DOI QR코드

DOI QR Code

Effect of degumming conditions on the fluorescence intensity of fluorescent silk cocoons: A combined experimental and molecular dynamics study

  • Chan Yeong, Yu (Department of Biomedical Engineering, Yonsei University) ;
  • Ezekiel Edward, Nettey-Oppong (Department of Biomedical Engineering, Yonsei University) ;
  • Elijah, Effah (Department of Biomedical Engineering, Yonsei University) ;
  • Su Min, Han (Department of Biomedical Engineering, Yonsei University) ;
  • Seong-Wan, Kim (Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Seung Ho, Choi (Department of Biomedical Engineering, Yonsei University)
  • 투고 : 2022.09.14
  • 심사 : 2022.10.18
  • 발행 : 2022.12.30

초록

Silk is a unique natural biopolymer with outstanding biocompatibility, high mechanical strength, and superior optical transparency. Due to its excellent properties, silk has been widely reported as an ideal biomaterial for several biomedical applications. Recently, fluorescent silk protein, a variant of native silk, has been reported as a biophotonic material with the potential for bioimaging and biosensing. Despite the realization of fluorescent silk, the traditional degumming process of fluorescence silk is crude and often results in fluorescence loss. The loss of fluorescent properties is attributed to the sensitivity of silk fibroin to temperature and solvent concentration during degumming. However, there is no comprehensive information on the influence of these processing parameters on fluorescence evolution and decay during fluorescent silk processing. Therefore, we conducted a spectroscopic study on fluorescence decay as a function of temperature, concentration, and duration for fluorescent silk cocoon degumming. Sodium carbonate solution was tested for degumming the fluorescent silk cocoons with different concentrations and temperatures; also, sodium carbonate solution is combined with Alcalase enzyme and triton x-100 to find optimal degumming conditions. Additionally, we conducted a molecular dynamics study to investigate the fundamental effect of temperature on the stability of the fluorescent protein. We observed degumming temperature as the prime source of fluorescent intensity reduction. From the MD study, fluorescence degradation originated from the thermal agitation of fluorescent protein Cα atoms and fluctuations of amino acid residues located in the chromophore region. Overall, degumming fluorescent silk with sodium carbonate and Alcalase enzyme solution at 25 ℃ preserved fluorescence.

키워드

과제정보

This work was carried out with the support of "Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ015373)" Rural Development Administration, Republic of Korea.

참고문헌

  1. Altman GH, Diaz F, Jakuba C, Calabro T, Horan RL, Chen JS, et al. (2003) Silk-based biomaterials. Biomaterials 24, 401-416. https://doi.org/10.1016/S0142-9612(02)00353-8
  2. Arami M, Rahimi S, Mivehie L, Mazaheri F, Mahmoodi NM (2007) Degumming of Persian silk with mixed proteolytic enzymes. J Appl Polym Sci 106, 267-275. https://doi.org/10.1002/app.26492
  3. Arooj M, Kim S, Sakkiah S, Cao GP, Lee Y, Lee KW (2013) Molecular modeling study for inhibition mechanism of human chymase and its application in inhibitor design. PLoS One 8, e62740.
  4. Brooks BR, Brooks III CL, Mackerell JR AD, Nilsson L, Petrella RJ, Roux B, et al. (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30, 1545-1614. https://doi.org/10.1002/jcc.21287
  5. Bucciarelli A, Quaranta A, Maniglio (2021) Imaging the morphological structure of silk fibroin constructs through fluorescence energy transfer and confocal microscopy. Electron Mater 2, 186-197. https://doi.org/10.3390/electronicmat2020015
  6. Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server; in The Proteomics Protocols Handbook. Walker JM (eds.), pp. 571-607, Humana Press, Totowa.
  7. Gil Pineda LI, Milko LN, He Y (2020) Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: a case study. Biophys Rep 6, 80-87. https://doi.org/10.1007/s41048-020-00107-w
  8. Hockney RW, Eastwood JW (1989) Computer simulation using particles. Adam Hilger, New York.
  9. Holland C, Numata K, Rnjak-Kovacina J, Seib FP (2019) The biomedical use of silk: past, present, future. Adv Healthc Mater 8, 1800465.
  10. Hu F, Lin NB, Liu XY (2020) Interplay between light and functionalized silk fibroin and applications. Iscience 23, 101035.
  11. Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, De Groot BL, et al. (2017) CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods 14, 71-73. https://doi.org/10.1038/nmeth.4067
  12. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14, 33-38. https://doi.org/10.1016/0263-7855(96)00018-5
  13. Iizuka T, Sezutsu H, Tatematsu K, Kobayashi I, Yonemura N, Uchino K, et al. (2013) Colored fluorescent silk made by transgenic silkworms. Adv Funct Mater 23, 5232-5239. https://doi.org/10.1002/adfm.201300365
  14. Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29, 1859-1865. https://doi.org/10.1002/jcc.20945
  15. Kim DW, Lee OJ, Kim SW, Ki CS, Chao JR, Yoo H, et al. (2015a) Novel fabrication of fluorescent silk utilized in biotechnological and medical applications. Biomaterials 70, 48-56. https://doi.org/10.1016/j.biomaterials.2015.08.025
  16. Kim DW, Lee OJ, Kim SW, Ki CS, Chao JR, Yoo H, et al. (2015b) Novel fabrication of fluorescent silk utilized in biotechnological and medical applications. Biomaterials 70, 48-56. https://doi.org/10.1016/j.biomaterials.2015.08.025
  17. Koehl A, Hu H, Maeda S, Zhang Y, Qu Q, Paggi JM, et al. (2018) Structure of the µ-opioid receptor-Gi protein complex. Nature 558, 547-552. https://doi.org/10.1038/s41586-018-0219-7
  18. Kurosaki S, Otsuka H, Kunitomo M, Koyama M, Pawankar R, Matumoto K (1999) Fibroin allergy IgE mediated hypersensitivity to silk suture materials. Nippon Ika Daigaku Zasshi 66, 41-44. https://doi.org/10.1272/jnms.66.41
  19. Kusurkar TS, Tandon I, Sethy NK, Bhargava K, Sarkar S, Singh SK, et al. (2013) Fluorescent silk cocoon creating fluorescent diatom using a "water glass-fluorophore ferry". Sci Rep 3, 3290.
  20. Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, et al. (2016) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J Chem Theory Comput 12, 405-413. https://doi.org/10.1021/acs.jctc.5b00935
  21. Lee OJ, Sultan MT, Hong H, Lee YJ, Lee JS, Lee H, et al. (2020) Recent advances in fluorescent silk fibroin. Front Mater 7, 50.
  22. Leem JW, Kim MS, Choi SH, Kim SR, Kim SW, Song YM, et al. (2020) Edible unclonable functions. Nat Commun 11, 328.
  23. Mohan R, Venugopal S (2012) Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus. Bioinformation 8, 722-728. https://doi.org/10.6026/97320630008722
  24. Nath O, Singh A, Singh IK (2017) In-Silico drug discovery approach targeting receptor tyrosine kinase-like orphan receptor 1 for cancer treatment. Sci Rep 7, 1-10. https://doi.org/10.1038/s41598-016-0028-x
  25. Nguyen TP, Nguyen QV, Nguyen VH, Le TH, Huynh VQN, Vo DVN, et al. (2019) Silk fibroin-based biomaterials for biomedical applications: a review. Polymers 11, 1933. https://doi.org/10.3390/polym11030481
  26. Pletnev S, Shcherbo D, Chudakov DM, Pletneva N, Merzilyak EM, Wlodawer A, et al. (2008) A crystallographic study of bright far-red fluorescent protein mkate reveals pH-induced cis-trans isomerization of the chromophore. J Biol Chem 283, 28980-28987. https://doi.org/10.1074/jbc.M800599200
  27. Pollock E, Glosli J (1996) Comments on P3M, FMM, and the Ewald method for large periodic coulombic systems. Comput Phys Commun 95, 93-110. https://doi.org/10.1016/0010-4655(96)00043-4
  28. Qiu J, Wang D, Zhang Y, Dong J, Wang J, Niu X (2013) Molecular modeling reveals the novel inhibition mechanism and binding mode of three natural compounds to staphylococcal α-hemolysin. PLoS One 8, e80197.
  29. Rahman MU, Rehman AU, Liu H, Chen HF (2020) Comparison and evaluation of force fields for intrinsically disordered proteins. J Chem Inf Model 60, 4912-4923. https://doi.org/10.1021/acs.jcim.0c00762
  30. Rieloff E, Skepo M. (2021) Molecular dynamics simulations of phosphorylated intrinsically disordered proteins: a force field comparison. Int J Mol Sci 22, 10174.
  31. Sahay A, Piprodhe A, Pise M (2020) In silico analysis and homology modeling of strictosidine synthase involved in alkaloid biosynthesis in catharanthus roseus. J Genet Eng Biotech 18, 1-6. https://doi.org/10.1186/s43141-019-0015-2
  32. Schicht M, Rausch F, Finotto S, Mathews M, Mattil A, Schubert M, et al. (2014) SFTA3 a novel protein of the lung: three-dimensional structure, characterisation and immune activation. Eur Resp J 44, 447-456. https://doi.org/10.1183/09031936.00179813
  33. Schrodinger L (2022) PyMOL [Internet]. Available from: http://www.pymol.org/pymol [accessed on 24 October 2022].
  34. Shao D, Zhang Q, Xu P, Jiang Z (2022) Effects of the temperature and salt concentration on the structural characteristics of the protein (PDB code 1BBL). Polymers 14, 2134.
  35. Thompson AP, Aktulga HM, Berger R, Bolintineanu DS, Brown WM, Crozier PS, et al. (2022) LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comput Phys Commun 271, 108171.
  36. Wen DL, Sun DH, Huang P, Huang W, Su M, Wang Y, et al. (2021) Recent progress in silk fibroin-based flexible electronics. Microsyst Nanoeng 7, 35.
  37. Yang Y, Shao Z, Chen X, Zhou P (2004) Optical spectroscopy to investigate the structure of regenerated Bombyx mori silk fibroin in solution. Biomacromolecules 5, 773-779. https://doi.org/10.1021/bm0343848
  38. Zuluaga-Velez A, Quintero-Martinez A, Orozco LM, Sepulveda-Arias JC (2021) Silk fibroin nanocomposites as tissue engineering scaffolds - a systematic review. Biomed Pharmacother 141, 111924.