فناوری در مهندسی هوافضا

فناوری در مهندسی هوافضا

کریستالوگرافی پروتئین‌ها در شرایط بی‌وزنی فضا

نوع مقاله : علمی- ترویجی

نویسنده
پژوهشگاه هوافضا، وزارت علوم، تحقیقات و فناوری، تهران، ایران
چکیده
امروزه شرایط خارق‌العاده فضا، به‌ ویژه ریزجاذبه، نه تنها برای تحقیقات در علوم فیزیک و مواد مورد استفاده قرار می‌گیرد، بلکه ابزاری منحصر به فرد را برای تحقیق در زمینه‌های مختلف علوم زیستی فراهم می‌نمایند. هدف اصلی مطالعات در شرایط بی‌وزنی،کشف نقش جاذبه بر تکامل و آینده حیات و توسعه و جهت گیری موجودات از تک سلولی تا انسان است. علاوه بر این، شرایط فضا می­تواند برای مطالعات مهندسی بافت نظیر رشد استخوان، غضروف و عروق، تحقیقات سرطان و دارو نیز به کار رود. در کریستالوگرافی، الگوهای تابش اشعه ایکس بر روی کریستال­ها برای تعیین ساختار سه بعدی پروتئین‌ها تجزیه و تحلیل می شود. از این طریق، ساختار دقیق مولکول پروتئینی بازسازی شده و عملکرد زیستی آن کشف می­گردد. این مرحله برای فرایند تحقیق در زیست شناسی، داروسازی و پزشکی حیاتی می­باشد. چالش برانگیزترین جنبه این فرایند، تولید میزان مناسبی از کریستال­های مرتب و منظم با حداقل مقدار موزائیک داخلی و ترکیب کم ناخالصی است. لازم به ذکر است که اغلب پروتئین‌ها تمایل به تشکیل کریستال‌های بزرگ و با کیفیت ندارند که این امر هم به شرایط کریستالوگرافی و هم به خود مولکول بستگی دارد. در شرایط عادی، جاذبه بر روند تبلور و کیفیت پروتئین‌ها تأثیر می­گذارد. در مقابل، شرایط بی‌وزنی فضا تا حدودی این معضل را حل نموده و می‌تواند منجر به تشکیل کریستال‌هایی با کیفیت بالاتر شود. بر اساس تحقیقات فضایی، بی‌وزنی می‌تواند به‌طور قابل توجهی بر رشد کریستال و ساختار پروتئین تاثیر بگذارد. این پژوهش به بررسی تأثیرات بی‌وزنی فضا بر کریستالوگرافی پروتئین، مزایا، چالش‌ها و فرصت‌هایی می­پردازد که این شرایط منحصر به فرد برای علم کریستالوگرافی ارائه می­نماید.
کلیدواژه‌ها
موضوعات

عنوان مقاله English

Crystallography of proteins in weightlessness conditions of space

نویسنده English

Maryam Salavatifar
Aerospace Research Institute, Ministry of Science, Research and Technology, Tehran, Iran
چکیده English

Today, the unique environment of space-particularly microgravity-is employed in physics and materials science research and serves as a valuable platform for advancing various fields within the life sciences. The primary objective of weightlessness research is to elucidate the role of gravity in the origin, development, and future of life, as well as in the physiological adaptation of organisms ranging from unicellular species to humans. Additionally, microgravity conditions enable the investigation of biological phenomena, including bone and cartilage formation, vascular development, cancer progression, and other biomedical processes. In protein crystallography, X-ray diffraction patterns generated from crystals are analyzed to determine the three-dimensional molecular structure. This approach enables the reconstruction of the protein’s precise architecture and reveals its biological functionality. Such structural insights are fundamental to research in biology, pharmacology, and medical sciences. A major challenge in this field is generating an adequate number of well-ordered crystals with minimal internal mosaicity and low impurity levels. Notably, most proteins do not readily form large, high-quality crystals, and successful crystallization depends heavily on both environmental parameters and the intrinsic properties of the molecule. Under terrestrial conditions, gravity imposes limitations on the crystallization process, often compromising crystal quality. In contrast, the microgravity environment of space partially mitigates these effects, frequently yielding crystals with superior structural integrity. Studies conducted in space have demonstrated that weightlessness can significantly influence crystal nucleation, growth dynamics, and final structural resolution. This research explores the impact of microgravity on protein crystallography, focusing on the advantages, limitations, and scientific opportunities it offers for advancing structural biology.

کلیدواژه‌ها English

Crystallography
Weightlessness
resolution
X-ray diffraction
[1] J. Balukovic, J. Slisko, and A. C. Cruz, "Thought experiments in teaching free-fall weightlessness: A critical review and an exploration of mercury’s behavior in "falling elevator"," EURASIA Journal of Mathematics, Science and Technology Education, vol. 13, no. 5, pp. 1283-1311, 2016, https://doi.org/10.12973/eurasia.2017.00671a.
[2] U. Proske and B. M. Weber, "Proprioceptive disturbances in weightlessness revisited," Npj Microgravity, vol. 9, no. 1, 2023, Art. no. 64, https://doi.org/10.1038/s41526-023-00318-8.
[3] A. McPherson and L. J. DeLucas, "Microgravity protein crystallization," Npj Microgravity, vol. 1, no. 1, pp. 1-20, 2015, https://doi.org/10.1038/npjmgrav.2015.10.
[4] D. R. Morrison, "Cell electrophoresis in microgravity: Past and future," Cell Electrophoresis, pp. 283-313, 2020, https://doi.org/10.1201/9781003069188-20.
[5] A. McPherson, "Protein crystallization," Protein Crystallography: Methods and Protocols, pp. 17-50, 2017, https://doi.org/10.1007/978-1-4939-7000-1_2.
[6] M. Abdalla, W. A. Eltayb, A. Samad, S. Elshareef, and T. Dafaalla, "Important factors influencing protein crystallization," Global Journal of Biotechnology and Biomaterial Science, vol. 2, no. 1, pp. 025-028, 2016, https://doi.org/10.17352/gjbbs.000008.
[7] V. Timofeev and V. Samygina, "Protein crystallography: Achievements and challenges," Crystals, vol. 13, no. 1, 2023, Art. no. 71, https://doi.org/10.3390/cryst13010071.
[8] H. M. Berman et al., "The protein data bank," Nucleic Acids Research, vol. 28, no. 1, pp. 235-242, 2000, https://doi.org/10.1093/nar/28.1.235.
[9] J. R. Helliwell and N. E. Chayen, "A down-to-Earth approach," Nature, vol. 448, no. 7154, pp. 658-659, 2007, https://doi.org/10.1038/448658a.
[10]N. E. Chayen, "Protein crystallization for genomics: throughput versus output," Journal of Structural and functional Genomics, vol. 4, pp. 115-120, 2003, https://doi.org/10.1023/a:1026174727482.
[11]E. H. Snell and J. R. Helliwell, "Macromolecular crystallization in microgravity," Reports on Progress in Physics, vol. 68, no. 4, 2005, Art. no. 799, https://doi.org/10.1088/0034-4885/68/4/r02.
[12]N. E. Chayen and J. R. Helliwell, "Microgravity protein crystallization: Are we reaping the full benefit of outer space," Annals of the New York Academy of Sciences, vol. 974, no. 1, pp. 591-597, 2002, https://doi.org/10.1111/j.1749-6632.2002.tb05933.x.
[13]N. Ramachandran and F. Leslie, "Using magnetic fields to control convection during protein crystallization-analysis and validation studies," Journal of Crystal Growth, vol. 274, no. 1-2, pp. 297-306, 2005, https://doi.org/10.1016/j.jcrysgro.2004.10.006.
[14]C. Y. Zhang et al., "Cycling temperature strategy: A method to improve the efficiency of crystallization condition screening of proteins," Crystal Growth and Design, vol. 8, no. 12, pp. 4227-4232, 2008, https://doi.org/10.1021/cg800689j.
[15]G. Sazaki, A. Moreno, and K. Nakajima, "Novel coupling effects of the magnetic and electric fields on protein crystallization," Journal of Crystal Growth, vol. 262, no. 1-4, pp. 499-502, 2004, https://doi.org/10.1016/j.jcrysgro.2003.09.050.
[16]Z. S. Derewenda, "The use of recombinant methods and molecular engineering in protein crystallization," Methods, vol. 34, no. 3, pp. 354-363, 2004, https://doi.org/10.1016/j.ymeth.2004.03.024.
[17]K. L. Longenecker, S. M. Garrard, P. J. Sheffield, and Z. S. Derewenda, "Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI," Acta Crystallographica Section D: Biological Crystallography, vol. 57, no. 5, pp. 679-688, 2001, https://doi.org/10.1107/s0907444901003122.
[18]M. Braddock, "From target identification to drug development in space: Using the microgravity assist," Current Drug Discovery Technologies, vol. 17, no. 1, pp. 45-56, 2020, https://doi.org/10.2174/1570163816666190112150014.
[19]K. Jackson et al., "An analysis of protein crystals grown under microgravity conditions," Crystals, vol. 14, no. 7, 2024, Art. no. 652, https://doi.org/10.3390/cryst14070652.
[20]G. Ruyters, C. Betzel, D. Grimm, G. Ruyters, C. Betzel, and D. Grimm, "Biotechnology, cell biology and microgravity," Biotechnology in Space, pp. 1-10, 2017, https://doi.org/10.1007/978-3-319-64054-9_1.
[21]W. Littke and C. John, "Protein single crystal growth under microgravity," Science, vol. 225, no. 4658, pp. 203-204, 1984, https://doi.org/10.1016/0022-0248(86)90183-1.
[22]H. F. Noller, "Structure of ribosomal RNA," Annual Review of Biochemistry, vol. 53, no. 1, pp. 119-162, 1984, https://doi.org/10.1146/annurev.biochem.53.1.119.
[23]G. Ruyters, C. Betzel, and D. Grimm, Biotechnology in Space, Springer, 2017, https://doi.org/10.1007/978-3-319-64054-9.
[24]V. A. Erdmann et al., "Crystallization of proteins under microgravity," FEBS Letters, vol. 259, no. 1, pp. 194-198, 1989, https://doi.org/10.1016/0014-5793(89)81526-1.
[25]R. Van Noorden, "Structural biology bags chemistry prize: Chemistry Nobel for trio who described the ribosome," Nature, vol. 461, no. 7266, pp. 860-861, 2009, https://doi.org/10.1038/461860a.
[26]J. M. Martin-Garcia, C. E. Conrad, J. Coe, S. Roy-Chowdhury, and P. Fromme, "Serial femtosecond crystallography: A revolution in structural biology," Archives of Biochemistry and Biophysics, vol. 602, pp. 32-47, 2016, https://doi.org/10.1016/j.abb.2016.03.036.
[27]R. Giegé, "A historical perspective on protein crystallization from 1840 to the present day," The FEBS Journal, vol. 280, no. 24, pp. 6456-6497, 2013, https://doi.org/10.1111/febs.12580.
[28]J. A. Gavira, "Current trends in protein crystallization," Archives of Biochemistry and Biophysics, vol. 602, pp. 3-11, 2016, https://doi.org/10.1016/j.abb.2015.12.010.
[29]A. McPherson, "Introduction to protein crystallization," Methods, vol. 34, no. 3, pp. 254-265, 2004, https://doi.org/10.1016/j.ymeth.2004.03.019.
[30]N. E. Chayen and E. Saridakis, "Protein crystallization: From purified protein to diffraction-quality crystal," Nature Methods, vol. 5, no. 2, pp. 147-153, 2008, https://doi.org/10.1038/nmeth.f.203.
[31] A. Martirosyan et al., "Effect of macromolecular mass transport in microgravity protein crystallization," Gravitational and Space Research, vol. 7, no. 1, pp. 33-44, 2019, https://doi.org/10.2478/gsr-2019-0005.
[32]R. Schubert, A. Meyer, D. Baitan, K. Dierks, M. Perbandt, and C. Betzel, "Real-time observation of protein dense liquid cluster evolution during nucleation in protein crystallization," Crystal Growth and Design, vol. 17, no. 3, pp. 954-958, 2017, https://doi.org/10.1021/acs.cgd.6b01826.
[33]P. Debye, "Lowering of freezing point and related phenomena," Physikalische Zeitschrift, vol. 24, pp. 185-206, 1923.
[34]L. A. Gonzalez-Ramirez, J. Carrera, J. A. Gavira, E. Melero-Garcia, and J. M. Garcia-Ruiz, "Granada crystallization facility-2: A versatile platform for crystallization in space," Crystal Growth and Design, vol. 8, no. 12, pp. 4324-4329, 2008, https://doi.org/10.1021/cg800788e.
[35] C. Sauter, B. Lorber, A. McPherson, and R. Giegé, "General methods," International Tables for Crystallography, pp. 99-121, 2012, https://doi.org/10.1107/97809553602060000812.
[36]P. G. Vekilov and J. I. D. Alexander, "Dynamics of layer growth in protein crystallization," Chemical Reviews, vol. 100, no. 6, pp. 2061-2090, 2000, https://doi.org/10.1021/cr9800558.
[37]N. Ramachandran, C. R. Baugher, and R. J. Naumann, "Modeling flows and transport in protein crystal growth," Microgravity Science and Technology, vol. 8, no. 3, pp. 170-179, 1995.
[38]F. Otálora, M. L. Novella, J. A. Gavira, B. R. Thomas, and J. M. García-Ruiz, "Experimental evidence for the stability of the depletion zone around a growing protein crystal under microgravity," Acta Crystallographica Section D: Biological Crystallography, vol. 57, no. 3, pp. 412-417, 2001, https://doi.org/10.1107/s0907444901000555.
[39]A. Chernov, J. Garcia-Ruiz, and B. Thomas, "Visualization of the impurity depletion zone surrounding apoferritin crystals growing in gel with holoferritin dimer impurity," Journal of Crystal Growth, vol. 232, no. 1-4, pp. 184-187, 2001, https://doi.org/10.1016/s0022-0248(01)01065-x.
[40]P. Eistrikh-Heller et al., "Crystallization in microgravity and the atomic-resolution structure of uridine phosphorylase from vibrio cholerae," Crystallography Reports, vol. 66, pp. 777-785, 2021, https://doi.org/10.1134/s1063774521050059
[41]K. Boyko, V. Timofeev, V. Samygina, I. Kuranova, V. Popov, and M. Koval’Chuk, "Protein crystallization under microgravity conditions: Analysis of the results of Russian experiments performed on the International Space Station in 2005- 2015," Crystallography Reports, vol. 61, pp. 718-729, 2016, https://doi.org/10.1134/s1063774516050059.
[42]T. Kinoshita, R. Maruki, M. Warizaya, H. Nakajima, and S. Nishimura, "Structure of a high-resolution crystal form of human triosephosphate isomerase: Improvement of crystals using the gel-tube method," Acta Crystallographica Section F: Structural Biology and Crystallization Communications, vol. 61, no. 4, pp. 346-349, 2005, https://doi.org/10.1134/s1063774516050059.
[43]M. Vallazza et al., "Crystallization and structure analysis of Thermus flavus 5S rRNA helix B," Acta Crystallographica Section D: Biological Crystallography, vol. 58, no. 10, pp. 1700-1703, 2002, https://doi.org/10.1107/s090744490201421x.
[44]R. Krauspenhaar et al., "Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 Å resolution," Acta Crystallographica Section D: Biological Crystallography, vol. 58, no. 10, pp. 1704-1707, 2002, https://doi.org/10.1107/s0907444902014270.
[45]J. Habash, T. J. Boggon, J. Raftery, N. E. Chayen, P. F. Zagalsky, and J. R. Helliwell, "Apocrustacyanin C1 crystals grown in space and on Earth using vapour-diffusion geometry: Protein structure refinements and electron-density map comparisons," Acta Crystallographica Section D: Biological Crystallography, vol. 59, no. 7, pp. 1117-1123, 2003, https://doi.org/10.2210/pdb1obu/pdb.
[46]A. E. Miele, L. Federici, G. Sciara, F. Draghi, M. Brunori, and B. Vallone, "Analysis of the effect of microgravity on protein crystal quality: The case of a myoglobin triple mutant," Acta Crystallographica Section D: Biological Crystallography, vol. 59, no. 6, pp. 982-988, 2003, https://doi.org/10.1107/s0907444903005924.
[47]A. Vahedi-Faridi, J. Porta, and G. E. Borgstahl, "Improved three-dimensional growth of manganese superoxide dismutase crystals on the International Space Station," Acta Crystallographica Section D: Biological Crystallography, vol. 59, no. 2, pp. 385-388, 2003, https://doi.org/10.1107/s0907444902020310.
[48]M. Ponassi, L. Felli, S. Parodi, U. Valbusa, and C. Rosano, "Crystals of the hydrogenase maturation factor HypF N-terminal domain grown in microgravity, display improved internal order," Journal of Crystal Growth, vol. 314, no. 1, pp. 246-251, 2011, https://doi.org/10.1016/j.jcrysgro.2010.12.011.
[49]D. Nichesola, M. Perduca, S. Capaldi, M. E. Carrizo, P. G. Righetti, and H. L. Monaco, "Crystal structure of chicken liver basic fatty acid-binding protein complexed with cholic acid," Biochemistry, vol. 43, no. 44, pp. 14072-14079, 2004, https://doi.org/10.1021/bi0489661.
[50]H. Tanaka et al., "Improvement in the quality of hematopoietic prostaglandin D synthase crystals in a microgravity environment," Journal of Synchrotron Radiation, vol. 18, no. 1, pp. 88-91, 2011, https://doi.org/10.1107/s0909049510037076.
[51]E. Smirnova et al., "Protein crystal growth on the Russian segment of the International Space Station," Crystallography Reports, vol. 54, pp. 901-911, 2009, https://doi.org/10.1134/s106377450905023x. 
[52]C. Evrard et al., "TIM crystals grown by capillary counterdiffusion: Statistical evidence of quality improvement in microgravity," Crystal Growth and Design, vol. 7, no. 11, pp. 2161-2166, 2007, https://doi.org/10.1021/cg700687t.
[53]H. Tanaka et al., "Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions," Acta Crystallographica Section F: Structural Biology and Crystallization Communications, vol. 63, no. 2, pp. 69-73, 2007, https://doi.org/10.1107/s1744309106054625.
[54]P. H. Małecki, W. Rypniewski, M. Szymański, J. Barciszewski, and A. Meyer, "Binding of the plant hormone kinetin in the active site of Mistletoe Lectin I from Viscum album," Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, vol. 1824, no. 2, pp. 334-338, 2012, https://doi.org/10.1016/j.bbapap.2011.10.013.
[55]A. Meyer, W. Rypniewski, M. Szymański, W. Voelter, J. Barciszewski, and C. Betzel, "Structure of mistletoe lectin I from Viscum album in complex with the phytohormone zeatin," Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, vol. 1784, no. 11, pp. 1590-1595, 2008, https://doi.org/10.1016/j.bbapap.2008.07.010.
[56]T. N. Safonova, N. N. Mordkovich, K. M. Polyakov, V. A. Manuvera, V. P. Veiko, and V. O. Popov, "Crystallization of uridine phosphorylase from Shewanella oneidensis MR-1 in the laboratory and under microgravity and preliminary X-ray diffraction analysis," Acta Crystallographica Section F: Structural Biology and Crystallization Communications, vol. 68, no. 11, pp. 1387-1389, 2012, https://doi.org/10.1107/s1744309112041784.
[57]K. Inaka et al., "High-quality protein crystal growth of mouse lipocalin-type prostaglandin D synthase in microgravity," Crystal Growth and Design, vol. 11, no. 6, pp. 2107-2111, 2011, https://doi.org/10.1021/cg101370v.
[58]V. Timofeev, E. Smirnova, L. Chupova, R. Esipov, and I. Kuranova, "Preparation of the crystal complex of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis with coenzyme A and investigation of its three-dimensional structure at 2.1-Å resolution," Crystallography Reports, vol. 55, pp. 1050-1059, 2010, https://doi.org/10.1134/s1063774510060234.
[59]V. Timofeev, E. Smirnova, L. Chupova, R. Esipov, and I. Kuranova, "Three-dimensional structure of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in the apo form and in complexes with coenzyme A and dephosphocoenzyme A," Crystallography Reports, vol. 57, pp. 96-104, 2012, https://doi.org/10.1134/s1063774512010142.
[60]I. Yoshizaki et al., "Growth rate measurements of lysozyme crystals under microgravity conditions by laser interferometry," Review of Scientific Instruments, vol. 84, no. 10, 2013, https://doi.org/10.1063/1.4826090.
[61]V. Timofeev, S. Kuznetsov, V. K. Akparov, G. Chestukhina, and I. Kuranova, "Three-dimensional structure of carboxypeptidase T from Thermoactinomyces vulgaris in complex with N-BOC-L-leucine," Biochemistry (Moscow), vol. 78, pp. 252-259, 2013, https://doi.org/10.1134/s0006297913030061.
[62]S. N. A. Mohamad Aris, A. L. Thean Chor, M. S. Mohamad Ali, M. Basri, A. B. Salleh, and R. N. Z. Raja Abd. Rahman, "Crystallographic analysis of ground and space thermostable T1 lipase crystal obtained via counter diffusion method approach," BioMed Research International, vol. 2014, no. 1, 2014, Art. no. 904381, https://doi.org/10.1155/2014/904381.
[63]V. Strelov, I. Kuranova, B. Zakharov, and A. Voloshin, "Crystallization in space: Results and prospects, " Crystallography Reports, vol. 59, pp. 781-806, 2014, https://doi.org/10.1134/s1063774514060285.
[64]V. K. Akparov, V. Timofeev, and I. Kuranova, "Crystallization and preliminary X-ray diffraction study of porcine carboxypeptidase B," Crystallography Reports, vol. 60, pp. 367-369, 2015, https://doi.org/10.1134/s1063774515030025.
[65]V. Timofeev, Y. A. Abramchik, N. Zhukhlistova, T. Muravieva, R. Esipov, and I. Kuranova, "Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 Å resolution," Crystallography Reports, vol. 61, pp. 44-54, 2016, https://doi.org/10.1134/s1063774516010247.
[66]H. Yoshida, A. Yoshihara, T. Ishii, K. Izumori, and S. Kamitori, "X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates," Applied Microbiology and Biotechnology, vol. 100, no. 24, pp. 10403-10415, 2016, https://doi.org/10.1007/s00253-016-7673-7.
[67]V. N. Drago et al., "Microgravity crystallization of perdeuterated tryptophan synthase for neutron diffraction," Npj Microgravity, vol. 8, no. 1, 2022, Art. no. 13, https://doi.org/10.1038/s41526-022-00199-3.
[68]W. E. Lutz et al., "Perfect crystals: Microgravity capillary counterdiffusion crystallization of human manganese superoxide dismutase for neutron crystallography," Npj Microgravity, vol. 9, no. 1, 2023, Art. no. 39, https://doi.org/10.1038/s41526-023-00288-x.
[69]F. Ferranti, M. Del Bianco, and C. Pacelli, "Advantages and limitations of current microgravity platforms for space biology research," Applied Sciences, vol. 11, no. 1, 2020, Art. no. 68, https://doi.org/10.3390/app11010068.
 
 

  • تاریخ دریافت 16 دی 1403
  • تاریخ بازنگری 17 بهمن 1403
  • تاریخ پذیرش 21 بهمن 1403
  • تاریخ اولین انتشار 01 اردیبهشت 1404