Modelling of lysozyme binding to a cation exchange surface at atomic detail: The role of flexibility

Biophysical Journal

Volumn 100, Issue 12, 2011, Pages 3016-3024

  Steudle, Alexander ^a   Pleiss, Jürgen ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79960323239     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.05.024     Document Type: Article

References (40)

1. Roth, C. M., and A. M. Lenhoff. 2003. Biopolymers at Interfaces. Marcel Dekker, New York.
2. Talasaz, A. H., M. Nemat-Gorgani, ..., R. W. Davis. 2006. Prediction of protein orientation upon immobilization on biological and nonbiological surfaces. Proc. Natl. Acad. Sci. USA. 103:14773-14778. (Pubitemid 44527804)
3. Subrahmanyam, S., S. A. Piletsky, and A. P. F. Turner. 2002. Application of natural receptors in sensors and assays. Anal. Chem. 74:3942- 3951. (Pubitemid 34912889)
4. Ratner, B. D., and S. J. Bryant. 2004. Biomaterials: where we have been and where we are going. Annu. Rev. Biomed. Eng. 6:41-75. (Pubitemid 39209492)
5. Roth, C. M., and A. M. Lenhoff. 1998. Biopolymers at Interfaces. Marcel Dekker, New York.
6. Berman, H., K. Henrick, and H. Nakamura. 2003. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10:980. (Pubitemid 37500485)
7. Yoon, B. J., and A. M. Lenhoff. 1992. Computation of the electrostatic interaction energy between a protein and a charged surface. J. Phys. Chem. 96:3130-3134.
8. Ravichandran, S., and J. Talbot. 2000. Mobility of adsorbed proteins: a Brownian dynamics study. Biophys. J. 78:110-120. (Pubitemid 30207123)
9. Ravichandran, S., J. D. Madura, and J. Talbot. 2001. A Brownian dynamics study of the initial stages of hen egg-white lysozyme adsorption at a solid interface. J. Phys. Chem. B. 105:3610-3613.
10. Agashe, M., V. Raut, ..., R. A. Latour. 2005. Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment. Langmuir. 21:1103-1117. (Pubitemid 40184815)
11. Chen, X., Q. Wang, ..., T. Wu. 2007. Adsorption of leucine-rich amelogenin protein on hydroxyapatite (001) surface through -COO- claws. J. Phys. Chem. C. 111:1284-1290. (Pubitemid 46347072)
12. Shen, J. W., T. Wu, ..., H. H. Pan. 2008. Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces. Biomaterials. 29:513-532. (Pubitemid 350100806)
13. Mulheran, P., and K. Kubiak. 2009. Protein adsorption mechanisms on solid surfaces: lysozyme-on-mica. Mol. Simul. 35:561-566.
14. Kubiak, K., and P. A. Mulheran. 2009. Molecular dynamics simulations of hen egg white lysozyme adsorption at a charged solid surface. J Phys Chem B. 113:189-200.
15. Kubiak-Ossowska, K., and P. A. Mulheran. 2010. What governs protein adsorption and immobilization at a charged solid surface? Langmuir. 26:7690-7694.
16. Dismer, F., and J. Hubbuch. 2010. 3D structure-based protein retention prediction for ion-exchange chromatography. J. Chromatogr. A. 1217: 1343-1353.
17. Raffaini, G., and F. Ganazzoli. 2003. Simulation study of the interaction of some albumin subdomains with a flat graphite surface. Langmuir. 19:3403-3412.
18. Raffaini, G., and F. Ganazzoli. 2004. Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface. Langmuir. 20:3371-3378.
19. Carlsson, F., E. Hyltner, ..., P. Linse. 2004. Lysozyme adsorption to charged surfaces. A Monte Carlo study. J. Phys. Chem. B. 108:9871- 9881.
20. Roth, C. M., and A. M. Lenhoff. 1993. Electrostatic and van der Waals contributions to protein adsorption: computation of equilibriumconstants. Langmuir. 9:962-972.
21. Roth, C. M., and A. M. Lenhoff. 1995. Electrostatic and van der Waals contributions to protein adsorption: comparison of theory and experiment. Langmuir. 11:3500-3509.
22. Noinville, V., C. Vidal-Madjar, and B. Sebille. 1995. Modeling of protein adsorption on polymer surfaces. Computation of adsorption potential. J. Phys. Chem. 99:1516-1522.
23. Sun, Y., W. J. Welsh, and R. A. Latour. 2005. Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation. Langmuir. 21:5616-5626. (Pubitemid 40850653)
24. Lu, D. R., and K. Park. 1989. Protein adsorption on polymer surfaces: calculation of adsorption. J. Biomater. Sci. Polym. Ed. 1:243-260.
25. Yao, Y., and A. M. Lenhoff. 2004. Electrostatic contributions to protein retention in ion-exchange chromatography. 1. Cytochrome C variants. Anal. Chem. 76:6743-6752. (Pubitemid 39507266)
26. Yao, Y., and A. M. Lenhoff. 2005. Electrostatic contributions to protein retention in ion-exchange chromatography. 2. Proteins with various degrees of structural differences. Anal. Chem. 77:2157-2165. (Pubitemid 40463833)
27. Dismer, F., and J. Hubbuch. 2007. A novel approach to characterize the binding orientation of lysozyme on ion-exchange resins. J. Chromatogr. A. 1149:312-320. (Pubitemid 46627656)
28. Schwalbe, H., S. B. Grimshaw, ..., L. J. Smith. 2001. A refined solution structure of hen lysozyme determined using residual dipolar coupling data. Protein Sci. 10:677-688. (Pubitemid 32240493)
29. Rypniewski, W. R., H. M. Holden, and I. Rayment. 1993. Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: an x-ray analysis at 1.8-A resolution. Biochemistry. 32:9851-9858. (Pubitemid 23296833)
30. Kuramitsu, S., and K. Hamaguchi. 1980. Analysis of the acid-base titration curve of hen lysozyme. J. Biochem. 87:1215-1219. (Pubitemid 10033333)
31. 1993. The Merck Index. Merck & Co.
32. Weisstein, E. W. "Mollweide Projection." From MathWorld-A Wolfram Web Resource.
33. DePhillips, P., and A. M. Lenhoff. 2001. Determinants of protein retention characteristics on cation-exchange adsorbents. J. Chromatogr. A. 933:57-72. (Pubitemid 33043741)
34. Rocchia, W., E. Alexov, and B. Honig. 2001. Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalentions. J. Phys. Chem. B. 105:6507-6514. (Pubitemid 35339019)
35. Rocchia, W., S. Sridharan, ..., B. Honig. 2002. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J. Comput. Chem. 23:128-137. (Pubitemid 34063137)
36. Case, D. A., T. A. Darden, ..., P. A. Kollman. 2004. AMBER 8, University of California, San Francisco, CA. http://ambermd.org/.
37. Thompson, M. A. ArgusLab 4.0.1. Planaria Software, Seattle, WA.
38. Frisch, M. J., G. W. Trucks, ..., J. A. Pople. 2001. Gaussian 98 (Revision A.11.3). Gaussian, Pittsburgh, PA. http://www.gaussian.com/.
39. Cieplak, P., W. D. Cornell, ..., P. A. Kollman. 1995. Application of the multimolecule and multiconformational RESP methodology to biopolymers - charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 16:1357-1377.
40. Ladiwala, A., K. Rege, ..., S. M. Cramer. 2003. Investigation of mobile phase salt type effects on protein retention and selectivity in cationexchange systems using quantitative structure retention relationship models. Langmuir. 19:8443-8454.