Molecular simulation of adsorption and its implications to protein chromatography: A review

Biochemical Engineering Journal

Volumn 48, Issue 3, 2010, Pages 408-415

  Zhang, Lin ^a   Sun, Yan ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

Adsorption; Bioseparation; Chromatography; Conformational transition; Molecular simulation; Retention behavior

Indexed keywords

ADSORPTION PHENOMENA; ALL-ATOM MODEL; BIO-SEPARATION; BONDING DENSITY; COARSE GRAINED MODELS; COMPUTATIONAL POWER; COMPUTATIONAL QUANTUM CHEMISTRY; CONFORMATIONAL TRANSITIONS; EXPERIMENTAL APPROACHES; LIGAND PARAMETERS; MOBILE-PHASE COMPOSITION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR INSIGHTS; MOLECULAR SIMULATIONS; MONTE CARLO SIMULATION; PROTEIN ADSORPTION; PROTEIN CHROMATOGRAPHY; PROTEIN ORIENTATION; PROTEIN-SURFACE INTERACTIONS; RESEARCH AND DEVELOPMENT; RESEARCH TOOLS; RETENTION BEHAVIOR; SCIENCE AND TECHNOLOGY; SMALL MOLECULES; SMALL SCALE; SOLID SURFACE; TIME AND SPACE;

ADSORBENTS; CHROMATOGRAPHIC ANALYSIS; CHROMATOGRAPHY; COMPUTATIONAL CHEMISTRY; COMPUTER SIMULATION; CONFORMATIONS; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION; MOLECULAR STRUCTURE; MONTE CARLO METHODS; PROTEINS; SURFACE MORPHOLOGY;

ADSORPTION;

ADSORPTION; ANALYTICAL PARAMETERS; BIOSEPARATION; CHROMATOGRAPHY; CONFORMATIONAL TRANSITION; DENSITY; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MONTE CARLO METHOD; MORPHOLOGY; PRIORITY JOURNAL; PROTEIN CHROMATOGRAPHY; PROTEIN INTERACTION; QUANTUM CHEMISTRY; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW; SURFACE PROPERTY; TEMPERATURE;

EID: 75349094390     PISSN: 1369703X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bej.2009.12.003     Document Type: Review

References (107)

1. Silva L.P. Imaging proteins with atomic force microscopy: an overview. Curr. Protein Pept. Sci. 6 (2005) 387-395
2. Merrett K., Cornelius R.M., McClung W.G., Unsworth L.D., and Sheardown H. Surface analysis methods for characterizing polymeric biomaterials. J. Biomater. Sci.: Polym. Ed. 13 (2002) 593-621
3. Wuthrich K. NMR studies of structure and function of biological macromolecules (Nobel Lecture). Angew. Chem. Int. Ed. 42 (2003) 3340-3363
4. Nienhaus G.U. Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis. Macromol. Biosci. 6 (2006) 907-922
5. Lu J.R., Zhao X.B., and Yaseen M. Protein adsorption studied by neutron reflection. Curr. Opin. Colloid Interface 12 (2007) 9-16
6. Chen S.F., Liu L.Y., Zhou J., and Jiang S.Y. Controlling antibody orientation on charged self-assembled monolayers. Langmuir 19 (2003) 2859-2864
7. Xiao Y.Z., Jones T.T., Laurent A.H., O C.J., Przybycien T.M., and Fernandez E.J. Protein instability during HIC: hydrogen exchange labeling analysis and a framework for describing mobile and stationary phase effects. Biotechnol. Bioeng. 96 (2007) 80-93
8. Yang K., Bai S., and Sun Y. Protein adsorption dynamics in cation-exchange chromatography quantitatively studied by confocal laser scanning microscopy. Chem. Eng. Sci. 63 (2008) 4045-4054
9. Mungikar A.A., and Forciniti D. Computer simulations and neutron reflectivity of proteins at interfaces. Chemphyschem 3 (2002) 993-999
10. Raffaini G., and Ganazzoli F. Understanding the performance of biomaterials through molecular modeling: crossing the bridge between their intrinsic properties and the surface adsorption of proteins. Macromol. Biosci. 7 (2007) 552-566
11. Lipkowitz K.B. Atomistic modeling of enantioselection in chromatography. J. Chromatogr. A 906 (2001) 417-442
12. Felinger A. Molecular dynamic theories in chromatography. J. Chromatogr. A 1184 (2008) 20-41
13. Frenkel D., and Smit B. Understanding Molecular Simulation: From Algorithms to Applications. 2nd ed. (2002), Academic Press, San Diego, CA
14. Karplus M. Molecular dynamics of biological macromolecules: a brief history and perspective. Biopolymers 68 (2003) 350-358
15. Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9 (2002) 646-652
16. Daggett V. Protein folding-simulation. Chem. Rev. 106 (2006) 1898-1916
17. Tozzini V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15 (2005) 144-150
18. Clementi C. Coarse-grained models of protein folding: toy models or predictive tools?. Curr. Opin. Struct. Biol. 18 (2008) 10-15
19. Maginn E.J. From discovery to data: what must happen for molecular simulation to become a mainstream chemical engineering tool. AIChE J. 55 (2009) 1304-1310
20. Slater G.W., Holm C., Chubynsky M.V., de H.H., Dube A., Grass K., Hickey O.A., Kingsburry C., Sean D., Shendruk T.N., and Nhan L.X. Modeling the separation of macromolecules: a review of current computer simulation methods. Electrophoresis 30 (2009) 792-818
21. Rafferty J.L., Siepmann J.I., and Schure M.R. Influence of bonded-phase coverage in reversed-phase liquid chromatography via molecular simulation. I. Effects on chain conformation and interfacial properties. J. Chromatogr. A 1204 (2008) 11-19
22. Rafferty J.L., Siepmann J.I., and Schure M.R. Influence of bonded-phase coverage in reversed-phase liquid chromatography via molecular simulation. II. Effects on solute retention. J. Chromatogr. A 1204 (2008) 20-27
23. Rafferty J.L., Siepmann J.I., and Schure M.R. The effects of chain length, embedded polar groups, pressure, and pore shape on structure and retention in reversed-phase liquid chromatography: molecular-level insights from Monte Carlo simulations. J. Chromatogr. A 1216 (2009) 2320-2331
24. Zhuravlev N.D., Siepmann J.I., and Schure M.R. Surface coverages of bonded-phase ligands on silica: a computational study. Anal. Chem. 73 (2001) 4006-4011
25. Lippa K.A., and Sander L.C. Identification of isolated cavity features within molecular dynamics simulated chromatographic surfaces. J. Chromatogr. A 1128 (2006) 79-89
26. Lippa K.A., Sander L.C., and Mountain R.D. Molecular dynamics simulations of alkylsilane stationary-phase order and disorder. 1. Effects of surface coverage and bonding chemistry. Anal. Chem. 77 (2005) 7852-7861
27. Lippa K.A., Sander L.C., and Mountain R.D. Molecular dynamics simulations of alkylsilane stationary-phase order and disorder. 2. Effects of temperature and chain length. Anal. Chem. 77 (2005) 7862-7871
28. Sander L.C., Lippa K.A., and Wise S.A. Order and disorder in alkyl stationary phases. Anal. Bioanal. Chem. 382 (2005) 646-668
29. Dou X., Wang H., and Han J.Y. Molecular dynamics simulation of the effects of mobile-phase modification on interactions in reversed-phase liquid chromatography. J. Liq. Chromatogr. Relat. Technol. 29 (2006) 2559-2569
30. Ban K., Saito Y., and Jinno K. Characterization of the microscopic surface structure of the octadecylsilica stationary phase using a molecular-dynamics simulation. Anal. Sci. 20 (2004) 1403-1408
31. Ban K., Saito Y., and Jinno K. Molecular-dynamics simulation for the characterization of liquid chromatographic stationary phase: effect of temperature. Anal. Sci. 21 (2005) 397-402
32. Ban K., and Jinno K. Molecular-dynamics simulation for liquid chromatographic interactions: effect of mobile phase composition. Anal. Sci. 17 (2001) 113-117
33. Zamolo L., Busini V., Moiani D., Moscatelli D., and Cavallotti C. Molecular dynamic investigation of the interaction of supported affinity ligands with monoclonal antibodies. Biotechnol. Progr. 24 (2008) 527-539
34. Busini V., Moiani D., Moscatelli D., Zamolo L., and Cavallotti C. Investigation of the influence of spacer arm on the structural evolution of affinity ligands supported on agarose. J. Phys. Chem. B 110 (2006) 23564-23577
35. Riccardi E., Wang J.C., and Liapis A.I. Porous polymer adsorbent media constructed by molecular dynamics modeling and simulations: the immobilization of charged ligands and their effect on pore structure and local nonelectroneutrality. J. Phys. Chem. B 113 (2009) 2317-2327
36. Zhang X., Wang J.C., Lacki K.M., and Liapis A.I. Construction by molecular dynamics modeling and simulations of the porous structures formed by dextran polymer chains attached on the surface of the pores of a base matrix: characterization of porous structures. J. Phys. Chem. B 109 (2005) 21028-21039
37. Riccardi E., Wang J.C., and Liapis A.I. Rational surface design for molecular dynamics simulations of porous polymer adsorbent media. J. Phys. Chem. B 112 (2008) 7478-7488
38. Zhang L., Zhao G.F., and Sun Y. Molecular insight into protein conformational transition in hydrophobic charge induction chromatography: a molecular dynamics simulation. J. Phys. Chem. B 113 (2009) 6873-6880
39. Wang F., Stuart S.J., and Latour R.A. Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics. Biointerphases 3 (2008) 9-18
40. Lipkowitz K.B. Atomistic modeling of enantioselective binding. Acc. Chem. Res. 33 (2000) 555-562
41. Schefzick S., Lindner W., Lipkowitz K.B., and Jalaie M. Enantiodiscrimination by a quinine-based chiral stationary phase: a computational study. Chirality 12 (2000) 7-15
42. Rafferty J.L., Zhang L., Siepmann J.I., and Schure M.R. Retention mechanism in reversed-phase liquid chromatography: a molecular perspective. Anal. Chem. 79 (2007) 6551-6558
43. Nita S., Cann N.M., and Horton J.H. Structure, selectivity, and solvation of a model chiral stationary phase. J. Phys. Chem. B 108 (2004) 3512-3522
44. Zhao C., and Cann N.M. Solvation of the Whelk-O1 chiral stationary phase: a molecular dynamics study. J. Chromatogr. A 1131 (2006) 110-129
45. Zhao C.F., and Cann N.M. The docking of chiral epoxides on the Whelk-O1 stationary phase: a molecular dynamics study. J. Chromatogr. A 1149 (2007) 197-218
46. Zhao C.F., and Cann N.M. Molecular dynamics study of chiral recognition for the Whelk-O1 chiral stationary phase. Anal. Chem. 80 (2008) 2426-2438
47. Zhao C.F., Diemert S., and Cann N.M. Rational optimization of the Whelk-O1 chiral stationary phase using molecular dynamics simulations. J. Chromatogr. A 1216 (2009) 5968-5978
48. Zheng J., Lennon E.M., Tsao H.K., Sheng Y.J., and Jiang S.Y. Transport of a liquid water and methanol mixture through carbon nanotubes under a chemical potential gradient. J. Chem. Phys. 122 (2005) 214702-214707
49. Fouqueau A., Meuwly M., and Bemish R.J. Adsorption of acridine orange at a C-8,C-18/water/acetonitrile interface. J. Phys. Chem. B 111 (2007) 10208-10216
50. Braun J., Fouqueau A., Bemish R.J., and Meuwly M. Solvent structures of mixed water/acetonitrile mixtures at chromatographic interfaces from computer simulations. Phys. Chem. Chem. Phys. 10 (2008) 4765-4777
51. Li X., and McGuffin V.L. Theoretical evaluation of methods for extracting retention factors and kinetic rate constants in liquid chromatography. J. Chromatogr. A 1203 (2008) 67-80
52. McGuffin V.L. Stochastic simulation as a unified approach to separation science. Anal. Bioanal. Chem. 381 (2005) 106-109
53. Krouskop P.E., and McGuffin V.L. Stochastic simulation of the partition mechanism with a heterogeneous surface phase. J. Chromatogr. A 959 (2002) 49-64
54. McGuffin V.L., Krouskop P.E., and Wu P.R. Stochastic simulation of the partition mechanism under diffusion-limited conditions in chromatography and electrochromatography. J. Chromatogr. A 828 (1998) 37-50
55. Cavazzini A., Dondi F., Jaulmes A., Vidal-Madjar C., and Felinger A. Monte Carlo model of nonlinear chromatography: correspondence between the microscopic stochastic model and the macroscopic Thomas kinetic model. Anal. Chem. 74 (2002) 6269-6278
56. Dondi F., Munari P., Remelli M., and Cavazzini A. Monte Carlo model of nonlinear chromatography. Anal. Chem. 72 (2000) 4353-4362
57. Felinger A., Cavazzini A., Remelli M., and Dondi F. Stochastic-dispersive theory of chromatography. Anal. Chem. 71 (1999) 4472-4479
58. Helgaker T., Klopper W., and Tew D.P. Quantitative quantum chemistry. Mol. Phys. 106 (2008) 2107-2143
59. Carrasco J., Michaelides A., and Scheffler M. Insight from first principles into the nature of the bonding between water molecules and 4d metal surfaces. J. Chem. Phys. 130 (2009) 184707-184711
60. Vassilev P., van Santen R.A., and Koper M. Ab initio studies of a water layer at transition metal surfaces. J. Chem. Phys. 122 (2005) 054701-12
61. Wang Y.X., and Balbuena P.B. Roles of proton and electric field in the electroreduction of o-2 on Pt(1 1 1) surfaces: results of an ab-initio molecular dynamics study. J. Phys. Chem. B 108 (2004) 4376-4384
62. Jiang D.E., and Carter E.A. Adsorption and diffusion energetics of hydrogen atoms on Fe(1 1 0) from first principles. Surf. Sci. 547 (2003) 85-98
63. Chretien S., and Salahub D.R. Kohn-Sham density-functional study of the adsorption of acetylene and vinylidene on iron clusters, Fe-n/Fe-n(+) (n = 1-4). J. Chem. Phys. 119 (2003) 12279-12290
64. Tkatchenko A., and von Lilienfeld O.A. Adsorption of ar on graphite using london dispersion forces corrected Kohn-Sham density functional theory. Phys. Rev. B 73 (2006) 153406-153414
65. Latour R.A. Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions. Biointerphases 3 (2008) FC2-FC12
66. Wilson K., Stuart S.J., Garcia A., and Latour R.A. A molecular modeling study of the effect of surface chemistry on the adsorption of a fibronectin fragment spanning the 7-10th type-III repeats. J. Biomed. Mater. Res. Part A 69A (2004) 686-698
67. Latour R.A., and Hench L.L. A theoretical analysis of the thermodynamic contributions for the adsorption of individual protein residues on functionalized surfaces. Biomaterials 23 (2002) 4633-4648
68. Latour R.A., and Rini C.J. Theoretical analysis of adsorption thermodynamics for hydrophobic peptide residues on SAM surfaces of varying functionality. J. Biomed. Mater. Res. Part A 60 (2002) 564-577
69. Zheng J., Li L.Y., Tsao H.K., Sheng Y.J., Chen S.F., and Jiang S.Y. Strong repulsive forces between protein and oligo (ethylene glycol) self-assembled monolayers: a molecular simulation study. Biophys. J. 89 (2005) 158-166
70. He Y., Hower J., Chen S.F., Bernards M.T., Chang Y., and Jiang S.Y. Molecular simulation studies of protein interactions with zwitterionic phosphorylcholine self-assembled monolayers in the presence of water. Langmuir 24 (2008) 10358-10364
71. Hower J.C., He Y., and Jiang S.Y. A molecular simulation study of methylated and hydroxyl sugar-based self-assembled monolayers: surface hydration and resistance to protein adsorption. J. Chem. Phys. 129 (2008) 215101-215107
72. Cormack A.N., Lewis R.J., and Goldstein A.H. Computer simulation of protein adsorption to a material surface in aqueous solution: biomaterials modeling of a ternary system. J. Phys. Chem. B 108 (2004) 20408-20418
73. Pastorino C., Binder K., Kreer T., and Muller M. Static and dynamic properties of the interface between a polymer brush and a melt of identical chains. J. Chem. Phys. 124 (2006) 064902-64911
74. Muller M., Pastorino C., and Servantie J. Hydrodynamic boundary condition of polymer melts at simple and complex surfaces. Comput. Phys. Commun. 180 (2009) 600-604
75. Pastorino C., Binder K., and Muller M. Coarse-grained description of a brush-melt interface in equilibrium and under flow. Macromolecules 42 (2009) 401-410
76. Szabelski P., Panczyk T., and Drach M. Monte Carlo modeling of chiral adsorption on nanostructured chiral surfaces and slit pores. Langmuir 24 (2008) 12972-12980
77. Cavallo A., Muller M., and Binder K. Unmixing of polymer blends confined in ultrathin films: crossover between two-dimensional and three-dimensional behavior. J. Phys. Chem. B 109 (2005) 6544-6552
78. Ivanov V.A., Marternyanova J.A., Muller M., Paul W., and Binder K. Conformational changes of a single semiflexible macromolecule near an adsorbing surface: a Monte Carlo simulation. J. Phys. Chem. B 113 (2009) 3653-3668
79. Zhou J., Tsao H.K., Sheng Y.J., and Jiang S.Y. Monte Carlo simulations of antibody adsorption and orientation on charged surfaces. J. Chem. Phys. 121 (2004) 1050-1057
80. Sheng Y.J., Tsao H.K., Zhou J., and Jiang S.Y. Orientation of a Y-shaped biomolecule adsorbed on a charged surface. Phys. Rev. E 66 (2002) 011911-11915
81. Zheng J., Li L.Y., Chen S.F., and Jiang S.Y. Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers. Langmuir 20 (2004) 8931-8938
82. Ravichandran S., Madura J.D., and Talbot J. A Brownian dynamics study of the initial stages of hen egg-white lysozyme adsorption at a solid interface. J. Phys. Chem. B 105 (2001) 3610-3613
83. Ravichandran S., and Talbot J. Mobility of adsorbed proteins: a Brownian dynamics study. Biophys. J. 78 (2000) 110-120
84. Agashe M., Raut V., Stuart S.J., and Latour R.A. Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment. Langmuir 21 (2005) 1103-1117
85. Zhdanov V.P., and Kasemo B. Monte Carlo simulations of the kinetics of protein adsorption. Surf. Rev. Lett. 5 (1998) 615-634
86. Zhdanov V.P., and Kasemo B. Monte Carlo simulation of diffusion of adsorbed proteins. Proteins 39 (2000) 76-81
87. Zhdanov V.P., and Kasemo B. Monte Carlo simulation of denaturation of adsorbed proteins. Proteins 30 (1998) 168-176
88. Zhdanov V.P., and Kasemo B. Monte Carlo simulation of the kinetics of protein adsorption. Proteins. 30 (1998) 177-182
89. Zhdanov V.P., and Kasemo B. Folding of bundles of alpha-helices in solution, membranes, and adsorbed overlayers. Proteins 42 (2001) 481-494
90. Zhdanov V.P., Rechendorff K., Hovgaard M.B., and Besenbacher F. Deposition at glancing angle, surface roughness, and protein adsorption: Monte Carlo simulations. J. Phys. Chem. B 112 (2008) 7267-7272
91. Rechendorff K., Hovgaard M.B., Foss M., Zhdanov V.P., and Besenbacher F. Enhancement of protein adsorption induced by surface roughness. Langmuir 22 (2006) 10885-10888
92. Zhdanov V.P., and Kasemo B. Ordering of adsorbed proteins. Proteins 40 (2000) 539-542
93. Elli S., Raffaini G., Ganazzoli F., Timoshenko E.G., and Kuznetsov Y.A. Surface adsorption of comb polymers by Monte Carlo simulations. Polymer 49 (2008) 1716-1724
94. Euston S.R. Computer simulation of proteins: adsorption, gelation and self-association. Curr. Opin. Colloid Interface 9 (2004) 321-327
95. Euston S.R., and Abu N.M. Simulating the equation of state of model globular proteins adsorbed at a surface. Langmuir 21 (2005) 4227-4235
96. Knotts T.A., Rathore N., and de Pablo J.J. Structure and stability of a model three-helix-bundle protein on tailored surfaces. Proteins 61 (2005) 385-397
97. Ganazzoli F., and Raffaini G. Computer simulation of polypeptide adsorption on model biomaterials. Phys. Chem. Chem. Phys. 7 (2005) 3651-3663
98. Raffaini G., and Ganazzoli F. Sequential adsorption of proteins and the surface modification of biomaterials: a molecular dynamics study. J. Mater. Sci.: Mater. Med. 18 (2007) 309-316
99. Raffaini G., and Ganazzoli F. Adsorption of charged albumin subdomains on a graphite surface. J. Biomed. Mater. Res. Part A 76A (2006) 638-645
100. Raffaini G., and Ganazzoli F. Surface ordering of proteins adsorbed on graphite. J. Phys. Chem. B 108 (2004) 13850-13854
101. Raffaini G., and Ganazzoli F. Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface. Langmuir 20 (2004) 3371-3378
102. Mantero S., Piuri D., Montevecchi F.M., Vesentini S., Ganazzoli F., and Raffaini G. Albumin adsorption onto pyrolytic carbon: a molecular mechanics approach. J. Biomed. Mater. Res. Part A 59 (2002) 329-339
103. Raffaini G., and Ganazzoli F. Protein adsorption on the hydrophilic surface of a glassy polymer: a computer simulation study. Phys. Chem. Chem. Phys. 8 (2006) 2765-2772
104. Zhang L., Lu D.N., and Liu Z. Dynamic control of protein conformation transition in chromatographic separation based on hydrophobic interactions: molecular dynamics simulation. J. Chromatogr. A 1216 (2009) 2483-2490
105. Euston S.R., Hughes P., Naser M.A., and Westacott R.E. Comparison of the adsorbed conformation of barley lipid transfer protein at the decane-water and vacuum-water interface: a molecular dynamics simulation. Biomacromolecules 9 (2008) 1443-1453
106. Kamal C., Ghanty T.K., Banerjee A., and Chakrabarti A. The van der Waals coefficients between carbon nanostructures and small molecules: a time-dependent density functional theory study. J. Chem. Phys. 131 (2009) 164708-164711
107. Senn H.M., and Thiel W. QM/MM studies of enzymes. Curr. Opin. Chem. Biol. 11 (2007) 182-187