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Volumn 117, Issue 15, 2013, Pages 3962-3975

Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; MOLECULAR DYNAMICS; PEPTIDES;

EID: 84876469199     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp311795b     Document Type: Article
Times cited : (98)

References (47)
  • 1
    • 34247245185 scopus 로고    scopus 로고
    • Peptide self-assembly at the nanoscale: A challenging target for computational and experimental biotechnology
    • Colombo, G.; Soto, P.; Gazit, E. Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology Trends Biotechnol. 2007, 25, 211-218
    • (2007) Trends Biotechnol. , vol.25 , pp. 211-218
    • Colombo, G.1    Soto, P.2    Gazit, E.3
  • 2
  • 3
    • 33749642847 scopus 로고    scopus 로고
    • Computational approaches to fibril structure and formation
    • Hall, C. K.; Wagoner, V. A. Computational approaches to fibril structure and formation Methods Enzymol. 2006, 412, 338-365
    • (2006) Methods Enzymol. , vol.412 , pp. 338-365
    • Hall, C.K.1    Wagoner, V.A.2
  • 4
    • 33748689799 scopus 로고    scopus 로고
    • Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
    • Ma, B. Y.; Nussinov, R. Simulations as analytical tools to understand protein aggregation and predict amyloid conformation Curr. Opin. Chem. Biol. 2006, 10, 445-452
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 445-452
    • Ma, B.Y.1    Nussinov, R.2
  • 5
    • 33646235847 scopus 로고    scopus 로고
    • Designing a nanotube using naturally occurring protein building blocks
    • Tsai, C. J.; Zheng, J.; Nussinov, R. Designing a nanotube using naturally occurring protein building blocks PLoS Comput. Biol. 2006, 2, 311-319
    • (2006) PLoS Comput. Biol. , vol.2 , pp. 311-319
    • Tsai, C.J.1    Zheng, J.2    Nussinov, R.3
  • 6
    • 33745152345 scopus 로고    scopus 로고
    • Rigid self-assembled hydrogel composed of a modified aromatic dipeptide
    • Mahler, A.; Reches, M.; Rechter, M.; Cohen, S.; Gazit, E. Rigid self-assembled hydrogel composed of a modified aromatic dipeptide Adv. Mater. 2006, 18, 1365-1370
    • (2006) Adv. Mater. , vol.18 , pp. 1365-1370
    • Mahler, A.1    Reches, M.2    Rechter, M.3    Cohen, S.4    Gazit, E.5
  • 7
    • 0037466613 scopus 로고    scopus 로고
    • Casting metal nanowires within discrete self-assembled peptide nano-tubes
    • Reches, M.; Gazit, E. Casting metal nanowires within discrete self-assembled peptide nano-tubes Science 2003, 300, 625-627
    • (2003) Science , vol.300 , pp. 625-627
    • Reches, M.1    Gazit, E.2
  • 8
    • 33744932979 scopus 로고    scopus 로고
    • The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's β-amyloid polypeptide
    • Görbitz, C. H. The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's β-amyloid polypeptide Chem. Commun. 2006, 14, 2332-2334
    • (2006) Chem. Commun. , vol.14 , pp. 2332-2334
    • Görbitz, C.H.1
  • 9
    • 33846593451 scopus 로고    scopus 로고
    • Microporous Organic Materials from Hydrophobic Dipeptides
    • Henrik, C.; Görbitz, C. H. Microporous Organic Materials from Hydrophobic Dipeptides Chem.-Eur. J. 2007, 13, 1022-1031
    • (2007) Chem. - Eur. J. , vol.13 , pp. 1022-1031
    • Henrik, C.1    Görbitz, C.H.2
  • 10
    • 0035802949 scopus 로고    scopus 로고
    • Nanotube Formation by Hydrophobic Dipeptides
    • Görbitz, C. H. Nanotube Formation by Hydrophobic Dipeptides Chem.-Eur. J. 2001, 7, 5153-5159
    • (2001) Chem. - Eur. J. , vol.7 , pp. 5153-5159
    • Görbitz, C.H.1
  • 12
    • 2342595738 scopus 로고    scopus 로고
    • Formation of closed-cage nanostructures by self-assembly of aromatic dipeptides
    • Reches, M.; Gazit, E. Formation of closed-cage nanostructures by self-assembly of aromatic dipeptides Nano Lett. 2004, 4, 581-585
    • (2004) Nano Lett. , vol.4 , pp. 581-585
    • Reches, M.1    Gazit, E.2
  • 13
    • 0036135139 scopus 로고    scopus 로고
    • A possible role for pi-stacking in the self-assembly of amyloid fibrils
    • Gazit, E. A possible role for pi-stacking in the self-assembly of amyloid fibrils FASEB J. 2002, 16, 77-83
    • (2002) FASEB J. , vol.16 , pp. 77-83
    • Gazit, E.1
  • 14
    • 0035823520 scopus 로고    scopus 로고
    • Analysis of the structural and functional elements of the minimal active fragment of islet amyloid polypeptide (IAPP) - An experimental support for the key role of the phenylalanine residue in amyloid formation
    • Azriel, R.; Gazit, E. Analysis of the structural and functional elements of the minimal active fragment of islet amyloid polypeptide (IAPP)-An experimental support for the key role of the phenylalanine residue in amyloid formation J. Biol. Chem. 2001, 276, 34156-34161
    • (2001) J. Biol. Chem. , vol.276 , pp. 34156-34161
    • Azriel, R.1    Gazit, E.2
  • 15
    • 79960184746 scopus 로고    scopus 로고
    • Solvent and surface controlled self-assembly of diphenylalanine peptide: From microtubes to Nanofibers
    • Huang, R.; Qi, W.; Su, R.; Zhao, J.; He, Z. Solvent and surface controlled self-assembly of diphenylalanine peptide: from microtubes to Nanofibers Soft Matter 2011, 7, 6418-6421
    • (2011) Soft Matter , vol.7 , pp. 6418-6421
    • Huang, R.1    Qi, W.2    Su, R.3    Zhao, J.4    He, Z.5
  • 16
    • 79958780904 scopus 로고    scopus 로고
    • Self-assembly into spheres of a hybrid diphenylalanine-porphyrin: Increased fluorescence lifetime, conserved electronic properties
    • Charalambidis, G.; Kasotakis, E.; Lazarides, Th.; Mitraki, A.; Coutsolelos, A. G. Self-assembly into spheres of a hybrid diphenylalanine- porphyrin: increased fluorescence lifetime, conserved electronic properties Chem.-Eur. J. 2011, 17, 7213-7219
    • (2011) Chem. - Eur. J. , vol.17 , pp. 7213-7219
    • Charalambidis, G.1    Kasotakis, E.2    Lazarides, Th.3    Mitraki, A.4    Coutsolelos, A.G.5
  • 17
    • 38449096286 scopus 로고    scopus 로고
    • Fmoc-Diphenylalanine self assembles to a hydrogel via a novel architecture based on pi-pi interlocked beta-sheets
    • Smith, A. M.; Williams, R. J.; Tang, C.; Coppo, P.; Collins, R. F.; Turner, M. L.; Saiani, A.; Ulijn, R. V. Fmoc-Diphenylalanine self assembles to a hydrogel via a novel architecture based on pi-pi interlocked beta-sheets Adv. Mater. 2008, 20, 37-41
    • (2008) Adv. Mater. , vol.20 , pp. 37-41
    • Smith, A.M.1    Williams, R.J.2    Tang, C.3    Coppo, P.4    Collins, R.F.5    Turner, M.L.6    Saiani, A.7    Ulijn, R.V.8
  • 19
    • 84856481596 scopus 로고    scopus 로고
    • The Rheological and Structural Properties of Fmoc-Peptide-Based Hydrogels: The Effect of Aromatic Molecular Architecture on Self-Assembly and Physical Characteristics
    • Orbach, R.; Mironi-Harpaz, I.; Adler-Abramovich, L.; Mossou, E.; Mitchell, E. P.; Forsyth, V. T.; Gazit, E.; Seliktar, D. The Rheological and Structural Properties of Fmoc-Peptide-Based Hydrogels: The Effect of Aromatic Molecular Architecture on Self-Assembly and Physical Characteristics Langmuir 2012, 28, 2015-2022
    • (2012) Langmuir , vol.28 , pp. 2015-2022
    • Orbach, R.1    Mironi-Harpaz, I.2    Adler-Abramovich, L.3    Mossou, E.4    Mitchell, E.P.5    Forsyth, V.T.6    Gazit, E.7    Seliktar, D.8
  • 20
    • 0030623382 scopus 로고    scopus 로고
    • Conformational transitions provoked by organic solvents in beta-lactoglobulin: Can a molten globule like intermediate be induced by the decrease in dielectric constant?
    • Uversky, V. N.; Narizhneva, N. V.; Kirschstein, S. O.; Winter, S.; Löber, G. Conformational transitions provoked by organic solvents in beta-lactoglobulin: can a molten globule like intermediate be induced by the decrease in dielectric constant? Fold. Des. 1997, 2, 163-172
    • (1997) Fold. Des. , vol.2 , pp. 163-172
    • Uversky, V.N.1    Narizhneva, N.V.2    Kirschstein, S.O.3    Winter, S.4    Löber, G.5
  • 21
    • 0032444658 scopus 로고    scopus 로고
    • Trifluoroethanol and colleagues: Cosolvents come of age. Recent studies with peptides and proteins
    • Buck, M. Trifluoroethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins Q. Rev. Biophys. 1998, 31, 297-355
    • (1998) Q. Rev. Biophys. , vol.31 , pp. 297-355
    • Buck, M.1
  • 22
    • 79958176947 scopus 로고    scopus 로고
    • Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - A Combined Molecular Dynamics and NMR Study
    • Hwang, S.; Shao, Q.; Williams, H.; Hilty, C.; Gao, Y. Q. Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins - a Combined Molecular Dynamics and NMR Study J. Phys. Chem. B 2011, 115, 6653-6660
    • (2011) J. Phys. Chem. B , vol.115 , pp. 6653-6660
    • Hwang, S.1    Shao, Q.2    Williams, H.3    Hilty, C.4    Gao, Y.Q.5
  • 24
    • 62349108293 scopus 로고    scopus 로고
    • Self-assembling dipeptides: Including solvent degrees of freedom in a coarse-grained model
    • Villa, A.; van der Vegt, N. F. A.; Peter, C. Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model Phys. Chem. Chem. Phys. 2009, 11, 2068-2076
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 2068-2076
    • Villa, A.1    Van Der Vegt, N.F.A.2    Peter, C.3
  • 25
    • 62349089500 scopus 로고    scopus 로고
    • Self-assembling dipeptides: Conformational sampling in solvent-free coarse-grained simulation
    • Villa, A.; Peter, C.; van der Vegt, N. F. A. Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation Phys. Chem. Chem. Phys. 2009, 11, 2077-2086
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 2077-2086
    • Villa, A.1    Peter, C.2    Van Der Vegt, N.F.A.3
  • 26
    • 85015514764 scopus 로고    scopus 로고
    • Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly
    • Frederix, P. W. J. M; Ulijn, R. V.; Hunt, N. T.; Tuttle, T. Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly J. Phys. Chem. Lett. 2011, 2 (19) 2380-2384
    • (2011) J. Phys. Chem. Lett. , vol.2 , Issue.19 , pp. 2380-2384
    • Frederix, P.W.J.M.1    Ulijn, R.V.2    Hunt, N.T.3    Tuttle, T.4
  • 27
    • 84864680942 scopus 로고    scopus 로고
    • Dissecting the Self-Assembly Pathway of Diphenylalanine-Based Nanovesicles and Nanotubes
    • Guo, C.; Luo, Y.; Zhou, R.; Wie, G. Dissecting the Self-Assembly Pathway of Diphenylalanine-Based Nanovesicles and Nanotubes ACS Nano 2012, 6, 3907-3918
    • (2012) ACS Nano , vol.6 , pp. 3907-3918
    • Guo, C.1    Luo, Y.2    Zhou, R.3    Wie, G.4
  • 28
    • 0035838258 scopus 로고    scopus 로고
    • Solvation properties of non-polar amino acids in water and methanol: A molecular dynamics study
    • Renzi, D.; Carlevaro, C. M.; Stoico, C.; Vericat, F. Solvation properties of non-polar amino acids in water and methanol: a molecular dynamics study Mol. Phys. 2001, 99, 913-922
    • (2001) Mol. Phys. , vol.99 , pp. 913-922
    • Renzi, D.1    Carlevaro, C.M.2    Stoico, C.3    Vericat, F.4
  • 29
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • Berendsen, H.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 1995, 91, 43-56
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 43-56
    • Berendsen, H.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 30
    • 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. Model. 2001, 7, 306-317
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 31
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4, 435-447
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 32
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi, G.; Donadio, D.; Parinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126, 014101-1-014101-7
    • (2007) J. Chem. Phys. , vol.126 , pp. 0141011-0141017
    • Bussi, G.1    Donadio, D.2    Parinello, M.3
  • 33
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
    • (2004) J. Comput. Chem. , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 34
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman, B. D. Reidel Publishing Company: Dordrecht
    • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction models for water in relation to protein hydration. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Company: Dordrecht, 1981; pp 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 35
    • 35949020425 scopus 로고
    • Replica Monte-Carlo Simulation of Spin-Glasses
    • Swendsen, R.; Wang, J. Replica Monte-Carlo Simulation of Spin-Glasses Phys. Rev. Lett. 1986, 57, 2607-2609
    • (1986) Phys. Rev. Lett. , vol.57 , pp. 2607-2609
    • Swendsen, R.1    Wang, J.2
  • 36
    • 0031578972 scopus 로고    scopus 로고
    • Parallel Tempering Algorithm for Conformational Studies of Biological Molecules
    • Hansmann, U. H. E. Parallel Tempering Algorithm for Conformational Studies of Biological Molecules Chem. Phys. Lett. 1997, 281, 140-150
    • (1997) Chem. Phys. Lett. , vol.281 , pp. 140-150
    • Hansmann, U.H.E.1
  • 37
    • 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, 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 38
    • 1642546396 scopus 로고    scopus 로고
    • Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm
    • Nymeyer, H.; Gnanakaran, S.; Garcia, A. E. Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm Methods Enzymol. 2004, 383, 119-149
    • (2004) Methods Enzymol. , vol.383 , pp. 119-149
    • Nymeyer, H.1    Gnanakaran, S.2    Garcia, A.E.3
  • 39
    • 0030516672 scopus 로고    scopus 로고
    • Exchange Monte Carlo Method and Application to Spin Glass Simulations
    • Hukushima, K.; Nemoto, K. Exchange Monte Carlo Method and Application to Spin Glass Simulations J. Phys. Soc. Jpn. 1996, 65, 1604-1608
    • (1996) J. Phys. Soc. Jpn. , vol.65 , pp. 1604-1608
    • Hukushima, K.1    Nemoto, K.2
  • 40
    • 0036467163 scopus 로고    scopus 로고
    • Structure of Met-Enkephalin in Explicit Aqueous Solution Using Replica Exchange Molecular Dynamics
    • Sanbonmatsu, K. Y.; Garcia, A. E. Structure of Met-Enkephalin in Explicit Aqueous Solution Using Replica Exchange Molecular Dynamics Proteins 2002, 46, 225-234
    • (2002) Proteins , vol.46 , pp. 225-234
    • Sanbonmatsu, K.Y.1    Garcia, A.E.2
  • 41
    • 34249933138 scopus 로고    scopus 로고
    • Hydrogen bonding definitions and dynamics in liquid water
    • Kumar, R.; Schmidt, J. R.; Skinner, J. L. Hydrogen bonding definitions and dynamics in liquid water J. Chem. Phys. 2007, 126, 204107-204119
    • (2007) J. Chem. Phys. , vol.126 , pp. 204107-204119
    • Kumar, R.1    Schmidt, J.R.2    Skinner, J.L.3
  • 42
    • 79957566339 scopus 로고
    • Pair interactions and hydrogen-bond networks in models of liquid methanol
    • Haughney, M.; Ferrario, M.; McDonald, I. R. Pair interactions and hydrogen-bond networks in models of liquid methanol Mol. Phys. 1986, 58, 849-853
    • (1986) Mol. Phys. , vol.58 , pp. 849-853
    • Haughney, M.1    Ferrario, M.2    McDonald, I.R.3
  • 43
    • 33845281708 scopus 로고
    • Molecular-Dynamics Simulation of Liquid Methanol
    • Haughney, M.; Ferrario, M.; McDonald, I. R. Molecular-Dynamics Simulation of Liquid Methanol J. Phys. Chem. 1987, 91, 4934-4940
    • (1987) J. Phys. Chem. , vol.91 , pp. 4934-4940
    • Haughney, M.1    Ferrario, M.2    McDonald, I.R.3
  • 44
  • 45
    • 71649114292 scopus 로고    scopus 로고
    • Amyloid-like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations
    • Tamamis, P.; Kasotakis, E.; Mitraki, A.; Archontis, G. Amyloid-like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations J. Chem. Phys. B 2009, 113, 15639-15647
    • (2009) J. Chem. Phys. B , vol.113 , pp. 15639-15647
    • Tamamis, P.1    Kasotakis, E.2    Mitraki, A.3    Archontis, G.4
  • 46
    • 77951561571 scopus 로고    scopus 로고
    • Predicting polymer dynamics at multiple length and time scales
    • Harmandaris, V.; Kremer, K. Predicting polymer dynamics at multiple length and time scales Soft Matter 2009, 5, 3920-3926
    • (2009) Soft Matter , vol.5 , pp. 3920-3926
    • Harmandaris, V.1    Kremer, K.2
  • 47
    • 61849150553 scopus 로고    scopus 로고
    • Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations
    • Harmandaris, V.; Kremer, K. Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations Macromolecules 2009, 42, 791-802
    • (2009) Macromolecules , vol.42 , pp. 791-802
    • Harmandaris, V.1    Kremer, K.2


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