Aier I, Varadwaj PK, Raj U (2016) Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Sci Rep. https://doi.org/10.1038/SREP34984
Article PubMed PubMed Central Google Scholar
Amorim-Carmo B, Parente AMS, Souza ES, Silva-Junior AA, Araújo RM, Fernandes-Pedrosa MF (2022) Antimicrobial peptide analogs from scorpions: modifications and structure-activity. Front Mol Biosci. https://doi.org/10.3389/FMOLB.2022.887763
Article PubMed PubMed Central Google Scholar
Basit A, Karim AM, Asif M, Ali T, Lee JH, Jeon JH, ur Rehman S, Lee SH (2021) Designing short peptides to block the interaction of SARS-CoV-2 and human ACE2 for COVID-19 therapeutics. Front Pharmacol. https://doi.org/10.3389/FPHAR.2021.731828
Article PubMed PubMed Central Google Scholar
P. Bauer, B. Hess, E. Lindahl, (2024) Downloads — GROMACS 2022 documentation, (n.d.). https://manual.gromacs.org/2022/download.html
Büyükkiraz ME, Kesmen Z (2022) Antimicrobial peptides (AMPs): a promising class of antimicrobial compounds. J Appl Microbiol 132:1573–1596. https://doi.org/10.1111/JAM.15314
Conde-Torres D, Calvelo M, Rovira C, Piñeiro Á, Garcia-Fandino R (2024) Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies. Comput Struct Biotechnol J 25:61–74. https://doi.org/10.1016/J.CSBJ.2024.04.022
Article PubMed PubMed Central CAS Google Scholar
Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an nlog(N) method for ewald sums in large systems particle mesh ewald: an n-log(N) method for ewald sums in large systems, citation. J Chem Phys 98:10089. https://doi.org/10.1063/1.464397
De Mandal S, Panda AK, Murugan C, Xu X, Kumar NS, Jin F (2021) Antimicrobial peptides: novel source and biological function with a special focus on entomopathogenic nematode/bacterium symbiotic complex. Front Microbiol. https://doi.org/10.3389/FMICB.2021.555022
Article PubMed PubMed Central Google Scholar
Filipe HAL, Loura LMS (2022) Molecular dynamics simulations: advances and applications. Molecules. https://doi.org/10.3390/MOLECULES27072105
Article PubMed PubMed Central Google Scholar
Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar AN, Domene C (2018) Understanding conformational dynamics of complex lipid mixtures relevant to biology. J Membr Biol 251:609–631. https://doi.org/10.1007/S00232-018-0050-Y
Article PubMed PubMed Central CAS Google Scholar
Giangaspero A, Sandri L, Tossi A (2001) Amphipathic α helical antimicrobial peptides. Eur J Biochem 268:5589–5600. https://doi.org/10.1046/J.1432-1033.2001.02494.X
Article PubMed CAS Google Scholar
Gonçalves S, Santos NC (2023) Membrane-peptide interactions: from basics to current applications 2.0. Int J Mol Sci 24(8):7202. https://doi.org/10.3390/IJMS24087202
Article PubMed PubMed Central Google Scholar
Guixà-González R, Rodriguez-Espigares I, Ramírez-Anguita JM, Carrió-Gaspar P, Martinez-Seara H, Giorgino T, Selent J (2014) Membplugin: studying membrane complexity in VMD. Bioinformatics 30:1478–1480. https://doi.org/10.1093/BIOINFORMATICS/BTU037
Hasan MM, Schaduangrat N, Basith S, Lee G, Shoombuatong W, Manavalan B (2020) Hlppred-fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation. Bioinformatics 36:3350–3356. https://doi.org/10.1093/BIOINFORMATICS/BTAA160
Article PubMed CAS Google Scholar
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:14631472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12%3c1463::AID-JCC4%3e3.0.CO;2-H
Klähn M, Zacharias M (2013) Transformations in plasma membranes of cancerous cells and resulting consequences for cation insertion studied with molecular dynamics. Phys Chem Chem Phys 15:14427–14441. https://doi.org/10.1039/C3CP52085D
Krieger E, Vriend G (2014) YASARA view - molecular graphics for all devices - from smartphones to workstations. Bioinformatics 30:2981–2982. https://doi.org/10.1093/BIOINFORMATICS/BTU426
Article PubMed PubMed Central CAS Google Scholar
Lamiable A, Thevenet P, Rey J, Vavrusa M, Derreumaux P, Tuffery P (2016) Pep-fold3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res 44:W449–W454. https://doi.org/10.1093/NAR/GKW329
Article PubMed PubMed Central CAS Google Scholar
Liang Q, Wu QY, Wang ZY (2014) Effect of hydrophobic mismatch on domain formation and peptide sorting in the multicomponent lipid bilayers in the presence of immobilized peptides. J Chem Phys. https://doi.org/10.1063/1.4891931
Lim KJ, Sung BH, Shin JR, Lee YW, Kim DJ, Yang KS, Kim SC (2013) A cancer specific cell-penetrating peptide, BR2, for the efficient delivery of an scFv into cancer cells. PLoS ONE. https://doi.org/10.1371/JOURNAL.PONE.0066084
Article PubMed PubMed Central Google Scholar
Lu L, Voth GA (2009) Systematic coarse-graining of a multicomponent lipid bilayer. J Phys Chem B 113:1501–1510. https://doi.org/10.1021/JP809604K
Article PubMed PubMed Central CAS Google Scholar
Malanovic N, Marx L, Blondelle SE, Pabst G, Semeraro EF (2020) Experimental concepts for linking the biological activities of antimicrobial peptides to their molecular modes of action. Biochim Biophys Acta Biomembr. https://doi.org/10.1016/J.BBAMEM.2020.183275
Article PubMed PubMed Central Google Scholar
Marrink SJ, Corradi V, Souza PCT, Ingólfsson HI, Tieleman DP, Sansom MSP (2019) Computational modeling of realistic cell membranes. Chem Rev 119:6184–6226. https://doi.org/10.1021/ACS.CHEMREV.8B00460
Article PubMed PubMed Central CAS Google Scholar
Mink C, Strandberg E, Wadhwani P, Melo MN, Reichert J, Wacker I, Castanho MARB, Ulrich AS (2021) Overlapping properties of the short membrane-active peptide BP100 with (i) polycationic TAT and (ii) α-helical magainin family peptides. Front Cell Infect Microbiol. https://doi.org/10.3389/FCIMB.2021.609542
Article PubMed PubMed Central Google Scholar
Monincová L, Buděšínský M, Slaninová J, Hovorka O, Cvačka J, Voburka Z, Fučík V, Borovičková L, Bednárová L, Straka J, Čeřovský V (2010) Novel antimicrobial peptides from the venom of the eusocial bee Halictus sexcinctus (Hymenoptera: Halictidae) and their analogs. Amino Acids 39:763–775. https://doi.org/10.1007/S00726-010-0519-1
Monincová L, Veverka V, Slaninová J, Buděšínský M, Fučík V, Bednárová L, Straka J, Čeřovský V (2014) Structure-activity study of macropin, a novel antimicrobial peptide from the venom of solitary bee Macropis fulvipes (Hymenoptera: Melittidae). J Pept Sci 20:375–384. https://doi.org/10.1002/PSC.2625
Munk JK, Uggerhøj LE, Poulsen TJ, Frimodt-Møller N, Wimmer R, Nyberg NT, Hansen PR (2013) Synthetic analogs of anoplin show improved antimicrobial activities. J Pept Sci 19:669–675. https://doi.org/10.1002/PSC.2548
Article PubMed CAS Google Scholar
Nan YH, Park IS, Hahm KS, Shin SY (2011) Antimicrobial activity, bactericidal mechanism and LPS-neutralizing activity of the cell-penetrating peptide pVEC and its analogs. J Pept Sci 17:812–817. https://doi.org/10.1002/PSC.1408
Article PubMed CAS Google Scholar
Nešuta O, Hexnerová R, Buděšínský M, Slaninová J, Bednárová L, Hadravová R, Straka J, Veverka V, Čeřovský V (2016) Antimicrobial peptide from the wild bee Hylaeus signatus venom and its analogues: structure-activity study and synergistic effect with antibiotics. J Nat Prod 79:1073–1083.
Comments (0)