Mechanism of Enhancing Antifreeze Protein Activity by Low Molecular Mass Molecules

doi:10.19894/j.issn.1000-0518.210018

Chinese Journal of Applied Chemistry ›› 2021, Vol. 38 ›› Issue (12): 1612-1620.DOI: 10.19894/j.issn.1000-0518.210018

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Mechanism of Enhancing Antifreeze Protein Activity by Low Molecular Mass Molecules

DING Ya-Li¹, HU Xiang-Xiang¹, FENG Xuan^2,3, ZHANG Ran^2*, SHI Tong-Fei^2,3*, WEI Lai¹

¹(Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China)
²(State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China)
³(School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China)

Received:2021-01-10 Revised:2021-03-26 Published:2021-12-01 Online:2022-02-01
Supported by:
National Natural Science Foundation of China(No.21604086)

Abstract

Abstract: Antifreeze proteins (AFPs) are able to generate a difference between the non-equilibrium freezing point and the melting point, which is called thermal hysteresis (TH). AFPs inspire the design of new materials for use in the field of food industry and biomedical applications such as cell and organ preservation. The TH activity of a specific AFP of a beetle named Dendroides canadensis (DAFP-1) can be enhanced by low molecular mass molecules such as glycerol, trehalose and citrate acid, however the mechanism remains elusive. In order to reveal the molecular mechanism of the corresponding enhancing effects, we use AutoDock4.2 software to explore the potential docking modes between DAFP-1 and these low molecular mass molecules. Through the comparison and analysis of binding energy and docking conformations, it is found that the physical mechanism of low molecular mass molecules promoting antifreeze activity is not only limited to the single site binding between Arg9 residues and low molecular mass molecules as predicted in literature, the enhancement can also happen through the combined docking sites such as Arg30 and Arg54. These new binding scenarios can promote the aggregation of multiple DAFP-1 proteins forming larger binding templates, which greatly improves the antifreeze activity of DAFP-1.

Key words: Antifreeze proteins, Arginine, Low molecular mass molecules, AutoDock

CLC Number:

O641

DING Ya-Li, HU Xiang-Xiang, FENG Xuan, ZHANG Ran, SHI Tong-Fei, WEI Lai. Mechanism of Enhancing Antifreeze Protein Activity by Low Molecular Mass Molecules[J]. Chinese Journal of Applied Chemistry, 2021, 38(12): 1612-1620.

References

[1] DEVRIE A L. Glycoproteins as biological antifreeze agents in antarctic fishes[J]. Science, 1971, 172(3988): 1152-1155.
[2] DUMAN J G. The role of macromolecular antifreeze in the darkling beetle, Meracantha contracta[J]. J Comp Physiol, 1977, 115(2): 279-286.
[3] URRUTIA M E, DUMAN J G, KNIGHT C A. Plant thermal hysteresis proteins[J]. Biochim Biophys Acta, 1992, 1121(1/2): 199-206.
[4] DUMAN J, WU D W, OLSEN T M, et al. Thermal-hysteresis proteins[J]. Adv Low-Temp Biol, 1993, 2: 131-182.
[5] MARKS S M, PATEL A J. Antifreeze protein hydration waters: unstructured unless bound to ice[J]. Proc Natl Acad Sci USA, 2018, 115(33): 8244-8246.
[6] GRABOWSKA J, KUFFEL A, ZIELKIEWIC J. Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface[J]. Phys Chem Chem Phys, 2018, 20(39): 25365-25376.
[7] HUDAIT A, ODENDAHL N, QIU Y, et al. Ice-nucleating and antifreeze proteins recognize ice through a diversity of anchored clathrate and ice-like motifs[J]. J Am Chem Soc, 2018, 140(14): 4905-4912.
[8] OUDE VRIELINK A S, ALOI A, OLIJVE L L, et al. Interaction of ice binding proteins with ice, water and ions[J]. Biointerphases, 2016, 11(1): 018906.
[9] DAVIES P L. Ice-binding proteins: a remarkable diversity of structures for stopping and starting ice growth[J]. Trends Biochem Sci, 2014, 39(11): 548-555.
[10] DUMAN J G. Antifreeze and ice nucleator proteins in terrestrial arthropods[J]. Annu Rev Physiol, 2001, 63(1): 327-357.
[11] HUDAIT A, QIU Y, ODENDAHL N, et al. Hydrogen-bonding and hydrophobic groups contribute equally to the binding of hyperactive antifreeze and ice nucleating proteins to ice[J]. J Am Chem Soc, 2019, 141(19): 7887-7898.
[12] ANDORFER C A, DUMAN J G. Isolation and characterization of cDNA clones encoding antifreeze proteins of the pyrochroid beetle Dendroides canadensis[J]. J Insect Physiol, 2000, 46(3): 365-372.
[13] WANG S, AMORNWITTAWAT N, JUWITA V, et al. Arginine, a key residue for the enhancing ability of an antifreeze protein of the beetle Dendroides canadensis[J]. Biochemistry, 2009, 48(40): 9696-9703.
[14] LIOU Y-C, TOCILJ A, DAVIES P L, et al. Mimicry of ice structure by surface hydroxyls and water of a β-helix antifreeze protein[J]. Nature, 2000, 406(6793): 322-324.
[15] GRAETHER S P, KUIPER M J, GAGNÉ S M, et al. β-Helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect[J]. Nature, 2000, 406(6793): 325-328.
[16] LEI W, DUMAN J G. Antifreeze proteins of the beetle Dendroides canadensis enhance one another′s activities[J]. Biochemistry, 2005, 44(30): 10305-10312.
[17] WU D W, DUMAN J G. Activation of antifreeze proteins from larvae of the beetle Dendroides canadensis[J]. J Comp Physiol B, 1991, 161(3): 279-283.
[18] AMORNWITTAWAT N, WANG S, BANATLAO J, et al. Effects of polyhydroxy compounds on beetle antifreeze protein activity[J]. Biochim Biophys Acta Proteins Proteom, 2009, 1794(2): 341-346.
[19] WEN X, WANG S, AMORNWITTAWAT N, et al. Interaction of reduced nicotinamide adenine dinucleotide with an antifreeze protein from Dendroides canadensis: mechanistic implication of antifreeze activity enhancement[J]. J Mol Recognit, 2011, 24(6): 1025-1032.
[20] DU N, LIU X Y, HEW C L. Aggregation of antifreeze protein and impact on antifreeze activity[J]. J Phys Chem B, 2006, 110(41): 20562-20567.
[21] MORRIS G M, HUEY R, LINDSTROM W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility[J]. J Comput Chem, 2009, 30(16): 2785-2791.
[22] MEISTER K, EBBINGHAUS S, XU Y, et al. Long-range protein-water dynamics in hyperactive insect antifreeze proteins[J]. Proc Natl Acad Sci USA, 2013, 110(5): 1617-1722.
[23] WATERHOUSE A, BERTONI M, BIENERT S, et al. Swiss-model: homology modelling of protein structures and complexes[J]. Nucleic Acids Res, 2018, 46(W1): W296-W303.
[24] 田亚利, 张聪杰. GaussView软件在分子和晶体结构模拟中的使用探究[J]. 化学教学, 2015(6): 90-93.
TIAN Y L, ZHANG C J. Investigation of the use of GaussView software in molecular and crystal structure simulation[J]. Educ Chem, 2015(6): 90-93.
[25] 韩运侠, 梁会琴, 陶亚萍, 等. 邻苯二甲酸二甲酯分子的密度泛函计算和振动光谱研究[J]. 光散射学报, 2015, 27(2): 159-66.
HAN Y X, LANG H Q, TAO Y P, et al. Density functional theroy calculations and vibrational spectra of dimethyl phthalate[J]. J Light Scattering, 2015, 27(2): 159-166.

Mechanism of Enhancing Antifreeze Protein Activity by Low Molecular Mass Molecules

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