Skip to main content
Log in

The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy

  • Original Article
  • Published:
Amino Acids Aims and scope Submit manuscript

Abstract

Antimicrobial peptides (AMPs) are part of the innate immune system of many species. AMPs are short sequences rich in charged and non-polar residues. They act on the lipid phase of the plasma membrane without requiring membrane receptors. Polybia-MP1 (MP1), extracted from a native wasp, is a broad-spectrum bactericide, an inhibitor of cancer cell proliferation being non-hemolytic and non-cytotoxic. MP1 mechanism of action and its adsorption mode is not yet completely known. Its adsorption to lipid bilayer and lytic activity is most likely dependent on the ionization state of its two acidic and three basic residues and consequently on the bulk pH. Here we investigated the effect of bulk acidic (pH 5.5) and neutral pH (7.4) solution on the adsorption, insertion, and lytic activity of MP1 and its analog H-MP1 to anionic (7POPC:3POPG) model membrane. H-MP1 is a synthetic analog of MP1 with lysines replaced by histidines. Bulk pH changes could modulate this peptide efficiency. The combination of different experimental techniques and molecular dynamics (MD) simulations showed that the adsorption, insertion, and lytic activity of H-MP1 are highly sensitive to bulk pH in opposition to MP1. The atomistic details, provided by MD simulations, showed peptides contact their N-termini to the bilayer before the insertion and then lay parallel to the bilayer. Their hydrophobic faces inserted into the acyl chain phase disturb the lipid-packing.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Agadi N, Vasudevan S, Kumar A (2018) Structural insight into the mechanism of action of antimicrobial peptide BMAP-28(1–18) and its analogue mutBMAP18. J Struct Biol 204(3):435–448

    CAS  PubMed  Google Scholar 

  • Alvares DS, Fanani ML, Ruggiero Neto J, Wilke N (2016) The interfacial properties of the peptide Polybia-MP1 and its interaction with DPPC are modulated by lateral electrostatic attractions. Biochim Biophys Acta (BBA) Biomembr 1858(2):393–402

    CAS  Google Scholar 

  • Alvares DS, Ruggiero Neto J, Ambroggio EE (2017a) Phosphatidylserine lipids and membrane order precisely regulate the activity of Polybia-MP1 peptide. Biochim Biophys Acta Biomembr 1859(6):1067–1074

    CAS  PubMed  Google Scholar 

  • Alvares DS, Wilke N, Ruggiero Neto J, Fanani ML (2017b) The insertion of Polybia-MP1 peptide into phospholipid monolayers is regulated by its anionic nature and phase state. Chem Phys Lipids 207:38–48

    CAS  PubMed  Google Scholar 

  • Alvares DS, Viegas TG, Ruggiero Neto J (2018a) The effect of pH on the lytic activity of a synthetic mastoparan-like peptide in anionic model membranes. Chem Phys Lipids 216:54–64

    CAS  PubMed  Google Scholar 

  • Alvares DS, Wilke N, Ruggiero Neto J (2018b) Effect of N-terminal acetylation on lytic activity and lipid-packing perturbation induced in model membranes by a mastoparan-like peptide. Biochim Biophys Acta (BBA) Biomembr 1860(3):737–748

    CAS  Google Scholar 

  • Alvares DS, Monti MR, Ruggiero Neto J, Wilke N (2021) The antimicrobial peptide Polybia-MP1 differentiates membranes with the hopanoid, diplopterol from those with cholesterol. BBA Adv 1:100002

  • Appelt C, Eisenmenger F, Kühne R, Schmieder P, Söderhäll JA (2005) Interaction of the antimicrobial peptide cyclo (RRWWRF) with membranes by molecular dynamics simulations. Biophys J 89(4):2296–2306

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bacalum M, Janosi L, Zorila F, Tepes A-M, Ionescu C, Bogdan E, Hadade N, Craciun L, Grosu I, Turcu I, Radu M (2017) Modulating short tryptophan- and arginine-rich peptides activity by substitution with histidine. Biochim Biophys Acta Gen Subj 1861(7):1844–1854

    CAS  PubMed  Google Scholar 

  • Bertrand B, Munusamy S, Espinosa-Romero J-F, Corzo G, Sosa IA, Galván-Hernández A, Ortega-Blake I, Hernández-Adame PL, Ruiz-García J, Velasco-Bolom J-L, Garduño-Juárez R (2020) Biophysical characterization of the insertion of two potent antimicrobial peptides-Pin2 and its variant Pin2[GVG] in biological model membranes. Biochim Biophys Acta (BBA) Biomembr 1862(2):183105

    CAS  Google Scholar 

  • Bogdanova LR, Valiullina YA, Faizullin DA, Kurbanov RKH, Ermakova EA (2020) Spectroscopic, zeta potential and molecular dynamics studies of the interaction of antimicrobial peptides with model bacterial membrane. Spectrochim Acta Part A Mol Biomol Spectrosc 242:118785

    CAS  Google Scholar 

  • Cabrera MPS, Costa STB, de Souza BM, Palma MS, Ruggiero JR, Ruggiero Neto J (2008) Selectivity in the mechanism of action of antimicrobial mastoparan peptide Polybia-MP1. Eur Biophys J EBJ 37(6):879–891

    Google Scholar 

  • Cabrera MPS, Alvares DS, Leite NB, de Souza BM, Palma MS, Riske KA, Ruggiero Neto J (2011) New insight into the mechanism of action of wasp mastoparan peptides: lytic activity and clustering observed with giant vesicles. Langmuir 27(17):10805–10813

    PubMed  Google Scholar 

  • Chen Y, Mant CT, Farmer SW, Hancock REW, Vasil ML, Hodges RS (2005) Rational design of alpha-helical antimicrobial peptides with enhanced activities and specificity/therapeutic index. J Biol Chem 280(13):12316–12329

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen L, Zhigang T, Voloshchuk N, Liang JF (2012) Lytic peptides with improved stability and selectivity designed for cancer treatment. J Pharm Sci 101(4):1508–1517

    CAS  PubMed  Google Scholar 

  • Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems. J Chem Phys 98(12):10089–10092

    CAS  Google Scholar 

  • Davidchack RL, Handel R, Tretyakov MV (2009) Langevin thermostat for rigid body dynamics. J Chem Phys 130(23):234101

    PubMed  Google Scholar 

  • de Souza BM, da Silva AVR, Resende VMF, Arcuri HA, Cabrera MPDS, Ruggiero Neto J, Palma MS (2009) Characterization of two novel polyfunctional mastoparan peptides from the venom of the social wasp Polybia paulista. Peptides 30(8):1387–1395

    PubMed  Google Scholar 

  • de Souza BM, Cabrera MPDS, Ruggiero Neto J, Palma MS (2011) Investigating the effect of different positioning of lysine residues along the peptide chain of mastoparans for their secondary structures and biological activities. Amino Acids 40(1):77–90

    CAS  PubMed  Google Scholar 

  • de Souza BM, Cabrera MPDS, Gomes PC, Dias NB, Stabeli RG, Leite NB, Ruggiero Neto J, Palma MS (2015) Structure-activity relationship of mastoparan analogs: effects of the number and positioning of Lys residues on secondary structure, interaction with membrane-mimetic systems and biological activity. Peptides 72:164–174

    PubMed  Google Scholar 

  • Demel RA, Geurts van Kessel WS, Zwaal RF, Roelofsen B, van Deenen LL (1975) Relation between various phospholipase actions on human red cell membranes and the interfacial phospholipid pressure in monolayers. Biochim Biophys Acta 406(1):97–107

    CAS  PubMed  Google Scholar 

  • Eftink MR, Ghiron CA (1976) Fluorescence quenching of indole and model micelle systems. J Phys Chem 80(5):486–493

    CAS  Google Scholar 

  • Elber R, Ruymgaart AP, Hess B (2011) SHAKE parallelization. Eur Phys J Spec Top 200(1):211–223

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ermakova E, Kurbanov R, Zuev Y (2019) Coarse-grained molecular dynamics of membrane semitoroidal pore formation in model lipid-peptide systems. J Mol Graph Model 87:1–10

    CAS  PubMed  Google Scholar 

  • Farrotti A, Bocchinfuso G, Palleschi A, Rosato N, Salnikov ES, Voievoda N, Bechinger B, Stella L (2015) Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case. Biochim Biophys Acta 1848(2):581–592

    CAS  PubMed  Google Scholar 

  • Feller SE, Zhang Y, Pastor RW, Brooks BR (1995) Constant pressure molecular dynamics simulation: the Langevin piston method. J Chem Phys 103(11):4613–4621

    CAS  Google Scholar 

  • Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins Struct Funct Bioinform 23(4):566–579

    Article  CAS  Google Scholar 

  • Giuliani A, Pirri G, Nicoletto SF (2007) Antimicrobial peptides: an overview of a promising class of therapeutics. Cent Eur J Biol 2(1):1–33

    CAS  Google Scholar 

  • Guixà-González R, Rodriguez-Espigares I, Ramírez-Anguita J, Carrió-Gaspar P, Martinez-Seara H, Giorgino T, Selent J (2014) MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics (Oxford, England) 30(10):1478–1480

    Google Scholar 

  • Hancock RE, Lehrer R (1998) Cationic peptides: a new source of antibiotics. Trends Biotechnol 16(2):82–88

    CAS  PubMed  Google Scholar 

  • Huang J, MacKerell AD (2013) CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34(25):2135–2145

    CAS  PubMed  PubMed Central  Google Scholar 

  • Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38

    CAS  PubMed  Google Scholar 

  • Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29(11):1859–1865

    CAS  PubMed  Google Scholar 

  • Jo S, Lim JB, Klauda JB, Im W (2009) CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes. Biophys J 97(1):50–58

    CAS  PubMed  PubMed Central  Google Scholar 

  • Knapp B, Ospina L, Deane CM (2018) Avoiding false positive conclusions in molecular simulation: the importance of replicas. J Chem Theory Comput 14(12):6127–6138

    CAS  PubMed  Google Scholar 

  • Lakowicz JR (2006) Principles of fluorescence spectroscopy, 3rd edn. Springer, Berlin

    Google Scholar 

  • Lau SY, Taneja AK, Hodges RS (1984) Synthesis of a model protein of defined secondary and quaternary structure. Effect of chain length on the stabilization and formation of two-stranded alpha-helical coiled-coils. J Biol Chem 259(21):13253–13261

    CAS  PubMed  Google Scholar 

  • Leite NB, Alvares DS, de Souza BM, Palma MS, Ruggiero Neto J (2014) Effect of the aspartic acid D2 on the affinity of Polybia-MP1 to anionic lipid vesicles. Eur Biophys J 43(4):121–130

    CAS  PubMed  Google Scholar 

  • Leite NB, Aufderhorst-Roberts A, Palma MS, Connell SD, Ruggiero Neto J, Beales PA (2015) PE and PS lipids synergistically enhance membrane poration by a peptide with anticancer properties. Biophys J 109(5):936–947

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lobley A, Whitmore L, Wallace BA (2002) DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra. Bioinformatics (Oxford, England) 18(1):211–212

    CAS  Google Scholar 

  • Luo P, Baldwin RL (1997) Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry 36(27):8413–8421

    CAS  PubMed  Google Scholar 

  • Makovitzki A, Baram J, Shai Y (2008) Antimicrobial lipopolypeptides composed of palmitoyl di- and tricationic peptides: in vitro and in vivo activities, self-assembly to nanostructures, and a plausible mode of action. Biochemistry 47(40):10630–10636

    CAS  PubMed  Google Scholar 

  • Mark P, Nilsson L (2001) Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J Phys Chem A 105(43):9954–9960

    CAS  Google Scholar 

  • Marsh D (1996) Lateral pressure in membranes. Biochim Biophys Acta (BBA) Rev Biomembr 1286(3):183–223

    CAS  Google Scholar 

  • Marsh D (2013) Handbook of lipid bilayers. CRC Press, Boca Raton

    Google Scholar 

  • Matsuzaki K, Murase O, Tokuda H, Funakoshi S, Fujii N, Miyajima K (1994) Orientational and aggregational states of magainin 2 in phospholipid bilayers. Biochemistry 33(11):3342–3349

    CAS  PubMed  Google Scholar 

  • Miasaki KMF, Wilke N, Ruggiero Neto J, Alvares DS (2020) N-terminal acetylation of a mastoparan-like peptide enhances PE/PG segregation in model membranes. Chem Phys Lipids 232:104975

    CAS  PubMed  Google Scholar 

  • Miyamoto S, Kollman PA (1992) Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 13(8):952–962. https://doi.org/10.1002/jcc.540130805

    Article  CAS  Google Scholar 

  • Orioni B, Bocchinfuso G, Kim JY, Palleschi A, Grande G, Bobone S, Park Y, Kim JI, Hahm K, Lorenzo S (2009) Membrane perturbation by the antimicrobial peptide PMAP-23: a fluorescence and molecular dynamics study. Biochim Biophys Acta (BBA) Biomembr 1788(7):1523–1533

    CAS  Google Scholar 

  • Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781–1802. https://doi.org/10.1002/jcc.20289

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Piggot TJ, Allison JR, Sessions RB, Essex JW (2017) On the calculation of acyl chain order parameters from lipid simulations. J Chem Theory Comput 13(11):5683–5696

    CAS  PubMed  Google Scholar 

  • Romo TD, Bradney LA, Greathouse DV (2011) Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Biochim Biophys Acta (BBA) Biomembr 1808(8):2019–2030

    CAS  Google Scholar 

  • Sani M-A, Le Brun AP, Separovic F (2020) The antimicrobial peptide maculatin self assembles in parallel to form a pore in phospholipid bilayers. Biochim Biophys Acta (BBA) Biomembr 1862(5):183204

    CAS  Google Scholar 

  • Santos NC, Prieto M, Castanho MARB (2003) Quantifying molecular partition into model systems of biomembranes: an emphasis on optical spectroscopic methods. Biochim Biophys Acta 1612(2):123–135

    CAS  PubMed  Google Scholar 

  • Silva ON, Alves ESF, de la Fuente-Núñez C, Ribeiro SM, Mandal SM, Gaspar D, Veiga AS, Castanho MARB, Andrade CAS, Nascimento JM, Fensterseifer ICM, Porto WF, Correa JR, Hancock REW, Korpole S, Oliveira AL, Liao LM, Franco OL (2016) Structural studies of a lipid-binding peptide from tunicate hemocytes with anti-biofilm activity. Sci Rep 6(1):27128

    CAS  PubMed  PubMed Central  Google Scholar 

  • Souza BM, Mendes MA, Santos LD, Marques MR, Cesar LMM, Almeida RNA, Pagnocca FC, Konno K, Palma MS (2005). Structural and functional characterization of two novel peptide toxins isolated from the venom of the social wasp Polybia paulista. Peptides. Elsevier B.V, pp 2157–2164. Accepted 2014-05-20T13:54:38Z

  • Souza LMP, Nascimento JB, Romeu AL, Estrada-López ED, Pimentel AS (2018) Penetration of antimicrobial peptides in a lung surfactant model. Colloids Surf B Biointerfaces 167:345–353

    CAS  PubMed  Google Scholar 

  • Tsai C-W, Hsu N-Y, Wang C-H, Lu C-Y, Chang Y, Tsai H-HG, Ruaan R-C (2009) Coupling molecular dynamics simulations with experiments for the rational design of indolicidin-analogous antimicrobial peptides. J Mol Biol 392(3):837–854

    CAS  PubMed  Google Scholar 

  • Vogt TCB, Bechinger B (1999) The interactions of histidine-containing amphipathic helical peptide antibiotics with lipid bilayers the effects of charges and pH. J Biol Chem 274(41):29115–29121

    CAS  PubMed  Google Scholar 

  • Voievoda N, Schulthess T, Bechinger B, Seelig J (2015) Thermodynamic and biophysical analysis of the membrane-association of a histidine-rich peptide with efficient antimicrobial and transfection activities. J Phys Chem B 119(30):9678–9687

    CAS  PubMed  Google Scholar 

  • Wang K, Zhang B, Zhang W, Yan J, Li J, Wang R (2008) Antitumor effects, cell selectivity and structure–activity relationship of a novel antimicrobial peptide polybia-MPI. Peptides 29(6):963–968

    CAS  PubMed  Google Scholar 

  • Wang Y, Schlamadinger DE, Kim JE, McCammon JA (2012) Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. Biochim Biophys Acta (BBA) Biomembr 1818(5):1402–1409

    CAS  Google Scholar 

  • Whitmore L, Wallace BA (2004) DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Res 32(Web Server issue):W668–W673

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zanin LPM, de Araujo AS, Juliano MA, Casella T, Nogueira MCL, Ruggiero Neto J (2016) Effects of N-terminus modifications on the conformation and permeation activities of the synthetic peptide L1A. Amino Acids 48(6):1433–1444

    CAS  PubMed  Google Scholar 

  • Zhan H, Lazaridis T (2012) Influence of the membrane dipole potential on peptide binding to lipid bilayers. Biophys Chem 161:1–7

    CAS  PubMed  Google Scholar 

  • Zhigang T, Young A, Murphy C, Liang JF (2009) The pH sensitivity of histidine-containing lytic peptides. J Pept Sci Off Publ Eur Pept Soc 15(11):790–795

    Google Scholar 

Download references

Acknowledgements

The authors acknowledges financial support from Brazilian agencies: São Paulo Research Foundation-FAPESP (JRN: grant # 2015/25619-9; MSP grant# 2016/16212-5 and ASA grant # 2010/18169-3. IBSM Ph.D. grant CAPES, TGV Ph.D. grant CNPq. MSP CNPq/INCT iiii. DSA has a Post-doctorate fellowship Grant# 2015/25620-7 and thanks UNESP and CAPES for former scholarships. JRN and MSP are researchers for Brazilian Counsil for Scientific and Technological Development (CNPq). This research was supported by resources supplied by the Center for Scientific Computing (NCC/GridUNESP) of the São Paulo State University (UNESP), the “Centro Nacional de Processamento de Alto Desempenho em São Paulo (CENAPAD-SP)”. We also thank the National Laboratory for Scientific Computing (LNCC/MCTI, Brazil) and providing HPC resources of the SDumont supercomputer, URL: http://sdumont.lncc.br.

Author information

Authors and Affiliations

Authors

Contributions

IBSM and ASA performed the simulations and computational analysis. TGV, DSA and JRN performed the experiments and experimental analysis, MSP and BMS synthesized and purified the peptides. All authors discussed the results and participated on writing and reviewing this paper.

Corresponding authors

Correspondence to João Ruggiero Neto or Alexandre Suman de Araujo.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

This article does not contain any studies with human participants or animals performed by any of the authors.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Additional information

Handling editor: F. Polticelli.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary material 1 (pdf 4417 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Martins, I.B.S., Viegas, T.G., dos Santos Alvares, D. et al. The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy. Amino Acids 53, 753–767 (2021). https://doi.org/10.1007/s00726-021-02982-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00726-021-02982-0

Keywords

Navigation