Understanding selectin counter-receptor binding from electrostatic energy computations and experimental binding studies

Journal of Physical Chemistry B

Volumn 117, Issue 51, 2013, Pages 16443-16454

  Woelke, Anna Lena ^a   Kuehne, Christian ^b   Meyer, Tim ^a   Galstyan, Gegham ^a   Dernedde, Jens ^b   Knapp, Ernst Walter ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING AFFINITIES; BLOOD VESSEL WALLS; ELECTROSTATIC ENERGIES; HARMFUL SUBSTANCES; INFLAMMATORY PROCESS; MODELING PROCEDURE; MOLECULAR COMPONENTS; WHITE BLOOD CELLS;

BINDING ENERGY; BLOOD VESSELS;

IMMUNE SYSTEM;

LIGAND; PEPTIDE FRAGMENT; PROTON; SELECTIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION; STATIC ELECTRICITY; THERMODYNAMICS;

LIGANDS; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTONS; SELECTINS; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84891468260     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4099123     Document Type: Article

References (56)

1. Ley, K.; Laudanna, C.; Cybulsky, M. I.; Nourshargh, S. Getting to the Site of Inflammation: the Leukocyte Adhesion Cascade Updated Nat. Rev. Immunol. 2007, 7, 678-689
2. Bhatia, S. K.; King, M. R.; Hammer, D. A. The State Diagram for Cell Adhesion Mediated by Two Receptors Biophys. J. 2003, 84, 2671-2690
3. Ley, K. The Role of Selectins in Inflammation and Disease Trends Mol. Med. 2003, 9, 263-268
4. Kneuer, C.; Ehrhardt, C.; Radomski, M. W.; Bakowsky, U. Selectins - Potential Pharmacological Targets? Drug Discovery Today 2006, 11, 1034-1040
5. Barthel, S. R.; Gavino, J. D.; Descheny, L.; Dimitroff, C. J. Targeting Selectins and Selectin Ligands in Inflammation and Cancer Expert Opin. Ther. Targets 2007, 11, 1473-1491
6. Romano, S. J.; Slee, D. H. Targeting Selectins for the Treatment of Respiratory Diseases Curr. Opin. Invest. Drugs 2001, 2, 907-913
7. Fasting, C.; Schalley, C. A.; Weber, M.; Seitz, O.; Hecht, S.; Koksch, B.; Dernedde, J.; Graf, C.; Knapp, E. W.; Haag, R. Multivalency as a Chemical Organization and Action Principle Angew. Chem., Int. Ed. Engl. 2012, 51, 10472-10498
8. Roskamp, M.; Enders, S.; Pfrengle, F.; Yekta, S.; Dekaris, V.; Dernedde, J.; Reissig, H. U.; Schlecht, S. Multivalent Interaction and Selectivities in Selectin Binding of Functionalized Gold Colloids Decorated with Carbohydrate Mimetics Org. Biomol. Chem. 2011, 9, 7448-7456
9. Sanders, W. J.; Gordon, E. J.; Dwir, O.; Beck, P. J.; Alon, R.; Kiessling, L. L. Inhibition of L-Selectin-Mediated Leukocyte Rolling by Synthetic Glycoprotein Mimics J. Biol. Chem. 1999, 274, 5271-5278
10. McEver, R. P.; Zhu, C. Rolling Cell Adhesion Annu. Rev. Cell Dev. Biol. 2010, 26, 363-396
11. Somers, W. S.; Tang, J.; Shaw, G. D.; Camphausen, R. T. Insights into the Molecular Basis of Leukocyte Tethering and Rolling Revealed by Structures of P- and E-Selectin Bound to SLe(X) and PSGL-1 Cell 2000, 103, 467-479
12. Poppe, L.; Brown, G. S.; Philo, J. S.; Nikrad, P. V.; Shah, B. H. Conformation of sLex Tetrasaccharide, Free in Solution and Bound to E-, P-, and L-Selectin J. Am. Chem. Soc. 1997, 119, 1727-1736
13. Mehta, P.; Cummings, R. D.; McEver, R. P. Affinity and Kinetic Analysis of P-Selectin Binding to P-Selectin Glycoprotein Ligand-1 J. Biol. Chem. 1998, 273, 32506-32513
14. Croce, K.; Freedman, S. J.; Furie, B. C.; Furie, B. Interaction between Soluble P-Selectin and Soluble P-Selectin Glycoprotein Ligand 1: Equilibrium Binding Analysis Biochemistry 1998, 37, 16472-16480
15. Klopocki, A. G.; Yago, T.; Mehta, P.; Yang, J.; Wu, T.; Leppanen, A.; Bovin, N. V.; Cummings, R. D.; Zhu, C.; McEver, R. P. Replacing a Lectin Domain Residue in L-Selectin Enhances Binding to P-Selectin Glycoprotein Ligand-1 But Not to 6-Sulfo-Sialyl Lewis x J. Biol. Chem. 2008, 283, 11493-11500
16. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
17. Mehta, P.; McEver, R. P. Structure of Lectin and EGF Domains of L-Selectin. To be published.
18. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 1983, 4, 187-217
19. Brooks, B. R.; Brooks, C. L., 3rd; Mackerell, A. D., Jr.; 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, 1545-1614
20. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
21. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., 3rd. Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations J. Comput. Chem. 2004, 25, 1400-1415
22. Guvench, O.; Greene, S. N.; Kamath, G.; Brady, J. W.; Venable, R. M.; Pastor, R. W.; Mackerell, A. D., Jr. Additive Empirical Force Field for Hexopyranose Monosaccharides J. Comput. Chem. 2008, 29, 2543-2564
23. Guvench, O.; Hatcher, E. R.; Venable, R. M.; Pastor, R. W.; Mackerell, A. D. CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses J. Chem. Theory Comput. 2009, 5, 2353-2370
24. Rabenstein, B.; Knapp, E. W. Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers Biophys. J. 2001, 80, 1141-1150
25. Kieseritzky, G.; Knapp, E. W. Optimizing pKa Computation in Proteins with pH Adapted Conformations Proteins 2008, 71, 1335-1348
26. Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: Oxford, U.K., 1989.
27. Koch, W.; Holthausen, M. C. Wie gut ist Dichtefunktionaltheorie? A Chemist's Guide to Density Functional Theory; Wiley-VCH: Weinheim, Germany, 2000.
28. Jaguar, version 7.7, 7.7; Schrödinger, LLC: New York, 2010.
29. Vosko, S. H.; Wilk, L.; Nusair, M. Accurate Spin-Dependent Electron Liquid Correlation Energies for Local Spin-Density Calculations-a Critical Analysis Can. J. Phys. 1980, 58, 1200-1211
30. Lee, C. T.; Yang, W. T.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron-Density Phys. Rev. B 1988, 37, 785-789
31. Becke, A. D. Density-Functional Thermochemistry. 3. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652
32. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab-Initio Calculation of Vibrational Absorption and Circular-Dichroism Spectra Using Density-Functional Force-Fields J. Phys. Chem. 1994, 98, 11623-11627
33. Hehre, W. J.; Ditchfield, J. A.; Pople, J. A. Self-Consistent Molecular-Orbital Methods 0.12. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular-Orbital Studies of Organic-Molecules J. Chem. Phys. 1972, 56, 2257-2261
34. Harihara, P. C.; Pople, J. A. Influence of Polarization Functions on Molecular-Orbital Hydrogenation Energies Theor. Chim. Acta. 1973, 28, 213-222
35. Francl, M. M.; Pietro, W. J.; Hehre, W. J.; Binkley, J. S.; Gordon, M. S.; Defrees, D. J.; Pople, J. A. Self-Consistent Molecular-Orbital Methods 0.23. A Polarization-Type Basis Set for 2Nd-Row Elements J. Chem. Phys. 1982, 77, 3654-3665
36. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. Application of Resp Charges to Calculate Conformational Energies, Hydrogen-Bond Energies, and Free-Energies of Solvation J. Am. Chem. Soc. 1993, 115, 9620-9631
37. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges-the Resp Model J. Phys. Chem. 1993, 97, 10269-10280
38. Sako, D.; Comess, K. M.; Barone, K. M.; Camphausen, R. T.; Cumming, D. A.; Shaw, G. D. A Sulfated Peptide Segment at the Amino Terminus of PSGL-1 is Critical for P-Selectin Binding Cell 1995, 83, 323-331
39. Pouyani, T.; Seed, B. PSGL-1 Recognition of P-Selectin is Controlled by a Tyrosine Sulfation Consensus at the PSGL-1 Amino Terminus Cell 1995, 83, 333-343
40. Im, W. P.; Lee, M. S.; Brooks, C. L. Generalized Born Model with a Simple Smoothing Function J. Comput. Chem. 2003, 24, 1691-1702
41. Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Electrostatics of Nanosystems: Application to Microtubules and the Ribosome Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037-10041
42. Rabenstein, B.; Knapp, E. W. Problems Evaluating Energetics of Electron Transfer from QA to QB: The Light Exposed and Dark-Adapted Bacterial Reaction Center ACS Symp. Ser. 2004, 883, 71-92
43. Gamiz-Hernandez, A. P.; Kieseritzky, G.; Galstyan, A. S.; Demir-Kavuk, O.; Knapp, E. W. Understanding Properties of Cofactors in Proteins: Redox Potentials of Synthetic Cytochromes b ChemPhysChem 2010, 11, 1196-1206
44. Aqvist, J. Ion Water Interaction Potentials Derived from Free-Energy Perturbation Simulations J. Phys. Chem. 1990, 94, 8021-8024
45. Wild, M. K.; Huang, M. C.; Schulze-Horsel, U.; van der Merwe, P. A.; Vestweber, D. Affinity, Kinetics, and Thermodynamics of E-Selectin Binding to E-Selectin Ligand-1 J. Biol. Chem. 2001, 276, 31602-31612
46. Kieseritzky, G.; Knapp, E. W. Charge Transport in the ClC-Type Chloride-Proton Anti-Porter from Escherichia Coli J. Biol. Chem. 2011, 286, 2976-2986
47. Wedepohl, S.; Kaup, M.; Riese, S. B.; Berger, M.; Dernedde, J.; Tauber, R.; Blanchard, V. N-Glycan Analysis of Recombinant L-Selectin Reveals Sulfated GalNAc and GalNAc-GalNAc Motifs J. Proteome Res. 2010, 9, 3403-3411
48. Knibbs, R. N.; Craig, R. A.; Maly, P.; Smith, P. L.; Wolber, F. M.; Faulkner, N. E.; Lowe, J. B.; Stoolman, L. M. Alpha(1,3)-Fucosyltransferase VII-Dependent Synthesis of P- and E-Selectin Ligands on Cultured T Lymphoblasts J. Immunol. 1998, 161, 6305-6315
49. Maly, P.; Thall, A.; Petryniak, B.; Rogers, C. E.; Smith, P. L.; Marks, R. M.; Kelly, R. J.; Gersten, K. M.; Cheng, G.; Saunders, T. L. The Alpha(1,3)Fucosyltransferase Fuc-TVII Controls Leukocyte Trafficking Through an Essential Role in L-, E-, and P-Selectin Ligand Biosynthesis Cell 1996, 86, 643-653
50. Erdmann, I.; Scheidegger, E. P.; Koch, F. K.; Heinzerling, L.; Odermatt, B.; Burg, G.; Lowe, J. B.; Kundig, T. M. Fucosyltransferase VII-Deficient Mice with Defective E-, P-, and L-Selectin Ligands Show Impaired CD4+ and CD8+ T Cell Migration into the Skin, But Normal Extravasation into Visceral Organs J. Immunol. 2002, 168, 2139-2146
51. Zhang, X.; Bogorin, D. F.; Moy, V. T. Molecular basis of the dynamic strength of the sialyl Lewis X - selectin interaction ChemPhysChem 2004, 5, 175-182
52. Enders, S.; Bernhard, G.; Zakrzewicz, A.; Tauber, R. Inhibition of L-Selectin Binding by Polyacrylamide-Based Conjugates Under Defined Flow Conditions Biochim. Biophys. Acta 2007, 1770, 1441-1449
53. Leppänen, A.; Yago, T.; Otto, V. I.; McEver, R. P.; Cummings, R. D. Model Glycosulfopeptides from P-Selectin Glycoprotein Ligand-1 Require Tyrosine Sulfation and a Core 2-Branched O-Glycan to Bind to L-Selectin J. Biol. Chem. 2003, 278, 26391-26400
54. Ullmann, G. M.; Knapp, E. W. Electrostatic Models for Computing Protonation and Redox Equilibria in Proteins Eur. Biophys. J. 1999, 28, 533-551
55. Enders, S.; Riese, S. B.; Bernhard, G.; Dernedde, J.; Reutter, W.; Tauber, R. Binding Activity of Recombinant Human L-Selectin-Fc(gamma) is Modified by Sialylation Biochem. Eng. J. 2010, 48, 253-259
56. Papp, I.; Dernedde, J.; Enders, S.; Haag, R. Modular Synthesis of Multivalent Glycoarchitectures and Their Unique Selectin Binding Behavior Chem. Commun. 2008, 5851-5853