RAS BiologyБиофизика Biophysics

  • ISSN (Print) 0006-3029
  • ISSN (Online) 3034-5278

Endolysins T5 and PlyG Dynamics: Comparative Analysis in silico

PII
S00063029250820082-1
DOI
10.31857/S00063029250820082
Publication type
Article
Status
Published
Authors
Volume/ Edition
Volume 70 / Issue number 2
Pages
295-304
Abstract
Bacteriophage endolysins are part of a lytic enzymes complex responsible for the destruction of the bacterial cell wall peptidoglycan. In this paper, the dynamic properties of bacteriophage T5 single-domain endolysin and the multi-domain endolysin PlyG of gamma phage are studied using molecular dynamics and normal mode analysis. The mechanism of activation of bacteriophage T5 endolysin by calcium and the discovery of a fundamental difference in the dynamic features of single-domain and multi-domain endolysins are explained.
Keywords
эндолизин молекулярная динамика анализ нормальных мод активация кальцием динамические особенности белков
Date of publication
24.10.2025
Year of publication
2025
Number of purchasers
0
Views
18

References

  1. 1. Love M. J., Bhandari D., Dobson R. C. J., and Billington C. Potential for bacteriophage endolysins to supplement or replace antibiotics in food production and clinical care. Antibiotics (Basel, Switzerland), 7 (1), 17 (2018). DOI: 10.3390/antibiotics7010017
  2. 2. Fischetti V. A. Development of phage lysins as novel therapeutics: A historical perspective. Viruses, 10 (6), 310 (2018). DOI: 10.3390/v10060310
  3. 3. Czaplewski L., Bax R., Clokie M., Dawson M., Fairhead H., Fischetti V. A., Foster S., Gilmore B. F., Hancock R. E., Harper D., Henderson I. R., Hilpert K., Jones B. V., Kadioglu A., Knowles D., Olafsdottir S., Payne D., Projan S., Shaunak S., Silverman J., Thomas C. M., Trust T. J., Warn P., and Rex J. H. Alternatives to antibiotics −a pipeline portfolio review. Lancet. Infectious Diseases, 16 (2), 239–251 (2016). DOI: 10.1016/S1473-3099(15)00466-1
  4. 4. Vermassen A., Leroy S., Talon R., Provot C., Popowska M., and Desvaux M. Cell wall hydrolases in bacteria: Insight on the diversity of cell wall amidases, glycosidases and peptidases toward peptidoglycan. Front. Microbiol., 10, 331 (2019). DOI: 10.3389/fmicb.2019.00331
  5. 5. Wang M., Zhang J., Wei J., Jiang L., Jiang L., Sun Y., Zeng Z., and Wang Z. Phage-inspired strategies to combat antibacterial resistance. Crit. Rev. Microbial., 50 (2), 196–211 (2024). DOI: 10.1080/1040841X.2023.2181056
  6. 6. Low L. Y., Yang C., Perego M., Osterman A., and Liddington R. Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins. J. Biol. Chem., 286 (39), 34391–34403 (2011). DOI: 10.1074/jbc.M111.244160
  7. 7. Payne K. M. and Hatfull G. F. Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities. PLoS One, 7 (3), e34052 (2012). DOI: 10.1371/journal.pone.0034052
  8. 8. Oliveira H., Melo L. D., Santos S. B., Nobrega F. L., Ferreira E. C., Cerca N., Azeredo J., and Kluskens L. D. Molecular aspects and comparative genomics of bacteriophage endolysins. J. Virol., 87 (8), 4558–4570 (2013). DOI: 10.1128/JVI.03277-12
  9. 9. Son B., Kong M., and Ryu S. The auxiliary role of the amidase domain in cell wall binding and exolytic activity of staphylococcal phage endolysins. Viruses, 10 (6), 284 (2018). DOI: 10.3390/v10060284
  10. 10. Khan F. M., Chen J. H., Zhang R., and Liu B. A comprehensive review of the applications of bacteriophage-derived endolysins for foodborne bacterial pathogens and food safety: recent advances, challenges, and future perspective. Front. Microbiol., 14, 1259210 (2023). DOI: 10.3389/fmicb.2023.1259210
  11. 11. Briers Y., Volckaert G., Cornelissen A., Lagaert S., Michiels C. W., Hertveldt K., and Lavigne R. Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophages phiKZ and EL. Mol. Microbiol., 65 (5), 1334–1344 (2007). DOI: 10.1111/j.1365-2958.2007.05870.x
  12. 12. Loessner M. J., Kramer K., Ebel F., and Scherer S. C-terminal domains of Listeria monocytogenes bacteriophage murein hydrolases determine specific recognition and high-affinity binding to bacterial cell wall carbohydrates. Mol. Microbiol., 44 (2), 335–349 (2002). DOI: 10.1046/j.1365-2958.2002.02889.x
  13. 13. Oechslin F., Menzi C., Moreillon P., and Resch G. The multidomain architecture of a bacteriophage endolysin enables intramolecular synergism and regulation of bacterial lysis. J. Biol. Chem., 296, 100639 (2021). DOI: 10.1016/j.jbc.2021.100639
  14. 14. Vazquez R., Garcia E., and Garcia P. Sequence-function relationships in phage-encoded bacterial cell wall lytic enzymes and their implications for phage-derived product design. J. Virol., 95 (14), e0032121 (2021). DOI: 10.1128/JVI.00321-21
  15. 15. Atilgan C., Okan O. B., and Atilgan A. R. How orientational order governs collectivity of folded proteins. Proteins: Structure, Function, and Bioinformatics, 78 (16), 3363–3375 (2010). DOI:10.1002/prot.22843
  16. 16. Leitner M. D. Frequency-resolved communication maps for proteins and other nanoscale materials. J. Chem. Phys., 130 (19), 195101 (2009). DOI: 10.1063/1.3130149
  17. 17. Cui Q. and Bahar I. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, 1st ed. (Chapman and Hall/CRC, 2005). DOI: 10.1201/9781420035070
  18. 18. Van Wynsberghe A. W. and Cui Q. Interpreting correlated motions using normal mode analysis. Structure, 14 (11), 1647–1653 (2006). DOI: 10.1016/j.str.2006.09.003
  19. 19. Mikoulinskaia G. V., Odinokova I. V., Zimin A. A., Lysanskaya V. Y., Feofanov S. A., and Stepnaya O. A. Identification and characterization of the metal ion-dependent L-alanoyl-D-glutamate peptidase encoded by bacteriophage T5. FEBS J., 276 (24), 7329–7342 (2009). DOI: 10.1111/j.1742-4658.2009.07443.x
  20. 20. Schuch R., Nelson D., and Fischetti V. A. A bacteriolytic agent that detects and kills Bacillus anthracis. Nature, 418 (6900), 884–889 (2002). DOI: 10.1038/nature01026
  21. 21. Case D. A., Aktulga H. M., Belfon K., Cerutti D. S., Cisneros G. A., Cruzeiro V. W. D., Forouzesh N., Giese T. J., Gotz A. W., Gohlke H., Izadi S., Kasavajhala K., Kaymak M. C., King E., Kurtzman T., Lee T.-S., Li P., Liu J., Luchko T., Luo R., Manathunga M., Machado M. R., Nguyen H. M., O’Hearn K. A., Onufriev A. V., Pan F., Pantano S., Qi R., Rahnamoun A., Risheh A., Schott-Verdugo S., Shajan A., Swails J., Wang J., Wei H., Wu X., Wu Y., Zhang Sh., Zhao Sh., Zhu Q., Cheatham III Th. E., Roe D. R., Roitberg A., Simmerling C., York D. M., Nagan M. C., and Merz K. M. Jr. AmberTools. J. Chem. Inf. Model., 63 (20), 6183–6191 (2023). DOI: 10.1021/acs.jcim.3c01153
  22. 22. Grant B. J., Rodrigues A. P., ElSawy K. M., McCammon J. A., and Caves L. S. Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics, 22 (21), 2695–2696 (2006). DOI: 10.1093/bioinformatics/btl461
  23. 23. Prokhorov D., Mikoulinskaia G., Kutyshenko V., and Uversky V. Structural basis of activation of zinc-dependent peptidase of the bacteriophage T5 by calcium ions: A glance at the ion-dependent functioning proteoforms. Preprints, 2024072561 (2024). DOI: 10.20944/preprints202407.2561.v1
QR
Translate

Индексирование

Scopus

Scopus

Scopus

Crossref

Scopus

Higher Attestation Commission

At the Ministry of Education and Science of the Russian Federation

Scopus

Scientific Electronic Library