Skip to content
2000
image of Design and Characterization of Antibacterial Peptide Nanofibrils as Components of Composites for Biomaterial Applications

Abstract

Purpose

The purpose of this study was to design and synthesize the ug46 peptide, incorporate its fibrils into composite materials, and evaluate its structural and antimicrobial properties. Another objective was to utilize spectroscopy and molecular simulation, enhanced by Machine Vision methods, to monitor the aggregation process of the ug46 peptide and assess its potential as a scaffold for an antimicrobial peptide.

Method

The structural analysis of the ug46 peptide reveals its dynamic conformational changes. Initially, the peptide exhibits a disordered structure with minimal α-helix content, but as incubation progresses, it aggregates into fibrils rich in β-sheets. This transformation was validated by CD and ThT assays, which showed decreased molar ellipticity and an increase in ThT fluorescence.

Results

Laser-induced fluorescence and molecular dynamics simulations further revealed the transition from a compact native state to extended “worm-like” filament structures, influenced by peptide concentration and temperature. TEM and AFM confirmed these changes, showing the evolution of protofibrils into mature fibrils with characteristic twists. When incorporated into chitosan-bioglass composites, these fibrils significantly enhanced antimicrobial activity against pathogens such as and .

Conclusion

Overall, ug46 peptide fibrils show promise as a multifunctional scaffold with structural and antimicrobial benefits in composite biomaterials.

Loading

Article metrics loading...

/content/journals/cpps/10.2174/0113892037353453241219185311
2025-02-19
2025-05-16
Loading full text...

Full text loading...

References

  1. Li J. Koh J.J. Liu S. Lakshminarayanan R. Verma C.S. Beuerman R.W. Membrane active antimicrobial peptides: Translating mechanistic insights to design. Front. Neurosci. 2017 11 FEB 73 10.3389/fnins.2017.00073 28261050
    [Google Scholar]
  2. Li L. Sun J. Xia S. Tian X. Cheserek M.J. Le G. Mechanism of antifungal activity of antimicrobial peptide APP, a cell-penetrating peptide derivative, against Candida albicans: Intracellular DNA binding and cell cycle arrest. Appl. Microbiol. Biotechnol. 2016 100 7 3245 3253 10.1007/s00253‑015‑7265‑y 26743655
    [Google Scholar]
  3. Grafskaia E. Pavlova E. Babenko V.V. Latsis I. Malakhova M. Lavrenova V. Bashkirov P. Belousov D. Klinov D. Lazarev V. The Hirudo medicinalis microbiome is a source of new antimicrobial peptides. Int. J. Mol. Sci. 2020 21 19 7141 10.3390/ijms21197141 32992666
    [Google Scholar]
  4. Zheng M. Wang R. Chen S. Zou Y. Yan L. Zhao L. Li X. Design, synthesis and antifungal activity of stapled aurein1.2 peptides. Antibiotics 2021 10 8 956 10.3390/antibiotics10080956 34439006
    [Google Scholar]
  5. Sepehri Z. Kiani Z. Kohan F. Alavian S.M. Ghavami S. Toll like receptor 4 and hepatocellular carcinoma; A systematic review. Life Sci. 2017 179 80 87 10.1016/j.lfs.2017.04.025 28472619
    [Google Scholar]
  6. Xia S Liu M Wang C. Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res. 2020 30 4 343 355 10.1038/s41422‑020‑0305‑x 32231345
    [Google Scholar]
  7. Souza P.F.N. Lopes F.E.S. Amaral J.L. Freitas C.D.T. Oliveira J.T.A. A molecular docking study revealed that synthetic peptides induced conformational changes in the structure of SARS-CoV-2 spike glycoprotein, disrupting the interaction with human ACE2 receptor. Int. J. Biol. Macromol. 2020 164 66 76 10.1016/j.ijbiomac.2020.07.174 32693122
    [Google Scholar]
  8. Loffredo M.R. Nencioni L. Mangoni M.L. Casciaro B. Antimicrobial peptides for novel antiviral strategies in the current post-COVID-19 pandemic. J. Pept. Sci. 2024 30 1 e3534 10.1002/psc.3534 37501572
    [Google Scholar]
  9. Gawde U. Chakraborty S. Waghu F.H. Barai R.S. Khanderkar A. Indraguru R. Shirsat T. Idicula-Thomas S. CAMPR4: A database of natural and synthetic antimicrobial peptides. Nucleic Acids Res. 2023 51 D1 D377 D383 10.1093/nar/gkac933 36370097
    [Google Scholar]
  10. Wu D. Gao Y. Qi Y. Chen L. Ma Y. Li Y. Peptide-based cancer therapy: Opportunity and challenge. Cancer Lett. 2014 351 1 13 22 10.1016/j.canlet.2014.05.002 24836189
    [Google Scholar]
  11. Ma R. Wong S.W. Ge L. Shaw C. Siu S.W.I. Kwok H.F. In vitro and md simulation study to explore physicochemical parameters for antibacterial peptide to become potent anticancer peptide. Mol. Ther. Oncolytics 2020 16 7 19 10.1016/j.omto.2019.12.001 31909181
    [Google Scholar]
  12. Park J. Kim H. Kang D.D. Park Y. Exploring the therapeutic potential of scorpion-derived Css54 peptide against candida albicans. J. Microbiol. 2024 62 2 101 112 10.1007/s12275‑024‑00113‑4 38589765
    [Google Scholar]
  13. Parachin N.S. Mulder K.C. Viana A.A.B. Dias S.C. Franco O.L. Expression systems for heterologous production of antimicrobial peptides. Peptides 2012 38 2 446 456 10.1016/j.peptides.2012.09.020 23022589
    [Google Scholar]
  14. Vilcinskas A. Evolutionary plasticity of insect immunity. J. Insect Physiol. 2013 59 2 123 129 10.1016/j.jinsphys.2012.08.018 22985862
    [Google Scholar]
  15. Tang S.S. Prodhan Z.H. Biswas S.K. Le C.F. Sekaran S.D. Antimicrobial peptides from different plant sources: Isolation, characterisation, and purification. Phytochemistry 2018 154 94 105 10.1016/j.phytochem.2018.07.002 30031244
    [Google Scholar]
  16. Soundrarajan N. Park S. Le Van Chanh Q. Protegrin-1 cytotoxicity towards mammalian cells positively correlates with the magnitude of conformational changes of the unfolded form upon cell interaction. Scient. Rep. 2019 9 1 1 12 10.1038/s41598‑019‑47955‑2
    [Google Scholar]
  17. Leszczyńska K. Namiot D. Byfield F.J. Cruz K. Zendzian-Piotrowska M. Fein D.E. Savage P.B. Diamond S. McCulloch C.A. Janmey P.A. Bucki R. Antibacterial activity of the human host defence peptide LL-37 and selected synthetic cationic lipids against bacteria associated with oral and upper respiratory tract infections. J. Antimicrob. Chemother. 2013 68 3 610 618 10.1093/jac/dks434 23134677
    [Google Scholar]
  18. Raheem N. Straus S.K. Mechanisms of action for antimicrobial peptides with antibacterial and antibiofilm functions. Front. Microbiol. 2019 10 2866 10.3389/fmicb.2019.02866 31921046
    [Google Scholar]
  19. Rahnamaeian M. Antimicrobial peptides. Plant Signal. Behav. 2011 6 9 1325 1332 10.4161/psb.6.9.16319 21847025
    [Google Scholar]
  20. Koo H. Allan R.N. Howlin R.P. Stoodley P. Hall-Stoodley L. Targeting microbial biofilms: Current and prospective therapeutic strategies. Nat. Rev. Microbiol. 2017 15 12 740 755 10.1038/nrmicro.2017.99 28944770
    [Google Scholar]
  21. Grooters K.E. Ku J.C. Richter D.M. Krinock M.J. Minor A. Li P. Kim A. Sawyer R. Li Y. Strategies for combating antibiotic resistance in bacterial biofilms. Front. Cell. Infect. Microbiol. 2024 14 1352273 10.3389/fcimb.2024.1352273 38322672
    [Google Scholar]
  22. Sawicka J. Iłowska E. Deptuła M. Sosnowski P. Sass P. Czerwiec K. Chmielewska K. Szymańska A. Pietralik-Molińska Z. Kozak M. Sachadyn P. Pikuła M. Rodziewicz-Motowidło S. Functionalized peptide fibrils as a scaffold for active substances in wound healing. Int. J. Mol. Sci. 2021 22 8 3818 10.3390/ijms22083818 33917000
    [Google Scholar]
  23. Liu H. Duan Z. Tang J. Lv Q. Rong M. Lai R. A short peptide from frog skin accelerates diabetic wound healing. FEBS J. 2014 281 20 4633 4643 10.1111/febs.12968 25117795
    [Google Scholar]
  24. Kruse HV Chakraborty S Chen R Protecting orthopaedic implants from infection: antimicrobial peptide Mel4 is non-toxic to bone cells and reduces bacterial colonisation when bound to plasma ion-implanted 3D-printed PAEK polymers. Cells. 2024 13 8 656 10.3390/cells13080656
    [Google Scholar]
  25. Gabbiani G. The myofibroblast in wound healing and fibrocontractive diseases. J. Pathol. 2003 200 4 500 503 10.1002/path.1427 12845617
    [Google Scholar]
  26. Park H.J. Salem M. Semlali A. Leung K.P. Rouabhia M. Antimicrobial peptide KSL-W promotes gingival fibroblast healing properties in vitro. Peptides 2017 93 33 43 10.1016/j.peptides.2017.05.003 28499840
    [Google Scholar]
  27. Christoffersen H.F. Andreasen M. Zhang S. Nielsen E.H. Christiansen G. Dong M. Skrydstrup T. Otzen D.E. Scaffolded multimers of hIAPP20–29 peptide fragments fibrillate faster and lead to different fibrils compared to the free hIAPP20–29 peptide fragment. Biochim. Biophys. Acta. Proteins Proteomics 2015 1854 12 1890 1897 10.1016/j.bbapap.2015.08.005 26284878
    [Google Scholar]
  28. Jia Q. Fu Z. Li Y. Kang Z. Wu Y. Ru Z. Peng Y. Huang Y. Luo Y. Li W. Hu Y. Sun X. Wang J. Deng Z. Wu C. Wang Y. Yang X. Hydrogel loaded with peptide-containing nanocomplexes: symphonic cooperation of photothermal antimicrobial nanoparticles and prohealing peptides for the treatment of infected wounds. ACS Appl. Mater. Interfaces 2024 16 11 13422 13438 10.1021/acsami.3c16061 38442213
    [Google Scholar]
  29. Mateescu M. Baixe S. Garnier T. Jierry L. Ball V. Haikel Y. Metz-Boutigue M.H. Nardin M. Schaaf P. Etienne O. Lavalle P. Antibacterial peptide-based gel for prevention of medical implanted-device infection. PLoS One 2015 10 12 e0145143 10.1371/journal.pone.0145143 26659616
    [Google Scholar]
  30. Fraczyk J. Lipinski W. Chaberska A. Search for fibrous aggregates potentially useful in regenerative medicine formed under physiological conditions by self-assembling short peptides containing two identical aromatic amino acid residues. Molecules. 2018 23 3 568 10.3390/molecules23030568 29498711
    [Google Scholar]
  31. Veiga S.A. Schneider J.P. Antimicrobial hydrogels for the treatment of infection. Biopolymers 2013 100 6 637 644 10.1002/bip.22412 24122459
    [Google Scholar]
  32. Annabi N. Rana D. Sani S.E. Portillo-Lara R. Gifford J.L. Fares M.M. Mithieux S.M. Weiss A.S. Engineering a sprayable and elastic hydrogel adhesive with antimicrobial properties for wound healing. Biomaterials 2017 139 229 243 10.1016/j.biomaterials.2017.05.011 28579065
    [Google Scholar]
  33. Biernat M. Ciołek L. Dzierżyńska M. Oziębło A. Sawicka J. Deptuła M. Bauer M. Kamysz W. Pikuła M. Jaegermann Z. Rodziewicz-Motowidło S. Porous chitosan/ZnO-doped bioglass composites as carriers of bioactive peptides. Int. J. Appl. Ceram. Technol. 2020 17 6 2807 2816 10.1111/ijac.13609
    [Google Scholar]
  34. Prabaharan M. Sivashankari P.R. Prospects of bioactive chitosan-based scaffolds in tissue engineering and regenerative medicine Chitin and Chitosan for Regenerative Medicine 2015 41 59 10.1007/978‑81‑322‑2511‑9_2
    [Google Scholar]
  35. Azeera M Vaidevi S. Kumar J. Shanmugarathinam A. Ruckmani K. Chitosan-based systems in tissue engineering Functional Chitosan: Drug Delivery and Biomedical Applications 2020 297 320 10.1007/978‑981‑15‑0263‑7_10
    [Google Scholar]
  36. Paradowska-Stolarz A. Mikulewicz M. Laskowska J. Karolewicz B. Owczarek A. The importance of chitosan coatings in dentistry. Mar. Drugs 2023 21 12 613 10.3390/md21120613 38132934
    [Google Scholar]
  37. Katunar M.R. Diaz F. Boccaccini A.R. Ballarre J. SiO2–CaO rod-like particles in chitosan matrix as bioactive coatings for stainless steel implants. Ceram. Int. 2023 49 23 38535 38543 10.1016/j.ceramint.2023.09.185
    [Google Scholar]
  38. Ji X. Shao H. Li X. Ullah M.W. Luo G. Xu Z. Ma L. He X. Lei Z. Li Q. Jiang X. Yang G. Zhang Y. Injectable immunomodulation-based porous chitosan microspheres/HPCH hydrogel composites as a controlled drug delivery system for osteochondral regeneration. Biomaterials 2022 285 121530 10.1016/j.biomaterials.2022.121530 35504181
    [Google Scholar]
  39. Kagan B.L. Jang H. Capone R. Arce T.F. Ramachandran S. Lal R. Nussinov R. Antimicrobial properties of amyloid peptides. Mol. Pharm. 2012 9 4 708 717 10.1021/mp200419b 22081976
    [Google Scholar]
  40. Sha X. Li P. Feng Y. Xia D. Tian X. Wang Z. Yang Y. Mao X. Liu L. Self-assembled peptide nanofibrils designed to release membrane-lysing antimicrobial peptides. ACS Appl. Bio Mater. 2020 3 6 3648 3655 10.1021/acsabm.0c00281 35025235
    [Google Scholar]
  41. Calabrese A.N. Liu Y. Wang T. Musgrave I.F. Pukala T.L. Tabor R.F. Martin L.L. Carver J.A. Bowie J.H. The amyloid fibril-forming properties of the amphibian antimicrobial peptide uperin 3.5. Chem. Bio. Chem. 2016 17 3 239 246 10.1002/cbic.201500518 26676975
    [Google Scholar]
  42. Jang H. Arce F.T. Mustata M. Ramachandran S. Capone R. Nussinov R. Lal R. Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link. Biophys. J. 2011 100 7 1775 1783 10.1016/j.bpj.2011.01.072 21463591
    [Google Scholar]
  43. Paiva K.B.S. Granjeiro J.M. Matrix metalloproteinases in bone resorption, remodeling, and repair. Prog. Mol. Biol. Transl. Sci. 2017 148 203 303 10.1016/bs.pmbts.2017.05.001 28662823
    [Google Scholar]
  44. Manon-Jensen T. Multhaupt H.A.B. Couchman J.R. Mapping of matrix metalloproteinase cleavage sites on syndecan-1 and syndecan-4 ectodomains. FEBS J. 2013 280 10 2320 2331 10.1111/febs.12174 23384311
    [Google Scholar]
  45. Krishna P.V.M. Reddy V.S. Kumar V.P. Suresh P. Antibiotic susceptibility pattern of Staphylococcus aureus and methicillin – resistant Staphylococcus aureus isolated from various clinical specimens in a tertiary care teaching hospital, Pondicherry. Indian J. Public Health Res. Dev. 2019 10 2 208 213 10.5958/0976‑5506.2019.00287.0
    [Google Scholar]
  46. Parastan R. Kargar M. Solhjoo K. Kafilzadeh F. Staphylococcus aureus biofilms: Structures, antibiotic resistance, inhibition, and vaccines. Gene Rep. 2020 20 100739 10.1016/j.genrep.2020.100739
    [Google Scholar]
  47. Idrees M. Sawant S. Karodia N. Rahman A. Staphylococcus aureus biofilm: Morphology, genetics, pathogenesis and treatment strategies. Int. J. Environ. Res. Public Health 2021 18 14 7602 10.3390/ijerph18147602 34300053
    [Google Scholar]
  48. Ciofu O. Tolker-Nielsen T. Tolerance and resistance of Pseudomonas aeruginosa biofilms to antimicrobial agents-how P. aeruginosa can escape antibiotics. Front. Microbiol. 2019 10 MAY 913 10.3389/fmicb.2019.00913 31130925
    [Google Scholar]
  49. Laborda P. Hernando-Amado S. Martínez J.L. Sanz-García F. Antibiotic resistance in pseudomonas. Adv. Exp. Med. Biol. 2022 1386 117 143 10.1007/978‑3‑031‑08491‑1_5 36258071
    [Google Scholar]
  50. Kowalska K. Carr D.B. Lipkowski A.W. Direct antimicrobial properties of substance P. Life Sci. 2002 71 7 747 750 10.1016/S0024‑3205(02)01740‑X 12074933
    [Google Scholar]
  51. Zarena D. Mishra B. Lushnikova T. Wang F. Wang G. The π configuration of the WWW motif of a short trp-rich peptide is critical for targeting bacterial membranes, disrupting preformed biofilms, and killing methicillin-resistant Staphylococcus aureus. Biochemistry 2017 56 31 4039 4043 10.1021/acs.biochem.7b00456 28731688
    [Google Scholar]
  52. Sahariah P. Sørensen K.K. Hjálmarsdóttir M.Á. Sigurjónsson Ó.E. Jensen K.J. Másson M. Thygesen M.B. Antimicrobial peptide shows enhanced activity and reduced toxicity upon grafting to chitosan polymers. Chem. Commun. 2015 51 58 11611 11614 10.1039/C5CC04010H 26096124
    [Google Scholar]
  53. Grafskaia E.N. Nadezhdin K.D. Talyzina I.A. Polina N.F. Podgorny O.V. Pavlova E.R. Bashkirov P.V. Kharlampieva D.D. Bobrovsky P.A. Latsis I.A. Manuvera V.A. Babenko V.V. Trukhan V.M. Arseniev A.S. Klinov D.V. Lazarev V.N. Medicinal leech antimicrobial peptides lacking toxicity represent a promising alternative strategy to combat antibiotic-resistant pathogens. Eur. J. Med. Chem. 2019 180 143 153 10.1016/j.ejmech.2019.06.080 31302447
    [Google Scholar]
  54. Li Y. Xu W. Tang Y. Image I. Tang Y. Image I. Y L Classification, prediction, and verification of the regioselectivity of fungal polyketide synthase product template domains. J. Biol. Chem. 2010 285 30 22764 22773 10.1074/jbc.M110.128504 20479000
    [Google Scholar]
  55. Balhara V. Schmidt R. Gorr S.U. DeWolf C. Membrane selectivity and biophysical studies of the antimicrobial peptide GL13K. Biochim. Biophys. Acta Biomembr. 2013 1828 9 2193 2203 10.1016/j.bbamem.2013.05.027 23747365
    [Google Scholar]
  56. Iłowska E. Barciszewski J. Jaskólski M. Moliński A. Kozak M. Szymańska A. Identification of a steric zipper motif in the amyloidogenic core of human cystatin C and its use for the design of self-assembling peptides. Int. J. Mol. Sci. 2022 23 10 5800 10.3390/ijms23105800 35628610
    [Google Scholar]
  57. Fonseca K.B. Maia F.R. Cruz F.A. Andrade D. Juliano M.A. Granja P.L. Barrias C.C. Enzymatic, physicochemical and biological properties of MMP-sensitive alginate hydrogels. Soft Matter 2013 9 12 3283 3292 10.1039/c3sm27560d
    [Google Scholar]
  58. Biancalana M. Makabe K. Koide A. Koide S. Molecular mechanism of thioflavin-T binding to the surface of β-rich peptide self-assemblies. J. Mol. Biol. 2009 385 4 1052 1063 10.1016/j.jmb.2008.11.006 19038267
    [Google Scholar]
  59. Rusakov K. El-Turabi A. Reimer L. Jensen P.H. Hanczyc P. Thioflavin T─a reporter of microviscosity in protein aggregation process: the study case of α-synuclein. J. Phys. Chem. Lett. 2024 15 25 6685 6690 10.1021/acs.jpclett.4c00699 38899873
    [Google Scholar]
  60. Rusakov K. Demianiuk S. Jalonicka E. Hanczyc P. Cavity lasing characteristics of thioflavin T and thioflavin X in different solvents and their interaction with DNA for the controlled reduction of a light amplification threshold in solid-state biofilms. ACS Appl. Opt. Mater. 2023 1 12 1922 1929 10.1021/acsaom.3c00264 38149104
    [Google Scholar]
  61. Hanczyc P. Fita P. Laser emission of thioflavin T uncovers protein aggregation in amyloid nucleation phase. ACS Photonics 2021 8 9 2598 2609 10.1021/acsphotonics.1c00082 34557567
    [Google Scholar]
  62. Schrödinger L. The PyMOL molecular graphics system. J. Biophy. Chem. 2015 6 2 54 63 10.4236/jbpc.2015.62006
    [Google Scholar]
  63. Ciołek L Krok-Borkowicz M Gąsiński A Biernat M Antosik A Pamuła E. Bioactive glasses enriched with strontium or zinc with different degrees of structural order as components of chitosan-based composite scaffolds for bone tissue engineering. Polymers. 2023 15 19 3994 10.3390/polym15193994 37836043
    [Google Scholar]
  64. Ciołek L. Chraniuk M. Bollin P. Biernat M. Panasiuk M. Nidzworski D. Gromadzka B. Jaegermann Z. Pamuła E. Bioactive glasses enriched with zinc and strontium: Synthesis, characterization, cytocompatibility with osteoblasts and antibacterial properties. Acta Bioeng. Biomech. 2023 25 4 69 80 10.37190/ABB‑02339‑2023‑02 39072467
    [Google Scholar]
  65. Garbo C. Locs J. D’Este M. Demazeau G. Mocanu A. Roman C. Horovitz O. Tomoaia-Cotisel M. Advanced Mg, Zn, Sr, Si multi-substituted hydroxyapatites for bone regeneration. Int. J. Nanomedicine 2020 15 1037 1058 10.2147/IJN.S226630 32103955
    [Google Scholar]
  66. Abedin F Kandel N Tatulian SA Effects of Aβ-derived peptide fragments on fibrillogenesis of Aβ. Sci Rep. 2021 1 1 19262 10.1038/s41598‑021‑98644‑y 34584131
    [Google Scholar]
  67. Portillo A. Hashemi M. Zhang Y. Breydo L. Uversky V.N. Lyubchenko Y.L. Role of monomer arrangement in the amyloid self-assembly. Biochim. Biophys. Acta. Proteins Proteomics 2015 1854 3 218 228 10.1016/j.bbapap.2014.12.009 25542374
    [Google Scholar]
  68. Biskupek I. Czaplewski C. Sawicka J. Prediction of aggregation of biologically-active peptides with the UNRES coarse-grained model. Biomolecules. 2022 12 8 1140 10.3390/biom12081140 36009034
    [Google Scholar]
  69. Microorganisms N.R.C. Bacteria, Their Smallest Representatives and Subcellular Structures, and the Purported Precambrian Fossil “Metallogenium”. Size Limits of Very Small Microorganisms: Proceedings of a Workshop. Washington (DC) National Academies Press (US) 1999
    [Google Scholar]
  70. Nakai R. Size matters: Ultra-small and filterable microorganisms in the environment. Microbes Environ. 2020 35 2 10.1264/jsme2.ME20025 32493880
    [Google Scholar]
  71. Filipović U. Dahmane R.G. Ghannouchi S. Zore A. Bohinc K. Bacterial adhesion on orthopedic implants. Adv. Colloid Interface Sci. 2020 283 102228 10.1016/j.cis.2020.102228 32858407
    [Google Scholar]
  72. Vestby LK Grønseth T Simm R Nesse LL Bacterial biofilm and its role in the pathogenesis of disease. Bact. Biof. 2020 9 2 59 10.3390/antibiotics9020059 32028684
    [Google Scholar]
  73. Sieradzan A.K. Czaplewski C. Krupa P. Mozolewska M.A. Karczyńska A.S. Lipska A.G. Lubecka E.A. Gołaś E. Wirecki T. Makowski M. Ołdziej S. Liwo A. Modeling the structure, dynamics, and transformations of proteins with the UNRES force field. Methods Mol. Biol. 2022 2376 399 416 10.1007/978‑1‑0716‑1716‑8_23 34845623
    [Google Scholar]
  74. Liwo A. Sieradzan A.K. Lipska A.G. Czaplewski C. Joung I. Żmudzińska W. Hałabis A. Ołdziej S. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. J. Chem. Phys. 2019 150 15 155104 10.1063/1.5093015 31005069
    [Google Scholar]
  75. Czaplewski C. Kalinowski S. Liwo A. Scheraga H.A. Application of multiplexed replica exchange molecular dynamics to the UNRES force field: tests with α and α+β proteins. J. Chem. Theory Comput. 2009 5 3 627 640 10.1021/ct800397z 20161452
    [Google Scholar]
  76. Khalili M. Liwo A. Jagielska A. Scheraga H.A. Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems. J. Phys. Chem. B 2005 109 28 13798 13810 10.1021/jp058007w 16852728
    [Google Scholar]
  77. Khalili M. Liwo A. Rakowski F. Grochowski P. Scheraga H.A. Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode. J. Phys. Chem. B 2005 109 28 13785 13797 10.1021/jp058008o 16852727
    [Google Scholar]
  78. Katzgraber HG Trebst S Huse DA Troyer M Feedback-optimized parallel tempering Monte Carlo. J. Statist. Mech. The. Experi. 2006 3 3 P03018 10.1088/1742‑5468/2006/03/P03018
    [Google Scholar]
  79. Sieradzan A.K. Sans-Duñó J. Lubecka E.A. Czaplewski C. Lipska A.G. Leszczyński H. Ocetkiewicz K.M. Proficz J. Czarnul P. Krawczyk H. Liwo A. Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. J. Comput. Chem. 2023 44 4 602 625 10.1002/jcc.27026 36378078
    [Google Scholar]
  80. Kumar S. Rosenberg J.M. Bouzida D. Swendsen R.H. Kollman P.A. THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 1992 13 8 1011 1021 10.1002/jcc.540130812
    [Google Scholar]
  81. Liwo A. Khalili M. Czaplewski C. Kalinowski S. Ołdziej S. Wachucik K. Scheraga H.A. Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. J. Phys. Chem. B 2007 111 1 260 285 10.1021/jp065380a 17201450
    [Google Scholar]
  82. Biernat M Woźniak A Chraniuk M. Effect of selected crosslinking and stabilization methods on the properties of porous chitosan composites dedicated for medical applications. Polymers 2023 15 11 2507 10.3390/POLYM15112507
    [Google Scholar]
  83. E2180 Standard Test Method for Determining the Activity of Incorporated Antimicrobial Agent. Available from: https://www.astm.org/e2180-18.html (Accessed April 30, 2024)
  84. Chraniuk M. Panasiuk M. Hovhannisyan L. Żołędowska S. Nidzworski D. Ciołek L. Woźniak A. Kubiś A. Karska N. Jaegermann Z. Rodziewicz-Motowidło S. Biernat M. Gromadzka B. Assessment of the toxicity of biocompatible materials supporting bone regeneration: impact of the type of assay and used controls. Toxics 2022 10 1 20 10.3390/toxics10010020 35051062
    [Google Scholar]
  85. Konno K. Hisada M. Fontana R. Lorenzi C.C.B. Naoki H. Itagaki Y. Miwa A. Kawai N. Nakata Y. Yasuhara T. Neto R.J. Azevedo D.W.F. Jr Palma M.S. Nakajima T. Anoplin, a novel antimicrobial peptide from the venom of the solitary wasp Anoplius samariensis. Biochim. Biophys. Acta Protein Struct. Mol. Enzymol. 2001 1550 1 70 80 10.1016/S0167‑4838(01)00271‑0 11738089
    [Google Scholar]
  86. Wojciechowska M. Macyszyn J. Miszkiewicz J. Grzela R. Trylska J. Stapled anoplin as an antibacterial agent. Front. Microbiol. 2021 12 772038 10.3389/fmicb.2021.772038 34966367
    [Google Scholar]
  87. Ifrah D. Doisy X. Ryge T.S. Hansen P.R. Structure-activity relationship study of anoplin. J. Pept. Sci. 2005 11 2 113 121 10.1002/psc.598 15635634
    [Google Scholar]
  88. Gou S. Li B. Ouyang X. Ba Z. Zhong C. Zhang T. Chang L. Zhu Y. Zhang J. Zhu N. Zhang Y. Liu H. Ni J. Novel broad-spectrum antimicrobial peptide derived from anoplin and its activity on bacterial pneumonia in mice. J. Med. Chem. 2021 64 15 11247 11266 10.1021/acs.jmedchem.1c00614 34180670
    [Google Scholar]
  89. Munk J.K. Uggerhøj L.E. Poulsen T.J. Frimodt-Møller N. Wimmer R. Nyberg N.T. Hansen P.R. Synthetic analogs of anoplin show improved antimicrobial activities. J. Pept. Sci. 2013 19 11 669 675 10.1002/psc.2548 24019229
    [Google Scholar]
/content/journals/cpps/10.2174/0113892037353453241219185311
Loading
/content/journals/cpps/10.2174/0113892037353453241219185311
Loading

Data & Media loading...

Supplements

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test