Effect of glycosylation on hydration behavior at the ice-binding surface of the Ocean Pout type III antifreeze protein: a molecular dynamics simulation

References

• Amanai, K. J., Wang, G., Tang, J., Wang, B., & Jiang, J. (2002). Shaggy/GSK3 antagonizes Hedgehog signalling by regulating Cubitus interruptus. Nature, 416, 548–552.
   PubMed Web of Science ®Google Scholar
• Barria, A., Muller, D., Derkach, V., Griffith, L. C., & Soderlin, R. (1997). Regulatory phosphorylation of AMPA-type glutamate receptors by CaM-KII during long-term potentiation. Science, 276, 2042–2045.10.1126/science.276.5321.2042
   PubMed Web of Science ®Google Scholar
• Bohne, A., Lang, E., & Von der Lieth, C. W. (1999). SWEET–WWW-based rapid 3D construction of oligo- and polysaccharides. Bioinformatics, 15, 767–768.10.1093/bioinformatics/15.9.767
   PubMed Web of Science ®Google Scholar
• Brooks, B. R., Brooks, C. L., 3rd, Mackerell, A. D., Jr., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30, 1545–1614.10.1002/jcc.v30:10
   PubMed Web of Science ®Google Scholar
• Carlson, W. B., Sjong, A., Adam, G. A., Wan, F. (2014). Hydrophilic agents in paints. US Patent.
   Google Scholar
• Chao, H., Sjnnichsen, F. D., DeLuca, C. I., Sykes, B. D., & Davies, P. L. (1994). Structure-function relationship in the globular type III antifreeze protein: Identification of a cluster of surface residues required for binding to ice. Protein Science, 3,1760–1776.
   PubMed Web of Science ®Google Scholar
• Daniel, S. C. Y., Wai-Ching, H., Steve, B., Yiqi, X. J. S., Choy, L. H., & Frank, S. (1998). Identification of the ice-binding surface on a type III antifreeze protein with a ‘flatness function’ algorithm. Biophysical Journal, 74, 2142–2151.
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. G. (1983). Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. Chemical Physics, 98, 10089–10092.
   Google Scholar
• Davies, P. L., & Hew, C. L. (1990). Biochemistry of fish antifreeze proteins. The FASEB Journal, 4, 2460–2468.
   PubMed Web of Science ®Google Scholar
• DeVries, A. L. (1983). Antifreeze peptides and glycopeptides in cold-water fishes. Annual Review of Physiology, 45, 245–260.10.1146/annurev.ph.45.030183.001333
   PubMed Web of Science ®Google Scholar
• DeVries, P. J. (1986). Hostplant records and natural history notes on Costa Rican butterflies (Papilionidae, Pieridae & NAymphalidae. Journal of Research on the Lepidoptera, 24, 290–333.
   Google Scholar
• DeVries, A. L., & Wohlschlag, D. E. (1969). Freezing resistance in some Antarctic fishes. Science, 163, 1074–1075.
   Web of Science ®Google Scholar
• Duman, R. S., Nakagawa, S., & Malberg, J. (2001). Regulation of adult neurogenesis by antidepressant treatment. Neuropsychopharmacology, 25, 836–844.10.1016/S0893-133X(01)00358-X
   PubMed Web of Science ®Google Scholar
• Duman, J. G., & Olsen, T. M. (1993). Thermal hysteresis protein activity in bacteria, fungi, and phylogenetically diverse plants. Cryobiology, 30, 322–328.10.1006/cryo.1993.1031
   Web of Science ®Google Scholar
• Foloppe, N., Nilsson, L., Jr, & MacKerell, A. D. (2001). Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics. Biopolymers, 61, 61–76.10.1002/(ISSN)1097-0282
   PubMed Web of Science ®Google Scholar
• Gourdine, J. P., Cioci, G., Miguet, L., Unverzagt, C., Silva, D. V., Varrot, A., & Gautier, C. (2008). High affinity interaction between a bivalve C-type lectin and a biantennary complex-type N-glycan revealed by crystallography and microcalorimetry. Journal of Biological Chemistry, 283, 30112–30120.10.1074/jbc.M804353200
   PubMed Web of Science ®Google Scholar
• Graether, S. P., Kuiper, M. J., Gagne, S. M., Walker, V. K., Jia, Z., Sykes, B. D., & Davies, P. L. (2000). Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect. Nature, 406, 325–328.
   PubMed Web of Science ®Google Scholar
• Graham, L. A., Liou, Y. C., Walker, V. K., & Davies, P. L. (1997). Hyperactive antifreeze protein from beetles. Nature, 388, 727–728.10.1038/41908
   PubMed Web of Science ®Google Scholar
• Graham, C. A., McIlhatton, B. P., Kirk, C. W., Beattie, E. D., Lyttle, K., Hart, P., … Nicholls, D. P. (2005). Genetic screening protocol for familial hypercholesterolemia which includes splicing defects gives an improved mutation detection rate. Atherosclerosis, 182, 331–340.10.1016/j.atherosclerosis.2005.02.016
   PubMed Web of Science ®Google Scholar
• Harding, M. M., Anderberg, P. I., & Haymet, A. D. (2003). ‘Antifreeze’ glycoproteins from polar fish. European Journal of Biochemistry, 270, 1381–1392.10.1046/j.1432-1033.2003.03488.x
   PubMedGoogle Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33–38.10.1016/0263-7855(96)00018-5
   PubMed Web of Science ®Google Scholar
• Jia, Z., & Davies, P. L. (2002). Antifreeze proteins: An unusual receptor–ligand interaction. Trends in Biochemical Sciences, 27, 101–106.10.1016/S0968-0004(01)02028-X
   PubMed Web of Science ®Google Scholar
• Jia, Z., DeLuca, C. I., Chao, H., & Davies, P. L. (1996). Structural basis for the binding of a globular antifreeze protein to ice. Nature, 384, 285–288.10.1038/384285a0
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926–935.10.1063/1.445869
   Web of Science ®Google Scholar
• Kathryn, V. (2002). Fish antifreeze protein. Science, 86, 471.
   Google Scholar
• Knight, C. A. (2000). Adding to the antifreeze agenda. Nature, 406, 249–251.
   PubMed Web of Science ®Google Scholar
• Knight, C. A., Driggers, E., & DeVries, A. L. (1993). Adsorption to ice of fish antifreeze glycopeptides 7 and 8. Biophysical Journal, 64, 252–259.10.1016/S0006-3495(93)81361-4
   PubMed Web of Science ®Google Scholar
• Kuiper, M. J., Davies, P. L., & Walker, V. K. (2001). A theoretical model of a plant antifreeze protein from lolium perenne. Biophysical Journal, 81, 3560–3565.10.1016/S0006-3495(01)75986-3
   PubMed Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101, 4177–4189.10.1063/1.467468
   Web of Science ®Google Scholar
• Midya, U. S., & Bandyopadhyay, S. (2014). Hydration behavior at the ice-binding surface of the tenebrio molitor antifreeze protein. The Journal of Physical Chemistry B, 118, 4743–4752.10.1021/jp412528b
   PubMed Web of Science ®Google Scholar
• Nada, H., & Furukawa, Y. (2012). Antifreeze proteins: Computer simulation studies on the mechanism of ice growth inhibition. Polymer Journal, 44, 690–698.10.1038/pj.2012.13
   Web of Science ®Google Scholar
• Nutt, D. R., & Smith, J. C. (2008). Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. Journal of the American Chemical Society, 130, 13066–13073.10.1021/ja8034027
   PubMed Web of Science ®Google Scholar
• Otting, G., & Wuethrich, K. (1989). Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules. Journal of the American Chemical Society, 111, 1871–1875.10.1021/ja00187a050
   Web of Science ®Google Scholar
• Pertaya, N., Marshall, C. B., DiPrinzio, C. L., Wilen, L., Thomson, E. S., Wettlaufer, J. S., … Braslavsky, I. (2007). Fluorescence microscopy evidence for quasi-permanent attachment of antifreeze proteins to ice surfaces. Biophysical Journal, 92, 3663–3673.10.1529/biophysj.106.096297
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. J. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26, 1781–1802.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Raymond, J. A., Wilson, P., & DeVries, A. L. (1989). Inhibition of growth of nonbasal planes in ice by fish antifreezes. Proceedings of the National Academy of Sciences, 86, 881–885.10.1073/pnas.86.3.881
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Sharpton, V. L., Brent Dalrymple, G., Marín, L. E., Ryder, G., Schuraytz, B. C., & Urrutia-Fucugauchi, J. U. (1992). New links between the Chicxulub impact structure and the Cretaceous/Tertiary boundary. Nature, 359, 819–821.10.1038/359819a0
   Web of Science ®Google Scholar
• Sidebottom, C., Buckley, S., Pudney, P., Twigg, S., Jarman, C., Holt, C., … Lillford, P. (2000). Phytochemistry. Heat-stable antifreeze protein from grass. Nature, 406, 256.
   PubMed Web of Science ®Google Scholar
• Smolin, N., & Daggett, V. (2008). Formation of ice-like water structure on the surface of an antifreeze protein. The Journal of Physical Chemistry B, 112, 6193–6202.10.1021/jp710546e
   PubMed Web of Science ®Google Scholar
• Sonnichsen, F. D., Sykes, B. D., Chao, H., & Davies, P. L. (1993). The nonhelical structure of antifreeze protein type III. Science, 259, 1154–1157.10.1126/science.8438165
   PubMed Web of Science ®Google Scholar
• Sun, T., Gauthier, S. Y., Campbell, R. L., & Davies, P. L. (2015). Revealing surface waters on an antifreeze protein by fusion protein crystallography combined with molecular dynamic simulations. The Journal of Physical Chemistry B, 119, 12808–12815.10.1021/acs.jpcb.5b06474
   PubMed Web of Science ®Google Scholar
• Tachibana, Y., Fletcher, G. L., Fujitani, N., Tsuda, S., Monde, K., & Nishimura, S. I. (2004). Antifreeze glycoproteins: Elucidation of the structural motifs that are essential for antifreeze activity. Angewandte Chemie International Edition, 43, 856–862.10.1002/(ISSN)1521-3773
   PubMed Web of Science ®Google Scholar
• Tomchaney, A. P., Morris, J. P., Kang, S. H., & Duman, J. G. (1982). Purification, composition, and physical properties of a thermal hysteresis ‘antifreeze’ protein from larvae of the beetle Tenebrio molitor. Biochemistry, 21, 716–721.10.1021/bi00533a020
   PubMed Web of Science ®Google Scholar
• Vries, W. D., Willemina, M. C., Kapteijn, E. G., & Van Der Beek, A. H. (1970). Molar growth yields and fermentation balances of lactobacillus casei L3 in batch cultures and in continuous cultures. Microbiology, 63, 333–345.
   Web of Science ®Google Scholar
• Wierzbicki, A., Dalal, P., Cheatham, T. E., Knickelbein, J. E., Haymet, A. D. J., & Maduraz, J. D. Antifreeze proteins at the ice/water interface: Three calculated discriminating properties for orientation of type I proteins. Biophysical Journal, 93,1442–1451.
   PubMed Web of Science ®Google Scholar
• Wilson, P. W. (1993). Explaining thermal hysteresis by the Kelvin effect. Cryoletters, 14, 31–36.
   Google Scholar
• Worrall, F., Wooff, D. A., & McIntyre, P. A. (2013). simple modelling approach for water quality: The example of an estuarine impoundment. Science of the Total Environment, 219, 41–51.
   Google Scholar
• Yang, D. S. C. (1993). Protein–ice interactions: Antifreeze proteins. The amphipathic helix. Boca Raton, FL: CRC Press.
   Google Scholar
• Yeh, Y., & Feeney, R. E. (1996). Antifreeze proteins:  Structures and mechanisms of function. Chemical Reviews, 96, 601–618.10.1021/cr950260c
   PubMed Web of Science ®Google Scholar