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Research Articles

Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35–56) in aqueous environment

Pages 302-317 | Received 24 Aug 2016, Accepted 16 Dec 2016, Published online: 23 Jan 2017

References

  • Amadei, A. , Linssen, A. , & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics , 17 , 412–425.10.1002/(ISSN)1097-0134
  • Berendsen, H. J. C. , Postma, J. P. M. , van Gunsteren, W. F. , & Hermans, J. (1981). Intermolecular forces . In B. Pullman Intermolecular Forces (pp. 331–342). Dordrecht: D Reidel Publishing Company.
  • Berendsen, H. J. C. , Grigera, J. R. , & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry , 91 , 6269–6271.10.1021/j100308a038
  • Berhanu, W. M. , & Hansmann, U. H. (2012). Side-chain hydrophobicity and the stability of Aβ 16-22 aggregates. Protein Science , 21 , 1837–1848.10.1002/pro.v21.12
  • Best, R. B. , & Mittal, J. (2011). Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences. Proteins: Structure, Function, and Bioinformatics , 79 , 1318–1328.10.1002/prot.22972
  • Cao, Z. , & Wang, J. (2010). A comparative study of two different force fields on structural and thermodynamics character of H1 peptide via molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics , 27 , 651–661.10.1080/07391102.2010.10508579
  • Cao, Z. , & Wang, J. (2010). A comparative study of different temperatures on computed structural character of H1 peptide via temperature replica exchange molecular dynamics simulations. Progress in Biochemistry and Biophysics , 37 , 319–325.10.3724/SP.J.1206.2009.00616
  • Cao, Z. , Liu, L. , & Wang, J. (2010). Effects of pH and temperature on the structural and thermodynamic character of α-syn12 peptide in aqueous solution. Journal of Biomolecular Structure and Dynamics , 28 , 343–353.10.1080/07391102.2010.10507364
  • Cao, Z. , Liu, L. , Wu, P. , & Wang, J. (2011). Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution. Acta Biochimica et Biophysica Sinica , 43 , 172–180.10.1093/abbs/gmr002
  • Cao, Z. , Liu, L. , Zhao, L. , & Wang, J. (2011). Effects of different force fields and temperatures on the structural character of abeta (12–28) peptide in aqueous solution. International Journal of Molecular Sciences , 12 , 8259–8274.10.3390/ijms12118259
  • Cino, E. A. , Choy, W. , & Karttunen, M. (2012). Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations. Journal of Chemical Theory and Computation , 8 , 2725–2740.10.1021/ct300323g
  • Conway, K. A. , Harper, J. D. , & Lansbury, P. T. (2000). Fibrils formed in vitro from α-synuclein and two mutant forms linked to Parkinson's disease are typical amyloid†. Biochemistry , 39 , 2552–2563.10.1021/bi991447r
  • Daidone, I. , Simona, F. , Roccatano, D. , Broglia, R. A. , Tiana, G. , Colombo, G. , & Di Nola, A. (2004). β-Hairpin conformation of fibrillogenic peptides: Structure and α-β transition mechanism revealed by molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics , 57 , 198–204.10.1002/prot.20178
  • Darden, T. , York, D. , & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics , 98 , 10089–10092.10.1063/1.464397
  • Daura, X. , Gademann, K. , Jaun, B. , Seebach, D. , van Gunsteren, W. F. , & Mark, A. E. (1999). Peptide folding: When simulation meets experiment. Angewandte Chemie International Edition , 38 , 236–240.10.1002/(ISSN)1521-3773
  • DeLano, W. L. (2002). The PyMOL molecular graphics system, 2002, Internet. Retrieved from http://www.pymol.org
  • Duan, Y. , Wu, C. , Chowdhury, S. , Lee, M. C. , Xiong, G. , Zhang, W. , … Caldwell, J. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry , 24 , 1999–2012.10.1002/(ISSN)1096-987X
  • Essmann, U. , Perera, L. , Berkowitz, M. L. , Darden, T. , Lee, H. , & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics , 103 , 8577–8593.10.1063/1.470117
  • Foloppe, N. , & MacKerell Jr., A. D. (2000). All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. Journal of Computational Chemistry , 21 , 86–104.10.1002/(SICI)1096-987X(20000130)21:2<>1.0.CO;2-6
  • Freddolino, P. L. , Liu, F. , Gruebele, M. , & Schulten, K. (2008). Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal , 94 , L75–L77.10.1529/biophysj.108.131565
  • Gerben, S. R. , Lemkul, J. A. , Brown, A. M. , & Bevan, D. R. (2014). Comparing atomistic molecular mechanics force fields for a difficult target: A case study on the Alzheimer’s amyloid β-peptide. Journal of Biomolecular Structure and Dynamics , 32 , 1817–1832.10.1080/07391102.2013.838518
  • Hess, B. , Bekker, H. , Berendsen, H. J. , & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry , 18 , 1463–1472.10.1002/(ISSN)1096-987X
  • Hess, B. , Kutzner, C. , van der Spoel, D. , & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation , 4 , 435–447.10.1021/ct700301q
  • Hornak, V. , Abel, R. , Okur, A. , Strockbine, B. , Roitberg, A. , & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics , 65 , 712–725.10.1002/prot.v65:3
  • Jorgensen, W. L. , Chandrasekhar, J. , Madura, J. D. , Impey, R. W. , & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics , 79 , 926–935.10.1063/1.445869
  • Jorgensen, W. L. , Maxwell, D. S. , & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society , 118 , 11225–11236.10.1021/ja9621760
  • Kabsch, W. , & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers , 22 , 2577–2637.10.1002/(ISSN)1097-0282
  • Kaminski, G. A. , Friesner, R. A. , Tirado-Rives, J. , & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides†. The Journal of Physical Chemistry B , 105 , 6474–6487.10.1021/jp003919d
  • Li, J. , Lakshminarayanan, R. , Bai, Y. , Liu, S. , Zhou, L. , Pervushin, K. , … Beuerman, R. W. (2012). Molecular dynamics simulations of a new branched antimicrobial peptide: A comparison of force fields. The Journal of Chemical Physics , 137 , 215101–215110.10.1063/1.4768899
  • MacKerell, A. D. , Bellott, M. , Dunbrack, R. L. , Evanseck, J. D. , Field, M. J. , … Karplus, M. (1998). Journal of Physical Chemistry B, 102 , 3586–3616.
  • MacKerell, A. D. , Banavali, N. , & Foloppe, N. (2000). Development and current status of the CHARMM force field for nucleic acids. Biopolymers , 56 , 257–265.10.1002/(ISSN)1097-0282
  • Mackerell, A. D. , Feig, M. , & Brooks, C. L. (2004). Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. Journal of Computational Chemistry , 25 , 1400–1415.10.1002/jcc.v25:11
  • Mahoney, M. W. , & Jorgensen, W. L. (2000). A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. The Journal of Chemical Physics , 112 , 8910–8922.10.1063/1.481505
  • Maisuradze, G. G. , Liwo, A. , & Scheraga, H. A. (2010). Relation between free energy landscapes of proteins and dynamics. Journal of Chemical Theory and Computation , 6 , 583–595.10.1021/ct9005745
  • Matthes, D. , & de Groot, B. L. (2009). Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes. Biophysical Journal , 97 , 599–608.10.1016/j.bpj.2009.04.061
  • Mirecka, E. A. , Shaykhalishahi, H. , Gauhar, A. , Akgül, Ş , Lecher, J. , … Hoyer, W. (2014). Sequestration of a β-hairpin for control of α-synuclein aggregation. Angewandte Chemie International Edition, 53 , 4227–4230.
  • Nguyen, P. H. , Stock, G. , Mittag, E. , Hu, C. K. , & Li, M. S. (2005). Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study. Proteins: Structure, Function, and Bioinformatics , 61 , 795–808.10.1002/prot.20696
  • Nosé, S. , & Klein, M. L. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics , 50 , 1055–1076.10.1080/00268978300102851
  • Oostenbrink, C. , Villa, A. , Mark, A. E. , & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry , 25 , 1656–1676.10.1002/(ISSN)1096-987X
  • Parrinello, M. , & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics , 52 , 7182–7190.10.1063/1.328693
  • Pronk, S. , Pall, S. , Schulz, R. , Larsson, P. , Bjelkmar, P. , Apostolov, R. , … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics , 29 , 845–854.10.1093/bioinformatics/btt055
  • Rochet, J. C. , & Lansbury, P. T. (2000). Amyloid fibrillogenesis: Themes and variations. Current Opinion in Structural Biology , 10 , 60–68.10.1016/S0959-440X(99)00049-4
  • Ross, C. A. , & Poirier, M. A. (2004). Protein aggregation and neurodegenerative disease. Nature Medicine , 10 , S10–S17.10.1038/nm1066
  • Sayle, R. A. , & Millner-White, E. J. (1995). RASMOL: Biomolecular graphics for all. Trends in Biochemical Sciences , 20 , 374–376.10.1016/S0968-0004(00)89080-5
  • Spillantini, M. G. , Schmidt, M. L. , Lee, V. M. Y. , Trojanowski, J. Q. , Jakes, R. , & Goedert, M. (1997). α-synuclein in Lewy bodies. Nature , 388 , 839–840.10.1038/42166
  • Sugita, Y. , & Okamoto, Y. (1999). Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters , 314 , 141–151.10.1016/S0009-2614(99)01123-9
  • van Gunsteren, W. F. , Billeter, S. R. , Eising, A. A. , Eising, A. A. , Hünenberger, P. H. , Krüger, P. K. H. C. , … Tironi, I. G. (1996). Biomolecular simulation: The GROMOS96 manual and user guide . Zurich, Switzerland: Hochschulverlag AG an der Zurich.
  • Wang, J. , Cieplak, P. , & Kollman, P. A. (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry , 21 , 1049–1074.10.1002/(ISSN)1096-987X
  • Yu, H. , Han, W. , Ma, W. , & Schulten, K. (2015). Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. The Journal of Chemical Physics , 143 , 243142–243142.10.1063/1.4936910
  • Zhang, J. , Qin, M. , & Wang, W. (2006). Folding mechanism of β-hairpins studied by replica exchange molecular simulations. Proteins: Structure, Function, and Bioinformatics , 62 , 672–685.
  • Zhou, R. (2003). Trp-cage: Folding free energy landscape in explicit water. Proceedings of the National Academy of Sciences , 100 , 13280–13285.10.1073/pnas.2233312100
  • Zhou, R. , Berne, B. J. , & Germain, R. (2001). The free energy landscape for β hairpin folding in explicit water. Proceedings of the National Academy of Sciences , 98 , 14931–14936.10.1073/pnas.201543998

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