Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Mücksch, Christian ^a   Urbassek, Herbert M ^a  

^a Rheinland Pfälzische Technische Universität Kaiserslautern Landau   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BONE MORPHOGENETIC PROTEIN 2; GRAPHITE; SODIUM CHLORIDE; WATER;

ADSORPTION KINETICS; ARTICLE; CONTROLLED STUDY; EXPERIMENTAL STUDY; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTEIN ADSORPTION; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN INTERACTION; PROTEIN TRANSPORT; PROTEIN UNFOLDING; SURFACE PROPERTY; ADSORPTION; CHEMISTRY; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

ADSORPTION; BONE MORPHOGENETIC PROTEIN 2; GRAPHITE; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS; WATER;

EID: 84878627749     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064883     Document Type: Article

References (43)

1. Ratner BD, Bryant SJ, (2004) Biomaterials: Where we have been and where we are going. Annu Rev Biomed Eng 6: 41.
2. Nakanishi K, Sakiyama T, Imamura K, (2001) On the adsorption of proteins on solid surfaces, a common but very complicated phenomenon. Journal of Bioscience and Bioengineering 91: 233.
3. Svaldo-Lanero T, Penco A, PratoM, Canepa M, Rolandi R, et al. (2008) Nanopatterning by protein unfolding. Soft Matter 4: 965-967.
4. Gray JJ, (2004) The interaction of proteins with solid surfaces. Current Opinion in Structural Biology 14: 110-115.
5. Wei T, Carignano MA, Szleifer I, (2011) Lysozyme adsorption on polyethylene surfaces: Why are long simulations needed? Langmuir 27: 12074-12081.
6. Raffaini G, Ganazzoli F, (2003) Simulation study of the interaction of some albumin subdomains with a flat graphite surface. Langmuir 19: 3403.
7. Raffaini G, Ganazzoli F, (2010) Protein adsorption on a hydrophbic surface: A molecular dynamics study of lysozyme on graphite. Langmuir 26: 5679-5689.
8. Sun Y, Dominy BN, Latour RA, (2007) Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface. Journal of Computational Chemistry 28: 1883-1892.
9. Voter AF, (1997) Hyperdynamics: Accelerated molecular dynamics of infrequent events. Phys Rev Lett 78: 3908-3911.
10. Hamelberg D, Mongan J, McCammon JA, (2004) Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. The Journal of Chemical Physics 120: 11919-11929.
11. Wang Y, Markwick PRL, de Oliveira CAF, McCammon JA, (2011) Enhanced lipid diffusion and mixing in accelerated molecular dynamics. Journal of Chemical Theory and Computation 7: 3199-3207.
12. Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC, (2012) Routine access to millisecond time scale events with accelerated molecular dynamics. Journal of Chemical Theory and Computation 8: 2997-3002.
13. Xin Y, Doshi U, Hamelberg D, (2010) Examining the limits of time reweighting and kramers' rate theory to obtain correct kinetics from accelerated molecular dynamics. The Journal of Chemical Physics 132: 224101.
14. Jennissen HP, (2002) Accelerated and improved osteointegration of implants biocoated with bone morphogenetic protein 2 (bmp-2). Ann NY Acad Sci 961: 139.
15. Sachse A, Wagner A, Keller M, Wagner O, Wetzel WD, et al. (2005) Osteointegration of hydroxyapatite-titanium implants coated with nonglycosylated recombinant human bone morphogenetic protein-2 (bmp-2) in aged sheep. Bone 37: 699-710.
16. Dong X, Wang Q, Wu T, Pan H, (2007) Understanding adsorption-desorption dynamics of bmp-2 on hydroxyapatite (001) surface. Biophysical Journal 93: 750-759.
17. Oliveira AF, Gemming S, Seifert G, (2010) Molecular dynamics simulations of bmp-2 adsorption on a hydrophobic surface. molekulardynamische simulation des bmp-2-adsorption auf einer hydrophoben oberfl̈ache. Materialwissenschaft und Werkstofftechnik 41: 1048-1053.
18. Utesch T, Daminelli G, Mroginski MA, (2011) Molecular dynamics simulations of the adsorption of bone morphogenetic protein-2 on surfaces with medical relevance. Langmuir 27: 13144-13153.
19. Mücksch C, Urbassek HM, (2011) Adsorption of bmp-2 on a hydrophobic graphite surface: A molecular dynamics study. Chemical Physics Letters 510: 252-256.
20. Winter M, Chuinard C, Cikes A, Pelegri C, Bronsard N, et al. (2009) Surgical management of elbow dislocation associated with non-reparable fractures of the radial head. Chirurgie de la Main 28: 158-167.
21. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with namd. Journal of Computational Chemistry 26: 1781-1802.
22. MacKerell AD, Bashford D, Bellott, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry B 102: 3586-3616.
23. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML, (1983) Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics 79: 926-935.
24. Scheufler C, Sebald W, Hülsmeyer M, (1999) Crystal structure of human bone morphogenetic protein-2 at 2.7 å resolution. Journal of Molecular Biology 287: 103-115.
25. 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.
26. Zuo A, Liang D, Sun P, Zhang R, Zhao R, et al. (2008) Bmp-2 modified hydroxyapatite/chitosan composite scaffold for bone engineering. The 2nd International Conference on Bioinformatics and Biomedical Engineering: 888-892.
27. Werder T, Walther JH, Jaffe RL, Halicioglu T, Koumoutsakos P, (2002) On the water-carbon interaction for use in molecular dynamics simulations of graphite and carbon nanotubes. Journal of the American Chemical Society 107: 1345.
28. Fowkes FM, Harkins WD, (1940) The state of monolayers adsorbed at the interface solid-aqueous solution. Journal of the American Chemical Society 62: 3377-3386.
29. Ryckaert JP, Ciccotti G, Berendsen HJ, (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics 23: 327-341.
30. Wang Y, Harrison CB, Schulten K, McCammon JA, (2011) Implementation of accelerated molecular dynamics in namd. Comput Sci Discov 4: 015002.
31. Wereszczynski J, McCammon J (2012) Computational Drug Discovery and Design, volume 819 of Methods in Molecular Biology. Springer New York, 515-524 pp.
32. de Oliveira CAF, Hamelberg D, McCammon JA, (2006) On the application of accelerated molecular dynamics to liquid water simulations. The Journal of Physical Chemistry B 110: 22695-22701.
33. 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.
34. Humphrey W, Dalke A, Schulten K, (1996) VMD - Visual Molecular Dynamics. Journal of Molecular Graphics 14: 33-38.
35. Stone J (1998) An Efficient Library for Parallel Ray Tracing and Animation. Master's thesis, Computer Science Department, University of Missouri-Rolla.
36. Grimme S, (2008) Gibt es spezielle nicht-kovalente π-π-stapelwechselwirkungen wirklich? Angewandte Chemie 120: 3478.
37. Rajesh C, Majumder C, Mizuseki H, Kawazoe Y, (2009) A theoretical study on the interaction of aromatic amino acids with graphene and single walled carbon nanotube. Journal of Chemical Physics 130: 124911-1.
38. Raffaini G, Ganazzoli F, (2004) Surface ordering of proteins adsorbed on graphite. The Journal of Physical Chemistry B 108: 13850-13854.
39. Zuckerman DM, (2011) Equilibrium sampling in biomolecular simulations. Annual Review of Biophysics 40: 41-62.
40. Wang F, Stuart S, Latour RA, (2008) Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics. Biointerphases 3: 9-18.
41. Grubmüller H, (1995) Predicting slow structural transitions in macromolecular systems: Conformational flooding. Phys Rev E 52: 2893-2906.
42. Lange OF, Schäfer LV, Grubmüller H, (2006) Flooding in gromacs: Accelerated barrier crossings in molecular dynamics. Journal of Computational Chemistry 27: 1693-1702.
43. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577.