Biomimetic design of affinity peptide ligand for capsomere of virus-like particle

Langmuir

Volumn 30, Issue 28, 2014, Pages 8500-8508

  Li, Yanying ^a   Liu, Xiaodan ^a   Dong, Xiaoyan ^a,b   Zhang, Lin ^a,b   Sun, Yan ^a,b  

^a TIANJIN UNIVERSITY   (China)

^b SynBio Research Platform   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AFFINITY CHROMATOGRAPHY; AMINO ACIDS; BIOMIMETICS; DESIGN; DIGITAL LIBRARIES; DRUG DELIVERY; LIGANDS; MOLECULAR DYNAMICS; PURIFICATION; VIRUSES;

AFFINITY PEPTIDES; BIOMIMETIC DESIGN; DOWNSTREAM PROCESS; MOLECULAR DYNAMICS SIMULATIONS; ONE-STEP PURIFICATION; SEPARATION AND PURIFICATION; STRUCTURE COMPARISONS; VIRUS-LIKE PARTICLES;

PEPTIDES;

CAPSID PROTEIN; PEPTIDE;

BIOMIMETICS; CHEMISTRY; POLYOMAVIRUS; PROCEDURES; VIRUS CAPSID;

BIOMIMETICS; CAPSID; CAPSID PROTEINS; PEPTIDES; POLYOMAVIRUS;

EID: 84904668062     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/la5017438     Document Type: Article

References (46)

1. Salunke, D. M.; Caspar, D. L. D.; Garcea, R. L. Self-assembly of purified polyomavirus capsid protein VP1 Cell. 1986, 46 (6) 895-904
2. Ghasparian, A.; Riedel, T.; Koomullil, J.; Moehle, K.; Gorba, C.; Svergun, D. I.; Perriman, A. W.; Mann, S.; Tamborrini, M.; Pluschke, G. Engineered synthetic virus-like particles and their use in vaccine delivery ChemBioChem 2011, 12 (1) 100-109
3. Uchida, M.; Morris, D. S.; Kang, S.; Jolley, C. C.; Lucon, J.; Liepold, L. O.; LaFrance, B.; Prevelige, P. E., Jr.; Douglas, T. Site-directed coordination chemistry with P22 virus-like particles Langmuir 2011, 28 (4) 1998-2006
4. Zhang, L.; Tang, R.; Bai, S.; Connors, N. K.; Lua, L. H.; Chuan, Y. P.; Middelberg, A. P.; Sun, Y. Molecular energetics in the capsomere of virus-like particle revealed by molecular dynamics simulations J. Phys. Chem. B 2013, 117 (18) 5411-5421
5. Stehle, T.; Yan, Y.; Benjamin, T. L.; Harrison, S. C. Structure of murine polyomavirus complexed with an oligosaccharide receptor fragment Nature 1994, 369, 160-163
6. Ding, Y.; Chuan, Y. P.; He, L.; Middelberg, A. P. J. Modeling the competition between aggregation and self-assembly during virus-like particle processing Biotechnol. Bioeng. 2010, 107 (3) 550-560
7. Chuan, Y. P.; Lua, L. H. L.; Middelberg, A. P. J. High-level expression of soluble viral structural protein in Escherichia coli J. Biotechnol. 2008, 134 (1) 64-71
8. Pattenden, L. K.; Middelberg, A. P. J.; Niebert, M.; Lipin, D. I. Towards the preparative and large-scale precision manufacture of virus-like particles Trends Biotechnol. 2005, 23 (10) 523-529
9. Liew, M. W. O.; Rajendran, A.; Middelberg, A. P. J. Microbial production of virus-like particle vaccine protein at gram-per-litre levels J. Biotechnol. 2010, 150 (2) 224-231
10. Kaufman, D. B.; Hentsch, M. E.; Baumbach, G. A.; Buettner, J. A.; Dadd, C. A.; Huang, P. Y.; Hammond, D. J.; Carbonell, R. G. Affinity purification of fibrinogen using a ligand from a peptide library Biotechnol. Bioeng. 2002, 77 (3) 278-289
11. Vutukuru, S.; Kane, R. S. Surface plasmon resonance spectroscopy-based high-throughput screening of ligands for use in affinity and displacement chromatography Langmuir 2008, 24 (20) 11784-11789
12. Makriyannis, T.; Clonis, Y. Design and study of peptide-ligand affinity chromatography adsorbents: Application to the case of trypsin purification from bovine pancreas Biotechnol. Bioeng. 1997, 53 (1) 49-57
13. Kelley, B. D.; Booth, J.; Tannatt, M.; Wu, Q.-L.; Ladner, R.; Yu, J.; Potter, D.; Ley, A. Isolation of a peptide ligand for affinity purification of factor VIII using phage display J. Chromatogr., A 2004, 1038 (1) 121-130
14. Huang, H.-J.; Yu, H. W.; Chen, C.-Y.; Hsu, C.-H.; Chen, H.-Y.; Lee, K.-J.; Tsai, F.-J.; Chen, C. Y.-C. Current developments of computer-aided drug design J. Taiwan. Inst. Chem. E 2010, 41 (6) 623-635
15. Wilson, G. L.; Lill, M. A. Integrating structure-based and ligand-based approaches for computational drug design Future Med. Chem. 2011, 3 (6) 735-750
16. Liu, F.-F.; Wang, T.; Dong, X.-Y.; Sun, Y. Rational design of affinity peptide ligand by flexible docking simulation J. Chromatogr., A 2007, 1146 (1) 41-50
17. Liu, F.-F.; Dong, X.-Y.; Wang, T.; Sun, Y. Rational design of peptide ligand for affinity chromatography of tissue-type plasminogen activator by the combination of docking and molecular dynamics simulations J. Chromatogr., A 2007, 1175 (2) 249-258
18. Zhang, L.; Sun, Y. Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: I. Construction of affinity binding model. Langmuir 30 (16), 4725-4733.
19. Zhang, L.; Zhang, C.; Sun, Y. Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: II. Inhibitor library, screening and experimental validation Langmuir 2014, 30 (16) 4734-4742
20. Delos, S. E.; Cripe, T. P.; Leavitt, A. D.; Greisman, H.; Garcea, R. L. Expression of the polyomavirus minor capsid proteins VP2 and VP3 in Escherichia coli: In vitro interactions with recombinant VP1 capsomeres J. Virol. 1995, 69 (12) 7734
21. Cai, X.; Chang, D.; Rottinghaus, S.; Consigli, R. A. Expression and purification of recombinant polyomavirus VP2 protein and its interactions with polyomavirus proteins J. Virol. 1994, 68 (11) 7609
22. Chen, X. S.; Stehle, T.; Harrison, S. C. Interaction of polyomavirus internal protein VP2 with the major capsid protein VP1 and implications for participation of VP2 in viral entry EMBO J. 1998, 17 (12) 3233-3240
23. Xue, Q.; Zhang, J.-L.; Zheng, Q.-C.; Cui, Y.-L.; Chen, L.; Chu, W.-T.; Zhang, H.-X. Exploring the Molecular Basis of dsRNA Recognition by Mss116p Using Molecular Dynamics Simulations and Free-Energy Calculations Langmuir 2013, 29 (35) 11135-11144
24. Zheng, J.; Yu, X.; Wang, J.; Yang, J.-C.; Wang, Q. Molecular modeling of two distinct triangular oligomers in amyloid β-protein J. Phys. Chem. B 2009, 114 (1) 463-470
25. Trott, O.; Olson, A. J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J. Comput. Chem. 2010, 31 (2) 455-461
26. London, N.; Raveh, B.; Cohen, E.; Fathi, G.; Schueler-Furman, O. Rosetta FlexPepDock web server - High resolution modeling of peptide-protein interactions Nucleic Acids Res. 2011, 39 (suppl 2) W249-W253
27. Zhou, J.; Zheng, J.; Jiang, S. 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
28. Zheng, J.; Jang, H.; Ma, B.; Nussinov, R. Annular structures as intermediates in fibril formation of Alzheimer Aβ17- 42 J. Phys. Chem. B 2008, 112 (22) 6856-6865
29. Yu, X.; Zheng, J. Polymorphic structures of Alzheimers β-amyloid globulomers PloS One 2011, 6 (6) e20575
30. Zhao, J.; Wang, Q.; Liang, G.; Zheng, J. Molecular dynamics simulations of low-ordered Alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers Langmuir. 2011, 27 (24) 14876-14887
31. Feng, H.; Becker, K. E.; Zhou, J.; Fichthorn, K. A. Molecular thin films on solid surfaces: Mechanisms of Melting Langmuir 2012, 28 (19) 7382-7392
32. Yu, X.; Wang, Q.; Lin, Y.; Zhao, J.; Zhao, C.; Zheng, J. Structure, orientation, and surface interaction of Alzheimer amyloid-β peptides on the graphite Langmuir 2012, 28 (16) 6595-6605
33. Lindahl, E.; Hess, B.; Van Der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Model. 2001, 7 (8) 306-317
34. Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126 (1) 014101
35. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N ·log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98 (12) 10089-10092
36. Hess, B.; Bekker, H.; Berendsen, H. J.; Fraaije, J. G. LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18 (12) 1463-1472
37. Li, J.; Zhang, L.; Sun, Y. Molecular basis of the initial platelet adhesion in arterial thrombosis: Molecular dynamics simulations J. Mol. Graphics Modell. 2012, 37, 49-58
38. Brooks, B. R.; Brooks, C. L.; MacKerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S. CHARMM: The biomolecular simulation program J. Comput. Chem. 2009, 30 (10) 1545-1614
39. Joshi, M.; Ebalunode, J. O.; Briggs, J. M. Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates Proteins: Struct., Funct., Bioinf. 2009, 75 (2) 323-335
40. Gorfe, A. A.; Jelesarov, I. Energetics of sequence-specific protein - DNA association: Computational analysis of integrase Tn916 binding to its target DNA Biochemistry. 2003, 42 (40) 11568-11576
41. Sanner, M. F. Python: A programming language for software integration and development J. Mol. Graphics Modell. 1999, 17 (1) 57-61
42. Das, R.; Baker, D. Macromolecular modeling with Rosetta Annu. Rev. Biochem. 2008, 77, 363-382
43. Huang, B.; Liu, F.-F.; Dong, X.-Y.; Sun, Y. Molecular mechanism of the affinity interactions between protein A and human immunoglobulin G1 revealed by molecular simulations J. Phys. Chem. B 2011, 115 (14) 4168-4176
44. Lafont, V.; Schaefer, M.; Stote, R. H.; Altschuh, D.; Dejaegere, A. Protein-protein recognition and interaction hot spots in an antigen-antibody complex: Free energy decomposition identifies "efficient amino acids" Proteins: Struct., Funct., Bioinf. 2007, 67 (2) 418-434
45. Nakanishi, A.; Nakamura, A.; Liddington, R.; Kasamatsu, H. Identification of amino acid residues within simian virus 40 capsid proteins Vp1, Vp2, and Vp3 that are required for their interaction and for viral infection J. Virol. 2006, 80 (18) 8891
46. Brady, J. N.; Consigli, R. A. Chromatographic separation of the polyoma virus proteins and renaturation of the isolated VP1 major capsid protein J. Virol. 1978, 27 (2) 436-442