Mesoscopic coarse-grained simulations of hydrophobic charge induction chromatography (HCIC) for protein purification

AIChE Journal

Volumn 61, Issue 6, 2015, Pages 2035-2047

  Yu, Gaobo ^a   Liu, Jie ^a   Zhou, Jian ^a  

^a SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Coarse graining; Hydrophobic charged induction chromatography; Molecular simulation; Protein adsorption; Protein orientation; Protein purification

Indexed keywords

ADSORPTION; ENZYMES; HYDROPHOBICITY; IONIC STRENGTH; LIGANDS; MOLECULAR ORIENTATION; PROBABILITY DISTRIBUTIONS; PURIFICATION; SUPERCONDUCTING MATERIALS; SURFACE CHEMISTRY;

COARSE GRAINING; MOLECULAR SIMULATIONS; PROTEIN ADSORPTION; PROTEIN ORIENTATION; PROTEIN PURIFICATION;

HYDROPHOBIC CHROMATOGRAPHY;

EID: 84929606884     PISSN: 00011541     EISSN: 15475905     Source Type: Journal    
DOI: 10.1002/aic.14805     Document Type: Article

References (66)

1. Burton S, Haggarty N, Harding D. One step purification of chymosin by mixed mode chromatography. Biotechnol. Bioeng. 1997;56:45-55.
2. Burton S, Harding D. Hydrophobic charge induction chromatography: salt independent protein adsorption and facile elution with aqueous buffers. J. Chromatogr. A. 1998;814:71-81.
3. Ghose S, Hubbard B, Cramer SM. Evaluation and comparison of alternatives to Protein A chromatography: mimetic and hydrophobic charge induction chromatographic stationary phases. J. Chromatogr. A. 2006;1122:144-152.
4. Zhao G, Sun Y. Displacement chromatography of proteins on hydrophobic charge induction adsorbent column. J. Chromatogr. A 2007;1165:109-115.
5. Shi QH, Shen FF, Sun S. Studies of lysozyme binding to histamine as a ligand for hydrophobic charge induction chromatography. Biotechnol. Progr. 2010;26:134-141.
6. Guerrier L, Girot P, Schwartz W, Boschetti E. New method for the selective capture of antibodies under physiolgical conditions. Bioseparation. 2000;9:211-221.
7. Guerrier L, Flayeux I, Boschetti E. A dual-mode approach to the selective separation of antibodies and their fragments. J. Chromatogr. B. 2001;755:37-46.
8. Schwartz W, Judd D, Wysocki M, Guerrier L, Birck-Wilson E, Boschetti E. Comparison of hydrophobic charge induction chromatography with affinity chromatography on protein A for harvest and purification of antibodies. J. Chromatogr. A. 2001;908:251-263.
9. Boschetti E. Antibody separation by hydrophobic charge induction chromatography. Trends Biotechnol. 2002;20:333-337.
10. Tong H-F, Lin D-Q, Yuan X-M, Yao S-J. Enhancing IgG purification from serum albumin containing feedstock with hydrophobic charge-induction chromatography. J. Chromatogr. A. 2012;1244:116-122.
11. Tong H-F, Lin D-Q, Gao D, Yuan X-M, Yao S-J. Caprylate as the albumin-selective modifier to improve IgG purification with hydrophobic charge-induction chromatography. J. Chromatogr. A. 2013;1285:88-96.
12. Zhao G, Peng G, Li F, Shi Q, Sun Y. 5-Aminoindole, a new ligand for hydrophobic charge induction chromatography. J. Chromatogr. A. 2008;1211:90-98.
13. Chen J, Tetrault J, Ley A. Comparison of standard and new generation hydrophobic interaction chromatography resins in the monoclonal antibody purification process. J. Chromatogr. A. 2008;1177:272-281.
14. Xia H-F, Lin D-Q, Chen Z-M, Yao S-J. Salt-promoted adsorption of an antibody onto hydrophobic charge-induction adsorbents. J. Chem. Eng. Data. 2010;55:5751-5758.
15. Ghose S, Hubbard B, Cramer SM. Protein interactions in hydrophobic charge induction chromatography (HCIC). Biotechnol. Progr. 2005;21:498-508.
16. Zhao G, Dong X-Y, Sun Y. Ligands for mixed-mode protein chromatography: principles, characteristics and design. J. Biotechnol. 2009;144:3-11.
17. Zhang L, Sun Y. Molecular simulation of adsorption and its implications to protein chromatography: a review. Biochem. Eng. J. 2010;48:408-415.
18. Xia H-F, Lin D-Q, Yao S-J. Hydrophobic charge induction chromatography: principles, characteristics and applications. Chem. Ind. Eng. Prog. 2010;29:1951-1956.
19. Zhou J, Chen S, Jiang S. Orientation of adsorbed antibodies on charged surfaces by computer simulation based on a united-residue model. Langmuir. 2003;19:3472-3478.
20. Zheng J, Li LY, Tsao, HK, Sheng YJ, Chen SF, Jiang SY. Strong repulsive forces between protein and oligo (ethylene glycol) self-assembled monolayers: a molecular simulation study. Biophys. J. 2005;89:158-166.
21. Zhou J, Thorpe IF, Izvekov S, Voth GA. Coarse-grained peptide modeling using a systematic multiscale approach. Biophys. J. 2007;92:4289-4303.
22. He Y, Hower J, Chen SF, Bernards MT, Chang Y, Jiang SY. Molecular simulation studies of protein interactions with zwitterionic phosphorylcholine self-assembled monolayers in the presence of water. Langmuir. 2008;24:10358-10364.
23. Zhong T, Ai P, Zhou J. Structures and properties of PAMAM dendrimer: a multi-scale simulation study. Fluid Phase. Equilibr 2011;302:43-47.
24. Xie Y, Zhou J, Jiang SY. Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces. J. Chem. Phys. 2010;132:065101.
25. Dong J, Zhou J. Solvent-responsive behavior of polymer-brush-modified amphiphilic gold nanoparticles. Macromol. Theor. Simul. 2013;22:174-186.
26. Liu J, Liao C, Zhou J. Multiscale simulations of protein G B1 adsorbed on charged self-assembled monolayers. Langmuir. 2013;29:11366-11374.
27. Xie Y, Liao C, Zhou J. Effects of external electric fields on lysozyme adsorption by molecular dynamics simulations. Biophys. Chem. 2013;179:26-34.
28. Sun D, Zhou J. Ionic liquid confined in nafion: toward molecular-level understanding. Aiche J. 2013;59:2630-2639.
29. Liu J, Yu G, Zhou J. Ribonuclease A adsorption onto charged self-assembled monolayers: a multiscale simulation study. Chem. Eng. Sci. 2015;121:331-339.
30. Peng C, Liu J, Zhao D, Zhou J. Adsorption of hydrophobin on different self-assembled monolayers: the role of the hydrophobic dipole and the electric dipole. Langmuir. 2014;30:11401-11411.
31. Zhao D, Peng C, Zhou J. Lipase adsorption on different nanomaterials: a multi-scale simulation study. Phys. Chem. Chem. Phys. 2015;17:840-850.
32. Latour RA. Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions (Review). Biointerphases. 2008;3:FC2-FC12.
33. Wang H-Y, Lin D-Q, Yao S-J, Yun J-X, Yao K-J. Molecular simulation of the interactions between 4-mercaptoethyl-pyridine ligand and IgG. Acta Chim. Sinica. 2010;68:1597-1602.
34. Lin D-Q, Tong H-F, Wang H-Y, Yao S-J. Molecular insight into the ligand-IgG interactions for 4-mercaptoethyl-pyridine based hydrophobic charge-induction chromatography. J. Phys. Chem. B. 2012;116:1393-1400.
35. Lin D-Q, Tong H-F, Wang H-Y, Shao S, Yao S-J. Molecular mechanism of hydrophobic charge-induction chromatography: interactions between the immobilized 4-mercaptoethyl-pyridine ligand and IgG. J. Chromatogr. A. 2012;1260:143-153.
36. Zhang L, Zhao G, Sun Y. Molecular insight into protein conformational transition in hydrophobic charge induction chromatography: a molecular dynamics simulation. J. Phys. Chem. B. 2009;113:6873-6880.
37. Zhang L, Zhao G, Sun Y. Molecular dynamics simulation and experimental validation of the effect of pH on protein desorption in hydrophobic charge induction chromatography. Mol. Simulat. 2010;36:1096-1103.
38. Zhang L, Zhao G, Sun Y. Effects of ligand density on hydrophobic charge induction chromatography: molecular dynamics simulation. J. Phys. Chem. B 2010;114:2203-2211.
39. Zhang L, Bai S, Sun Y. Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme. J. Mol. Graph. Model. 2011;29:906-914.
40. Wei T, Carignano MA, Szleifer I. Lysozyme adsorption on polyethylene surfaces: why are long simulations needed? Langmuir. 2011;27:12074-12081.
41. Wei T, Carignano MA, Szleifer I. Molecular dynamics simulation of lysozyme adsorption/desorption on hydrophobic surfaces. J. Phys. Chem. B. 2012;116:10189-10194.
42. Yu G, Liu J, Zhou J. Mesoscopic coarse-grained simulations of lysozyme adsorption. J. Phys. Chem. B. 2014;118:4451-4460.
43. Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B. 2007;111:7812-7824.
44. Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink S-J. The MARTINI coarse-grained force field: extension to Proteins. J. Chem Theory Comput. 2008;4:819-834.
45. Wu Z, Cui QA, Yethiraj A. A new coarse-grained model for water: the importance of electrostatic interactions. J. Phys. Chem. B 2010;114:10524-10529.
46. Wu Z, Cui Q, Yethiraj A. a new coarse-grained force field for membrane-peptide simulations. J. Chem Theory Comput. 2011;7:3793-3802.
47. Fumi FG, Tosi MP. Ionic sizes and born repulsive parameters in the NaCl-type alkali halides I: the Huggins-Mayer and Pauling forms. J. Phys. Chem. Solids. 1964;25:31-43.
48. Tosi MP, Fumi FG. Ionic sizes and born repulsive parameters in the NaCl-type alkali halides II: the generalized Huggins-Mayer form. J. Phys. Chem. Solids. 1964;25:45-52.
49. Essmann U, Perera L, Berkowitz ML, Darden T, Hsing L, Pedersen L. G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995;103:8577-8593.
50. Darden T, Pearlman D, Pedersen LG. Ionic charging free energies: spherical versus periodic boundary conditions. J. Chem. Phys. 1998;109:10921-10935.
51. Sun Y, Welsh WJ, Latour RA. Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation. Langmuir. 2005;21:5616-5626.
52. Dismer F, Petzold M, Hubbuch J. Effects of ionic strength and mobile phase pH on the binding orientation of lysozyme on different ion-exchange adsorbents. J. Chromatogr. A. 2008;1194:11-21.
53. Tiemeyer S, Paulus M, Tolan M. Effect of surface charge distribution on the adsorption orientation of proteins to lipid monolayers. Langmuir. 2010;26:14064-14067.
54. Periole X, Marrink S-J. The Martini coarse-grained force field. In: Monticelli L, Salonen E, editors. Biomolecular Simulations, Vol. 924. New York: Humana Press, 2013:533-565.
55. Periole X, Cavalli M, Marrink SJ, Ceruso MA. Combining an elastic network with a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition. J. Chem Theory Comput. 2009;5:2531-2543.
56. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids. Res. 2004;32:W665-W667.
57. Hess B, van Der Spoel D, Lindahl E. Gromacs User Manual Version 4.5.4. Netherland: University of Groningen, 2010.
58. Yesylevskyy SO, Schafer LV, Sengupta D, Marrink SJ. Polarizable water model for the coarse-grained MARTINI force field. Plos Comput. Biol. 2010;6:e1000810.
59. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984;81:3684-3690.
60. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996;14:33-38.
61. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera-A visualization system for exploratory research and analysis. J. Comput. Chem. 2004;25:1605-1612.
62. Sigal GB, Mrksich M, Whitesides GM. Effect of surface wettability on the adsorption of proteins and detergents. J. Am. Chem. Soc. 1998;120:3464-3473.
63. Chen X, Yang T, Kataoka S, Cremer PS. Specific ion effects on interfacial water structure near macromolecules. J. Am. Chem. Soc. 2007;129:12272-12279.
64. Feng H, Zhou J, Lu X. Molecular dynamics simulations on the interfacial structures of electrolyte solutions. Acta Chim. Sinica. 2009;67:2407-2412.
65. Feng H, Zhou J, Lu X, Fichthorn KA. Communication: molecular dynamics simulations of the interfacial structure of alkali metal fluoride solutions. J. Chem. Phys. 2010;133: 061103.
66. Zhou J, Lu X, Wang Y, Shi J. Molecular dynamics study on ionic hydration. Fluid. Phase. Equilibr. 2002;194-197:257-270.