Density functional theory study on the cross-linking of mussel adhesive proteins

Journal of Physical Chemistry B

Volumn 119, Issue 17, 2015, Pages 5496-5504

  Matin, Mohammad A ^a   Chitumalla, Ramesh Kumar ^a   Lim, Manho ^a   Gao, Xingfa ^b   Jang, Joonkyung ^a  

^a Pusan National University   (South Korea)

^b INSTITUTE OF HIGH ENERGY PHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COORDINATION REACTIONS; IRON COMPOUNDS; LIGANDS; MECHANICAL PROPERTIES; METAL IONS; METALS; MOLLUSCS; PROTEINS; TRANSITION METAL COMPOUNDS; TRANSITION METALS;

COORDINATION COMPLEX; COVALENT CROSSLINKING; DENSITY FUNCTIONAL THEORY STUDIES; MOLECULAR ORIGINS; MUSSEL ADHESIVE PROTEINS; PHYSISORPTION ENERGY; POLYMERIC LIGANDS; TRIVALENT METAL IONS;

DENSITY FUNCTIONAL THEORY;

ADHESIVE PROTEIN, MUSSEL; CROSS LINKING REAGENT; DOPA; LIGAND; ORGANOMETALLIC COMPOUND; PROTEIN;

CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION; PROTEIN STABILITY; QUANTUM THEORY; THERMODYNAMICS;

CROSS-LINKING REAGENTS; DIHYDROXYPHENYLALANINE; LIGANDS; MODELS, MOLECULAR; ORGANOMETALLIC COMPOUNDS; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEINS; QUANTUM THEORY; THERMODYNAMICS;

EID: 84928974324     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b01152     Document Type: Article

References (56)

1. Weisser, J. T.; Nilges, M. J.; Sever, M. J.; Wilker, J. J. Epr Investigation and Spectral Simulations of Iron-Catecholate Complexes and Iron-Peptide Models of Marine Adhesive Cross-Links Inorg. Chem. 2006, 45, 7736-7747
2. Waite, J. H.; Qin, X. Polyphosphoprotein from the Adhesive Pads of Mytilus edulis Biochemistry 2001, 40, 2887-2893
3. Mian, S. A.; Saha, L. C.; Jang, J.; Wang, L.; Gao, X.; Nagase, S. Density Functional Theory Study of Catechol Adhesion on Silica Surfaces J. Phys. Chem. C 2010, 114, 20793-20800
4. Mian, S.; Gao, X.; Nagase, S.; Jang, J. Adsorption of Catechol on a Wet Silica Surface: Density Functional Theory Study Theor. Chem. Acc. 2011, 130, 333-339
5. Deming, T. J. Mussel Byssus and Biomolecular Materials Curr. Opin. Chem. Biol. 1999, 3, 100-105
6. Lee, H.; Scherer, N. F.; Messersmith, P. B. Single-Molecule Mechanics of Mussel Adhesion Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 12999-13003
7. Sever, M. J.; Weisser, J. T.; Monahan, J.; Srinivasan, S.; Wilker, J. J. Metal-Mediated Cross-Linking in the Generation of a Marine-Mussel Adhesive Angew. Chem., Int. Ed. 2004, 43, 448-450
8. Avdeef, A.; Sofen, S. R.; Bregante, T. L.; Raymond, K. N. Coordination Chemistry of Microbial Iron Transport Compounds. 9. Stability Constants for Catechol Models of Enterobactin J. Am. Chem. Soc. 1978, 100, 5362-5370
9. Monahan, J.; Wilker, J. J. Specificity of Metal Ion Cross-Linking in Marine Mussel Adhesives Chem. Commun. 2003, 1672-1673
10. Holten-Andersen, N.; Harrington, M. J.; Birkedal, H.; Lee, B. P.; Messersmith, P. B.; Lee, K. Y. C.; Waite, J. H. pH-Induced Metal-Ligand Cross-Links Inspired by Mussel Yield Self-Healing Polymer Networks with near-Covalent Elastic Moduli Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 2651-2655
11. Monahan, J.; Wilker, J. J. Cross-Linking the Protein Precursor of Marine Mussel Adhesives: Bulk Measurements and Reagents for Curing Langmuir 2004, 20, 3724-3729
12. Taylor, S. W.; Waite, J. H.; Ross, M. M.; Shabanowitz, J.; Hunt, D. F. trans -2,3- cis -3,4-Dihydroxyproline, a New Naturally Occurring Amino Acid, Is the Sixth Residue in the Tandemly Repeated Consensus Decapeptides of an Adhesive Protein from Mytilus Edulis J. Am. Chem. Soc. 1994, 116, 10803-10804
13. Fullenkamp, D. E.; Barrett, D. G.; Miller, D. R.; Kurutz, J. W.; Messersmith, P. B. pH-Dependent Cross-Linking of Catechols through Oxidation via Fe3+ and Potential Implications for Mussel Adhesion RSC Adv. 2014, 4, 25127-25134
14. Ceylan, H.; Urel, M.; Erkal, T. S.; Tekinay, A. B.; Dana, A.; Guler, M. O. Mussel Inspired Dynamic Cross-Linking of Self-Healing Peptide Nanofiber Network Adv. Funct. Mater. 2013, 23, 2081-2090
15. Barrett, D. G.; Fullenkamp, D. E.; He, L.; Holten-Andersen, N.; Lee, K. Y. C.; Messersmith, P. B. pH-Based Regulation of Hydrogel Mechanical Properties through Mussel-Inspired Chemistry and Processing Adv. Funct. Mater. 2013, 23, 1111-1119
16. Harrington, M. J.; Masic, A.; Holten-Andersen, N.; Waite, J. H.; Fratzl, P. Iron-Clad Fibers: A Metal-Based Biological Strategy for Hard Flexible Coatings Science 2010, 328, 216-220
17. Zhang, F.; Sababi, M.; Brinck, T.; Persson, D.; Pan, J.; Claesson, P. M. In Situ Investigations of Fe3+ Induced Complexation of Adsorbed Mefp-1 Protein Film on Iron Substrate J. Colloid Interface Sci. 2013, 404, 62-71
18. Vreven, T.; Byun, K. S.; Komáromi, I.; Dapprich, S.; Montgomery, J. A.; Morokuma, K.; Frisch, M. J. Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM J. Chem. Theory Comput. 2006, 2, 815-826
19. Singh, U. C.; Kollman, P. A. A Combined Ab Initio Quantum Mechanical and Molecular Mechanical Method for Carrying out Simulations on Complex Molecular Systems: Applications to the CH3Cl + Cl- Exchange Reaction and Gas Phase Protonation of Polyethers J. Comput. Chem. 1986, 7, 718-730
20. Zeng, H.; Hwang, D. S.; Israelachvili, J. N.; Waite, J. H. Strong Reversible Fe3+-Mediated Bridging between DOPA-Containing Protein Films in Water Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 12850-12853
21. Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652
22. Horsman, G. P.; Jirasek, A.; Vaillancourt, F. H.; Barbosa, C. J.; Jarzecki, A. A.; Xu, C.; Mekmouche, Y.; Spiro, T. G.; Lipscomb, J. D.; Blades, M. W. Spectroscopic Studies of the Anaerobic Enzyme-Substrate Complex of Catechol 1,2-Dioxygenase J. Am. Chem. Soc. 2005, 127, 16882-16891
23. Šbestík, J.; Šfařík, M.; Bouř, P. Ferric Complexes of 3-Hydroxy-4-Pyridinones Characterized by Density Functional Theory and Raman and Uv-Vis Spectroscopies Inorg. Chem. 2012, 51, 4473-4481
24. Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations J. Am. Chem. Soc. 1992, 114, 10024-10035
25. Bakowies, D.; Thiel, W. Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches J. Phys. Chem. 1996, 100, 10580-10594
26. Taylor, S. W.; Chase, D. B.; Emptage, M. H.; Nelson, M. J.; Waite, J. H. Ferric Ion Complexes of a DOPA-Containing Adhesive Protein from Mytilus Edulis Inorg. Chem. 1996, 35, 7572-7577
27. Yapo-Kicho, D.; Lagant, P.; Vergoten, G. The SPASIBA Force Field for Studying Iron-Tannins Interactions: Application to Fe3+/Fe2+ Catechol Complexe Int. J. Mol. Sci. 2007, 8, 259-272
28. Cox, D. D.; Que, L. Functional Models for Catechol 1,2-Dioxygenase. The Role of the Iron(III) Center J. Am. Chem. Soc. 1988, 110, 8085-8092
29. Karadakov, P. B.; Morokuma, K. ONIOM as an Efficient Tool for Calculating NMR Chemical Shielding Constants in Large Molecules Chem. Phys. Lett. 2000, 317, 589-596
30. Rega, N.; Iyengar, S. S.; Voth, G. A.; Schlegel, H. B.; Vreven, T.; Frisch, M. J. Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach J. Phys. Chem. B 2004, 108, 4210-4220
31. Humbel, S.; Sieber, S.; Morokuma, K. The IMOMO Method: Integration of Different Levels of Molecular Orbital Approximations for Geometry Optimization of Large Systems: Test for n -Butane Conformation and SN2 Reaction: RCl+Cl- J. Chem. Phys. 1996, 105, 1959-1967
32. Vreven, T.; Morokuma, K. Investigation of the S0-S1 Excitation in Bacteriorhodopsin with the Oniom(MO:MM) Hybrid Method Theor. Chem. Acc. 2003, 109, 125-132
33. Vreven, T.; Morokuma, K. On the Application of the IMOMO (Integrated Molecular Orbital + Molecular Orbital) Method J. Comput. Chem. 2000, 21, 1419-1432
34. Derat, E.; Bouquant, J.; Humbel, S. On the Link Atom Distance in the ONIOM Scheme. An Harmonic Approximation Analysis J. Mol. Struct.: THEOCHEM 2003, 632, 61-69
35. Théry, V.; Rinaldi, D.; Rivail, J.-L.; Maigret, B.; Ferenczy, G. G. Quantum Mechanical Computations on Very Large Molecular Systems: The Local Self-Consistent Field Method J. Comput. Chem. 1994, 15, 269-282
36. Frisch, M. J.; T, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, revision B.01; Gaussian, Inc.: Wallingford, CT, 2010.
37. Myradalyyev, S.; Limpanuparb, T.; Wang, X.; Hirao, H. Comparative Computational Analysis of Binding Energies between Several Divalent First-Row Transition Metals (Cr2+, Mn2+, Fe2+, Co2+, Ni2+, and Cu2+) and Ligands (Porphine, Corrin, and Tmc) Polyhedron 2013, 52, 96-101
38. Boys, S. F.; Bernardi, F. The Calculation of Small Molecular Interactions by the Differences of Separate Total Energies. Some Procedures with Reduced Errors Mol. Phys. 1970, 19, 553-566
39. Merrick, J. P.; Moran, D.; Radom, L. An Evaluation of Harmonic Vibrational Frequency Scale Factors J. Phys. Chem. A 2007, 111, 11683-11700
40. Furche, F.; Burke, K. In Annual Reports in Computational Chemistry; David, C. S., Ed.; Elsevier: New York, 2005; Vol. 1, pp 19-30.
41. Yanai, T.; Tew, D. P.; Handy, N. C. A New Hybrid Exchange-Correlation Functional Using the Coulomb-Attenuating Method (CAM-B3LYP) Chem. Phys. Lett. 2004, 393, 51-57
42. Raymond, K. N.; Isied, S. S.; Brown, L. D.; Fronczek, F. R.; Nibert, J. H. Coordination Isomers of Biological Iron Transport Compounds. VI. Models of the Enterobactin Coordination Site. A Crystal Field Effect in the Structure of Potassium Tris(catecholato)chromate(III) and -Ferrate(III) Sesquihydrates, K3[M(O2C6H4)3]·1.5H2O, M = Chromium, Iron J. Am. Chem. Soc. 1976, 98, 1767-1774
43. Öhrström, L.; Michaud-Soret, I. Fe-Catecholate and Fe-Oxalate Vibrations and Isotopic Substitution Shifts from Dft Quantum Chemistry J. Phys. Chem. A 1999, 103, 256-264
44. Ros, P.; Schuit, G. C. A. Molecular Orbital Calculations on Copper Chloride Complexes Theor. Chim. Acta 1966, 4, 1-12
45. Salama, S.; Stong, J. D.; Neilands, J. B.; Spiro, T. G. Electronic and Resonance Raman Spectra of Iron(III) Complexes of Enterobactin, Catechol, and N -Methyl-2,3-dihydroxybenzamide Biochemistry 1978, 17, 3781-3785
46. Aakesson, R.; Pettersson, L. G. M.; Sandstroem, M.; Wahlgren, U. Ligand Field Effects in the Hydrated Divalent and Trivalent Metal Ions of the First and Second Transition Periods J. Am. Chem. Soc. 1994, 116, 8691-8704
47. Yang, Y.; Ratner, M. A.; Schatz, G. C. Multireference Ab Initio Study of Ligand Field D-D Transitions in Octahedral Transition-Metal Oxide Clusters J. Phys. Chem. C 2014, 118, 29196-29208
48. Reed, A. E.; Weinstock, R. B.; Weinhold, F. Natural Population Analysis J. Chem. Phys. 1985, 83, 735-746
49. Singh, U. C.; Kollman, P. A. An Approach to Computing Electrostatic Charges for Molecules J. Comput. Chem. 1984, 5, 129-145
50. Breneman, C. M.; Wiberg, K. B. Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis J. Comput. Chem. 1990, 11, 361-373
51. Chirlian, L. E.; Francl, M. M. Atomic Charges Derived from Electrostatic Potentials: A Detailed Study J. Comput. Chem. 1987, 8, 894-905
52. Hu, H.; Lu, Z.; Yang, W. Fitting Molecular Electrostatic Potentials from Quantum Mechanical Calculations J. Chem. Theory Comput. 2007, 3, 1004-1013
53. Vega-Arroyo, M.; LeBreton, P. R.; Rajh, T.; Zapol, P.; Curtiss, L. A. Density Functional Study of the TiO2-Dopamine Complex Chem. Phys. Lett. 2005, 406, 306-311
54. Barone, V.; Cossi, M. Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model J. Phys. Chem. A 1998, 102, 1995-2001
55. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V. Energies, Structures, and Electronic Properties of Molecules in Solution with the C-PCM Solvation Model J. Comput. Chem. 2003, 24, 669-681
56. Tomasi, J.; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models Chem. Rev. 2005, 105, 2999-3094