Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: I. Construction of an affinity binding model

Langmuir

Volumn 30, Issue 16, 2014, Pages 4725-4733

  Zhang, Lin ^a   Sun, Yan ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADHESION; BINDING ENERGY; BIOMIMETICS; COMPUTER SIMULATION; MOLECULAR DYNAMICS;

AFFINITY BINDING; BINDING FREE ENERGY; BIOMIMETIC DESIGN; COLLAGEN SURFACE; HYDROPHOBIC INTERACTIONS; MOLECULAR DETERMINANTS; MOLECULAR DYNAMICS SIMULATIONS; PLATELET ADHESION;

COLLAGEN;

COLLAGEN; PLASMA PROTEIN; PLATELET ADHESION INHIBITOR; PROTEIN BINDING; VERY LATE ACTIVATION ANTIGEN 2;

BIOMIMETICS; CHEMICAL PHENOMENA; CHEMISTRY; MOLECULAR DYNAMICS; PROCEDURES;

BIOMIMETICS; BLOOD PROTEINS; COLLAGEN; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INTEGRIN ALPHA2BETA1; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING;

EID: 84899638672     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/la404599s     Document Type: Article

References (45)

1. Furie, B.; Furie, B. C. Mechanisms of Disease: Mechanisms of Thrombus Formation New Engl. J. Med. 2008, 359, 938-949
2. Meadows, T. A.; Bhatt, D. L. Clinical Aspects of Platelet Inhibitors and Thrombus Formation Circ. Res. 2007, 100, 1261-1275
3. Blann, A. D. Platelets: The Universal Killer? Biochim. Biophys. Acta, Mol. Basis Dis. 2007, 1772, 715-717
4. Andrews, R. K.; Gardiner, E. E.; Shen, Y.; Berndt, M. C. Platelet Interactions in Thrombosis IUBMB Life 2004, 56, 13-18
5. Ajjan, R. A.; Ariens, R. Cardiovascular Disease and Heritability of the Prothrombotic State Blood Rev. 2009, 23, 67-78
6. Varga-Szabo, D.; Pleines, I.; Nieswandt, B. Cell Adhesion Mechanisms in Platelets Arterioscl. Throm. Vas. 2008, 28, 403-412
7. Gibbins, J. M. Platelet Adhesion Signalling and the Regulation of Thrombus Formation J. Cell Sci. 2004, 117, 3415-3425
8. Wei, A. H.; Schoenwaelder, S. M.; Andrews, R. K.; Jackson, S. P. New Insights Into the Haemostatic Function of Platelets Br. J. Hamaetol. 2009, 147, 415-430
9. Rivera, J.; Lozano, M. L.; Navarro-Nunez, L.; Vicente, V. Platelet Receptors and Signaling in the Dynamics of Thrombus Formation Haematol. Hematol. J. 2009, 94, 700-711
10. Sachs, N.; Sonnenberg, A. Cell-Matrix Adhesion of Podocytes in Physiology and Disease Nat. Rev. Nephrol. 2013, 9, 200-210
11. Nieswandt, B.; Pleines, I.; Bender, M. Platelet Adhesion and Activation Mechanisms in Arterial Thrombosis and Ischaemic Stroke J. Thromb. Haemost. 2011, 91, 92-104
12. Xu, H. F.; Bihan, D.; Chang, F.; Huang, P. H.; Farndale, R. W.; Leitinger, B. Discoidin Domain Receptors Promote Alpha 1 Beta 1-and Alpha 2 Beta 1-Integrin Mediated Cell Adhesion to Collagen by Enhancing Integrin Activation PLoS One 2012, 7, e52209
13. Knight, C. G.; Morton, L. F.; Onley, D. J.; Peachey, A. R.; Messent, A. J.; Smethurst, P. A.; Tuckwell, D. S.; Farndale, R. W.; Barnes, M. J. Identification in Collagen Type I of an Integrin Alpha(2)Beta(1)-Binding Site Containing an Essential Ger Sequence J. Biol. Chem. 1998, 273, 33287-33294
14. Kamata, T.; Liddington, R. C.; Takada, Y. Interaction Between Collagen and the Alpha(2) I-Domain of Integrin Alpha(2)Beta(1)-Critical Role of Conserved Residues in the Metal Ion-Dependent Adhesion Site (Midas) Region J. Biol. Chem. 1999, 274, 32108-32111
15. Emsley, J.; Knight, C. G.; Farndale, R. W.; Barnes, M. J.; Liddington, R. C. Structural Basis of Collagen Recognition by Integrin Alpha 2 Beta 1 Cell 2000, 101, 47-56
16. Siebert, H. C.; Burg-Roderfeld, M.; Eckert, T.; Stotzel, S.; Kirch, U.; Diercks, T.; Humphries, M. J.; Frank, M.; Wechselberger, R.; Tajkhorshid, E.; Oesser, S. Interaction of the Alpha 2a Domain of Integrin with Small Collagen Fragments Protein Cell 2010, 1, 393-405
17. Zaman, M. H. Understanding the Molecular Basis for Differential Binding of Integrins to Collagen and Gelatin Biophys. J. 2007, 92, L17-L19
18. Attwood, S. J.; Simpson, A.; Hamaia, S. W.; Bihan, D.; Roy, D.; Farndale, R. W.; Welland, M. E. Measurement of the Interaction Between Recombinant I-Domain From Integrin Alpha 2 Beta 1 and a Triple Helical Collagen Peptide with the Gfoger Binding Motif Using Molecular Force Spectroscopy Int. J. Mol. Sci. 2013, 14, 2832-2845
19. Karplus, M.; McCammon, J. A. Molecular Dynamics Simulations of Biomolecules Nat. Struct. Biol. 2002, 9, 646-652
20. Daggett, V. Protein Folding-Simulation Chem. Rev. 2006, 106, 1898-1916
21. Nimlos, M. R.; Beckham, G. T.; Matthews, J. F.; Bu, L. T.; Himmel, M. E.; Crowley, M. F. Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-Binding Module On Cellulose J. Biol. Chem. 2012, 287, 20603-20612
22. Priyadarzini, T.; Selvin, J.; Gromiha, M. M.; Fukui, K.; Veluraja, K. Theoretical Investigation On the Binding Specificity of Sialyldisaccharides with Hemagglutinins of Influenza a Virus by Molecular Dynamics Simulations J. Biol. Chem. 2012, 287, 34547-34557
23. 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, 6595-6605
24. Zhao, J.; Wang, Q.; Liang, G.; Zheng, J. Molecular Dynamics Simulations of Low-Ordered Alzheimer Beta-Amyloid Oligomers From Dimer to Hexamer On Self-Assembled Monolayers Langmuir 2011, 27, 14876-14887
25. Feng, H. J.; Becker, K. E.; Zhou, J.; Fichthorn, K. A. Molecular Thin Films On Solid Surfaces: Mechanisms of Melting Langmuir 2012, 28, 7382-7392
26. 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, 17418-17424
27. McCully, M. E.; Beck, D.; Daggett, V. Multimolecule Test-Tube Simulations of Protein Unfolding and Aggregation Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17851-17856
28. Hopping, G.; Kellock, J.; Caughey, B.; Daggett, V. Designed Trpzip-3 B-Hairpin Inhibits Amyloid Formation in Two Different Amyloid Systems ACS Med. Chem. Lett. 2013, 4, 824-828
29. 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
30. Zheng, J.; Yu, X.; Wang, J.; Yang, J.; Wang, Q. Molecular Modeling of Two Distinct Triangular Oligomers in Amyloid Beta-Protein J. Phys. Chem. B 2010, 114, 463-470
31. Zou, H. J.; Luo, C.; Zheng, S. X.; Luo, X. M.; Zhu, W. L.; Chen, K. X.; Shen, J. H.; Jiang, H. L. Molecular Insight Into the Interaction Between Ifabp and Pa by Using Mm-Pbsa and Alanine Scanning Methods J. Phys. Chem. B 2007, 111, 9104-9113
32. Huang, B.; Liu, F. F.; Dong, X. Y.; Sun, Y. Molecular Mechanism of the Affinity Interactions Between Protein a and Human Innmunoglobulin G1 Revealed by Molecular Simulations J. Phys. Chem. B 2011, 115, 4168-4176
33. Li, J.; Zhang, L.; Sun, Y. Molecular Basis of the Initial Platelet Adhesion in Arterial Thrombosis: Molecular Dynamics Simulations J. Mol. Graph. Model. 2012, 37, 49-58
34. 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, 5411-5421
35. Chang, N. Computational Studies on the Factors Influencing Stabilities of Collagen-Like Peptides. M.S. Thesis, Massachusetts Institute of Technology, 2004.
36. Lindahl, E.; Hess, B.; van, S. D. Gromacs 3.0: A Package for Molecular Simulation and Trajectory Analysis J. Mol. Model. 2001, 7, 306-317
37. Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling. J. Chem. Phys. 2007, 126.
38. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. Lincs: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
39. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N [Center-Dot] Log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
40. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. Charmm: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30, 1545-1614
41. 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 2009, 75, 323-335
42. 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, 11568-11576
43. 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 2007, 67, 418-434
44. Knight, C. G.; Morton, L. F.; Peachey, A. R.; Tuckwell, D. S.; Farndale, R. W.; Barnes, M. J. The Collagen-Binding a-Domains of Integrins Alpha(1)Beta(1) and Alpha(2)Beta(1) Recognize the Same Specific Amino Acid Sequence, Gfoger, in Native (Triple-Helical) Collagens J. Biol. Chem. 2000, 275, 35-40
45. Emsley, J.; King, S. L.; Bergelson, J. M.; Liddington, R. C. Crystal Structure of the I Domain From Integrin A2B1 J. Biol. Chem. 1997, 272, 28512-28517