Erratum: Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules (BMC Biophysics (2014) 7:4 DOI: 10.1186/2046-1682-7-4);Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

BMC Biophysics

Volumn 7, Issue 1, 2014, Pages

  Mereghetti, Paolo ^a,b   Martinez, Michael ^a   Wade, Rebecca C ^a,c  

^a HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

^b CENTER FOR NANOTECHNOLOGY INNOVATION NEST   (Italy)

^c UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

Brownian dynamics simulation; Continuum solvent electrostatics; Debye H ckel; Discretization grid; Finite difference; Ionic strength; Poisson Boltzmann equation; Protein diffusion; Second virial coefficient; Small angle scattering intensity

Indexed keywords

BOVINAE;

EID: 84928103638     PISSN: 20461682     EISSN: 20461682     Source Type: Journal    
DOI: 10.1186/s13628-020-0026-z     Document Type: Erratum

References (44)

1. McGuffee SR, Elcock AH. Atomically detailed simulations of concentrated protein solutions: The effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems. J Am Chem Soc 2006, 128:12098-12110.
2. Geyer T, Winter U. An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations. J Chem Phys 2009, 130:114905.
3. Mereghetti P, Gabdoulline RR, Wade RC. Brownian dynamics simulation of protein solutions: structural and dynamical properties. Biophys J 2010, 99(11):3782-91.
4. Ando T, Skolnick J. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci 2010, 107(43):18457-18462.
5. McGuffee SR, Elcock AH. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 2010, 6(3):e1000694.
6. Wieczorek G, Zielenkiewicz P. Influence of macromolecular crowding on protein-protein association rates - a Brownian dynamics study. Biophys J 2008, 95:5030-5036.
7. Goodsell DS, Olson AJ. Automated docking of substrates to proteins by simulated annealing. Proteins: Struct Function Genet 1990, 8(8):195-202.
8. Gabdoulline RR, Wade RC. Simulation of the diffusional association of barnase and barstar. Biophys J 1997, 72(5):1917-1929.
9. Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985, 28(7):849-857.
10. Wu X, Milne J, Borgnia M, Rostapshov A, Subramaniam S,. BR B A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J Struct Biol 2003, 141:63-76. BR B.
11. Sherwood P, Brooks BR, Sansom MSP. Multiscale methods for macromolecular simulations. Curr Opin Struct Biol 2008, 18(5):630-640.
12. Mereghetti P, Wade RC. Atomic detail Brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions. J Phys Chem B 2012, 116:8523-8533.
13. Sharp K. Incorporating solvent and ion screening into molecular dynamics using the finite-differnece Poisson-Boltzmann method. J Comp Chem 1991, 12(4):454-468.
14. Lu BZ, Chen WZ, Wang CX,. Xu Xj Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation. Proteins: Struct Function Bioinform 2002, 48(3):497-504. Xu Xj.
15. Prabhu NV, Zhu P, Sharp KA. Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. J Comp Chem 2004, 25(16):2049-2064.
16. Wang J, Tan C, Lu Q, Luo R,. Tan Yh Poisson-Boltzmann Solvents in Molecular Dynamics Simulations. Commun Comput Phys 2008, 3(5):1010-1031. Tan Yh.
17. Ermak DL, McCammon JA. Brownian dynamics with hydrodynamic interactions. J Chem Phys 1978, 69:1352-1360.
18. Urbina-Villalba G, Garcia-Sucre M, Toro-Mendoza J. Average hydrodynamic correction for the Brownian dynamics calculation of flocculation rates in concentrated dispersions?. Phys Rev E 2003, 68:061408.
19. de la Torre JG, Huertas ML, Carrasco B. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys J 2000, 78:719-730.
20. Tokuyama M, Oppenheim I. Dynamics of hard-sphere suspensions. Phys Rev E 1994, 50:R16-R19.
21. Tokuyama M, Oppenheim I. On the theory of concentrated hard-sphere suspensions. Physica A 1995, 216:85-119.
22. Tokuyama M, Moriki T, Kimura Y. Self-diffusion of biomolecules in solution. Physical Rev E 2011, 83(5):1-8.
23. Cichocki B, Ekiel-Jezewska ML, Wajnryb E. Lubrication corrections for three-particle contribution to short-time self-diffusion coefficients in colloidal dispersions. J Chem Phys 1999, 111(7):3265-3273.
24. Gabdoulline RR, Wade RC. On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events. J Am Chem Soc 2009, 131(26):9230-9238.
25. Gabdoulline RR, Wade RC. Effective charges for macromolecules in solvent. J Phys Chem 1996, 100:3868-3878.
26. Elcock A, Gabdoulline R, Wade R, McCammon J. Computer simulation of protein-protein association kinetics: Acetylcholinesterase- Fasciculin. J Mol Biol 1999, 291:149-162.
27. Neal BL, Asthagiri D, Lenhoff AM. Molecular origins of osmotic second virial coefficients of proteins. Biophys J 1998, 75:2469-2477.
28. Elcock AH, McCammon JA. Calculation of weak protein-protein interactions: the pH dependence of the second Virial coefficient. Biophys J 2001, 80:613-625.
29. Hill TL. An introduction to statistical thermodynamics 1986, New York: Dover Publications Inc.
30. da Silva MA, Itri R, Arêas EPG. Lysozyme viscoelastic matrices in tetramethylurea/water media: a small angle X-ray scattering study. Biophys Chem 2002, 99(2):169-179.
31. Zhang F, Jacobs RMJ, Martin CM, Schreiber F,. Skoda MWa Protein interactions studied by SAXS: effect of ionic strength and protein concentration for BSA in aqueous solutions. J Phys Chem B 2007, 111:251-9. Skoda MWa.
32. Heinen M, Zanini F, Roosen-Runge F, Zhang F, Hennig M, Seydel T, Schweins R, Sztucki M, Antalík M, Schreiber F, Nägele G,. Fedunová D Viscosity and diffusion: crowding and salt effects in protein solutions. Soft Matter 2012, 8(5):1404. Fedunová D.
33. Allen MP, Tildesley DJ. Computer Simulations of Liquids 1989, USA: Oxford University Press.
34. Asthagiri D, Paliwal A, Abras D, Lenhoff AM, Paulaitis ME. A consistent experimental and modeling approach to light-scattering studies of protein-protein interactions in solution. Biophysical J 2005, 88:3300-3309.
35. Price WS, Tsuchiya F, Arata Y. Lysozyme aggregation and solution properties studied using PGSE NMR diffusion measurements. J Am Chem Soc 1999, 121:11503-11512.
36. Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. modbase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2009, 37(suppl 1):D347-D354.
37. Balbo J, Mereghetti P, Herten DP, Wade R. The shape of protein crowders is a major determinant of protein diffusion. Biophys J 2013, 104(7):1576-1584.
38. Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A. H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 2005, 33:W368-W371.
39. Jorgensen WL, Tirado-Rives J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 1988, 110(6):1657-1666.
40. Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Andrew I, Antosiewicz J, Gilsong MK, Bagheri B, Scott LR, McCammon JA. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Comput Phys Commun 1995, 91(1-3):57-95.
41. Balescu RC. Equilibrium and Non-Equilibrium Statistical Mechanics 1975, New York: John Wiley & Sons.
42. Nägele G. On the dynamics and structure of charge-stabilized suspensions. Phys Rep 1996, 272:215-375.
43. Fukasawa T, Sato T. Versatile application of indirect Fourier transformation to structure factor analysis: from X-ray diffraction of molecular liquids to small angle scattering of protein solutions. Phys Chem Chem Phys 2011, 13(8):3187-3196.
44. Stylianopoulos T, Poh MZ, Insin N, Bawendi MG, Fukumura D, Munn LL, Jain RK. Diffusion of particles in the extracellular matrix: the effect of repulsive electrostatic interactions. Biophys J 2010, 99(5):1342-1349.