Langevin dynamics simulations reveal biologically relevant folds arising from the incorporation of a torsional potential

Journal of Theoretical Biology

Volumn 265, Issue 3, 2010, Pages 245-249

  Anjukandi, Padmesh ^a   Pereira, Gerald G ^b,c   Williams, Martin A K ^a,c  

^a MASSEY UNIVERSITY   (New Zealand)

^b CSIRO   (Australia)

^c MACDIARMID INSTITUTE FOR ADVANCED MATERIALS AND NANOTECHNOLOGY   (New Zealand)

Author keywords

Brownian motion; Conformations; Langevin dynamics simulation; Torsional potential

Indexed keywords

POLYMER;

BROWNIAN MOTION; COMPUTER SIMULATION; POLYMERASE CHAIN REACTION; TORSION;

ARTICLE; CONFORMATION; CONTROLLED STUDY; MATHEMATICAL MODEL; MECHANICAL TORSION; PRIORITY JOURNAL; RIGIDITY; SIMULATION; SOLVATION; SOLVENT EFFECT; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION;

COMPUTER SIMULATION; MODELS, CHEMICAL; MOLECULAR CONFORMATION; POLYMERS; TORSION, MECHANICAL;

EID: 77954622615     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.05.011     Document Type: Article

References (27)

1. Allen M.P., Tildesley D.J. Computer Simulation of Liquids 1987, Clarendon Press, Oxford.
2. Banavar J.R., Maritan A. Colloquium: geometrical approach to protein folding: a tube picture. Rev. Mod. Phys. 2003, 75:23-34.
3. Banavar J.R., Maritan A. Computational approach to protein folding problem. PROTEINS: Structure, Function and Genetics 2007, 42:433-435.
4. Banavar, J.R., Maritan, A., 2007b. Physics of proteins, Annu. Rev. Biophys. Biomol. Struct. 261-280.
5. Bryngelson J.D., Wolynes P.G. Spin glasses and the statistical mechanics of protein folding. Proc. Nat. Acad. Sci. 1987, 84:7524-7528.
6. Chakrabarty S., Bagchi B. Self-organization of n-alkane chains in water: length dependent crossover from helix and toroid to molten globule. J. Phys. Chem. B Lett. 2009, 113:8446-8448.
7. Creighton T.E. PROTEINS-Structure and Molecular properties 1999, Freeman, New York.
8. Edwards S.A., Williams D.R.M. Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations. Macromolecules 2005, 38:10590-10595.
9. Hargittai I., Hargittai M. Molecular structure of hyaluronan: an introduction. Struct. Chem. 2008, 19:697-717.
10. Kemp J.P., Chen Z.Y. Formation of helical states in wormlike polymer chains. Phys. Rev. Lett. 1998, 81:3880-3883.
11. Kumar V., Jenson I., Jacobsen J.L., Guttmann A.J. Role of conformational entropy in force-induced biopolymer unfolding. Phys. Rev. Lett. 2007, 98:128101(1)-128101(4).
12. Lee N.K., Thirumalai D. Pulling-speed-dependent force-extension profiles for semiflexible chains. Biophys. J. 2004, 86(5):2641-2649.
13. Liu C., Muthukumar M. Langevin dynamics simulations of early-stage polymer nucleation and crystallization. J. Chem. Phys. 1998, 109:2536-2542.
14. Maurice R.G., Matthai C.C. Force-extension curves for a single polymer chain under varying solvent conditions. Phys. Rev. E 1999, 60:3165-3169.
15. Maritan A., Micheletti C., Trovato A., Banavar J.R. Optimal shapes of compact strings. Nature 2000, 406:287-290.
16. Miller I.C.B., Keentok M., Pereira G.G., Williams D.R.M. Semiflexible polymer condensates in poor solvents: toroid versus spherical geometries. Phys. Rev. E 2005, 71:031802(1)-031802(9).
17. Pande V.S., Rokhsar D.S. Folding pathway of a lattice model for proteins. Proc. Nat. Acad. Sci. 1999, 96:1273-1278.
18. Pereira G.G., Williams D.R.M. Kinetic pathways for the collapse of semiflexible polymers. Aust. NZ. Ind. Appl. Math. J. 2004, 45(E):c163-c173.
19. Pereira G.G., Williams D.R.M. Crystalline toroidal globules of DNA and other semi-flexible polymers: jumps in radius caused by hexagonal packing. Europhys. Lett. 2000, 50:559-564.
20. Schnurr B., MacKintosh F.C., Williams D.R.M. Dynamical intermediates in the collapse of semiflexible polymers in poor solvents. Europhys. Lett. 2000, 51(3):279-285.
21. Sletmoen M., Maurstad G., Stokke B.T. Potentials of bionanotechnology in the study and manufacturing of self-assembled biopolymer complexes and gels. Food Hydrocolloids 2008, 22:2-11.
22. Srinivas G., Bagchi B. Detection of collapsed and ordered polymer structures by fluorescence resonance energy transfer in stiff homopolymers: bimodality in the reaction efficiency distribution. J. Chem. Phys. 2002, 116:837-844.
23. Vogel T., Neuhaus T., Bachmann M., Janke W. Thickness-dependent secondary structure formation of tubelike polymers. Europhys. Lett. 2009, 85. 10003(p1)-10003(p5).
24. Watson J.D., Crick F.H.C. A structure for deoxyribose nuclic acid. Nature 1953, 3:737-738.
25. Welch P., Muthukumar M. Molecular mechanisms of polymer crystallization from solution. Phys. Rev. Lett. 2001, 87:218302(1)-218302(4).
26. Zhang Q., Lu Z., Hu H., Yang W., Marszalek P.E. Direct detection of the formation of V-amylose helix by single molecule force spectroscopy. J. Am. Chem. Soc. 2006, 128(29):9387-9393.
27. Zhang L., Wang C., Cui S., Wang Z., Zhang X. Single-molecule force spectroscopy on curdlan: unwinding helical structures and random coils. Nano Lett. 2003, 3:1119-1124.