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Akbari Azam, Maryam, Motalebi, Abbas Ali, Nassiri, Mohammadreaza, Anvar, Amir. (1404). The Recombinant Production of Novel Bovine Lactoferricin Engineered Peptide Using Molecular Dynamics Simulation. سامانه مدیریت نشریات علمی, 80(4), 995-1003. doi: 10.61882/ARI.80.4.995
Maryam Akbari Azam; Abbas Ali Motalebi; Mohammadreaza Nassiri; Amir Ali Anvar. "The Recombinant Production of Novel Bovine Lactoferricin Engineered Peptide Using Molecular Dynamics Simulation". سامانه مدیریت نشریات علمی, 80, 4, 1404, 995-1003. doi: 10.61882/ARI.80.4.995
Akbari Azam, Maryam, Motalebi, Abbas Ali, Nassiri, Mohammadreaza, Anvar, Amir. (1404). 'The Recombinant Production of Novel Bovine Lactoferricin Engineered Peptide Using Molecular Dynamics Simulation', سامانه مدیریت نشریات علمی, 80(4), pp. 995-1003. doi: 10.61882/ARI.80.4.995
Akbari Azam, Maryam, Motalebi, Abbas Ali, Nassiri, Mohammadreaza, Anvar, Amir. The Recombinant Production of Novel Bovine Lactoferricin Engineered Peptide Using Molecular Dynamics Simulation. سامانه مدیریت نشریات علمی, 1404; 80(4): 995-1003. doi: 10.61882/ARI.80.4.995

The Recombinant Production of Novel Bovine Lactoferricin Engineered Peptide Using Molecular Dynamics Simulation

Archives of Razi Institute
مقاله 21، دوره 80، شماره 4، مهر و آبان 2025، صفحه 995-1003    اصل مقاله (467.97 K)
نوع مقاله: Original Articles
شناسه دیجیتال (DOI): 10.61882/ARI.80.4.995
نویسندگان
Maryam Akbari Azam1؛ Abbas Ali Motalebi1؛ Mohammadreaza Nassiri* 2؛ Amir Ali Anvar1
1Department of Food Hygiene, Science and Research Branch, Islamic Azad University, Tehran. Iran.
2Department of Animal Science, Faculty of agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
چکیده
Antimicrobial peptides (AMPs) are native and safe short peptides that are considered one of the best alternatives for antibiotics. Although numerous studies have been conducted on AMPs, their mode of action has not yet been fully understood. Computational peptide engineering can provide valuable insight into the stability and potency of AMPs against targets. In the present study, we performed a molecular dynamics simulation study to understand the mode of action of Bovine Lfcin and to improve the interactions between Bovine Lfcin (wild and mutant types) and DNA (an important intracellular target), DNAK (an important protein in pathogenicity, mostly in gram-negative bacteria), and LysM (an important surface protein in gram-positive bacteria). The nucleotide sequence of Lfcin peptide was synthesized and cloned in pET22b (+). Induction of gene expression was done using 1mM IPTG and recombinant peptide was purified using His-tag marker. The antimicrobial peptide activity was performed on Escherichia coli O157 and Bacillus subtilis Gram- negative and positive bacteria using disk diffusion methods, respectively. Our results showed that all the changes in Bovine Lfcin wild type observed in this study improved the peptide-DNA, DNAK, and LysM interactions. Based on the results, removing the PHE25 residue from the wild type Bovine Lfcin peptide had more significant effects on complex formation with DNA, DNAK, and LysM. The recombinant production of a Lfcin peptide with a molecular weight of ~5 KDa was confirmed by SDS PAGE. The performance of Lfcin peptide on pathogenic bacteria was strong and it had the strongest effect in concentrations of 6 and 8 mg/ml for gram positive and negative bacteria, respectively.
کلیدواژه‌ها
Antimicrobial peptides, Bovine Lfcin؛ Recombinant Protein
عنوان مقاله [English]
تولید نوترکیب پپتید ضدمیکروبی مهندسی شده لاکتوفرسین با استفاده از محاسبات دینامیک مولکلولی
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مراجع
  1. Kaufmann H, Medzhitov R, Gordon S. The Innate Immune Response to Infection. Washington, DC, USA: ASM Press. 2004. P. 324-450.
  2. Coccolini C, Berselli E, Blanco-Llamero C. Biomedical and Nutritional Applications of Lactoferrin. Int J Pept Res Ther. 2023; 29, 71.
  3. Elass-Rochard E, Roseanu A, Legrand D, Trif M, Salmon V, Motas C, Montreuil J, Spik G. Lactoferrin-lipopolysaccharide interaction: involvement of the 28-34 loop region of human lactoferrin in the high-affinity binding to Escherichia coli 055B5 lipopolysaccharide. Biochem J. 1995; 15;312 ( Pt 3)(Pt 3):839-45.
  4. Ramírez-Rico G, Martinez-Castillo M, Avalos-Gómez C, de la Garza M. Bovine apo-lactoferrin affects the secretion of proteases in Mannheimia haemolytica Access Microbiol. 2021; 25;3(10):000269.
  5. Gu Y, Stansfeld PJ, Zeng Y, Dong H, Wang W, Dong C. Lipopolysaccharide is inserted into the outer membrane through an intramembrane hole, a lumen gate, and the lateral opening of LptD. Structure. 2015; 3;23(3):496-504.
  6. Li J, Koh JJ, Liu S, Lakshminarayanan R, Verma CS, Beuerman RW. Membrane Active Antimicrobial Peptides: Translating Mechanistic Insights to Design. Front Neurosci. 2017; 14;11:73.
  7. Vorland LH. Lactoferrin: a multifunctional glycoprotein. Acta Pathologica, Microbiologica et Immunologica Scandinavica. 1999;107(11):971–981.
  8. Farnaud S, Evans RW. Lactoferrin—a multifunctional protein with antimicrobial properties. Molecular Immunology. 2003;40(7):395–405.
  9. Zhang QY, Yan ZB, Meng YM. Antimicrobial peptides: mechanism of action, activity and clinical potential. Military Med Res. 2021;8, 48.
  10. Hiltunen T, Virta M, Laine AL. Antibiotic resistance in the wild: an eco-evolutionary perspective. Philos Trans R Soc Lond B Biol Sci. 2017;372(1712):20160039.
  11. Wang J, Dou X, Song J, Lyu Y, Zhu X, Xu L. Antimicrobial peptides: promising alternatives in the post feeding antibiotic era. Med Res Rev. 2019;39(3):831–59.
  12. Assoni L, Milani B, Carvalho MR, Nepomuceno LN, Waz NT, Guerra MES, Converso TR, Darrieux M. Resistance Mechanisms to Antimicrobial Peptides in Gram-Positive Bacteria. Front Microbiol. 2020; 21;11:593215.
  13. Pirtskhalava M, Vishnepolsky B, Grigolava M, Managadze G. Physicochemical Features and Peculiarities of Interaction of AMP with the Membrane. Pharmaceuticals (Basel). 2021 17;14(5):471.
  14. Lyu Z; Yang P; Lei J; Zhao J. Biological Function of Antimicrobial Peptides on Suppressing Pathogens and Improving Host Immunity. 2023; 12, 1037.
  15. Wadhwani P, Epand RF, Heidenreich N, Bürck J, Ulrich AS, Epand RM. Membrane-active peptides and the clustering of anionic lipids. Biophys J. 2012; 18;103(2):265-74.
  16. Stark M, Liu LP, Deber CM. Cationic hydrophobic peptides with antimicrobial activity. Antimicrob Agents Chemother. 2002; 46(11):3585-90.
  17. Lei J, Sun L, Huang S, Zhu C, Li P, He J, Mackey V, Coy DH, He Q. The antimicrobial peptides and their potential clinical applications. Am J Transl Res. 2019;15;11(7):3919-3931.
  18. Kumar P, Kizhakkedathu JN, Straus SK. Antimicrobial Peptides: Diversity, Mechanism of Action and Strategies to Improve the Activity and Biocompatibility In Vivo. Biomolecules. 2018;19;8(1):4.
  19. Paiva AD, Breukink E, Mantovani HC. Role of lipid II and membrane thickness in the mechanism of action of the lantibiotic bovicin HC5. Antimicrob Agents Chemother. 2011; 55(11):5284-93.
  20. Oñate-Garzón J, Manrique-Moreno M, Trier S. Antimicrobial activity and interactions of cationic peptides derived from Galleria mellonella cecropin D-like peptide with model membranes. J Antibiot. 2017; 70, 238–245.
  21. Hollmann A, Martinez M, Maturana P, Semorile LC, Maffia PC. Antimicrobial Peptides: Interaction With Model and Biological Membranes and Synergism With Chemical Antibiotics. Front Chem. 2018; 5;6:204.
  22. Palmer N, Maasch JRMA, Torres MDT, de la Fuente-Nunez C. Molecular Dynamics for Antimicrobial Peptide Discovery. Infect Immun. 2021;17;89(4):e00703-20.
  23. Śledź P, Caflisch A. Protein structure-based drug design: from docking to molecular dynamics. Curr Opin Struct Biol. 2018;48:93–102.
  24. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics. 2006;Chapter 5:Unit-5.6.
  25. Laskowski RA, MacArthur MW, Moss DS, Thornton PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993;26, 283-291.
  26. Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1-2:19–25.
  27. MacKerell AD Jr, Banavali N, Foloppe N. Development and current status of the CHARMM force field for nucleic acids. Biopolymers. 2000-2001;56(4):257-65.
  28. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction Models for Water in Relation to Protein Hydration. In: Pullman, B. (eds) Intermolecular Forces. The Jerusalem Symposia on Quantum Chemistry and Biochemistry. 1981; vol 14. Springer, Dordrecht.
  29. Nosé S, Klein ML. Constant pressure molecular dynamics for molecular systems, Molecular Physics. 1983;50:5, 1055-1076.
  30. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res. 2000;33(12):889-97.
  31. Taghizadegan N, Firozrai M, Nassiri M. Ariannejad H. Use of Molecular Dynamic Tools in Engineering of Onconase Enzyme to Increase Cellular Uptake and Evade RI. Int J Pept Res Ther. 2020; 26, 737–743.
  32. Schimek C, Egger E, Tauer C, Striedner G, Brocard C, Cserjan-Puschmann M, Hahn R. Extraction of recombinant periplasmic proteins under industrially relevant process conditions: Selectivity and yield strongly depend on protein titer and methodology. Biotechnol Prog. 2020;Sep;36(5):e2999.
  33. Huang YC, Lin YM, Chang TW, Wu SJ, Lee .S. The flexible and clustered lysine residues of human ribonuclease 7 are critical for membrane permeability and antimicrobial activity, J BiolChem. 2007;(282): 4626-4633.
  34. Mercer DK, Torres MDT, Duay SS, Lovie E, Simpson L, von Köckritz-Blickwede M, de la Fuente-Nunez C, O'Neil DA, Angeles-Boza AM. Antimicrobial Susceptibility Testing of Antimicrobial Peptides to Better Predict Efficacy. Front Cell Infect Microbiol. 2020;7;10:326.
  35. O'Neill J. Tackling drug-resistant infections globally: Final report and recommendations: Review on antimicrobial resistance. 2016; 1–76.
  36. El-Kafrawy SA, Abbas AT, Oelkrug C, Tahoon M, Ezzat S, Zumla A, Azhar EI. IgY antibodies: The promising potential to overcome antibiotic resistance. Front Immunol. 2023;20;14:1065353.
  37. Bahar AA, Ren D. Antimicrobial peptides. Pharmaceuticals (Basel) 2013;6:1543–75.
  38. Zanetti Cathelicidins, multifunctional peptides of the innate immunity. J Leukoc Biol. 2004;75:39–48.
  39. Lei J, Sun L, Huang S, Zhu C, Li P, He J, Mackey V, Coy DH, He Q. The antimicrobial peptides and their potential clinical applications. Am J Transl Res. 2019;15;11(7):3919-3931.
  40. Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, Wang Y, Roux B, Aksimentiev A, Luthey-Schulten Z, Kalé LV, Schulten K, Chipot C, Tajkhorshid E. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys. 2020; 153:044130.
  41. Pourmousa M, Song HD, He Y, Heinecke JW, Segrest JP, Pastor RW. Tertiary structure of apolipoprotein A-I in nascent high-density lipoproteins. Proc Natl Acad Sci U S A. 2018;115:5163–5168.
  42. Nguyen LT, Haney EF, Vogel HJ. The expanding scope of antimicrobial peptide structures and their modes of action. Trends Biotechnol.2011; 29:464–472.
  43. Koehbach J, Craik DJ. The vast structural diversity of antimicrobial peptides. Trends Pharmacol Sci. 2019; 40:517–528.
  44. Torres MDT, Pedron CN, Araújo I, Silva PI, Silva FD, Oliveira VX. Decoralin analogs with increased resistance to degradation and lower hemolytic activity. ChemistrySelect. 2017; 2:18–23.
  45. Potaman VN, Sinden RR. DNA: Alternative Conformations and Biology. In: Madame Curie Bioscience Database [Internet]. Austin (TX). Landes Bioscience. 2000-2013; Available from: https://www.ncbi.nlm.nih.gov/books/NBK6545/.
  46. Fourie KR; Wilson HL. Understanding GroEL and DnaK Stress Response Proteins as Antigens for Bacterial Diseases. 2020; 8, 773.
  47. Shao X, Jiang M, Yu Z. Surface display of heterologous proteins in Bacillus thuringiensis using a peptidoglycan hydrolase anchor. Microb Cell Fact. 2009; 8, 48 (2009).
  48. Rizzetto G, Gambini D, Maurizi A, Molinelli E, De Simoni E, Pallotta F, Brescini L, Cirioni O, Offidani A, Simonetti O, Giacometti A. The sources of antimicrobial peptides against Gram-positives and Gramnegatives: our research experience. Infez Med. 2023;1;31(3):306-322.
  49. Sinha M, Kaushik S, Kaur P, Sharma S, Singh TP. Antimicrobial lactoferrin peptides: the hidden players in the protective function of a multifunctional protein. Int J Pept. 2013;2013:390230.
  50. Munk JK, Ritz C, Fliedner FP, Frimodt-Møller N, Hansen PR. Novel method to identify the optimal antimicrobial peptide in a combination matrix, using anoplin as an example. Antimicrob Agents Chemother. 2014;58(2):1063-70.
  51. Chen L, Shen T, Liu Y. Enhancing the antibacterial activity of antimicrobial peptide PMAP-37(F34-R) by cholesterol modification. BMC Vet Res. 2020;16, 419.
  52. Wiradharma N, Sng MYS, Khan M, Ong ZY, Yang YY. Rationally designed α-helical broad-spectrum antimicrobial peptides with idealized facial amphiphilicity. Macromol Rapid Commun. 2013;34(1):74–80.
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