Laser-Induced Crystallization of Standard Proteins on Ultra-Hydrophobic Surface and Characterization Using Raman Spectroscopy

B. Sudarshan Acharya
Manipal Academy of Higher Education, Karnataka, India

Sajan D. George
Manipal Academy of Higher Education, Karnataka, India

Abdul Ajees Abdul Salam (Login required)
Manipal Academy of Higher Education, Karnataka, India


Paper #7785 received 25 Feb 2023; revised manuscript received 20 Jul 2023; accepted for publication 21 Jul 2023; published online 4 Sep 2023.

Abstract

Structural information helps to understand the function of the proteins and provides potential protein-ligand interactions of new drugs. X-ray crystallography is a powerful technique to determine the structure in three-dimensional geometry. However, obtaining high-quality single crystals remains an obstacle in macromolecular crystallography. Laser-induced crystallization is emerging as an alternative technique to circumvent this problem. In this study, we have prepared ultra-hydrophobic surfaces and used them for protein crystallization. Three model proteins, lysozyme, ferritin, and proteinase K, with distinct hydrophobicity, were used for this study. The protein droplet placed on three surfaces (non-siliconized, siliconized, and candle soot films) is exposed to a diode laser (785 nm, 75 mW). Ultra-hydrophobic candle soot surfaced coverslips rapidly yielded the crystals in conventional and laser-exposed droplets. Proteinase K nucleated faster than the lysozyme/ferritin on candle soot coated surface, compared to the regular coverslips suggesting that ultra-hydrophobic surfaces assisted laser-induced crystallization will play an essential role in protein crystallization.

Keywords

protein crystallization; ultra-hydrophobic surfaces; laser-induced crystallization

Full Text:

PDF

References


1. M. Kashii, H. Kitano, Y. Hosokawa, H. Adachi, Y. Mori, T. Sasaki, H. Masuhara, K. Takano, H. Matsumura, and T. Inoue, “Femtosecond laser processing of protein crystals in crystallization drop,” Japanese Journal of Applied Physics 44(6L), L873 (2005).

2. M. A. Dessau, Y. Modis, “Protein crystallization for X-ray crystallography,” Journal of Visualized Experiments 47, e2285 (2011).

3. A. Moreno, “Advanced methods of protein crystallization,” Protein Crystallography. Methods in Molecular Biology 1607, A. Wlodawer, Z. Dauter, M. Jaskolski (Eds.), Humana Press, New York (2017).

4. J. M. Keith (Ed.), “Data, sequence analysis and evolution. Preface,” Methods in Molecular Biology 452, Totowa, NJ (2008).

5. A. McPherson, J. A. Gavira, “Introduction to protein crystallization,” Acta Crystallographica Section F: Structural Biology Communications 70(1), 2–20 (2014).

6. S. Thippeshappa, S. D. George, A. Bankapur, S. Chidangil, D. Mathur, and A. A. A. Salam, “Effect of biocompatible nucleants in rapid crystallization of natural amino acids using a CW Nd:YAG laser,” Scientific Reports 8, 16018 (2018).

7. C. N. Nanev, E. Saridakis, L. Govada, S. C. Kassen, H. V. Solomon, and N. E. Chayen, “Hydrophobic Interface-Assisted Protein Crystallization: Theory and Experiment,” ACS Applied Materials & Interfaces 11(13), 12931–12940 (2019).

8. T. A. J. Grell, M. A. Pinard, D. Pettis, and K. Aslan, “Rapid crystallization of glycine using metal-assisted and microwave-accelerated evaporative crystallization: The effect of engineered surfaces and sample volume,” Nano Biomedicine and Engineering 4(3), 125–131 (2012).

9. T. Shilpa, S. D. George, A. Bankapur, and S. Chidangil, A. K. Dharmadhikari, D. Mathur, S. M. Kumar, K. Byrappa, and A. A. A. Salam, “Effect of nucleants in photothermally assisted crystallization,” Photochemical & Photobiological Sciences 16(6), 870–882 (2017).

10. B. A. Garetz, J. E. Aber, N. L. Goddard, R. G. Young, and A. S. Myerson, “Nonphotochemical, polarization-dependent, laser-induced nucleation in supersaturated aqueous urea solutions,” Physical Review Letters 77(16), 3475–3476 (1996).

11. T. Shilpa, S. G. Bhat, V. R. Rodrigus, S. George, A. K. Dharmadhikari, C. Santhosh, and A. A. Ajees, “Small and macromolecules crystallization induced by focused ultrafast laser,” Proceedings of the Indian National Science Academy 81(2), 517–523 (2015).

12. T. Rungsimanon, K. I. Yuyama, T. Sugiyama, and H. Masuhara, “Crystallization in unsaturated glycine/D2O solution achieved by irradiating a focused continuous wave near infrared laser,” Crystal Growth & Design 10(11), 4686–4688 (2010).

13. A. Caciagli, R. Singh, D. Joshi, R. Adhikari, and E. Eiser, “Controlled Optofluidic Crystallization of Colloids Tethered at Interfaces,” Physical Review Letters 125(6), 068001 (2020).

14. K. I. Yuyama, K.-D. Chang, J. R. Tu, H. Masuhara, and T. Sugiyama, “Rapid localized crystallization of lysozyme by laser trapping,” Physical Chemistry Chemical Physics 20(9), 6034–6039 (2018).

15. J. R. Tu, A. Miura, K. I. Yuyama, H. Masuhara, and T. Sugiyama, “Crystal growth of lysozyme controlled by laser trapping,” Crystal Growth & Design 14(1), 15–22 (2014).

16. J. J. K. Chen, K.-I. Yuyama, T. Sugiyama, and H. Masuhara, “Bubble generation and molecular crystallization at solution surface by intense continuous-wave laser irradiation,” Applied Physics Express 11(8), 085502 (2018).

17. S. Pathak, J. A. Dharmadhikari, A. A. Thamizhavel, D. Mathur, and A. K. Dharmadhikari, “Growth of micro-crystals in solution by in-situ heating via continuous wave infrared laser light and an absorber,” Journal of Crystal Growth 433, 43–47 (2016).

18. E. Pechkova, G. Maksimov, E. Parshina, E. Maksimov, N. Kutusov, N. Brazhe, I. Tarasova, S. Fiordoro, and N. Claudio, “Raman spectroscopy of protein crystal nucleation and growth,” American Journal of Biochemistry and Biotechnology 10(3), 202–207 (2014).

19. A. Rygula, K. Majzner, K. M. Marzec, A. Kaczor, M. Pilarczyk, and M. Baranska, “Raman spectroscopy of proteins: A review,” Journal of Raman Spectroscopy 44(8), 1061–1076 (2013).

20. A. V. Frontzek, L. Paccou, Y. Guinet, and A. Hédoux, “Study of the phase transition in lysozyme crystals by Raman spectroscopy,” Biochimica et Biophysica Acta (BBA)-General Subjects 1860(2), 412–423 (2016).

21. V. Kocherbitov, J. Latynis, A. Misiuì, J. Barauskas, and G. Niaura, “Hydration of lysozyme studied by Raman spectroscopy,” The Journal of Physical Chemistry B 117(17), 4981–4992 (2013).

22. G. Anderle, R. Mendelsohn, “Fourier Transform-Infrared Studies of the Amide III Spectral Region,” Biophysical Journal 52(1), 69–74 (1987).

23. B. R. Silver, V. Fülöp, and P. R. Unwin, “Protein crystallization at oil / water interfaces,” New Journal of Chemistry 35(3), 602–606 (2011).

24. R. Silver, J. M. A. Grime, New Approaches to Protein Crystallization, Ph.D. Thesis, University of Warwick (2013).

25. Y.-S. Jun, D. Kim, and C. W. Neil, “Heterogeneous Nucleation and Growth of Nanoparticles at Environmental Interfaces,” Accounts of Chemical Research 49(9), 1681–1690 (2016).

26. J. R. Hunter, P. K. Kilpatrick, and R. G. Carbonell, “Lysozyme Adsorption at the Air / Water Interface,” Journal of Colloid and Interface Science 137(2), 462–482 (1990).

27. C. J. J. Gerard, G. Ferry, L. M. Vuillard, J. A. Boutin, N. Ferte, R. Grossier, N. Candoni, and S. Veesler, “A Chemical Library to Screen Protein and Protein–Ligand Crystallization Using a Versatile Microfluidic Platform,” Crystal Growth & Design 18(9), 5130–5137 (2018).

28. D. Tsekova, S. Dimitrova, and C. N. Nanev, “Heterogeneous nucleation (and adhesion) of lysozyme crystals,” Journal of Crystal Growth 196(2–4), 226–233 (1999).

29. E. Pechkova, C. Nicolini, “Accelerated protein crystal growth by protein thin film template,” Journal of Crystal Growth 231(4), 599–602 (2001).

30. T. Yamazaki, Y. Kimura, P. G. Vekilov, E. Furukawa, M. Shirai, H. Matsumoto, A. E. S. V. Driessche, and K. Tsukamoto, “Two types of amorphous protein particles facilitate crystal nucleation,” Proceedings of the National Academy of Sciences 114(9), 2154–2159 (2017).

31. E. Saridakis, S. Khurshid, L. Govada, Q. Phan, D. Hawkins, G. V Crichlow, E. Lolis, S. M. Reddy s, and N. E. Chayen, “Protein crystallization facilitated by molecularly imprinted polymers,” Proceedings of the National Academy of Sciences 108(27), 11081–11086 (2011).

32. F. Artusio, R. Pisano, “Surface-induced crystallization of pharmaceuticals and biopharmaceuticals : a review,” International Journal of Pharmaceutics 547(1–2), 190–280 (2018).

33. X. Lin, S. Park, D. Choi, J. Heo, and J. Hong, “Mechanically durable superhydrophobic PDMS-candle soot composite coatings with high biocompatibility,” Journal of Industrial and Engineering Chemistry 74, 79–85 (2019).

34. B. N. Sahoo, S. Nanda, J. A. Kozinski, and S. K. Mitra, “PDMS/camphor soot composite coating: towards a self-healing and a self-cleaning superhydrophobic surface,” RSC Advances 7(25), 15027–15040 (2017).

35. E. Saridakis, N. E. Chayen, “Towards a ‘universal’ nucleant for protein crystallization,” Trends in Biotechnology 27(2), 99–106 (2009).

36. C. N. Nanev, E. Saridakis, and N. E. Chayen, “Protein crystal nucleation in pores,” Scientific Reports 7, 35821 (2017).

37. M. A. Hough, “Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data,” Acta Crystallographica Section D: Biological Crystallography 71, 27–35 (2015).

38. G. Gouadec, P. Colomban, “Raman Spectroscopy of nanomaterials: How spectra relate to disorder, particle size and mechanical properties,” Progress in Crystal Growth and Characterization of Materials 53(1), 1–56 (2007).

39. N. Kuhar, S. Sil, T. Verma, and S. Umapathy, “Challenges in application of Raman spectroscopy to biology and materials,” RSC Advances 8(46), 25888–25908 (2018).

40. N. A. Nevskaya, Y. N. Chirgadze, “Infrared spectra and resonance interactions of amide‐I and II vibrations of α‐helix,” Biopolymers: Original Research on Biomolecules 15(4), 637–648 (1976).

41. A. C. S. Talari, Z. Movasaghi, S. Rehman, and I. U. Rehman, “Raman spectroscopy of biological tissues,” Applied Spectroscopy Reviews 50(1), 46–111 (2015).

42. C. Camerlingo, M. Lisitskiy, M. Lepore, M. Portaccio, D. Montorio, S. D. Prete, and G. Cennamo, “Characterization of human tear fluid by means of surface-enhanced raman spectroscopy,” Sensors 19(5), 1177 (2019).

43. N. S. Myshakina, Z. Ahmed, and S. A. Asher, “Dependence of Amide Vibrations on Hydrogen Bonding,” Journal of Physical Chemistry B 112(38), 11873–11877 (2008).

44. C. Betzel, G. P. Pal, and W. Saenger, “Three‐dimensional structure of proteinase K at 0.15‐nm resolution,” European Journal of Biochemistry 178(1), 155–171 (1988).

45. B. Xu, N. D. Chasteen, “Iron oxidation chemistry in ferritin. Increasing Fe/O2 stoichiometry during core formation,” Journal of Biological Chemistry 266(30), 19965–19970 (1991).

46. K. D. Welch, M. E. Van Eden, and S. D. Aust, “Modification of ferritin during iron loading,” Free Radical Biology and Medicine 31(8), 999–1006 (2001).

47. A. M. Koorts, M. Viljoen, “Ferritin and ferritin isoforms I : Structure – function relationships , synthesis , degradation and secretion,” Archives of Physiology and Biochemistry 1(113), 30–54 (2007).






© 2014-2024 Samara National Research University. All Rights Reserved.
Public Media Certificate (RUS). 12+