Silk fibroin hydrogel not only has biocompatibility, but also has environmental response ability. It plays an important role in the development of material. The gelation mechanism of silk fibroin hydrogel is very important to textile and medicine fields. The molecular dynamics simulation was used to discuss the structure and non-bond interaction of silk fibroin hydrogel. The results show that the non-bond interactions between silk fibroin molecules and water molecules have certain influence on the formation of silk fibroin hydrogel. According to the hydrogen bond analysis, the hydrogen bonds are mainly formed between random coil peptide fragments at the two ends of silk fibroin molecules and residues 252-254 are the key residues. The electrostatic and polar solvation interactions between silk fibroin molecules plays a major role in cross-linking of the coil segments of two silk fibroin molecules.
Citation: Xuewei Jiang, Lu Zheng, Huhe Wu, Jun Zhang. Investigations into the role of non-bond interaction on gelation mechanism of silk fibroin hydrogel[J]. Mathematical Biosciences and Engineering, 2021, 18(4): 4071-4083. doi: 10.3934/mbe.2021204
Silk fibroin hydrogel not only has biocompatibility, but also has environmental response ability. It plays an important role in the development of material. The gelation mechanism of silk fibroin hydrogel is very important to textile and medicine fields. The molecular dynamics simulation was used to discuss the structure and non-bond interaction of silk fibroin hydrogel. The results show that the non-bond interactions between silk fibroin molecules and water molecules have certain influence on the formation of silk fibroin hydrogel. According to the hydrogen bond analysis, the hydrogen bonds are mainly formed between random coil peptide fragments at the two ends of silk fibroin molecules and residues 252-254 are the key residues. The electrostatic and polar solvation interactions between silk fibroin molecules plays a major role in cross-linking of the coil segments of two silk fibroin molecules.
| [1] | X. Li, S. Yan, J. Qu, M. Li, D. Ye, R. You, et al., Soft freezing-induced self-assembly of silk fibroin for tunable gelation, Int. J. Biol. Macromol., 117 (2018), 691-695. |
| [2] |
Y. X. He, N. N. Zhang, W. F. Li, N. Jia, B. Y. Chen, K. Zhou, et al., N-terminal domain of bombyx mori fibroin mediates the assembly of silk in response to pH decrease, J. Mol. Biol., 418 (2012), 197-207. doi: 10.1016/j.jmb.2012.02.040
|
| [3] |
A. E. Thurber, F. G. Omenetto, D. L. Kaplan, In vivo bioresponses to silk proteins, Biomaterials, 71 (2015), 145-157. doi: 10.1016/j.biomaterials.2015.08.039
|
| [4] |
Y. Feng, X. Li, M. Li, D Ye, Q. Zhang, R You, et al., Facile preparation of biocompatible silk fibroin/cellulose nanocomposite films with high mechanical performance, ACS Sustainable Chem. Eng., 5 (2017), 6227-6236. doi: 10.1021/acssuschemeng.7b01161
|
| [5] |
X. Li, J. Zhang, Y. Feng, S. Yan, Q. Zhang, R. You, Tuning the structure and performance of silk biomaterials by combining mulberry and non-mulberry silk fibroin, Polym. Degrad. Stab., 147 (2018), 57-63. doi: 10.1016/j.polymdegradstab.2017.11.013
|
| [6] |
H. Tao, D. L. Kaplan, F. G. Omenetto, Silk materials—a road to sustainable high technology, Adv. Mater., 24 (2012), 2824-2837. doi: 10.1002/adma.201104477
|
| [7] |
A. Motta, L. Fambri, C. Migliaresi, Regenerated silk fibroin films: Thermal and dynamic mechanical analysis, Macromol. Chem. Phys., 203 (2002), 1658-1665. doi: 10.1002/1521-3935(200207)203:10/11<1658::AID-MACP1658>3.0.CO;2-3
|
| [8] |
Z. Shao, F. Vollrath. Surprising strength of silkworm silk, Nature, 418 (2002), 741. doi: 10.1038/418741a
|
| [9] |
H. J. Kim, U. J. Kim, G. Vunjak-Novakovic, B. H. Min, D. L. Kaplan, Influence of macroporous protein scaffolds on bone tissue engineering from bone marrow stem cells, Biomaterials, 26 (2005), 4442-4452. doi: 10.1016/j.biomaterials.2004.11.013
|
| [10] |
S. Cao, R. Tang, G. Sudlow, Z. Wang, K. K. Liu, J. Luan, et al., Shape-dependent biodistribution of biocompatible silk microcapsules, ACS Appl. Mater. Interfaces, 11 (2019), 5499-5508. doi: 10.1021/acsami.8b17809
|
| [11] | J. H. Choi, D. K. Kim, J. E. Song, J. M. Oliveira, R. L. Reis, G. Khang, Silk fibroin-based scaffold for bone tissue engineering, in Novel Biomaterials for Regenerative Medicine, Springer, (2018), 371-387. |
| [12] |
N. H. Romano, D Sengupta, C. Chung, S. C. Heilshorn, Protein-engineered biomaterials: Nanoscale mimics of the extracellular matrix, Biochim. Biophys. Acta, 1810 (2011), 339-349. doi: 10.1016/j.bbagen.2010.07.005
|
| [13] | D. D. McKinnon, D. W. Domaille, T. E. Brown, K. A. Kyburz, E. Kiyotake, J. N. Cha, et al., Measuring cellular forces using bis-aliphatic hydrazone crosslinked stress-relaxing hydrogels, Soft Matter, 10 (2014), 9230-9236. |
| [14] |
R. V. Rughani, M. C. Branco, D. J. Pochan, J. P. Schneider, De novo design of a shear-thin recoverable peptide-based hydrogel capable of intrafibrillar photopolymerization, Macromolecules, 43 (2010), 7924-7930. doi: 10.1021/ma1014808
|
| [15] |
L. Yu, J. Ding, Injectable hydrogels as unique biomedical materials, Chem. Soc. Rev., 37 (2008), 1473-1481. doi: 10.1039/b713009k
|
| [16] |
S. Bai, X. Zhang, Q. Lu, W. Sheng, L. Liu, B. Dong, et al., Reversible hydrogel-solution system of silk with high beta-sheet content, Biomacromolecules, 15 (2014), 3044-3051. doi: 10.1021/bm500662z
|
| [17] |
H. Meng, J. Zheng, X. Wen, Z. Cai, J. Zhang, T. Chen, pH- and sugar-induced shape memory hydrogel based on reversible phenylboronic acid-diol ester bonds, Macromol. Rapid Commun., 36 (2015), 533-537. doi: 10.1002/marc.201400648
|
| [18] |
X. Wang, J. Kluge, G. G. Leisk, D. L. Kaplan, Sonication-induced gelation of silk fibroin for cell encapsulation, Biomaterials, 29 (2008), 1054-1064. doi: 10.1016/j.biomaterials.2007.11.003
|
| [19] | K. Mita, S. Ichimura, T. C. James, Highly repetitive structure and its organization of the silk fibroin gene, J. Mol. Evol., 38 (1994), 583-592. |
| [20] |
G. H. Altman, F. Diaz, C. Jakuba, T. Calabro, R. L. Horan, J. Chen, et al., Silk-based biomaterials, Biomaterials, 24 (2003), 401-416. doi: 10.1016/S0142-9612(02)00353-8
|
| [21] |
B. Liu, Y. Song, L. Jin, Z. Wang, D. Pu, S. Lin, et al., Silk structure and degradation, Colloids Surf. B, 131 (2015), 122-128. doi: 10.1016/j.colsurfb.2015.04.040
|
| [22] |
V. Pandey, T. Haider, P. Jain, P. N. Gupta, V. Soni, Silk as a leading-edge biological macromolecule for improved drug delivery, J. Drug Delivery Sci. Technol., 55 (2020), 101294. doi: 10.1016/j.jddst.2019.101294
|
| [23] |
C. W. P. Foo, D. L. Kaplan, Genetic engineering of fibrous proteins: spider dragline silk and collagen, Adv. Drug Delivery Rev., 54 (2002), 1131-1143. doi: 10.1016/S0169-409X(02)00061-3
|
| [24] | S. Inoue, K. Tanaka, F. Arisaka, S. Kimura, K. Ohtomo, S. Mizuno, Silk fibroin of bombyx mori is secreted, assembling a high molecular mass elementary unit consisting of H-chain, L-chain, and P25, with a 6: 6: 1 molar ratio, J. Biol. Chem., 275 (2000), 40517-40528. |
| [25] |
Z. Chen, H. Zhang, Z. Lin, Y. Lin, J. H. Esch, X. Y. Liu, Programing performance of silk fibroin materials by controlled nucleation, Adv. Funct. Mater., 26 (2016), 8978-8990. doi: 10.1002/adfm.201602908
|
| [26] |
Y. Yang, W. Wu, H. Liu, H. Xu, Y. Zhong, L. Zhang, et al. Aggregation behaviors of thermo-responsive methylcellulose in water: A molecular dynamics simulation study, J. Mol. Graphics Modell., 97 (2020), 107554. doi: 10.1016/j.jmgm.2020.107554
|
| [27] |
E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, et al., UCSF Chimera—A visualization system for exploratory research and analysis, J. Comput. Chem., 25 (2004), 1605-1612. doi: 10.1002/jcc.20084
|
| [28] |
Y. Wang, Q. Wei, S. Wang, W. Chai, Y. Zhang, Structural and water diffusion of Poly(acryl amide)/Poly(vinyl alcohol) blend films: Experiment and molecular dynamics simulations, J. Mol. Graphics Modell., 71 (2017), 40-49. doi: 10.1016/j.jmgm.2016.11.001
|
| [29] |
S. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys., 117 (1995), 1-19. doi: 10.1006/jcph.1995.1039
|
| [30] |
H. Attouch, R. Cominetti, A dynamical approach to convex minimization coupling approximation with the steepest descent method, J. Diff. Equations, 128 (1996), 519-540. doi: 10.1006/jdeq.1996.0104
|
| [31] | W. H. Press, B. P. Flannery, S. A. Teukolsky, W. T. Vetterling, P. B. Kramer, Numerical recipes, The art of scientific computing, Phys. Today, 40 (1987), 120-122. |
| [32] |
B. T. Polyak, The conjugate gradient method in extremal problems, Ussr Comput. Math. Math. Phys., 9 (1969), 94-112. doi: 10.1016/0041-5553(69)90035-4
|
| [33] |
V. Krä utler, W. F. Van Gunsteren, P. H. Hünenberger, A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations, J. Comput. Chem., 22 (2001), 501-508. doi: 10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V
|
| [34] |
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. R. Haak, Molecular-dynamics with coupling to an external bath, J. Chem. Phys., 81 (1984), 3684-3690. doi: 10.1063/1.448118
|
| [35] |
S. E. Feller, Y. Zhang, R. W. Pastor, Constant pressure molecular dynamics simulation: The Langevin piston method, J. Chem. Phys., 103 (1995), 4613-4621. doi: 10.1063/1.470648
|
| [36] |
J. A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K. E. Hauser, C. Simmerling, ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB, J. Chem. Theory Comput., 11 (2015), 3696-3713. doi: 10.1021/acs.jctc.5b00255
|
| [37] |
M. P. Eastwood, C. Hardin, Z. Luthey-Schulten, P. G. Wolynes, Evaluating protein structure-prediction schemes using energy landscape theory, IBM J. Res. Dev., 45 (2001), 475-497. doi: 10.1147/rd.453.0475
|
| [38] |
H. Zhao, Y. Li, A novel pH/temperature-responsive hydrogel based on tremella polysaccharide and poly(N-isopropylacrylamide), Colloids Surf. A, 586 (2020), 124270. doi: 10.1016/j.colsurfa.2019.124270
|
| [39] |
S. Mathesan, A. Rath, P. Ghosh, Molecular mechanisms in deformation of cross-linked hydrogel nanocomposite, Mater. Sci. Eng. C, 59 (2016), 157-167. doi: 10.1016/j.msec.2015.09.087
|
| [40] |
S. G. Lee, G. F. Brunello, S. S. Jang, D. G. Bucknall, Molecular dynamics simulation study of P (VP-co-HEMA) hydrogels: effect of water content on equilibrium structures and mechanical properties, Biomaterials, 30 (2009), 6130-6141. doi: 10.1016/j.biomaterials.2009.07.035
|
| [41] |
R. E. Marsh, R. B. Corey, L. Pauling, An investigation of the structure of silk fibroin, Biochim. Biophys. Acta, 16 (1955), 1-34. doi: 10.1016/0006-3002(55)90178-5
|
| [42] |
G. Freddi, P. Monti, M. Nagura, Y. Gotoh, M. Tsukada, Structure and molecular conformation of tussah silk fibroin films: Effect of heat treatment, J. Polym. Sci. Part B, 35 (1997), 841-847. doi: 10.1002/(SICI)1099-0488(19970415)35:5<841::AID-POLB13>3.0.CO;2-A
|
| [43] |
M. Tsukada, G. Freddi, N. Kasai, P. Monti, Structure and molecular conformation of tussah silk fibroin films treated with water-methanol solutions: Dynamic mechanical and thermomechanical behavior, J. Polym. Sci. Part B, 36 (1998), 2717-2724. doi: 10.1002/(SICI)1099-0488(19981115)36:15<2717::AID-POLB5>3.0.CO;2-O
|
| [44] |
W. R. Taylor, The classification of amino acid conservation, J. Theor. Biol., 119 (1986), 205-218. doi: 10.1016/S0022-5193(86)80075-3
|
| [45] |
J. W. West, D. E. Patton, T. Scheuer, Y. Wang, A. L. Goldin, W. A. Catterall, A cluster of hydrophobic amino acid residues required for fast Na(+)-channel inactivation, Proc. Natl. Acad. Sci., 89 (1992), 10910-10914. doi: 10.1073/pnas.89.22.10910
|
| [46] |
J. L. Regier, F. Shen, S. J. Triezenberg, Pattern of aromatic and hydrophobic amino acids critical for one of two subdomains of the VP16 transcriptional activator, Proc. Natl. Acad. Sci., 90 (1993), 883-887. doi: 10.1073/pnas.90.3.883
|
| [47] | J. Yu, H. K. Chan, T. Gengenbach, J. A Denman, Protection of hydrophobic amino acids against moisture-induced deterioration in the aerosolization performance of highly hygroscopic spray-dried powders, Eur. J. Pharm. Biopharm., 119 (2017), 224-234. |
| [48] |
K. Chen, Y. Jiang, L. Du, L. Kurgan, Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs, J. Comput. Chem., 30 (2009), 163-172. doi: 10.1002/jcc.21053
|
| [49] | A. T. Zikri, H. D. Pranowo, W. Haryadi, Stability, hydrogen bond occupancy analysis and binding free energy calculation from flavonol docked in DAPK1 active site using molecular dynamic simulation approaches, Indones. J. Chem., 21 (2021). |
| [50] |
C. H. Görbitz, Hydrogen-bond distances and angles in the structures of amino acids and peptides, Acta Crystallogr. Sec. B, 45 (1989), 390-395. doi: 10.1107/S0108768189003666
|
| [51] |
B. R. Miller, T. D. McGee, J. M. Swails, N. Homeyer, H. Gohlke, A. E. Roitberg, MMPBSA.py: An efficient program for end-state free energy calculations, J. Chem. Theory Comput., 8 (2012), 3314-3321. doi: 10.1021/ct300418h
|
| [52] |
M. G. Montalbán, S. Chakraborty, J. Peñ a-García, H. Verli, G. Villora, H. Pérez-Sánchez, et al., Molecular insight into silk fibroin based delivery vehicle for amphiphilic drugs: Synthesis, characterization and molecular dynamics studies, J. Mol. Liq., 299 (2020), 112156. doi: 10.1016/j.molliq.2019.112156
|
| [53] |
S. C. C. van der Lubbe, F. Zaccaria, X. Sun, C. F. Guerra, Secondary electrostatic interaction model revised: Prediction comes mainly from measuring charge accumulation in hydrogen-bonded monomers, J. Am. Chem. Soc., 141 (2019), 4878-4885. doi: 10.1021/jacs.8b13358
|
| [54] |
X. Wu, J. Hou, M. Li, J. Wang, D. L. Kaplan, S. Lu, Sodium dodecyl sulfate-induced rapid gelation of silk fibroin, Acta Biomater., 8 (2012), 2185-2192. doi: 10.1016/j.actbio.2012.03.007
|
| [55] |
J. H. Park, M. H. Kim, L. Jeong, D. Cho, O. H. Kwon, W. H. Park, Effect of surfactants on sol-gel transition of silk fibroin, J. Sol. Gel. Sci. Technol., 71 (2014), 364-371. doi: 10.1007/s10971-014-3379-4
|
| [56] |
Z. Li, Z. Zheng, Y. Yang, G. Fang, J. Yao, Z. Shao, et al., Robust protein hydrogels from silkworm silk, ACS Sustainable Chem. Eng., 4 (2016), 1500-1506. doi: 10.1021/acssuschemeng.5b01463
|
| [57] |
H. Mrad, S. Alix, S. Migneault, A. Koubaa, P. Perré, Numerical and experimental assessment of water absorption of wood-polymer composites, Measurement, 115 (2018), 197-203. doi: 10.1016/j.measurement.2017.10.011
|
| [58] | W. Fan, P. Zhao, J. Kang, G. Nan, Application of molecular simulation technology to emulsified asphalt study, J. China Univ. Pet., 38 (2014), 179-185. |
| [59] |
L. He, B. Niemeyer, A novel correlation for protein diffusion coefficients based on molecular weight and radius of gyration, Biotechnol. Prog., 19 (2003), 544-548. doi: 10.1021/bp0256059
|
| [60] |
Z. J. Derlacki, A. J. Easteal, A.V. J. Edge, L. A. Woolf, Z. Roksandic, Diffusion coefficients of methanol and water and the mutual diffusion coefficient in methanol-water solutions at 278 and 298 K, J. Phys. Chem. B, 89 (1985), 5318-5322. doi: 10.1021/j100270a039
|
| [61] |
Y. Huang, K. Bailey, S. Wang, X. Feng, Silk fibroin films for potential applications in controlled release, React. Funct. Polym., 116 (2017), 57-68. doi: 10.1016/j.reactfunctpolym.2017.05.007
|
| [62] |
A. Rattanamanee, H. Niamsup, L. Srisombat. W. Punyodom, R. Watanesk, S. Watanesk, Role of chitosan on some physical properties and the urea controlled release of the silk fibroin/gelatin hydrogel, J. Polym. Environ., 23 (2015), 334-340. doi: 10.1007/s10924-014-0703-6
|
| [63] |
T. Asakura, M. Demura, H. Ogawa, K. Matsushita, M. Imanari, NMR imaging of diffusion of small organic molecules in silk fibroin gel, Macromolecules, 24 (1991), 620-622. doi: 10.1021/ma00002a045
|
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Xuewei Jiang, Lu Zheng, Huhe Wu, Jun Zhang. Investigations into the role of non-bond interaction on gelation mechanism of silk fibroin hydrogel[J]. Mathematical Biosciences and Engineering, 2021, 18(4): 4071-4083. doi: 10.3934/mbe.2021204
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