Conformations of myoglobin-derived peptides at the air-water interface

Langmuir

Volumn 32, Issue 18, 2016, Pages 4405-4414

  Cheung, David L ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

AIR; BIOINFORMATICS; EMULSIFICATION; OILS AND FATS; PEPTIDES;

AIR WATER INTERFACES; CONFORMATIONAL CHANGE; LIQUID INTERFACE; MOLECULAR SIMULATIONS; NATIVE ENVIRONMENT; OIL WATER INTERFACES; PROTEIN STRUCTURES; SOLUTION CONFORMATIONS;

PHASE INTERFACES;

MYOGLOBIN; PEPTIDE FRAGMENT; WATER;

AIR; CHEMISTRY; MOLECULAR MODEL; PROTEIN SECONDARY STRUCTURE; SURFACE PROPERTY;

AIR; MODELS, MOLECULAR; MYOGLOBIN; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, SECONDARY; SURFACE PROPERTIES; WATER;

EID: 85002822681     PISSN: 07437463     EISSN: 15205827     Source Type: Journal    
DOI: 10.1021/acs.langmuir.5b04619     Document Type: Review

References (65)

1. Yano, Y. F. Kinetics of protein unfolding at interfaces. J. Phys.: Condens. Matter 2012, 24, 503101.
2. Linder, M. B. Hydrophobins: Proteins that self assemble at interfaces. Curr. Opin. Colloid Interface Sci. 2009, 14, 356-363.
3. Mackenzie, C. D.; Smith, B. O.; Meister, A.; Blume, A.; Zhao, X.; Lu, J. R.; Kennedy, M. W.; Cooper, A. Ranaspumin-2: structure and function of a surfactant protein from the foam nests of a tropical frog. Biophys. J. 2009, 96, 4984-92.
4. Vance, S. J.; Mcdonald, R. E.; Cooper, A.; Smith, B. O.; Kennedy, M. W. The structure of latherin, a surfactant allergen protein from horse sweat and saliva. J. R. Soc., Interface 2013, 10, 20130453.
5. Reis, P.; Holmberg, K.; Watzke, H.; Leser, M. E.; Miller, R. Lipases at interfaces: a review. Adv. Colloid Interface Sci. 2009, 147-148, 237-250.
6. Dickinson, E. Colloid science of mixed ingredients. Soft Matter 2006, 2, 642.
7. DeGrado, W.; Lear, J. Induction of peptide conformation at apolar water interfaces. 1. A study with model peptides of defined hydrophobic periodicity. J. Am. Chem. Soc. 1985, 107, 7684-7689.
8. Dexter, A. F.; Malcolm, A. S.; Middelberg, A. P. J. Reversible active switching of the mechanical properties of a peptide film at a fluid-fluid interface. Nat. Mater. 2006, 5, 502-6.
9. Gidalevitz, D.; Huang, Z.; Rice, S. A. Protein folding at the air-water interface studied with X-ray reflectivity. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 2608-11.
10. Zhao, X.; Pan, F.; Lu, J. R. Interfacial assembly of proteins and peptides: recent examples studied by neutron reflection. J. R. Soc., Interface 2009, 6,S659-70.
11. Husband, F. A.; Garrood, M. J.; Mackie, A. R.; Burnett, G. R.; Wilde, P. J. Adsorbed protein secondary and tertiary structures by circular dichroism and infrared spectroscopy with refractive index matched emulsions. J. Agric. Food Chem. 2001, 49, 859-866.
12. Miles, A. J.; Wallace, B. A. Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics. Chem. Soc. Rev. 2006, 35, 39-51.
13. Zhai, J. L.; Day, L.; Aguilar, M.-I.; Wooster, T. J. Protein folding at emulsion oil/water interfaces. Curr. Opin. Colloid Interface Sci. 2013, 18, 257-271.
14. Day, L.; Zhai, J.; Xu, M.; Jones, N. C.; Hoffmann, S. V.; Wooster, T. J. Conformational changes of globular proteins adsorbed at oil-in-water emulsion interfaces examined by Synchrotron Radiation Circular Dichroism. Food Hydrocolloids 2014, 34, 78-87.
15. Euston, S. R.; Hughes, P.; Naser, M. A.; Westacott, R. E. Comparison of the adsorbed conformation of barley lipid transfer protein at the decane-water and vacuum-water interface: a molecular dynamics simulation. Biomacromolecules 2008, 9, 1443-53.
16. Euston, S. R. Molecular simulation of adsorption of hydrophobin HFBI to the air-water, DPPC-water and decane-water interfaces. Food Hydrocolloids 2014, 42, 66-74.
17. Dalgicdir, C.; Globisch, C.; Peter, C.; Sayar, M. Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces. PLoS Comput. Biol. 2015, 11, e1004328.
18. Zare, D.; McGrath, K. M.; Allison, J. R. Deciphering β-Lactoglobulin Interactions at an Oil-Water Interface: A Molecular Dynamics Study. Biomacromolecules 2015, 16, 1855-1861.
19. Euston, S. R. Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models. Biomacromolecules 2010, 11, 2781-7.
20. Cheung, D. L. Molecular simulation of hydrophobin adsorption at an oil-water interface. Langmuir 2012, 28, 8730-6.
21. Schulz, A.; Fioroni, M.; Linder, M. B.; Nessel, A.; Bocola, M.; Subkowski, T.; Schwaneberg, U.; Böker, A.; Rodríguez-Ropero, F. Exploring the mineralization of hydrophobins at a liquid interface. Soft Matter 2012, 8, 11343-11352.
22. James, J. J.; Lakshmi, B. S.; Seshasayee, A. S. N.; Gautam, P. Activation of Candida rugosa lipase at alkane-aqueous interfaces: a molecular dynamics study. FEBS Lett. 2007, 581, 4377-83.
23. Xue, Y.; He, L.; Middelberg, A. P. J.; Mark, A. E.; Poger, D. Determining the Structure of Interfacial Peptide Films: Comparing Neutron Reflectometry and Molecular Dynamics Simulations. Langmuir 2014, 30, 10080.
24. Iglesias-Fernández, J.; Darré, L.; Kohlmeyer, A.; Thomas, R. K.; Shen, H.-H.; Domene, C. Surfactin at the Water/Air Interface and in Solution. Langmuir 2015, 31, 11097-11104.
25. Trodler, P.; Schmid, R. D.; Pleiss, J. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC Struct. Biol. 2009, 9, 38.
26. Sugita, Y.; Okamoto, Y. Replica exchange molecular dynamics method for protein folding simulation. Chem. Phys. Lett. 1999, 314, 141-151.
27. Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120, 11919-11929.
28. De Simone, A.; Kitchen, C.; Kwan, A. H.; Sunde, M.; Dobson, C. M.; Frenkel, D. Intrinsic disorder modulates protein self-assembly and aggregation. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 6951-6956.
29. Deighan, M.; Pfaendtner, J. Exhaustively Sampling Peptide Adsorption with Metadynamics. Langmuir 2013, 29, 7999-8009.
30. Levine, Z. A.; Fischer, S. A.; Shea, J. E.; Pfaendtner, J. Trp-Cage Folding on Organic Surfaces. J. Phys. Chem. B 2015, 119, 10417-10425.
31. Watson, H. C. The Stereochemistry of the Protein Myoglobin. Prog. Stereochem. 1969, 4, 299.
32. Poon, S.; Clarke, A. E.; Schultz, C. J. Structure-function analysis of the emulsifying and interfacial properties of apomyoglobin and derived peptides. J. Colloid Interface Sci. 1999, 213, 193-203.
33. Sankaranarayanan, K.; Dhathathreyan, A.; Krägel, J.; Miller, R. Interfacial viscoelasticity of myoglobin at air/water and air/solution interfaces: Role of folding and clustering. J. Phys. Chem. B 2012, 116, 895-902.
34. Holt, S. A.; McGillivray, D. J.; Poon, S.; White, J. W. Protein Deformation and Surfactancy at an Interface. J. Phys. Chem. B 2000, 104, 7431-7438.
35. Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982, 157, 105-132.
36. Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.; Wilkins, M.; Appel, R.; A, B. Protein Identification and Analysis Tools on the ExPASy Server. The Proteomics Protocols Handbook 2005, 571-601.
37. Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 13749-54.
38. Bussi, G. Hamiltonian replica exchange in GROMACS: a flexible implementation. Mol. Phys. 2014, 112, 379-384.
39. Abrams, C.; Bussi, G. Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. Entropy 2014, 16, 163-199.
40. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, flexible, and free. J. Comput. Chem. 2005, 26, 1701-1718.
41. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 2008, 4, 435-447.
42. Tribello, G. A.; Bonomi, M.; Branduardi, D.; Camilloni, C.; Bussi, G. PLUMED 2: New feathers for an old bird. Comput. Phys. Commun. 2014, 185, 604-613.
43. Schmid, N.; Eichenberger, A. P.; Choutko, A.; Riniker, S.; Winger, M.; Mark, A. E.; Van Gunsteren, W. F. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur. Biophys. J. 2011, 40, 843-856.
44. Berendsen, H.; Grigera, J. R.; Straatsma, T. P. The missing term in effective pair potentials. J. Phys. Chem. 1987, 91, 6269-6271.
45. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103, 8577.
46. Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 2007, 126, 014101.
47. 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.
48. Michaud-Agrawal, N.; Denning, E. J.; Woolf, T. B.; Beckstein, O. MDAnalysis: A Toolkit for the Analysis of MolecularDynamics Simulations. J. Comput. Chem. 2011, 32, 2319-2327.
49. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; Van Gunsteren, W. F.; Mark, A. E. Peptide Folding: When Simulation Meets Experiment. Angew. Chem., Int. Ed. 1999, 38, 236-240.
50. Vink, R. L. C.; Horbach, J.; Binder, K. Capillary waves in a colloid-polymer interface. J. Chem. Phys. 2005, 122, 134905.
51. Radzicka, A.; Wolfenden, R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 1988, 27, 1664-1670.
52. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graphics 1996, 14, 33-38.
53. Frishman, D.; Argos, P. Knowledge-based protein secondary structure assignment. Proteins: Struct., Funct., Genet. 1995, 23, 566-579.
54. Park, S.; Schulten, K. Calculating potentials of mean force from steered molecular dynamics simulations. J. Chem. Phys. 2004, 120, 5946-61.
55. Fiorin, G.; Klein, M. L.; Hénin, J. Using collective variables to drive molecular dynamics simulations. Mol. Phys. 2013, 111, 3345-3362.
56. Laio, A.; Gervasio, F. L. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep. Prog. Phys. 2008, 71, 126601.
57. Hirst, J. D.; Brooks, C. L. Molecular Dynamics Simulations of Isolated Helixes of Myoglobin. Biochemistry 1995, 34, 7614-7621.
58. Vega, C.; de Miguel, E. Surface tension of the most popular models of water by using the test-area simulation method. J. Chem. Phys. 2007, 126, 154707.
59. Zhai, J.; Hoffmann, S. V.; Day, L.; Lee, T.-H.; Augustin, M. A.; Aguilar, M.-I.; Wooster, T. J. Conformational changes of α-lactalbumin adsorbed at oil-water interfaces: interplay between protein structure and emulsion stability. Langmuir 2012, 28, 2357-67.
60. Zhai, J.; Miles, A. J.; Pattenden, L. K.; Lee, T.-H.; Augustin, M. A.; Wallace, B. A.; Aguilar, M.-I.; Wooster, T. J. Changes in beta-lactoglobulin conformation at the oil/water interface of emulsions studied by synchrotron radiation circular dichroism spectroscopy. Biomacromolecules 2010, 11, 2136-42.
61. Wijesinha-Bettoni, R.; Gao, C.; Jenkins, J. A.; Mackie, A. R.; Wilde, P. J.; Mills, E. N. C.; Smith, L. J. Heat treatment of bovine α-lactalbumin results in partially folded, disulfide bond shuffled states with enhanced surface activity. Biochemistry 2007, 46, 9774-9784.
62. Gao, C.; Wijesinha-Bettoni, R.; Wilde, P. J.; Mills, E. N. C.; Smith, L. J.; Mackie, A. R. Surface Properties Are Highly Sensitive to Small pH Induced Changes in the 3-D Structure of α-Lactalbumin. Biochemistry 2008, 47, 1659-1666.
63. van Gunsteren, W. F.; Daura, X.; Mark, A. E. Encyclopedia of Computational Chemistry; John Wiley & Sons, Ltd, 2002.
64. Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25, 1656-1676.
65. Sakakibara, K.; Fujisawa, T.; Hill, J. P.; Ariga, K. Conformational interchange of a carbohydrate by mechanical compression at the air-water interface. Phys. Chem. Chem. Phys. 2014, 16, 10286-94.