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BioTechnologia
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3/2024
vol. 105
 
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RESEARCH PAPERS

Investigation of the new substitution glycine to alanine within the Kringle-2 domain of reteplase: a molecular dynamics study

Kaveh Haji-Allahverdipoor
1
,
Habib Eslami
2
,
Koosha Rokhzadi
1
,
Mokhtar Jalali Javaran
3
,
Sajad Rashidi Monfared
3
,
Mohamad Bagher Khademerfan
1

  1. Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
  2. Department of Pharmacology and Toxicology, Faculty of Pharmacy, Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medicinal Sciences, Bandar Abbas, Iran
  3. Department of Plant Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
BioTechnologia vol. 105 (3) ∙ pp. 201–213 ∙ 2024
Online publish date: 2024/09/30
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1. Abraham M.J., Murtola T., Schulz R., Páll S., Smith J.C., Hess B., et al. (2015) GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1: 19–25.
2. Anfray A., et al. (2021) Single-and two-chain tissue-type plasminogen activator treatments differentially influence cerebral recovery after stroke. Experim. Neurol. 338: 113606.
3. Bertrand T., Lesept F., Chevilley A., Lenoir S., Aimable M., Briens A., et al. (2015) Conformations of tissue plasminogen activator (tPA) orchestrate neuronal survival by a crosstalk between EGFR and NMDAR. Cell Death Dis. 6(10): e1924.
4. David C.C., Jacobs D.J. (2014) Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol. Biol. 1084: 193–226.
5. De Vos A.M., Ultsch M.H., Kelley R.F., Padmanabhan K., Tulinsky A., Westbrook M.L., et al. (1992) Crystal structur of the kringle 2 domain of tissue plasminogen activator at 2.4-. ANG. resolution. Biochemistry 31(1): 270–279.
6. Falconi M., Parrilli L., Battistoni A., Desideri A. (2002) Flexibility in monomeric Cu, Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation. Proteins 47(4): 513–520.
7. Giuliani A. (2017) The application of principal component analysis to drug discovery and biomedical data. Drug Discov. Today 22(7): 1069–1076.
8. Grant B.J., Rodrigues A.P., ElSawy K.M., McCammon J.A., Caves L.S. (2006) Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics 22(21): 2695–2696.
9. Jickling G.C., Liu D., Stamova B., Ander B.P., Zhan X., Lu A., et al. (2014) Hemorrhagic transformation after ischemic stroke in animals and humans. J. Cerebr. Blood Flow Metabol. 34(2): 185–199.
10. Keragala C.B., Woodruff T.M., Liu Z., Niego B., Ho H., McQuilten Z., et al. (2020) Tissue-type plasminogen activator and tenecteplase-mediated increase in blood brain barrier permeability involves cell intrinsic complement. Front. Neurol. 11: 577272.
11. Eslami H., Rokhzadi K., Basiri M., Esmaeili-Mahani S., Mahmoodi Z., Haji-Allahverdipoor K. (2024) Direct interaction of minocycline to p47phox contributes to its attenuation of TNF-α-mediated neuronal PC12 cell death: experimental and simulation validation. Cell Biochem. Biophys. https:// doi.org/10.1007/s12013-024-01382-x
12. Kulshreshtha S., Chaudhary V., Goswami G.K., Mathur N. (2016) Computational approaches for predicting mutant protein stability. J. Comput. Aided Mol. Design 30: 401–412.
13. Lopez-Atalaya J.P., Roussel B.D., Levrat D., Parcq J., Nicole O., Hommet Y., et al. (2008) Toward safer thrombolytic agents in stroke: molecular requirements for NMDA receptor-mediated neurotoxicity. J. Cerebr. Blood Flow Me-tabol. 28(6): 1212–1221.
14. Nicole O., Docagne F., Ali C., Margaill I., Carmeliet P., MacKenzie E.T., et al. (2001) The proteolytic activity of tissue-plasminogen activator enhances NMDA receptor-mediated signaling. Nature Med. 7(1): 59–64.
15. Pace C.N., Fu H., Fryar K.L., Landua J., Trevino S.R., Shirley B.A., et al. (2011) Contribution of hydrophobic inter-actions to protein stability. J. Mol. Biol. 408(3): 514–528.
16. Parcq J., Bertrand T., Baron A., Hommet Y., Angles-Cano E., Vivien D. (2013) Molecular requirements for safer generation of thrombolytics by bioengineering the tissue-type plasminogen activator A chain. J. Thromb. Haemost. 11(3): 539–546.
17. Pontiggia F., Pachov D., Clarkson M., Villali J., Hagan M., Pande V., et al. (2015) Free energy landscape of activation in a signalling protein at atomic resolution. Nature Commun. 6(1): 7284.
18. RCSB (2021) PDB Data Bank https://www.rcsb.org/
19. Renatus M., Engh R.A., Stubbs M.T., Huber R., Fischer S., Kohnert U., et al. (1997) Lysine 156 promotes the ano-malous proenzyme activity of tPA: X-ray crystal structure of single-chain human tPA. The EMBO J. 16(16): 4797–4805.
20. Rocco A.G., Mollica L., Gianazza E., Calabresi L., Franceschini G., Sirtori C.R., et al. (2006) A model structure for the heterodimer apoA-IMilano–apoA-II supports its peculiar susceptibility to proteolysis. Biophys. J. 91(8): 3043–3049.
21. Salleh A.B., Rahim A., Rahman R., Leow T.C., Basri M. (2012) The role of Arg157Ser in improving the compactness and stability of ARM lipase. J. Comput. Sci. Syst. Biol. 5(2): 39–46.
22. Salsbury Jr. F.R. (2010) Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Curr. Opin. Pharmacol. 10(6): 738–744.
23. Saravanan P., Dubey V.K., Patra S. (2014) Emulating structural stability of Pseudomonas mendocina lipase: in silico mutagenesis and molecular dynamics studies. J. Mol. Model. 20: 1–12.
24. Touw W.G., Baakman C., Black J., Te Beek T.A., Krieger E., Joosten R.P., et al. (2015) A series of PDB-related data-banks for everyday needs. Nucl. Acids Res. 43(D1): D364–D368.
25. Turner P. (2005) XMGRACE, Version 5.1. 19. Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology, Beaverton, OR.
26. Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J.C. (2005) GROMACS: fast, flexible, and free. J. Comput. Chem. 26(16): 1701–1718.
27. Webb B., Sali A. (2016) Comparative protein structure modeling using MODELLER. Curr. Protocol. Bioinformatics 54(1): 5.6.1–5.6.37.
28. Wijesinha-Bettoni R., Alexeev Y., Johnson P., Marsh J., Sancho A.I., Abdullah U.S., et al. (2010) The structural characteristics of nonspecific lipid transfer proteins explain their resistance to gastroduodenal proteolysis. Biochemistry 49(10): 2130–2139.
29. Yepes M., Roussel B.D., Ali C., Vivien D. (2009) Tissue-type plasminogen activator in the ischemic brain: more than a thrombolytic. Trends Neurosci. 32(1): 48–55.
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