نانومقیاس

نانومقیاس

مطالعه مقایسه‌ای نوع وحشی و جهش‌یافته آنزیم کربنیک انیدراز II انسانی با استفاده از شبیه‌سازی دینامیک مولکولی

نوع مقاله : مقاله پژوهشی

نویسندگان
1 گروه بیوفیزیک، دانشکده علوم زیستی، دانشگاه تربیت مدرس، تهران، ایران.
2 گروه بیوفیزیک، دانشکده علوم زیستی، دانشگاه تربیت مدرس، تهران، ایران
چکیده
آنزیم کربنیک انیدراز II پروتئینی سیتوزولی واقع در غشای گلبول‌های قرمز است که در فرایندهای فیزیولوژیکی و پاتولوژیکی مختلفی شرکت دارد. این آنزیم به‌طور مؤثر هیدراتاسیون برگشت‌پذیر دی‌اکسید کربن را نیز کاتالیز می‌کند. با توجه ‌به نقش مهم آنزیم مذکور، در این مطالعه از روش محاسباتی شبیه‌سازی دینامیک مولکولی (MD) برای مطالعه ساختار و دینامیک آنزیم وحشی و چند آنزیم‌ جهش‌یافته استفاده شد. بر اساس مطالعات تجربی گذشته، آنزیم‌های جهش‌یافته این مطالعه، در جهت افزایش فعالیت سینتیکی و یا تغییر در پایداری آنزیم اثرگذار هستند. در ابتدا مطالعات مکانیک کوانتومی و سپس MD انجام شد. طبق نتایج، مشاهده شد که آنزیم طبیعی ازنظر انرژی پتانسیل و انرژی آزاد گیبس در وضعیت مطلوب و پایداری قرار دارد، همچنین با توجه ‏به RMSD،RMSF وRg مشخص شد آنزیم جهش‌یافته‌ای که بر فعالیت آنزیم تأثیرگذار است نسبت به سایر آنزیم‌ها دارای پایداری بیشتر، نوسانات و شعاع ژیراسیون کمتری است. در دو جهش‌یافته دیگر که بر پایداری آنزیم نیز اثرگذار بودند، نسبت به دو آنزیم قبل، پایداری کمتر و نوسانات و سطح انرژی پتانسیل بالاتری مشاهده شد، که باعث ناپایداری این آنزیم‏ها در طول شبیه‌سازی می‌شد. این نتایج می‌توانند در مهندسی و طراحی واریانت‌های جدیدی از آنزیم کربنیک انیدراز کمک‌کننده باشند.
کلیدواژه‌ها

موضوعات


عنوان مقاله English

Comparative study of wild-type and mutant human carbonic anhydrase II enzymes using molecular dynamics simulation

نویسندگان English

Maryam Mapar 1
Majid Taghdir 2
Bijan Ranjbar 2
1 Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran , Iran
2 Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
چکیده English

The human enzyme carbonic anhydrase II (HCA II) is a cytosolic protein located in the membrane of red blood cells, and it is involved in various physiological and pathological processes. It can catalyze the reversible hydration of carbon dioxide efficiently. Given the critical role of the HCA II, computational methods such as molecular dynamics simulation (MD) are used to study the structure and dynamics of the wild-type and the mutant enzymes. Based on the previous experimental studies, mutant enzymes enhance kinetic activity or decrease stability. Before MD, quantum mechanics studies were performed. The native enzyme was in a stable state after MD in terms of potential energy and Gibbs-free energy. As evidenced by RMSD, RMSF, and Rg, One of the mutated enzymes that affect the activity of the enzyme has more stability, less fluctuation, and less Rg than other enzymes. In two other mutants that also affected the stability of the enzyme, compared to the previous two enzymes, lower stability, more fluctuations, and potential energy level were observed, which caused the instability of these enzymes during the simulation. These results can help in the engineering and design of new variants of carbonic anhydrase enzyme.

کلیدواژه‌ها English

Human Carbonic Anhydrase II
Molecular Dynamics
Mutation
Stability
Activity
[1] Hewett-Emmett, D. and R.E. Tashian, Functional diversity, conservation, and convergence in the evolution of the α-, β-, and γ-carbonic anhydrase gene families. Molecular phylogenetics and evolution, 1996. 5(1): p. 50-77.
[2] Salemi, Z., S. Hosseinkhani, B. Ranjbar, and M. Nemat-Gorgani, Interaction of native and apo-carbonic anhydrase with hydrophobic adsorbents: A comparative structure-function study. BMB Reports, 2006. 39(5): p. 636-641.
[3] Center of Computational Structural Biology (CCSB) - Scripps Research. 2021. Revision 8604f73b.
[4] Shaik, N.A., et al., Molecular modelling and dynamics of CA2 missense mutations causative to carbonic anhydrase 2 deficiency syndrome. Journal of Biomolecular Structure and Dynamics, 2020. 38(14): p. 4067-4080.
[5] Fisher, Z., et al., Kinetic and structural characterization of thermostabilized mutants of human carbonic anhydrase II. Protein Engineering, Design & Selection, 2012. 25(7): p. 347-355.
[6] Silverman, D.N. and S. Lindskog, The catalytic mechanism of carbonic anhydrase: implications of a rate-limiting protolysis of water. Accounts of Chemical Research, 1988. 21(1): p. 30-36.
[7] Wambo, T.O., L.Y. Chen, S.F. McHardy, and A.T. Tsin, Molecular dynamics study of human carbonic anhydrase II in complex with Zn2+ and acetazolamide on the basis of all-atom force field simulations. Biophysical chemistry, 2016. 214: p. 54-60.
[8] Aggarwal, M., C.D. Boone, B. Kondeti, and R. McKenna, Structural annotation of human carbonic anhydrases. Journal of enzyme inhibition and medicinal chemistry, 2013. 28(2): p. 267-277.
[9] Bauer, C., G. Gros, and H. Bartels, Biophysics and Physiology of Carbon Dioxide: Symposium Held at the University of Regensburg (FRG) April 17–20, 1979. 2013: Springer Science & Business Media.
[10] Mishra, C.B., M. Tiwari, and C.T. Supuran, Progress in the development of human carbonic anhydrase inhibitors and their pharmacological applications: Where are we today? Medicinal Research Reviews, 2020. 40(6): p. 2485-2565.
[11] Liang, J.-Y. and W.N. Lipscomb, Binding of substrate CO2 to the active site of human carbonic anhydrase II: a molecular dynamics study. Proceedings of the National Academy of Sciences, 1990. 87(10): p. 3675-3679.
[12] Håkansson, K. and A. Wehnert, Structure of cobalt carbonic anhydrase complexed with bicarbonate. Journal of molecular biology, 1992. 228(4): p. 1212-1218.
[13] Fisher, S.Z., et al., Speeding up proton transfer in a fast enzyme: Kinetic and crystallographic studies on the effect of hydrophobic amino acid substitutions in the active site of human carbonic anhydrase II. Biochemistry, 2007. 46(12): p. 3803-3813.
[14] Elleby, B., B. Sjöblom, and S. Lindskog, Changing the efficiency and specificity of the esterase activity of human carbonic anhydrase II by site‐specific mutagenesis. European journal of biochemistry, 1999. 262(2): p. 516-521.
[15] Carlsson, U. and B.-H. Jonsson, Folding and stability of human carbonic anhydrase II. The carbonic anhydrases: New horizons, 2000: p. 241-259.
[16] Mahon, B.P., M.A. Pinard, and R. McKenna, Targeting carbonic anhydrase IX activity and expression. Molecules, 2015. 20(2): p. 2323-2348.
[17] DeepView–Swiss, P., Home Page. Viewer http://www. expasy. org/spdbv (accessed Jan 2008).(b) Guex, N.; Peitsch, M. C. Electrophoresis, 1997. 18: p. 2714-2723.
[18] Sarraf, N., A. Saboury, B. Ranjbar, and A. Moosavi-Movahedi, Structural and functional changes of bovine carbonic anhydrase as a consequence of temperature. Acta Biochimica Polonica, 2004. 51(3): p. 665-671.
[19] Chen, G., D. Lu, J. Wu, and Z. Liu, Detachment of HCO3–from the Active Site of Carbonic Anhydrase: Molecular Dynamics Simulation and Machine Learning. The Journal of Physical Chemistry C, 2018. 122(35): p. 20539-20549.
[20] Ryckaert, J.-P., G. Ciccotti, and H.J. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of computational physics, 1977. 23(3): p. 327-341.
[21] Nasiripourdori, A., B. Ranjbar, and H. Naderi-Manesh, Binding of long-chain α-neurotoxin would stabilize the resting state of nAChR: A comparative study with α-conotoxin. Theoretical Biology and Medical Modelling, 2009. 6: p. 1-15.
[22] Amadei, A., A.B. Linssen, and H.J. Berendsen, Essential dynamics of proteins. Proteins: Structure, Function, and Bioinformatics, 1993. 17(4): p. 412-425.
[23] Tavassoli, Z., M. Taghdir, and B. Ranjbar, Renin inhibition by soyasaponin I: A potent native anti-hypertensive compound. Journal of Biomolecular Structure and Dynamics, 2018. 36(1): p. 166-176.
[24] Schreiner, W., R. Karch, B. Knapp, and N. Ilieva, Relaxation estimation of RMSD in molecular dynamics immunosimulations. Computational and mathematical methods in medicine, 2012. 2012.
[25] Rahimi, M., M. Taghdir, and F. Abasi Joozdani, Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease. Scientific Reports, 2023. 13(1): p. 14179.
[26] Dabirmanesh, B., et al., Inhibition mediated stabilization effect of imidazolium based ionic liquids on alcohol dehydrogenase. Journal of Molecular Liquids, 2012. 170: p. 66-71.
[27] Ali, S., et al., Identification and evaluation of inhibitors of lipase from Malassezia restricta using virtual high-throughput screening and molecular dynamics studies. International journal of molecular sciences :(4)20.2019,p. 884.
[28] Karbassi, F., et al., Activity, structural and stability changes of mushroom tyrosinase by sodium dodecyl sulfate. Colloids and surfaces B: Biointerfaces, 2003. 32(2): p. 137-143.
[29] Kannan, K., et al., Crystal structure of human erythrocyte carbonic anhydrase B. Three-dimensional structure at a nominal 2.2-A resolution. Proceedings of the National Academy of Sciences, 1975. 72(1): p. 51-55.
[30] Sarraf, N., A. Saboury, B. Ranjbar, and M. Nemat-Gorgani, Effect of some amino acids on the structure and activity of carbonic anhydrase. Asian Journal of Chemistry, 2005. 17(4): p. 2385.
[31] Ranjbar, B., K. Khalifeh, and S. Shirdel, Biophysical Chemistry. 2023, Iran: Tarbiat Modares University. 416. [In persian].
 
دوره 11، شماره 1
بهار 1403
صفحه 53-42

  • تاریخ دریافت 08 اسفند 1402
  • تاریخ پذیرش 18 اردیبهشت 1403