Multiscale simulations of protein G B1 adsorbed on charged self-assembled monolayers

Langmuir

Volumn 29, Issue 36, 2013, Pages 11366-11374

  Liu, Jie ^a   Liao, Chenyi ^a   Zhou, Jian ^a  

^a SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ATTRACTIVE INTERACTIONS; CARBOXYL-FUNCTIONALIZED; ELECTROSTATIC INTERACTION ENERGY; MOLECULAR DYNAMICS SIMULATIONS; NEGATIVELY CHARGED SURFACES; ORIENTATION DISTRIBUTIONS; REPULSIVE INTERACTIONS; ROOT-MEAN SQUARE DEVIATION;

CHARGED PARTICLES; CONFORMATIONS; EFFICIENCY; ELECTROSTATIC SEPARATORS; EXPERIMENTS; MOLECULAR DYNAMICS; MONTE CARLO METHODS; ORGANIC POLYMERS; SELF ASSEMBLED MONOLAYERS; SUPERCONDUCTING MATERIALS; VAN DER WAALS FORCES;

ANTIBODIES;

BACTERIAL PROTEIN; IGG FC BINDING PROTEIN, STREPTOCOCCUS; IGG FC-BINDING PROTEIN, STREPTOCOCCUS; IMMOBILIZED PROTEIN; IMMUNOGLOBULIN G;

ADSORPTION; ARTICLE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PROTEIN TERTIARY STRUCTURE; SURFACE PROPERTY; THERMODYNAMICS;

ADSORPTION; BACTERIAL PROTEINS; IMMOBILIZED PROTEINS; IMMUNOGLOBULIN G; MOLECULAR DYNAMICS SIMULATION; MONTE CARLO METHOD; PROTEIN STRUCTURE, TERTIARY; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 84884187910     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/la401171v     Document Type: Article

References (60)

1. Gray, J. J. The interaction of proteins with solid surfaces Curr. Opin. Struc. Biol. 2004, 14 (1) 110-115
2. Tanaka, T.; Matsunaga, T. Fully automated chemiluminescence immunoassay of insulin using antibody-protein A-bacterial magnetic particle complexes Anal. Chem. 2000, 72 (15) 3518-3522
3. Neubert, H.; Jacoby, E. S.; Bansal, S. S.; Iles, R. K.; Cowan, D. A.; Kicman, A. T. Enhanced affinity capture MALDI-TOF MS: Orientation of an immunoglobulin G using recombinant protein G Anal. Chem. 2002, 74 (15) 3677-3683
4. Song, H. Y.; Zhou, X. D.; Hobley, J.; Su, X. D. Comparative study of random and oriented antibody immobilization as measured by dual polarization interferometry and surface plasmon resonance spectroscopy Langmuir 2012, 28 (1) 997-1004
5. Wang, H.; Castner, D. G.; Ratner, B. D.; Jiang, S. Y. Probing the orientation of surface-immobilized immunoglobulin G by time-of-flight secondary ion mass spectrometry Langmuir. 2004, 20 (5) 1877-1887
6. Gao, D.; McBean, N.; Schultz, J. S.; Yan, Y. S.; Mulchandani, A.; Chen, W. F. Fabrication of antibody arrays using thermally responsive elastin fusion proteins J. Am. Chem. Soc. 2006, 128 (3) 676-677
7. Bae, Y. M.; Oh, B. K.; Lee, W.; Lee, W. H.; Choi, J. W. Study on orientation of immunoglobulin G on protein G layer Biosens. Bioelectron. 2005, 21 (1) 103-110
8. Jung, Y.; Lee, J. M.; Jung, H.; Chung, B. H. Self-directed and self-oriented immobilization of antibody by protein G-DNA conjugate Anal. Chem. 2007, 79 (17) 6534-6541
9. Ha, T. H.; Jung, S. O.; Lee, J. M.; Lee, K. Y.; Lee, Y.; Park, J. S.; Chung, B. H. Oriented immobilization of antibodies with GST-fused multiple F-c-specific B-domains on a gold surface Anal. Chem. 2007, 79 (2) 546-556
10. Kim, E. S.; Shim, C. K.; Lee, J. W.; Park, J. W.; Choi, K. Y. Synergistic effect of orientation and lateral spacing of protein G on an on-chip immunoassay Analyst. 2012, 137 (10) 2421-2430
11. Lee, J. H.; Choi, H. K.; Lee, S. Y.; Lim, M. W.; Chang, J. H. Enhancing immunoassay detection of antigens with multimeric protein Gs Biosens. Bioelectron. 2011, 28 (1) 146-151
12. Johnson, B. N.; Mutharasan, R. pH effect on protein G orientation on gold surfaces and characterization of adsorption thermodynamics Langmuir 2012, 28 (17) 6928-6934
13. Baugh, L.; Weidner, T.; Baio, J. E.; Nguyen, P. C. T.; Gamble, L. J.; Slayton, P. S.; Castner, D. G. Probing the orientation of surface-immobilized protein G B1 using ToF-SIMS, Sum Frequency Generation, and NEXAFS Spectroscopy Langmuir. 2010, 26 (21) 16434-16441
14. Baio, J. E.; Weidner, T.; Baugh, L.; Gamble, L. J.; Stayton, P. S.; Castner, D. G. Probing the orientation of electrostatically immobilized protein G B1 by time-of-flight secondary ion spectrometry, sum frequency generation, and near-edge X-ray adsorption fine structure spectroscopy Langmuir 2012, 28 (4) 2107-2112
15. Kim, H.; Kang, D. Y.; Goh, H. J.; Oh, B. K.; Singh, R. P.; Oh, S. M.; Choi, J. W. Analysis of direct immobilized recombinant protein G on a gold surface Ultramicroscopy 2008, 108 (10) 1152-1156
16. Choi, J. W.; Park, K. S.; Lee, W. C.; Oh, B. K.; Chun, B. S.; Paek, S. H. Regulation of anti-LDL immobilization on self-assembled protein G layer using CHAPS and its application to immunosensor Mater. Sci. Eng., C 2004, 24 (1-2) 241-245
17. Xie, Y.; Liu, M. F.; Zhou, J. Molecular dynamics simulations of peptide adsorption on self-assembled monolayers Appl. Surf. Sci. 2012, 258 (20) 8153-8159
18. Zhang, A. J.; Xie, Y.; Zhou, J. Experimental control and characterization of proteins orientation on surfaces Prog. Chem. 2009, 21, 1408-1417
19. Sheng, Y. B.; Wang, W.; Chen, P. Adsorption of an ionic complementary peptide on the hydrophobic graphite surface J. Phys. Chem. C 2010, 114 (1) 454-459
20. Yu, X.; Wang, Q. M.; Lin, Y. A.; Zhao, J.; Zhao, C.; Zheng, J. Structure, orientation, and surface interaction of alzheimer amyloid-beta peptides on the graphite Langmuir 2012, 28 (16) 6595-6605
21. Wei, T.; Carignano, M. A.; Szleifer, I. Lysozyme adsorption on polyethylene surfaces: Why are long simulations needed? Langmuir 2011, 27 (19) 12074-12081
22. Trzaskowski, B.; Leonarski, F.; Les, A.; Adamowicz, L. Modeling tubulin at interfaces. Immobilization of microtubules on self-assembled monolayers J. Phys. Chem. B 2005, 109 (37) 17734-17742
23. Xie, Y.; Liao, C. Y.; Zhou, J. Effects of external electric fields on lysozyme adsorption by molecular dynamics simulations Biophys. Chem. 2013, 179, 26-34
24. Agashe, M.; Raut, V.; Stuart, S. J.; Latour, R. A. Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment Langmuir 2005, 21 (3) 1103-1117
25. Hsu, H. J.; Sheu, S. Y.; Tsay, R. Y. Preferred orientation of albumin adsorption on a hydrophilic surface from molecular simulation Colloids Surf. B 2008, 67 (2) 183-191
26. Friedel, M.; Baumketner, A.; Shea, J. E. Effects of surface tethering on protein folding mechanisms Proc. Natl. Acad. Sci. U.S.A. 2006, 103 (22) 8396-8401
27. Friedel, M.; Baumketner, A.; Shea, J. E. Stability of a protein tethered to a surface J. Chem. Phys. 2007, 126, 095101
28. Wang, H.; He, Y.; Ratner, B. D.; Jiang, S. Y. Modulating cell adhesion and spreading by control of FnIII(7-10) orientation on charged self-assembled monolayers (SAMs) of alkanethiolates J. Biomed. Mater. Res. A 2006, 77A (4) 672-678
29. Boughton, A. P.; Andricioaei, I.; Chen, Z. Surface orientation of magainin 2: Molecular Dynamics Simulation and sum frequency generation vibrational spectroscopic studies Langmuir 2010, 26 (20) 16031-16036
30. Nordgren, C. E.; Tobias, D. J.; Klein, M. L.; Blasie, J. K. Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces Biophys. J. 2002, 83 (6) 2906-2917
31. Trzaskowski, B.; Leonarski, F.; Les, A.; Adamowicz, L. Altering the orientation of proteins on self-assembled monolayers: A computational study Biomacromolecules 2008, 9 (11) 3239-3245
32. Zhou, J.; Chen, S. F.; Jiang, S. Y. Orientation of adsorbed antibodies on charged surfaces by computer simulation based on a united-residue model Langmuir 2003, 19 (8) 3472-3478
33. Zhou, J.; Zheng, J.; Jiang, S. Y. Molecular simulation studies of the orientation and conformation of cytochrome c adsorbed on self-assembled monolayers J. Phys. Chem. B 2004, 108 (45) 17418-17424
34. Hagiwara, T.; Sakiyama, T.; Watanabe, H. Molecular simulation of bovine beta-lactoglobulin adsorbed onto a positively charged solid surface Langmuir 2009, 25 (1) 226-234
35. Knotts, T. A.; Rathore, N.; de Pabloz, J. J. An entropic perspective of protein stability on surfaces Biophys. J. 2008, 94 (11) 4473-4483
36. Wei, S.; Knotts, T. A. Predicting stability of alpha-helical, orthogonal-bundle proteins on surfaces J. Chem. Phys. 2010, 133, 115102
37. Xie, Y.; Zhou, J.; Jiang, S. Y. Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces J. Chem. Phys. 2010, 132 (6) 065101
38. Bauer, M. C.; Xue, W. F.; Linse, S. Protein GB1 folding and assembly from structural elements Int. J. Mol. Sci. 2009, 10 (4) 1552-1566
39. Wu, X. M.; Yang, G.; Zhou, L. J. Identifying the intermediates during the folding/unfolding of protein GB1 with MD simulations Theor. Chem. Acc. 2012, 131 (5) 1229
40. Gallagher, T.; Alexander, P.; Bryan, P.; Gilliland, G. L. Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR Biochemistry-U.S.. 1994, 33 (15) 4721-4729
41. Hess, B.; van der Spoel, D.; Lindahl, E.; Apol, E.; Apostolov, R.; Berendsen, H. J. C.; van Buuren, A.; Bjelkmar, P.; van Drunen, R.; Feenstra, A.; Groenhof, G.; Kasson, P.; Larsson, P.; Meulenhoff, P.; Murtola, T.; Pall, S.; Pronk, S.; Schultz, R.; Shirts, M.; Sijbers, A.; Tieleman, P. Gromacs User Manual v.4.5; RIT: Uppsala, Sweden, 2010
42. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: San Carlos, CA, 2002; http://www.pymol.org.
43. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105 (28) 6474-6487
44. Kony, D.; Damm, W.; Stoll, S.; van Gunsteren, W. F. An improved OPLS-AA force field for carbohydrates J. Comput. Chem. 2002, 23 (15) 1416-1429
45. Chatterjee, S.; Debenedetti, P. G.; Stillinger, F. H.; Lynden-Bell, R. M. A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models J. Chem. Phys. 2008, 128 (12) 124511
46. Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31 (3) 1695-1697
47. Nose, S. A unified formulation of the constant temperature molecular dynamics methods J. Chem. Phys. 1984, 81 (1) 511-519
48. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18 (12) 1463-1472
49. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Hsing, L.; Pedersen, L. G. A smooth particle mesh Ewald method J. Chem. Phys. 1995, 103 (19) 8577-8593
50. Humphrey, W.; Dalke, A.; Schulten, K. VMD: visual molecular dynamics J. Mol. Graphics 1996, 14 (1) 33-38
51. Ravichandran, S.; Madura, J. D.; Talbot, J. A Brownian dynamics study of the initial stages of hen egg-white lysozyme adsorption at a solid interface J. Phys. Chem. B 2001, 105 (17) 3610-3613
52. Zhou, J.; Tsao, H. K.; Sheng, Y. J.; Jiang, S. Y. Monte Carlo simulations of antibody adsorption and orientation on charged surfaces J. Chem. Phys. 2004, 121 (2) 1050-1057
53. Chen, S. F.; Liu, L. Y.; Zhou, J.; Jiang, S. Y. Controlling antibody orientation on charged self-assembled monolayers Langmuir 2003, 19 (7) 2859-2864
54. Sheinerman, F. B.; Brooks, C. L. A molecular dynamics simulation study of segment B1 of protein G Proteins 1997, 29 (2) 193-202
55. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22 (12) 2577-637
56. Guss, B.; Eliasson, M.; Olsson, A.; Uhlen, M.; Frej, A. K.; Jornvall, H.; Flock, J. I.; Lindberg, M. Structure of the IgG-binding regions of streptococcal protein G EMBO J. 1986, 5 (7) 1567-1575
57. Kato, K.; Lian, L. Y.; Barsukov, I. L.; Derrick, J. P.; Kim, H.; Tanaka, R.; Yoshino, A.; Shiraishi, M.; Shimada, I.; Arata, Y. Model for the complex between protein G and an antibody Fc fragment in solution Structure 1995, 3 (1) 79-85
58. Sloan, D. J.; Hellinga, H. W. Dissection of the protein G B1 domain binding site for human IgG Fc fragment Protein Sci. 1999, 8 (8) 1643-1648
59. Sauer-Eriksson, A. E.; Kleywegt, G. J.; Uhlen, M.; Jones, T. A. Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG Structure 1995, 3 (3) 265-278
60. Wiseman, M. E.; Frank, C. W. Antibody adsorption and orientation on hydrophobic surfaces Langmuir 2012, 28 (3) 1765-1774