로고    scopus 로고
    • Suppression of IAPP fibrillation at anionic lipid membranes via IAPP-derived amyloid inhibitors and insulin
    • D. Sellin, L.-M. Yan, A. Kapurniotu, R. Winter, Suppression of IAPP fibrillation at anionic lipid membranes via IAPP-derived amyloid inhibitors and insulin, Biophys. Chem. 150 (2010) 73-79.
    • (2010) Biophys. Chem. , vol.150 , pp. 73-79
    • Sellin, D.1    Yan, L.-M.2    Kapurniotu, A.3    Winter, R.4
  • 6
    • 0034677739 scopus 로고    scopus 로고
    • Preparation of synthetic human islet amyloid polypeptide (IAPP) in a stable conformation to enable study of conversion to amyloid-like fibrils
    • DOI 10.1016/S0014-5793(00)01287-4, PII S0014579300012874
    • C.E. Higham, E.T. Jaikaran, P.E. Fraser, M. Gross, A. Clark, Preparation of synthetic human islet amyloid polypeptide (iapp) in a stable conformation to enable study of conversion to amyloid-like fibrils, FEBS Lett. 470 (2000) 55-60. (Pubitemid 30155623)
    • (2000) FEBS Letters , vol.470 , Issue.1 , pp. 55-60
    • Higham, C.E.1    Jaikaran, E.T.A.S.2    Fraser, P.E.3    Gross, M.4    Clark, A.5
  • 8
    • 0034977531 scopus 로고    scopus 로고
    • Islet amyloid polypeptide: Identification of long-range contacts and local order on the fibrillogenesis pathway
    • S.B. Padrick, A.D. Miranker, Islet amyloid polypeptide: identification of long-range contacts and local order on the fibrillogenesis pathway, J. Mol. Biol. 308 (2001) 783-794.
    • (2001) J. Mol. Biol. , vol.308 , pp. 783-794
    • Padrick, S.B.1    Miranker, A.D.2
  • 9
    • 70349560017 scopus 로고    scopus 로고
    • NMR spectroscopic investigation of early events in IAPP amyloid fibril formation
    • R. Mishra, M. Geyer, R. Winter, NMR spectroscopic investigation of early events in IAPP amyloid fibril formation, Chembiochem 10 (2009) 1769-1772.
    • (2009) Chembiochem , vol.10 , pp. 1769-1772
    • Mishra, R.1    Geyer, M.2    Winter, R.3
  • 10
    • 33845960266 scopus 로고    scopus 로고
    • Direct detection of transient alpha-helical states in islet amyloid polypeptide
    • DOI 10.1110/ps.062486907
    • J.A. Williamson, A.D. Miranker, Direct detection of transient alpha-helical states in islet amyloid polypeptide, Protein Sci. 16 (2007) 110-117. (Pubitemid 46036503)
    • (2007) Protein Science , vol.16 , Issue.1 , pp. 110-117
    • Williamson, J.A.1    Miranker, A.D.2
  • 11
    • 33747119677 scopus 로고    scopus 로고
    • Conserved and cooperative assembly of membrane-bound alpha-helical states of islet amyloid polypeptide
    • DOI 10.1021/bi060579z
    • J.D. Knight, J.A. Hebda, A.D. Miranker, Conserved and cooperative assembly of membrane-bound alpha-helical states of islet amyloid polypeptide, Biochemistry 45 (2006) 9496-9508. (Pubitemid 44223253)
    • (2006) Biochemistry , vol.45 , Issue.31 , pp. 9496-9508
    • Knight, J.D.1    Hebda, J.A.2    Miranker, A.D.3
  • 13
    • 0030015420 scopus 로고    scopus 로고
    • Alpha-helical, but not beta-sheet, propensity of proline is determined by peptide environment
    • S.C. Li, N.K. Goto, K.A. Williams, C.M. Deber, Alpha-helical, but not beta-sheet, propensity of proline is determined by peptide environment, Proc. Natl Acad. Sci. USA 93 (1996) 6676-6681.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 6676-6681
    • Li, S.C.1    Goto, N.K.2    Williams, K.A.3    Deber, C.M.4
  • 14
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of alpha helices
    • J.S. Richardson, D.C. Richardson, Amino acid preferences for specific locations at the ends of alpha helices, Science 240 (1988) 1648-1652.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 15
    • 0037470589 scopus 로고    scopus 로고
    • Full-length rat amylin forms fibrils following substitution of single residues from human amylin
    • J. Green, C. Goldsbury, T. Mini, S. Sunderji, P. Frey, J. Kistler, G. Cooper, U. Aebi, Full-length rat amylin forms fibrils following substitution of single residues from human amylin, J. Mol. Biol. 326 (2003) 1147-1156.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1147-1156
    • Green, J.1    Goldsbury, C.2    Mini, T.3    Sunderji, S.4    Frey, P.5    Kistler, J.6    Cooper, G.7    Aebi, U.8
  • 16
    • 0033579545 scopus 로고    scopus 로고
    • Analysis of amylin cleavage products provides new insights into the amyloidogenic region of human amylin
    • M.R. Nilsson, D.P. Raleigh, Analysis of amylin cleavage products provides new insights into the amyloidogenic region of human amylin, J. Mol. Biol. 294 (1999) 1375-1385.
    • (1999) J. Mol. Biol. , vol.294 , pp. 1375-1385
    • Nilsson, M.R.1    Raleigh, D.P.2
  • 17
    • 11144243803 scopus 로고    scopus 로고
    • Contribution of the intrinsic disulfide to the assembly mechanism of islet amyloid
    • DOI 10.1110/ps.041051205
    • B.W. Koo, A.D. Miranker, Contribution of the intrinsic disulfide to the assembly mechanism of islet amyloid, Protein Sci. 14 (2005) 231-239. (Pubitemid 40054136)
    • (2005) Protein Science , vol.14 , Issue.1 , pp. 231-239
    • Koo, B.W.1    Miranker, A.D.2
  • 18
    • 0033963034 scopus 로고    scopus 로고
    • Molden: A pre- and post-processing program for molecular and electronic structures
    • G. Schaftenaar, J. Noordik, Molden: a pre- and post-processing program for molecular and electronic structures, J. Comput.-Aided Mol. Des. 14 (2000) 123-134.
    • (2000) J. Comput.-Aided Mol. Des. , vol.14 , pp. 123-134
    • Schaftenaar, G.1    Noordik, J.2
  • 19
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • DOI 10.1002/elps.1150181505
    • N. Guex, M. Peitsch, SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling, Electrophoresis 18 (1997) 2714-2723. http://www.expasy.org/spdbv/. (Pubitemid 28059943)
    • (1997) Electrophoresis , vol.18 , Issue.15 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 20
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: A package for molecular simulation and trajectory analysis
    • E. Lindahl, B. Hess, D. van der Spoel, Gromacs 3.0: a package for molecular simulation and trajectory analysis, J. Mol. Model. 7 (2001) 306-317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 21
    • 0029633168 scopus 로고
    • Gromacs: A message-passing parallel molecular dynamics implementation
    • H.J.C. Berendsen, D. van der Spoel, R. van Drunen, Gromacs: a message-passing parallel molecular dynamics implementation, Comp. Phys. Comm. 91 (1995) 43-56.
    • (1995) Comp. Phys. Comm. , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 23
    • 33645941402 scopus 로고
    • The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
    • W.L. Jorgensen, J. Tirado-Rives, The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin, J. Am. Chem. Soc. 110 (1988) 1657-1666.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 24
    • 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
    • G. Kaminski, R. Friesner, J. Tirado-Rives, W. Jorgensen, Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides, J. Phys. Chem. B 105 (2001) 6474-6487.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
    • Kaminski, G.1    Friesner, R.2    Tirado-Rives, J.3    Jorgensen, W.4
  • 26
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, C. Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22 (1983) 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 27
    • 0036174712 scopus 로고    scopus 로고
    • Continuum secondary structure captures protein flexibility
    • DOI 10.1016/S0969-2126(02)00700-1, PII S0969212602007001
    • C.A.F. Andersen, A.G. Palmer, S. Brunak, B. Rost, Continuum secondary structure captures protein flexibility, Structure 10 (2002) 175-184. (Pubitemid 34164596)
    • (2002) Structure , vol.10 , Issue.2 , pp. 175-184
    • Andersen, C.A.F.1    Palmer, A.G.2    Brunak, S.3    Rost, B.4
  • 28
    • 33947315642 scopus 로고    scopus 로고
    • Secondary structure assignment that accurately reflects physical and evolutionary characteristics
    • M.V. Cubellis, F. Cailliez, S.C. Lovell, Secondary structure assignment that accurately reflects physical and evolutionary characteristics, BMC Bioinform. 6 (Suppl 4) (2005) S8.
    • (2005) BMC Bioinform. , vol.6 , Issue.SUPPL. 4
    • Cubellis, M.V.1    Cailliez, F.2    Lovell, S.C.3
  • 29
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • D. Eisenberg, A. McLachlan, Solvation energy in protein folding and binding, Nature 319 (1986) 199-203. (Pubitemid 16128783)
    • (1986) Nature , vol.319 , Issue.6050 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 30
    • 13444250015 scopus 로고    scopus 로고
    • Formation of spanning water networks on protein surfaces via 2D percolation transition
    • A. Oleinikova, N. Smolin, I. Brovchenko, A. Geiger, R. Winter, Formation of spanning water networks on protein surfaces via 2D percolation transition, J. Phys. Chem. B 109 (2005) 1988-1998.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 1988-1998
    • Oleinikova, A.1    Smolin, N.2    Brovchenko, I.3    Geiger, A.4    Winter, R.5
  • 31
    • 77950850164 scopus 로고    scopus 로고
    • Volumetric properties of human islet amyloid polypeptide in liquid water
    • I. Brovchenko, M.N. Andrews, A. Oleinikova, Volumetric properties of human islet amyloid polypeptide in liquid water, Phys. Chem. Chem. Phys. 12 (2010) 4233-4238.
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 4233-4238
    • Brovchenko, I.1    Andrews, M.N.2    Oleinikova, A.3
  • 34
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • S. Nosé, A molecular dynamics method for simulations in the canonical ensemble, Mol. Phys. 52 (1984) 255-268.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 35
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W. Hoover, Canonical dynamics: equilibrium phase-space distributions, Phys. Rev. A 31 (1985) 1695-1697.
    • (1985) Phys. Rev. , vol.31 , pp. 1695-1697
    • Hoover, W.1
  • 36
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • M. Parrinello, A. Rahman, Polymorphic transitions in single crystals: a new molecular dynamics method, J. Appl. Phys. 52 (1981) 7182-7190.
    • (1981) J. Appl. Phys. , vol.52 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 37
    • 84926811618 scopus 로고
    • Constant pressure molecular dynamics for molecular systems
    • S. Nosé, M. Klein, Constant pressure molecular dynamics for molecular systems, Mol. Phys. 50 (1983) 1055-1076.
    • (1983) Mol. Phys. , vol.50 , pp. 1055-1076
    • Nosé, S.1    Klein, M.2
  • 38
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithims for rigid water models
    • S. Miyamoto, P. Kollman, SETTLE: an analytical version of the SHAKE and RATTLE algorithims for rigid water models, J. Comput. Chem. 12 (1992) 952-962.
    • (1992) J. Comput. Chem. , vol.12 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.2
  • 39
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes
    • J. Ryckaert, G. Ciccotti, H.J.C. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes, J. Comput. Phys. 23 (1977) 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 40
    • 33846823909 scopus 로고
    • Particle mesh ewald: An N-log(N) method for ewald sums in large systems
    • T. Darden, D. York, L. Pedersen, Particle mesh ewald: an N-log(N) method for ewald sums in large systems, J. Chem. Phys. 98 (1993) 1311-1327.
    • (1993) J. Chem. Phys. , vol.98 , pp. 1311-1327
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 43
    • 70149116768 scopus 로고    scopus 로고
    • Association of highly compact type II diabetes related islet amyloid polypeptide intermediate species at physiological temperature revealed by diffusion NMR spectroscopy
    • R. Soong, J.R. Brender, P.M. Macdonald, A. Ramamoorthy, Association of highly compact type II diabetes related islet amyloid polypeptide intermediate species at physiological temperature revealed by diffusion NMR spectroscopy, J. Am. Chem. Soc. 131 (2009) 7079-7085.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 7079-7085
    • Soong, R.1    Brender, J.R.2    Macdonald, P.M.3    Ramamoorthy, A.4
  • 45
    • 79955976097 scopus 로고    scopus 로고
    • From Computational Biophysics to Systems Biology (CBSB08)
    • NIC-Directors
    • U.H.E. Hansmann, J.H. Meinke, S. Mohanty, W. Nadler, O. Zimmermann (Eds.), From Computational Biophysics to Systems Biology (CBSB08), NIC series, NIC-Directors, 40, 2008. http://www.fz-juelich.de/nic-series/volume40/volume40. html.
    • (2008) NIC Series , vol.40
    • Hansmann, U.H.E.1    Meinke, J.H.2    Mohanty, S.3    Nadler, W.4    Zimmermann, O.5
  • 46
    • 58049176407 scopus 로고    scopus 로고
    • Which properties of a spanning network of hydration water enable biological functions?
    • I. Brovchenko, A. Oleinikova, Which properties of a spanning network of hydration water enable biological functions? Chemphyschem 9 (2008) 2695-2702.
    • (2008) Chemphyschem , vol.9 , pp. 2695-2702
    • Brovchenko, I.1    Oleinikova, A.2
  • 48
    • 0032972592 scopus 로고    scopus 로고
    • Effects of sequential proline substitutions on amyloid formation by human amylin 20-29
    • D.F. Moriarty, D.P. Raleigh, Effects of sequential proline substitutions on amyloid formation by human amylin 20-29, Biochemistry 38 (1999) 1811-1818.
    • (1999) Biochemistry , vol.38 , pp. 1811-1818
    • Moriarty, D.F.1    Raleigh, D.P.2
  • 49
    • 0035823520 scopus 로고    scopus 로고
    • Analysis of the minimal amyloid-forming fragment of the islet amyloid polypeptide. An experimental support for the key role of the phenylalanine residue in amyloid formation
    • R. Azriel, E. Gazit, Analysis of the minimal amyloid-forming fragment of the islet amyloid polypeptide. An experimental support for the key role of the phenylalanine residue in amyloid formation, J. Biol. Chem. 276 (2001) 34156-34161.
    • (2001) J. Biol. Chem. , vol.276 , pp. 34156-34161
    • Azriel, R.1    Gazit, E.2
  • 50
    • 67650533782 scopus 로고    scopus 로고
    • Three-dimensional structure and orientation of rat islet amyloid polypeptide protein in a membrane environment by solution nmr spectroscopy
    • R.P.R. Nanga, J.R. Brender, J. Xu, K. Hartman, V. Subramanian, A. Ramamoorthy, Three-dimensional structure and orientation of rat islet amyloid polypeptide protein in a membrane environment by solution nmr spectroscopy, J. Am. Chem. Soc. 131 (2009) 8252-8261.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 8252-8261
    • Nanga, R.P.R.1    Brender, J.R.2    Xu, J.3    Hartman, K.4    Subramanian, V.5    Ramamoorthy, A.6
  • 51
  • 52
    • 73249115986 scopus 로고    scopus 로고
    • Human islet amyloid polypeptide monomers form ordered beta-hairpins: A possible direct amyloidogenic precursor
    • N.F. Dupuis, C. Wu, J.-E. Shea, M.T. Bowers, Human islet amyloid polypeptide monomers form ordered beta-hairpins: a possible direct amyloidogenic precursor, J. Am. Chem. Soc. 131 (2009) 18283-18292.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 18283-18292
    • Dupuis, N.F.1    Wu, C.2    Shea, J.-E.3    Bowers, M.T.4
  • 55
    • 41649117851 scopus 로고    scopus 로고
    • Sedimentation studies on human amylin fail to detect low-molecular-weight oligomers
    • S.M. Vaiana, R. Ghirlando, W.-M. Yau, W.A. Eaton, J. Hofrichter, Sedimentation studies on human amylin fail to detect low-molecular-weight oligomers, Biophys. J. 94 (2008) L45-L47.
    • (2008) Biophys. J. , vol.94
    • Vaiana, S.M.1    Ghirlando, R.2    Yau, W.-M.3    Eaton, W.A.4    Hofrichter, J.5
  • 56
    • 13844279124 scopus 로고    scopus 로고
    • Persistence of Vision Pty. Ltd, Williamstown, Victoria, Australia, 20048
    • Persistence of Vision Pty. Ltd., Persistence of Vision (TM) Raytracer, Persistence of Vision Pty. Ltd, Williamstown, Victoria, Australia, 20048 http://www.povray.org/.
    • Persistence of Vision (TM) Raytracer
  • 57
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • M.F. Sanner, A.J. Olson, J.C. Spehner, Reduced surface: an efficient way to compute molecular surfaces, Biopolymers 38 (1996) 305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 58
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • J. Kyte, R. Doolittle, A simple method for displaying the hydropathic character of a protein, J. Mol. Biol. 157 (1982) 105-132.
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.2


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