Potent Activity of Hybrid Arthropod Antimicrobial Peptides Linked by Glycine Spacers
Language English Country Switzerland Media electronic
Document type Journal Article
Grant support
LOEWE Centre for Translational Biodiversity Genomics
Hessisches Ministerium für Wissenschaft und Kunst
RVO: RO0516
European Regional Development Fund
ANR-10-LABX-62-IBEID
French Governments`Investissement dÀvenir
PubMed
34445625
PubMed Central
PMC8396199
DOI
10.3390/ijms22168919
PII: ijms22168919
Knihovny.cz E-resources
- Keywords
- Escherichia coli, antimicrobial peptide, glycine spacer, hybrid peptide, insect, scorpion,
- MeSH
- Anti-Bacterial Agents chemistry pharmacology MeSH
- Apoptosis MeSH
- Bacteria drug effects MeSH
- Arthropods chemistry MeSH
- Pore Forming Cytotoxic Proteins chemistry pharmacology MeSH
- Glycine chemistry MeSH
- Hemolysis drug effects MeSH
- Cricetinae MeSH
- Cells, Cultured MeSH
- Kidney drug effects MeSH
- Mice MeSH
- Animals MeSH
- Check Tag
- Cricetinae MeSH
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Anti-Bacterial Agents MeSH
- Pore Forming Cytotoxic Proteins MeSH
- Glycine MeSH
Arthropod antimicrobial peptides (AMPs) offer a promising source of new leads to address the declining number of novel antibiotics and the increasing prevalence of multidrug-resistant bacterial pathogens. AMPs with potent activity against Gram-negative bacteria and distinct modes of action have been identified in insects and scorpions, allowing the discovery of AMP combinations with additive and/or synergistic effects. Here, we tested the synergistic activity of two AMPs, from the dung beetle Copris tripartitus (CopA3) and the scorpion Heterometrus petersii (Hp1090), against two strains of Escherichia coli. We also tested the antibacterial activity of two hybrid peptides generated by joining CopA3 and Hp1090 with linkers comprising two (InSco2) or six (InSco6) glycine residues. We found that CopA3 and Hp1090 acted synergistically against both bacterial strains, and the hybrid peptide InSco2 showed more potent bactericidal activity than the parental AMPs or InSco6. Molecular dynamics simulations revealed that the short linker stabilizes an N-terminal 310-helix in the hybrid peptide InSco2. This secondary structure forms from a coil region that interacts with phosphatidylethanolamine in the membrane bilayer model. The highest concentration of the hybrid peptides used in this study was associated with stronger hemolytic activity than equivalent concentrations of the parental AMPs. As observed for CopA3, the increasing concentration of InSco2 was also cytotoxic to BHK-21 cells. We conclude that AMP hybrids linked by glycine spacers display potent antibacterial activity and that the cytotoxic activity can be modulated by adjusting the nature of the linker peptide, thus offering a strategy to produce hybrid peptides as safe replacements or adjuncts for conventional antibiotic therapy.
Department of Virology Veterinary Research Institute Hudcova 70 62100 Brno Czech Republic
LOEWE Centre for Translational Biodiversity Genomics Senckenberganlage 25 60325 Frankfurt Germany
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Stern S., Chorzelski S., Franken L., Völler S., Rentmeister H., Grosch B. Breaking through the Wall: A Call for Concerted Action on Antibiotics Research and Development. Global Union for Antibiotics Research and Development (GUARD) Initiative; Berlin, Germany: 2017.
Taneja N., Kaur H. Insights into Newer Antimicrobial Agents Against Gram-Negative Bacteria. Microbiol. Insights. 2016;9:9–19. doi: 10.4137/MBI.S29459. PubMed DOI PMC
Kudryashova E., Seveau S.M., Kudryashov D.S. Targeting and Inactivation of Bacterial Toxins by Human Defensins. Biol. Chem. 2017;398:1069–1085. doi: 10.1515/hsz-2017-0106. PubMed DOI PMC
Jenssen H., Hamill P., Hancock R.E.W. Peptide Antimicrobial Agents. Clin. Microbiol. Rev. 2006;19:491–511. doi: 10.1128/CMR.00056-05. PubMed DOI PMC
Lei J., Sun L., Huang S., Zhu C., Li P., He J., Mackey V., Coy D.H., He Q. The Antimicrobial Peptides and Their Potential Clinical Applications. Am. J. Transl. Res. 2019;11:3919–3931. PubMed PMC
Mylonakis E., Podsiadlowski L., Muhammed M., Vilcinskas A. Diversity, Evolution and Medical Applications of Insect Antimicrobial Peptides. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2016;371 doi: 10.1098/rstb.2015.0290. PubMed DOI PMC
Tonk M., Vilcinskas A. The Medical Potential of Antimicrobial Peptides from Insects. Curr. Top. Med. Chem. 2017;17:554–575. doi: 10.2174/1568026616666160713123654. PubMed DOI
Vilcinskas A., Mukherjee K., Vogel H. Expansion of the Antimicrobial Peptide Repertoire in the Invasive Ladybird Harmonia Axyridis. Proc. R. Soc. B Biol. Sci. 2013;280:20122113. doi: 10.1098/rspb.2012.2113. PubMed DOI PMC
Gerardo N.M., Altincicek B., Anselme C., Atamian H., Barribeau S.M., de Vos M., Duncan E.J., Evans J.D., Gabaldón T., Ghanim M., et al. Immunity and Other Defenses in Pea Aphids, Acyrthosiphon Pisum. Genome Biol. 2010;11:R21. doi: 10.1186/gb-2010-11-2-r21. PubMed DOI PMC
Choi J.H., Jang A.Y., Lin S., Lim S., Kim D., Park K., Han S.-M., Yeo J.-H., Seo H.S. Melittin, a Honeybee Venom-Derived Antimicrobial Peptide, May Target Methicillin-Resistant Staphylococcus Aureus. Mol. Med. Rep. 2015;12:6483–6490. doi: 10.3892/mmr.2015.4275. PubMed DOI PMC
Lu X., Shen J., Jin X., Ma Y., Huang Y., Mei H., Chu F., Zhu J. Bactericidal Activity of Musca Domestica Cecropin (Mdc) on Multidrug-Resistant Clinical Isolate of Escherichia Coli. Appl. Microbiol. Biotechnol. 2012;95:939–945. doi: 10.1007/s00253-011-3793-2. PubMed DOI
Oñate-Garzón J., Manrique-Moreno M., Trier S., Leidy C., Torres R., Patiño E. Antimicrobial Activity and Interactions of Cationic Peptides Derived from Galleria Mellonella Cecropin D-like Peptide with Model Membranes. J. Antibiot. (Tokyo) 2017;70:238–245. doi: 10.1038/ja.2016.134. PubMed DOI
Ulvatne H., Karoliussen S., Stiberg T., Rekdal O., Svendsen J.S. Short Antibacterial Peptides and Erythromycin Act Synergically against Escherichia Coli. J. Antimicrob. Chemother. 2001;48:203–208. doi: 10.1093/jac/48.2.203. PubMed DOI
Zerweck J., Strandberg E., Kukharenko O., Reichert J., Bürck J., Wadhwani P., Ulrich A.S. Molecular Mechanism of Synergy between the Antimicrobial Peptides PGLa and Magainin 2. Sci. Rep. 2017;7:13153. doi: 10.1038/s41598-017-12599-7. PubMed DOI PMC
Bagheri M., Beyermann M., Dathe M. Immobilization Reduces the Activity of Surface-Bound Cationic Antimicrobial Peptides with No Influence upon the Activity Spectrum. Antimicrob. Agents Chemother. 2009;53:1132–1141. doi: 10.1128/AAC.01254-08. PubMed DOI PMC
Liu S.P., Zhou L., Lakshminarayanan R., Beuerman R.W. Multivalent Antimicrobial Peptides as Therapeutics: Design Principles and Structural Diversities. Int. J. Pept. Res. Ther. 2010;16:199–213. doi: 10.1007/s10989-010-9230-z. PubMed DOI PMC
McKenna M. Antibiotic Resistance: The Last Resort. Nature. 2013;499:394–396. doi: 10.1038/499394a. PubMed DOI
Mojsoska B., Zuckermann R.N., Jenssen H. Structure-Activity Relationship Study of Novel Peptoids That Mimic the Structure of Antimicrobial Peptides. Antimicrob. Agents Chemother. 2015;59:4112–4120. doi: 10.1128/AAC.00237-15. PubMed DOI PMC
Klubthawee N., Adisakwattana P., Hanpithakpong W., Somsri S., Aunpad R. A Novel, Rationally Designed, Hybrid Antimicrobial Peptide, Inspired by Cathelicidin and Aurein, Exhibits Membrane-Active Mechanisms against Pseudomonas Aeruginosa. Sci. Rep. 2020;10:9117. doi: 10.1038/s41598-020-65688-5. PubMed DOI PMC
Hwang J.-S., Lee J., Kim Y.-J., Bang H.-S., Yun E.-Y., Kim S.-R., Suh H.-J., Kang B.-R., Nam S.-H., Jeon J.-P., et al. Isolation and Characterization of a Defensin-Like Peptide (Coprisin) from the Dung Beetle, Copris Tripartitus. Int. J. Pept. 2009;2009:136284. doi: 10.1155/2009/136284. PubMed DOI PMC
Kim I.-W., Kim S.-J., Kwon Y.-N., Yun E.-Y., Ahn M.-Y., Kang D.-C., Hwang J.-S. Effects of the Synthetic Coprisin Analog Peptide, CopA3 in Pathogenic Microorganisms and Mammalian Cancer Cells. J. Microbiol. Biotechnol. 2012;22:156–158. doi: 10.4014/jmb.1109.09014. PubMed DOI
Lee J.H., Kim I.-W., Kim S.-H., Yun E.-Y., Nam S.-H., Ahn M.-Y., Kang D.-C., Hwang J.S. Anticancer Activity of CopA3 Dimer Peptide in Human Gastric Cancer Cells. BMB Rep. 2015;48:324–329. doi: 10.5483/BMBRep.2015.48.6.073. PubMed DOI PMC
Yan R., Zhao Z., He Y., Wu L., Cai D., Hong W., Wu Y., Cao Z., Zheng C., Li W. A New Natural α-Helical Peptide from the Venom of the Scorpion Heterometrus Petersii Kills HCV. Peptides. 2011;32:11–19. doi: 10.1016/j.peptides.2010.10.008. PubMed DOI
Lee E., Kim J.-K., Shin S., Jeong K.-W., Shin A., Lee J., Lee D.G., Hwang J.-S., Kim Y. Insight into the Antimicrobial Activities of Coprisin Isolated from the Dung Beetle, Copris Tripartitus, Revealed by Structure–Activity Relationships. Biochim. Biophys. Acta BBA-Biomembr. 2013;1828:271–283. doi: 10.1016/j.bbamem.2012.10.028. PubMed DOI
Meletiadis J., Pournaras S., Roilides E., Walsh T.J. Defining Fractional Inhibitory Concentration Index Cutoffs for Additive Interactions Based on Self-Drug Additive Combinations, Monte Carlo Simulation Analysis, and In Vitro-In Vivo Correlation Data for Antifungal Drug Combinations against Aspergillus Fumigatus. Antimicrob. Agents Chemother. 2010;54:602–609. doi: 10.1128/AAC.00999-09. PubMed DOI PMC
Rios A.C., Moutinho C.G., Pinto F.C., Del Fiol F.S., Jozala A., Chaud M.V., Vila M.M.D.C., Teixeira J.A., Balcão V.M. Alternatives to Overcoming Bacterial Resistances: State-of-the-Art. Microbiol. Res. 2016;191:51–80. doi: 10.1016/j.micres.2016.04.008. PubMed DOI
Li Y., Xiang Q., Zhang Q., Huang Y., Su Z. Overview on the Recent Study of Antimicrobial Peptides: Origins, Functions, Relative Mechanisms and Application. Peptides. 2012;37:207–215. doi: 10.1016/j.peptides.2012.07.001. PubMed DOI
Aoki W., Ueda M. Characterization of Antimicrobial Peptides toward the Development of Novel Antibiotics. Pharmaceuticals. 2013;6:1055–1081. doi: 10.3390/ph6081055. PubMed DOI PMC
Kim J.-S., Jeong J.-H., Kim Y. Design and Engineering of Antimicrobial Peptides Based on LPcin-YK3, an Antimicrobial Peptide Derivative from Bovine Milk. J. Microbiol. Biotechnol. 2018;28:381–390. doi: 10.4014/jmb.1711.11057. PubMed DOI
Zhao J., Zhao C., Liang G., Zhang M., Zheng J. Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities. J. Chem. Inf. Model. 2013;53:3280–3296. doi: 10.1021/ci400477e. PubMed DOI
Sani M.-A., Saenger C., Juretic D., Separovic F. Glycine Substitution Reduces Antimicrobial Activity and Helical Stretch of DiPGLa-H in Lipid Micelles. J. Phys. Chem. B. 2017;121:4817–4822. doi: 10.1021/acs.jpcb.7b03067. PubMed DOI
Taraballi F., Natalello A., Campione M., Villa O., Doglia S.M., Paleari A., Gelain F. Glycine-Spacers Influence Functional Motifs Exposure and Self-Assembling Propensity of Functionalized Substrates Tailored for Neural Stem Cell Cultures. Front. Neuroeng. 2010;3 doi: 10.3389/neuro.16.001.2010. PubMed DOI PMC
Ishida A., Watanabe G., Oshikawa M., Ajioka I., Muraoka T. Glycine Substitution Effects on the Supramolecular Morphology and Rigidity of Cell-Adhesive Amphiphilic Peptides. Chem. Weinh. Bergstr. Ger. 2019;25:13523–13530. doi: 10.1002/chem.201902083. PubMed DOI
Ruiz N., Kahne D., Silhavy T.J. Advances in Understanding Bacterial Outer-Membrane Biogenesis. Nat. Rev. Microbiol. 2006;4:57–66. doi: 10.1038/nrmicro1322. PubMed DOI
Nikaido H. Molecular Basis of Bacterial Outer Membrane Permeability Revisited. Microbiol. Mol. Biol. Rev. 2003;67:593–656. doi: 10.1128/MMBR.67.4.593-656.2003. PubMed DOI PMC
Carnicelli V., Lizzi A.R., Ponzi A., Amicosante G., Bozzi A., Giulio A. Interaction between Antimicrobial Peptides ( AMPs ) and Their Primary Target, the Biomembranes. [(accessed on 12 February 2021)]; Available online: https://www.semanticscholar.org/paper/Interaction-between-antimicrobial-peptides-(-AMPs-)-Carnicelli-Lizzi/cabb4ef72c702f54978fe84b3963f0e05bcf02f4.
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 doi: 10.3389/fnins.2017.00073. PubMed DOI PMC
Brogden K.A. Antimicrobial Peptides: Pore Formers or Metabolic Inhibitors in Bacteria? Nat. Rev. Microbiol. 2005;3:238–250. doi: 10.1038/nrmicro1098. PubMed DOI
Hollmann A., Martinez M., Maturana P., Semorile L.C., Maffia P.C. Antimicrobial Peptides: Interaction With Model and Biological Membranes and Synergism With Chemical Antibiotics. Front. Chem. 2018;6 doi: 10.3389/fchem.2018.00204. PubMed DOI PMC
Melo M.N., Sousa F.J.R., Carneiro F.A., Castanho M.A.R.B., Valente A.P., Almeida F.C.L., Da Poian A.T., Mohana-Borges R. Interaction of the Dengue Virus Fusion Peptide with Membranes Assessed by NMR: The Essential Role of the Envelope Protein Trp101 for Membrane Fusion. J. Mol. Biol. 2009;392:736–746. doi: 10.1016/j.jmb.2009.07.035. PubMed DOI PMC
Kumar P., Kizhakkedathu J.N., Straus S.K. Antimicrobial Peptides: Diversity, Mechanism of Action and Strategies to Improve the Activity and Biocompatibility In Vivo. Biomolecules. 2018;8:4. doi: 10.3390/biom8010004. PubMed DOI PMC
Yeaman M.R., Yount N.Y. Mechanisms of Antimicrobial Peptide Action and Resistance. Pharmacol. Rev. 2003;55:27–55. doi: 10.1124/pr.55.1.2. PubMed DOI
Sitaram N., Nagaraj R. Interaction of Antimicrobial Peptides with Biological and Model Membranes: Structural and Charge Requirements for Activity. Biochim. Biophys. Acta. 1999;1462:29–54. doi: 10.1016/S0005-2736(99)00199-6. PubMed DOI
Wimley W.C. Describing the Mechanism of Antimicrobial Peptide Action with the Interfacial Activity Model. ACS Chem. Biol. 2010;5:905–917. doi: 10.1021/cb1001558. PubMed DOI PMC
Wu Q., Patočka J., Kuča K. Insect Antimicrobial Peptides, a Mini Review. Toxins. 2018;10:461. doi: 10.3390/toxins10110461. PubMed DOI PMC
Lee T.-H., Hall K.N., Aguilar M.-I. Antimicrobial Peptide Structure and Mechanism of Action: A Focus on the Role of Membrane Structure. Curr. Top. Med. Chem. 2016;16:25–39. doi: 10.2174/1568026615666150703121700. PubMed DOI
Cheng J.T.J., Hale J.D., Elliott M., Hancock R.E.W., Straus S.K. The Importance of Bacterial Membrane Composition in the Structure and Function of Aurein 2.2 and Selected Variants. Biochim. Biophys. Acta. 2011;1808:622–633. doi: 10.1016/j.bbamem.2010.11.025. PubMed DOI
Sparr E., Ash W.L., Nazarov P.V., Rijkers D.T.S., Hemminga M.A., Tieleman D.P., Killian J.A. Self-Association of Transmembrane Alpha-Helices in Model Membranes: Importance of Helix Orientation and Role of Hydrophobic Mismatch. J. Biol. Chem. 2005;280:39324–39331. doi: 10.1074/jbc.M502810200. PubMed DOI
Hu J., Chen C., Zhang S., Zhao X., Xu H., Zhao X., Lu J.R. Designed Antimicrobial and Antitumor Peptides with High Selectivity. Biomacromolecules. 2011;12:3839–3843. doi: 10.1021/bm201098j. PubMed DOI
Sánchez A., Vázquez A. Bioactive Peptides: A Review. Food Qual. Saf. 2017;1:29–46. doi: 10.1093/fqs/fyx006. DOI
Sd S. Net charge, hydrophobicity and specific amino acids contribute to the activity of antimicrobial peptides. J. Health Transl. Med. 2014;17:1–7. doi: 10.22452/jummec.vol17no1.1. DOI
Friedrich C.L., Moyles D., Beveridge T.J., Hancock R.E.W. Antibacterial Action of Structurally Diverse Cationic Peptides on Gram-Positive Bacteria. Antimicrob. Agents Chemother. 2000;44:2086–2092. doi: 10.1128/AAC.44.8.2086-2092.2000. PubMed DOI PMC
Toniolo C., Crisma M., Bonora G.M., Benedetti E., Blasio B.D., Pavone V., Pedone C., Santini A. Preferred Conformation of the Terminally Blocked (Aib)10 Homo-Oligopeptide: A Long, Regular 310-Helix. Biopolymers. 1991;31:129–138. doi: 10.1002/bip.360310112. DOI
Conlon J.M., Al-Kharrge R., Ahmed E., Raza H., Galadari S., Condamine E. Effect of Aminoisobutyric Acid (Aib) Substitutions on the Antimicrobial and Cytolytic Activities of the Frog Skin Peptide, Temporin-1DRa. Peptides. 2007;28:2075–2080. doi: 10.1016/j.peptides.2007.07.023. PubMed DOI
Dathe M., Nikolenko H., Meyer J., Beyermann M., Bienert M. Optimization of the Antimicrobial Activity of Magainin Peptides by Modification of Charge. FEBS Lett. 2001;501:146–150. doi: 10.1016/S0014-5793(01)02648-5. PubMed DOI
Matsuzaki K., Sugishita K., Harada M., Fujii N., Miyajima K. Interactions of an Antimicrobial Peptide, Magainin 2, with Outer and Inner Membranes of Gram-Negative Bacteria. Biochim. Biophys. Acta. 1997;1327:119–130. doi: 10.1016/S0005-2736(97)00051-5. PubMed DOI
Andrä J., Monreal D., de Tejada G.M., Olak C., Brezesinski G., Gomez S.S., Goldmann T., Bartels R., Brandenburg K., Moriyon I. Rationale for the Design of Shortened Derivatives of the NK-Lysin-Derived Antimicrobial Peptide NK-2 with Improved Activity against Gram-Negative Pathogens. J. Biol. Chem. 2007;282:14719–14728. doi: 10.1074/jbc.M608920200. PubMed DOI
Jiang Z., Kullberg B.J., van der Lee H., Vasil A.I., Hale J.D., Mant C.T., Hancock R.E.W., Vasil M.L., Netea M.G., Hodges R.S. Effects of Hydrophobicity on the Antifungal Activity of Alpha-Helical Antimicrobial Peptides. Chem. Biol. Drug Des. 2008;72:483–495. doi: 10.1111/j.1747-0285.2008.00728.x. PubMed DOI PMC
Takahashi D., Shukla S.K., Prakash O., Zhang G. Structural Determinants of Host Defense Peptides for Antimicrobial Activity and Target Cell Selectivity. Biochimie. 2010;92:1236–1241. doi: 10.1016/j.biochi.2010.02.023. PubMed DOI
Thaker H.D., Cankaya A., Scott R.W., Tew G.N. Role of Amphiphilicity in the Design of Synthetic Mimics of Antimicrobial Peptides with Gram-Negative Activity. ACS Med. Chem. Lett. 2013;4:481–485. doi: 10.1021/ml300307b. PubMed DOI PMC
Zhang S.-K., Song J., Gong F., Li S.-B., Chang H.-Y., Xie H.-M., Gao H.-W., Tan Y.-X., Ji S.-P. Design of an α-Helical Antimicrobial Peptide with Improved Cell-Selective and Potent Anti-Biofilm Activity. Sci. Rep. 2016;6:27394. doi: 10.1038/srep27394. PubMed DOI PMC
Rodríguez A., Villegas E., Montoya-Rosales A., Rivas-Santiago B., Corzo G. Characterization of Antibacterial and Hemolytic Activity of Synthetic Pandinin 2 Variants and Their Inhibition against Mycobacterium Tuberculosis. PLoS ONE. 2014;9:e101742. doi: 10.1371/journal.pone.0101742. PubMed DOI PMC
Yin L.M., Edwards M.A., Li J., Yip C.M., Deber C.M. Roles of Hydrophobicity and Charge Distribution of Cationic Antimicrobial Peptides in Peptide-Membrane Interactions. J. Biol. Chem. 2012;287:7738–7745. doi: 10.1074/jbc.M111.303602. PubMed DOI PMC
Chen Y., Guarnieri M.T., Vasil A.I., Vasil M.L., Mant C.T., Hodges R.S. Role of Peptide Hydrophobicity in the Mechanism of Action of Alpha-Helical Antimicrobial Peptides. Antimicrob. Agents Chemother. 2007;51:1398–1406. doi: 10.1128/AAC.00925-06. PubMed DOI PMC
Bjellqvist B., Hughes G.J., Pasquali C., Paquet N., Ravier F., Sanchez J.C., Frutiger S., Hochstrasser D. The Focusing Positions of Polypeptides in Immobilized PH Gradients Can Be Predicted from Their Amino Acid Sequences. Electrophoresis. 1993;14:1023–1031. doi: 10.1002/elps.11501401163. PubMed DOI
Bjellqvist B., Basse B., Olsen E., Celis J.E. Reference Points for Comparisons of Two-Dimensional Maps of Proteins from Different Human Cell Types Defined in a PH Scale Where Isoelectric Points Correlate with Polypeptide Compositions. Electrophoresis. 1994;15:529–539. doi: 10.1002/elps.1150150171. PubMed DOI
Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server. In: Walker J.M., editor. The Proteomics Protocols Handbook. Humana Press; Totowa, NJ, USA: 2005. pp. 571–607. (Springer Protocols Handbooks).
Yang J., Zhang Y. I-TASSER Server: New Development for Protein Structure and Function Predictions. Nucleic Acids Res. 2015;43:W174–W181. doi: 10.1093/nar/gkv342. PubMed DOI PMC
Sastry G.M., Adzhigirey M., Day T., Annabhimoju R., Sherman W. Protein and Ligand Preparation: Parameters, Protocols, and Influence on Virtual Screening Enrichments. J. Comput. Aided Mol. Des. 2013;27:221–234. doi: 10.1007/s10822-013-9644-8. PubMed DOI
Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.C., Williams K.L., Appel R.D., Hochstrasser D.F. Protein Identification and Analysis Tools in the ExPASy Server. Methods Mol. Biol. Clifton NJ. 1999;112:531–552. doi: 10.1385/1-59259-584-7:531. PubMed DOI
Lomize M.A., Pogozheva I.D., Joo H., Mosberg H.I., Lomize A.L. OPM Database and PPM Web Server: Resources for Positioning of Proteins in Membranes. Nucleic Acids Res. 2012;40:D370–D376. doi: 10.1093/nar/gkr703. PubMed DOI PMC
Bowers K.J., Chow E., Xu H., Dror R.O., Eastwood M.P., Gregersen B.A., Klepeis J.L., Kolossvary I., Moraes M.A., Sacerdoti F.D., et al. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters; Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, Association for Computing Machinery; Tampa, FL, USA. 11 November 2006;
Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983;79:926–935. doi: 10.1063/1.445869. DOI
Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters. Proteins. 2006;65:712–725. doi: 10.1002/prot.21123. PubMed DOI PMC
Lindorff-Larsen K., Piana S., Palmo K., Maragakis P., Klepeis J.L., Dror R.O., Shaw D.E. Improved Side-Chain Torsion Potentials for the Amber Ff99SB Protein Force Field. Proteins. 2010;78:1950–1958. doi: 10.1002/prot.22711. PubMed DOI PMC
Wang J., Cieplak P., Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000;21:1049–1074. doi: 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F. DOI
Klauda J.B., Venable R.M., Freites J.A., O’Connor J.W., Tobias D.J., Mondragon-Ramirez C., Vorobyov I., MacKerell A.D., Pastor R.W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. J. Phys. Chem. B. 2010;114:7830–7843. doi: 10.1021/jp101759q. PubMed DOI PMC
Hoover W.G. Canonical Dynamics: Equilibrium Phase-Space Distributions. Phys. Rev. A. 1985;31:1695–1697. doi: 10.1103/PhysRevA.31.1695. PubMed DOI
Martyna G.J., Tobias D.J., Klein M.L. Constant Pressure Molecular Dynamics Algorithms. J. Chem. Phys. 1994;101:4177–4189. doi: 10.1063/1.467468. DOI
Tuckerman M., Berne B.J., Martyna G.J. Reversible Multiple Time Scale Molecular Dynamics. J. Chem. Phys. 1992;97:1990–2001. doi: 10.1063/1.463137. DOI
Humphrey W., Dalke A., Schulten K. VMD: Visual Molecular Dynamics. J. Mol. Graph. 1996;14:33–38. doi: 10.1016/0263-7855(96)00018-5. PubMed DOI
Tonk M., Cabezas-Cruz A., Valdés J.J., Rego R.O.M., Chrudimská T., Strnad M., Šíma R., Bell-Sakyi L., Franta Z., Vilcinskas A., et al. Defensins from the Tick Ixodes Scapularis Are Effective against Phytopathogenic Fungi and the Human Bacterial Pathogen Listeria Grayi. Parasit. Vectors. 2014;7:554. doi: 10.1186/s13071-014-0554-y. PubMed DOI PMC
Tonk M., Pierrot C., Cabezas-Cruz A., Rahnamaeian M., Khalife J., Vilcinskas A. The Drosophila Melanogaster Antimicrobial Peptides Mtk-1 and Mtk-2 Are Active against the Malarial Parasite Plasmodium Falciparum. Parasitol. Res. 2019;118:1993–1998. doi: 10.1007/s00436-019-06305-x. PubMed DOI
Bolouri Moghaddam M.R., Tonk M., Schreiber C., Salzig D., Czermak P., Vilcinskas A., Rahnamaeian M. The Potential of the Galleria Mellonella Innate Immune System Is Maximized by the Co-Presentation of Diverse Antimicrobial Peptides. Biol. Chem. 2016;397:939–945. doi: 10.1515/hsz-2016-0157. PubMed DOI