Peptide folding problem: A molecular dynamics study on polyalanines using different force fields

International Journal of Peptide Research and Therapeutics

Volumn 19, Issue 2, 2013, Pages 117-123

  Raucci, Raffaele ^a   Colonna, Giovanni ^a   Castello, Giuseppe ^b   Costantini, Susan ^b  

^a SECOND UNIVERSITY OF NAPLES   (Italy)

^b NATIONAL CANCER INSTITUTE   (Italy)

Author keywords

Force fields; Helicity; Molecular dynamics; Peptide folding; Polyalanines; Simulations

Indexed keywords

PEPTIDE; POLYALANINE; UNCLASSIFIED DRUG;

ARTICLE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 84878012857     PISSN: 15733149     EISSN: 15733904     Source Type: Journal    
DOI: 10.1007/s10989-012-9322-z     Document Type: Article

References (26)

1. Box VG (1997) The molecular mechanics of quantized valence bonds. J Mol Model 3:124-141
2. Brown LY, Brown SA (2004) Alanine tracts: the expanding story of human illness and trinucleotide repeats. Trends Genet 20:51-58
3. Cornell WD, Cieplak P, Bayly CI et al (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179-5197
4. Fu C-F, Tian SX (2011) A comparative study for molecular dynamics simulations of liquid benzene. J Chem Theory Comput 7:2240-2252
5. Garcia AE (2004) Characterization of non-alpha helical conformations in Ala peptides. Polymer 45:669-676
6. Guvench O, MacKerell AD Jr (2008) Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol 443:63-88
7. Hooft RWW, Sander C, Vriend G (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comput Appl Biosci 13:425-430
8. Jorgensen WL, Chandrasekhar J, Madura J, Impey R, Klein M (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935
9. Jorgensen WL, Maxwell DS, Tirado-Rives J (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
10. Lacroix E, Viguera AR, Serrano L (1998) Elucidating the folding problem of alpha-helices: local motifs long-range electrostatics ionic strength dependence and prediction of NMR parameters. J Mol Biol 284:173-191
11. Levitt M (1983) Molecular dynamics of native protein: I Computer simulation of trajectories. J Mol Biol 168:595-620
12. Levitt M, Hirshberg M, Sharon R, Daggett V (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput Phys Commun 91:215-231
13. Lovell SC, Davis IW, Arendall WB, De Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Cα geometry: ψ and Cβ deviation. Proteins Struct Funct Genet 2003(50):437-450
14. Miick SM, Martinez GV, Fiori WR, Todd AP, Millhauser GL (1992) Short alanine-based peptides may form 3(10)-helices and not alpha-helices in aqueous solution. Nature 359:653-655
15. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM (1992) Stereochemical quality of protein structure coordinates. Proteins Struct Function Genetics 12:345-364
16. Mu Y, Kosov DS, Stock G (2003) Conformational dynamics of trialanine in water 2 comparison of AMBER, CHARMM, GROMOS and OPLS force fields to NMR and infrared experiments. J Phys Chem B 107:5064-5073
17. Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004) 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 25:1656-1676
18. Paladino A, Colonna G, Facchiano AM, Costantini S (2010) Functional hypothesis on miraculin' sweetness by a molecular dynamics approach. BBRC 396:726-730
19. Pereiaslavets LB, Finkel'shtein AV (2010) Atomic force field FFsol for calculation of molecular interactions of in water environment. Mol Biol (Mosk) 44:340-354
20. Perutz MF (1996) Glutamine repeats and inherited neurodegenerative diseases: molecular aspects. Curr Opin Struct Biol 6:848-858
21. Perutz MF (1999) Glutamine repeats and neurodegenerative diseases: molecular aspects. Trends Biochem Sci 24:58-63
22. Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Proteins Chem 66:27-85
23. Schuler LD, Daura X, van Gunsteren WF (2001) An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J Comput Chem 22:1205-1218
24. Sorin EJ, Pande VS (2005) Empirical force field assessment: the interplay between backbone torsions and non-covalent term scaling. J Comput Chem 26:682-690
25. Thompson EJ, DePaul AJ, Patel SS, Sorin EJ (2010) Evaluating molecular mechanical potentials for helical peptides and proteins. PLoS One 5:e10056
26. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast flexible and free. J Comput Chem 26:1701-1718