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Pastuszak K, Palusińska-Szysz M, Wiącek AE, Jurak M. Thermodynamic Study on Biomimetic Legionella gormanii Bacterial Membranes. Molecules 2024; 29:4367. [PMID: 39339363 PMCID: PMC11434087 DOI: 10.3390/molecules29184367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/30/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
The presented studies were aimed at determining the interactions in model membranes (Langmuir monolayers) created of phospholipids (PL) isolated from Legionella gormanii bacteria cultured with (PL + choline) or without (PL - choline) choline and to describe the impact of an antimicrobial peptide, human cathelicidin LL-37, on PL's monolayer behavior. The addition of choline to the growth medium influenced the mutual proportions of phospholipids extracted from L. gormanii. Four classes of phospholipids-phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), cardiolipin (CL), and their mixtures-were used to register compression isotherms with or without the LL-37 peptide in the subphase. Based on them the excess area (Ae), excess (ΔGe), and total (ΔGm) Gibbs energy of mixing were determined. The thermodynamic analyses revealed that the PL - choline monolayer showed greater repulsive forces between molecules in comparison to the ideal system, while the PL + choline monolayer was characterized by greater attraction. The LL-37 peptide affected the strength of interactions between phospholipids' molecules and reduced the monolayers stability. Accordingly, the changes in interactions in the model membranes allowed us to determine the difference in their susceptibility to the LL-37 peptide depending on the choline supplementation of bacterial culture.
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Affiliation(s)
- Katarzyna Pastuszak
- Department of Interfacial Phenomena, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland; (K.P.); (A.E.W.)
| | - Marta Palusińska-Szysz
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Agnieszka Ewa Wiącek
- Department of Interfacial Phenomena, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland; (K.P.); (A.E.W.)
| | - Małgorzata Jurak
- Department of Interfacial Phenomena, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland; (K.P.); (A.E.W.)
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2
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Ouyang J, Sheng Y, Wang W. Recent Advances of Studies on Cell-Penetrating Peptides Based on Molecular Dynamics Simulations. Cells 2022; 11:cells11244016. [PMID: 36552778 PMCID: PMC9776715 DOI: 10.3390/cells11244016] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
With the ability to transport cargo molecules across cell membranes with low toxicity, cell-penetrating peptides (CPPs) have become promising candidates for next generation peptide-based drug delivery vectors. Over the past three decades since the first CPP was discovered, a great deal of work has been done on the cellular uptake mechanisms and the applications for the delivery of therapeutic molecules, and significant advances have been made. But so far, we still do not have a precise and unified understanding of the structure-activity relationship of the CPPs. Molecular dynamics (MD) simulations provide a method to reveal peptide-membrane interactions at the atomistic level and have become an effective complement to experiments. In this paper, we review the progress of the MD simulations on CPP-membrane interactions, including the computational methods and technical improvements in the MD simulations, the research achievements in the CPP internalization mechanism, CPP decoration and coupling, and the peptide-induced membrane reactions during the penetration process, as well as the comparison of simulated and experimental results.
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Affiliation(s)
- Jun Ouyang
- School of Public Courses, Bengbu Medical College, Bengbu 233030, China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yuebiao Sheng
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- High Performance Computing Center, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
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3
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Agadi N, Maity A, Jha AK, Chakrabarti R, Kumar A. Distinct mode of membrane interaction and disintegration by diverse class of antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184047. [PMID: 36100074 DOI: 10.1016/j.bbamem.2022.184047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/18/2022] [Accepted: 09/06/2022] [Indexed: 12/29/2022]
Abstract
The exploitation of conventional antibiotics in conjunction with the adeptness of microbes has led to the emergence of multi-drug-resistant pathogens. This has posed a severe threat to combating life-threatening infectious diseases. Antimicrobial peptides (AMP), which are considered to be the first line of defense in all living organisms, are being developed for therapeutic use. Herein, we determined the NMR solution structure of Rhesus macaque Myeloid Alpha Defensin-4 (RMAD4), a defensin AMP. Additionally, the distinct modes of membrane perturbation for two structurally dissimilar classes of AMPs was studied using biophysical methods namely, Solid-state 31P NMR, DSC and cryo-TEM. The cathelicidin - Bovine myeloid antimicrobial peptide (BMAP-28 (1-18)), which adopts a helical conformation, and the defensin RMAD4 peptide that natively folds to form β-sheets appeared to engage differently with the bacterial membrane. The helical BMAP-28 (1-18) peptide initiates lipid segregation and membrane thinning followed by pore formation, while the β-stranded RMAD4 peptide demonstrates fragmentation of the bilayer by the carpet or detergent-like mechanism of action. Molecular dynamics studies sufficiently corroborated these findings. The structure and mechanism of action of the AMPs studied using experimental and computational approaches are believed to help in providing a platform for the rational design of new competent and cost-effective antimicrobial peptides for therapeutic applications.
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Affiliation(s)
- Nutan Agadi
- Centre for Research in Nanotechnology and Science (CRNTS), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Akash Kumar Jha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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4
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Sun L, Wang S, Tian F, Zhu H, Dai L. Organizations of melittin peptides after spontaneous penetration into cell membranes. Biophys J 2022; 121:4368-4381. [PMID: 36199252 PMCID: PMC9703044 DOI: 10.1016/j.bpj.2022.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
The antimicrobial peptide, melittin, is a potential next-generation antibiotic because melittin can spontaneously form pores in bacterial cell membranes and cause cytoplasm leakage. However, the organizations of melittin peptides in cell membranes remain elusive, which impedes the understanding of the poration mechanism. In this work, we use coarse-grained and all-atom molecular dynamics (MD) simulations to investigate the organizations of melittin peptides during and after spontaneous penetration into DPPC/POPG lipid bilayers. We find that the peptides in lipid bilayers adopt either a transmembrane conformation or a U-shaped conformation, which are referred to as T- and U-peptides, respectively. Several U-peptides and/or T-peptides aggregate to form stable pores. We analyze a T-pore consisting of four T-peptides and a U-pore consisting of three U-peptides and one T-peptide. In both pores, peptides are organized in a manner such that polar residues face inward and hydrophobic residues face outward, which stabilizes the pores and produces water channels. Compared with the U-pore, the T-pore has lower energy, larger pore diameter, and higher permeability. However, the T-pore occurs less frequently than the U-pore in our simulations, probably because the formation of the T-pore is kinetically slower than the U-pore. The stability and permeability of both pores are confirmed by 300 ns all-atom MD simulations. The peptide organizations obtained in this work should deepen the understanding of the stability, poration mechanism, and permeability of melittin, and facilitate the optimization of melittin to enhance the antibacterial ability.
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Affiliation(s)
- Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon, Hong Kong, China.
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5
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Ghosh S, Chatterjee S, Satpati P. Effect of a monovalent salt on the energetics of an antimicrobial-peptide: micelle dissociation. Phys Chem Chem Phys 2022; 24:23669-23678. [PMID: 36148810 DOI: 10.1039/d2cp02735f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Antimicrobial peptides (AMPs) are promising antimicrobial and therapeutic agents. Recently, we synthesized a cationic 14 residue AMP (LL-14: LKWLKKLLKWLKKL), which showed high broad-spectrum antimicrobial activity. However, the antimicrobial activity of LL-14 was compromised in the presence of NaCl. Salt sensitivity of antimicrobial potency is one of the fundamental limitations of AMP therapeutics. Thus, understanding the thermodynamics of AMP binding to simple membrane-mimetic systems and the effect of NaCl that contributes to their stability is crucial for designing promising AMPs against microbial infection. In this work, we reported computational analysis of LL-14 binding to SDS micelles (the simplest bacterial membrane mimic) at various NaCl concentrations (0.0%, 0.5%, 1.0% w/v). The thermodynamics of LL-14 dissociation from the SDS micelles was estimated by employing steered molecular dynamics (SMD) simulation followed by umbrella sampling. The results indicated that the increase in NaCl concentration systematically disfavoured the LL-14:SDS binding, primarily by stabilizing the dissociative state (i.e., free LL-14 and free micelles in water). We proposed a kinetic scheme in which the salt-induced selective stabilization of the dissociative state increased the activation barrier for the peptide:micelle binding event resulting in reduced affinity. Center-of-mass pulling indicated that the interactions involving the N-terminal of the LL-14 (residues 1-6) and SDS micelle were crucial for the stability of the LL-14:SDS complex, and LL-14 underwent a conformational change (helix → unstructured) before dissociating from the SDS micelle. The observed structural features from the peptide:micelle dissociation pathway corroborate our previous simulations as well as circular dichroism (CD), and fluorescence experiments.
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Affiliation(s)
- Suvankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Xie YY, Qin XT, Zhang J, Sun MY, Wang FP, Huang M, Jia SR, Qi W, Wang Y, Zhong C. Self-assembly of peptide nanofibers with chirality-encoded antimicrobial activity. J Colloid Interface Sci 2022; 622:135-146. [DOI: 10.1016/j.jcis.2022.04.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/12/2022]
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7
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Ghosh S, Chatterjee S, Satpati P. Effect of Leu/Val Mutation on the Energetics of Antimicrobial Peptide:Micelle Binding. J Phys Chem B 2022; 126:5262-5273. [PMID: 35815580 DOI: 10.1021/acs.jpcb.2c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recently, we had reported a synthetic positively charged leucine-rich 14-residue-long antimicrobial peptide (AMP, LL-14: NH3+-LKWLKKLLKWLKKL-CONH2), which was highly active and cytotoxic relative to its valine analogue (VV-14). However, the thermodynamics underlying this differential toxicity and antimicrobial activity was unclear. Understanding the energetics of peptide binding to micelles (simplest membrane mimic, viz., SDS as a bacterial membrane and DPC as a eukaryotic membrane) and the effect of Leu → Val peptide mutations on the stability of the peptide:micelle complexes are of great academic interest and relevant for the rational design of potent and selective AMPs for therapeutic use. Here, we have reported the molecular dynamics free energy simulations that allowed us to quantitatively estimate the strength of peptide discrimination (based on single- or multiple-site Leu/Val mutations in LL-14) by membrane mimetic micelles (SDS and DPC) and decipher the energetics underlying peptide selectivity by micelles. The Leu-containing peptide (LL-14) was found to be preferred for micelle (SDS and DPC) binding relative to its Val analogues (single or multiple Val mutants). The strength of the preference depended on the position of the Leu/Val mutation in the peptide. Surprisingly, the N-terminal LL-14 single mutation (Leu → Val: L1V) was found to fine-tune the electrostatic interactions, resulting in the highest peptide selectivity (ΔΔG ∼ 8 kcal/mol for both SDS and DPC). However, the mechanism of L1V peptide selectivity was distinctly different for SDS and DPC micelles. SDS ensured high selectivity by disrupting the peptide:micelle salt bridge, whereas DPC desolvated the broken-peptide-backbone hydrogen bond in the V1 peptide:micelle complex. Mutations (Leu → Val) in the middle positions of the LL-14 (4th, 7th, 8th, and 11th) were disfavored by the micelles primarily due to the loss of peptide:micelle hydrophobic interactions. Peptides differing at the C-terminal (i.e., L14V) were recognized by SDS micelles (ΔΔG ∼ 4 kcal/mol) by altering peptide:micelle interactions. L14V mutation, on the other hand, did not play any role in the peptide:DPC binding, as no direct interactions between the C-terminal and DPC micelle were observed due to obvious electrostatic reasons. The strength of selectivity favoring LL-14 binding against VV-14 was found to be much higher for DPC micelles (ΔΔG ∼ 25 kcal/mol) relative to SDS micelles (ΔΔG ∼ 19 kcal/mol). The loss of the peptide:micelle hydrophobic contact in response to LL-14 → VV-14 mutation was found to be significantly larger for DPC relative to SDS micelles, resulting in higher discriminatory power for the former. Peptide:SDS salt bridges seemed to prevent the loss of peptide:micelle hydrophobic contact to some extent, leading to weaker selectivity for SDS micelles. High selectivity of DPC micelles provided an efficient mechanism for VV-14 dissociation from DPC micelles, whereas low-selectivity of SDS micelles ensured binding of both LL-14 and VV-14. To the best of our knowledge, this is the first study in which the experimental observations (antimicrobial activity and toxicity) between leucine-rich and valine-rich peptides have been explained by establishing a direct link between the energetics and structures.
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Affiliation(s)
- Suvankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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8
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Soybean peptide inhibits the biofilm of periodontopathic bacteria via bactericidal activity. Arch Oral Biol 2022; 142:105497. [PMID: 35849907 DOI: 10.1016/j.archoralbio.2022.105497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/09/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022]
Abstract
OBJECTIVE This study aimed to clarify the antibacterial mechanism and antibiofilm effect of soybean-derived peptide BCBS-11 against periodontopathic bacteria. DESIGN The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of BCBS-11 against Porphyromonas gingivalis (P. gingivalis), Fusobacterium nucleatum (F. nucleatum), and Streptococcus mitis (S. mitis) were determined for the antibacterial mechanism. The effect of BCBS-11 on membrane permeability and depolarization activity were investigated using propidium iodide (PI) staining and 3, 3'-dipropylthiadicarbocyanine iodide (DiSC3-(5)) analysis. Monospecies and multispecies biofilms were cultured on 96-well plates. The amount of biofilm was determined using crystal violet staining to determine the inhibition of biofilm formation and the eradication of established biofilm using BCBS-11. The cytotoxicity of BCBS-11 was evaluated using 3-(4, 5-Dimethylthiazol-2-yl)- 2, 5-diphenyltetrazolium bromide (MTT) assay. RESULTS The MIC and MBC indicated the bactericidal activity of BCBS-11 against P. gingivalis and F. nucleatum. The PI staining revealed that BCBS-11 disrupted the bacterial membrane integrity. The DiSC3-(5) analysis indicated that BCBS-11 depolarized the bacterial cytoplasmic membrane. These results indicate the antimicrobial action of BCBS-11 through membrane disruption and the collapse of membrane electrochemical gradient. BCBS-11 significantly inhibited the monospecies biofilm formation of P. gingivalis and F. nucleatum and also inhibited dual-species biofilm. BCBS-11 was not cytotoxic toward human oral epithelial cells. CONCLUSIONS BCBS-11 inhibits the monospecies and multispecies biofilm formation of P. gingivalis and F. nucleatum, and their bactericidal activity results from membrane disruption.
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9
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Ghosh S, Pandit G, Debnath S, Chatterjee S, Satpati P. Effect of monovalent salt concentration and peptide secondary structure in peptide-micelle binding. RSC Adv 2021; 11:36836-36849. [PMID: 35494385 PMCID: PMC9043568 DOI: 10.1039/d1ra06772a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Recently, we reported a cationic 14 residue peptide LL-14 (LKWLKKLLKWLKKL) with salt-sensitive broad-spectrum antimicrobial potency. However, the mechanism of its salt (NaCl) sensitivity remained unclear. In this study, we have reported computational (∼14.2 μs of MD) and experimental (CD, fluorescence) investigations to examine the salt-sensitivity and the role of peptide secondary structure on LL-14 binding to simple membrane mimetic (SDS, DPC) systems. LL-14 was shown to adopt a random coil (Pc) conformation in water and α-helical conformation (Ph) in the peptide:SDS micelle complex, accompanied by tryptophan burial, using both simulations and experiments. Simulations successfully deconvoluted the LL-14:micelle binding event in terms of secondary structure (random coil Pcversus helix Ph) and gave atomic insight into the initial and final LL-14:SDS complexes. Electrostatics drove the N-terminus (L1 and K2) of LL-14 (Pc or Ph) to bind the SDS micellar surface, initiating complex formation. LL-14 in amphipathic Ph conformation bound faster and buried deeper into the SDS micelle relative to Pc. Increasing NaCl concentration incrementally delayed LL-14:micelle binding by shielding the overall charges of the interacting partners. LL-14 binding to the SDS micelle was significantly faster relative to that of the zwitterionic DPC micelle due to electrostatic reasons. Cationic α-helical amphipathic peptides (with positively charged N-terminus) with low salt-ion concentration seemed to be ideal for faster SDS binding. We report computational (∼14.2 μs of MD) and experimental (CD, fluorescence) investigations to examine the salt-sensitivity and the role of the peptide secondary structure on LL-14 binding to simple membrane mimetic systems.![]()
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Affiliation(s)
- Suvankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2582249 +91-361-2583205
| | - Gopal Pandit
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2583310
| | - Swapna Debnath
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2583310
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2583310
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati 781039 Assam India +91-361-2582249 +91-361-2583205
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10
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Identification of the Ricin-B-Lectin LdRBLk in the Colorado Potato Beetle and an Analysis of Its Expression in Response to Fungal Infections. J Fungi (Basel) 2021; 7:jof7050364. [PMID: 34066637 PMCID: PMC8148562 DOI: 10.3390/jof7050364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 01/15/2023] Open
Abstract
Ricin-B-lectins (RBLs) have been identified in many groups of organisms, including coleopterans insects, particularly the Colorado potato beetle Leptinotarsa decemlineata (LdRBLs). We hypothesized that one of these LdRBLs (LdRBLk) may be involved in the immune response to fungal infections. We performed a theoretical analysis of the structure of this protein. Additionally, the expression levels of the LdRBlk gene were measured in L. decemlineata in response to infections with the fungi Metarhizium robertsii and Beauveria bassiana. The expression levels of LdRBlk in the L. decemlineata cuticle and fat body were increased in response to both infections. The induction of LdRBlk expression was dependent on the susceptibility of larvae to the fungi. Upregulation of the LdRBlk gene was also observed in response to other stresses, particularly thermal burns. Elevation of LdRBlk expression was frequently observed to be correlated with the expression of the antimicrobial peptide attacin but was not correlated with hsp90 regulation. Commercially available β-lectin of ricin from Ricinuscommunis was observed to inhibit the germination of conidia of the fungi. We suggest that LdRBLk is involved in antifungal immune responses in the Colorado potato beetle, either exerting fungicidal properties directly or acting as a modulator of the immune response.
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11
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Chakraborty A, Kobzev E, Chan J, de Zoysa GH, Sarojini V, Piggot TJ, Allison JR. Molecular Dynamics Simulation of the Interaction of Two Linear Battacin Analogs with Model Gram-Positive and Gram-Negative Bacterial Cell Membranes. ACS OMEGA 2021; 6:388-400. [PMID: 33458490 PMCID: PMC7807746 DOI: 10.1021/acsomega.0c04752] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Antimicrobial peptides (AMPs) are a potential solution to the increasing threat of antibiotic resistance, but successful design of active but nontoxic AMPs requires understanding their mechanism of action. Molecular dynamics (MD) simulations can provide atomic-level information regarding how AMPs interact with the cell membrane. Here, we have used MD simulations to study two linear analogs of battacin, a naturally occurring cyclic, lipidated, nonribosomal AMP. Like battacin, these analogs are active against Gram-negative multidrug resistant and Gram-positive bacteria, but they are less toxic than battacin. Our simulations show that this activity depends upon a combination of positively charged and hydrophobic moieties. Favorable interactions with negatively charged membrane lipid head groups drive association with the membrane and insertion of hydrophobic residues, and the N-terminal lipid anchors the peptides to the membrane surface. Both effects are required for stable membrane binding.
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Affiliation(s)
- Aparajita Chakraborty
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
| | - Elisey Kobzev
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
- School
of Computational and Natural Sciences, Massey
University Auckland, Auckland 0632, New Zealand
| | - Jonathan Chan
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Department
of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, United
Kingdom
| | | | - Vijayalekshmi Sarojini
- School of
Chemical Sciences, University of Auckland, Auckland 1010, New Zealand
- MacDiarmid
Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Thomas J. Piggot
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
- Chemical
Biological and Radiological Sciences, Defence
Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Jane R Allison
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Centre
for Theoretical Chemistry and Physics, Massey
University Auckland, Auckland 0632, New Zealand
- Biomolecular
Interaction Centre, University of Canterbury, Christchurch 8041, New Zealand
- Digital
Life Institute, University of Auckland, Auckland 1010, New Zealand
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12
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Acaroğlu Degitz İ, Hakkı Gazioğlu B, Burak Aksu M, Malta S, Demir Sezer A, Eren T. Antibacterial and hemolytic activity of cationic polymer-vancomycin conjugates. Eur Polym J 2020. [DOI: 10.1016/j.eurpolymj.2020.110084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Downing R, Volpe Bossa G, May S. Saddle-curvature instability of lipid bilayer induced by amphipathic peptides: a molecular model. SOFT MATTER 2020; 16:5032-5043. [PMID: 32452495 DOI: 10.1039/d0sm00499e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amphipathic peptides that partition into lipid bilayers affect the curvature elastic properties of their host. Some of these peptides are able to shift the Gaussian modulus to positive values, thus triggering an instability with respect to the formation of saddle curvatures. To characterize the generic aspects of the underlying mechanism, we employ a molecular lipid model that accounts for the interfacial tension between the polar and apolar regions of the membrane, for interactions between the lipid headgroups, and for the energy to stretch or compress the hydrocarbon chains. Peptides are modeled as cylinders that partition into the host membrane in a parallel orientation where they diminish the space available to the lipid headgroups and chains. The penetration depth into the membrane is determined by the angular size of the peptide's hydrophilic region. We demonstrate that only peptides with a small angular size of their hydrophilic region have an intrinsic tendency to render the Gaussian modulus more positive, and we identify conditions at which the Gaussian modulus adopts a positive sign upon increasing the peptide concentration. Our model allows us to also incorporate electrostatic interactions between cationic peptides and anionic lipids on the level of the linear Debye-Hückel model. We show that electrostatic interactions tend to shift the Gaussian modulus toward more positive values. Steric and electrostatic lipid-peptide interactions jointly decrease the effective interaction strength in the headgroup region of the host membrane thus suggesting a generic mechanisms of how certain amphipathic peptides are able to induce the formation of saddle curvatures.
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Affiliation(s)
- Rachel Downing
- Department of Physics, North Dakota State University, Fargo North Dakota 58108-6050, USA
| | - Guilherme Volpe Bossa
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil.
| | - Sylvio May
- Department of Physics, North Dakota State University, Fargo North Dakota 58108-6050, USA
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14
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Joodaki F, Martin LM, Greenfield ML. Planarity and out-of-plane vibrational modes of tryptophan and tyrosine in biomolecular modeling. Phys Chem Chem Phys 2019; 21:23943-23965. [PMID: 31596287 DOI: 10.1039/c9cp04798k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tryptophan and tyrosine are amino acids that play significant roles in the folding processes of proteins at water-membrane interfaces because of their amphipathic heteroaromatic rings. Employing appropriate heteroaromatic molecular structures is essential for obtaining accurate dynamics and predictive capabilities in molecular simulations of these amino acids. In this study, molecular dynamics simulations that applied the most recent version of the CHARMM36 force field were conducted on aqueous solutions of tryptophan and of tyrosine. Geometric analysis and dynamics quantified how aromatic rings deviated from planar structures and exhibited out-of-plane fluctuations. Radial distribution functions showed possible biological significance because the extent of ring planarity slightly affected local water concentrations near aromatic rings. Instantaneous all-atom normal mode analysis (NMA) and Fourier transformation of time autocorrelation functions of out-of-plane displacements were applied to study out-of-plane vibrations of atoms in these rings. The NMA started with minimum energy configurations and then averaged over fluctuations in aqueous solution. The frequencies and frequency patterns that were obtained for tryptophan and tyrosine with CHARMM36 differed from literature reports of Raman spectra, infrared spectra, and frequencies calculated using quantum mechanics, with some out-of-plane modes found at higher frequencies. Effects of imposing improper torsion potentials and changing torsion angle force constants were investigated for all atoms in the rings of tryptophan and tyrosine. Results show that these coarse force field variations only affect planarity and out-of-plane vibrations of atoms within the rings, and not other vibrations. Although increasing improper torsion force constants reduced deviations from aromatic ring planarity significantly, it increased out-of-plane mode frequencies. Reducing torsion angle force constants (with and without improper torsions) shifted modes to lower frequencies. A combination of decreasing most torsion angle force constants for ring atoms in both amino acids and including improper torsion forces attained frequencies and frequency patterns for out-of-plane normal modes that were more similar to the literature spectra. These force field variations decreased the extents of out-of-plane vibrations within the heteroaromatic rings of tryptophan, especially around the nitrogen atom in the ring, but not within the heteroaromatic ring of tyrosine. Conclusions were unaffected by the peptide endgroup, water, or simulation ensemble.
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Affiliation(s)
- Faramarz Joodaki
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, USA.
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15
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Antimicrobial Peptides in the Cross Hairs of Computer Simulations. Biophys J 2019; 113:1-3. [PMID: 28700907 DOI: 10.1016/j.bpj.2017.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/02/2017] [Indexed: 11/21/2022] Open
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Abstract
Brettanomyces bruxellensis has been described as the principal spoilage yeast in the winemaking industry. To avoid its growth, wine is supplemented with SO2, which has been questioned due to its potential harm to health. For this reason, studies are being focused on searching for, ideally, natural new antifungals. On the other hand, it is known that in wine production there are a variety of microorganisms, such as yeasts and bacteria, that are possible biological controls. Thus, it has been described that some microorganisms produce antimicrobial peptides, which might control yeast and bacteria populations. Our laboratory has described the Candida intermedia LAMAP1790 strain as a natural producer of antimicrobial compounds against food spoilage microorganisms, as is B. bruxellensis, without affecting the growth of S. cerevisiae. We have demonstrated the proteinaceous nature of the antimicrobial compound and its low molecular mass (under 10 kDa). This is the first step to the possible use of C. intermedia as a selective bio-controller of the contaminant yeast in the winemaking industry.
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17
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Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630158 DOI: 10.1098/rstb.2016.0219] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Graduate Program in Chemistry, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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18
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Xiang N, Lyu Y, Zhu X, Bhunia AK, Narsimhan G. Effect of physicochemical properties of peptides from soy protein on their antimicrobial activity. Peptides 2017; 94:10-18. [PMID: 28587835 DOI: 10.1016/j.peptides.2017.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 10/19/2022]
Abstract
Antimicrobial peptides (AMPs) kill microbial cells through insertion and damage/permeabilization of the cytoplasmic cell membranes and has applications in food safety and antibiotic replacement. Soy protein is an attractive, abundant natural source for commercial production of AMPs. In this research, explicit solvent molecular dynamics (MD) simulation was employed to investigate the effects of (i) number of total and net charges, (ii) hydrophobicity (iii) hydrophobic moment and (iv) helicity of peptides from soy protein on their ability to bind to lipid bilayer and their transmembrane aggregates to form pores. Interaction of possible AMP segments from soy protein with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPC/POPG) bilayers, a mimic of bacterial cell membrane, was investigated. Pore formation was insensitive to helicity and occurred for hydrophobicity threshold in the range of -0.3-0kcal/mol, hydrophobic moment threshold of 0.3kcal/mol, net charge threshold of 2. Though low hydrophobicity and high number of charges help in the formation of water channel for transmembrane aggregates, insertion of peptides with these properties requires overcome of energy barrier, as shown by potential of mean force calculations, thereby resulting in low antimicrobial activity. Experimental evaluation of antimicrobial activity of these peptides against Gram positive L. monocytogenes and Gram negative E. coli as obtained by spot-on-lawn assay was consistent with simulation results. These results should help in the development of guidelines for selection of peptides with antimicrobial activity based on their physicochemical properties.
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Affiliation(s)
- Ning Xiang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Yuan Lyu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Xiao Zhu
- Research Computing, Rosen Center for Advanced Computing, Purdue University, West Lafayette, IN 47907,United States
| | - Arun K Bhunia
- Department of Food Science, Purdue University, West Lafayette, IN 47907, United States; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, United States
| | - Ganesan Narsimhan
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, United States.
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19
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Farrotti A, Conflitti P, Srivastava S, Ghosh JK, Palleschi A, Stella L, Bocchinfuso G. Molecular Dynamics Simulations of the Host Defense Peptide Temporin L and Its Q3K Derivative: An Atomic Level View from Aggregation in Water to Bilayer Perturbation. Molecules 2017; 22:molecules22071235. [PMID: 28737669 PMCID: PMC6152314 DOI: 10.3390/molecules22071235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 12/03/2022] Open
Abstract
Temporin L (TempL) is a 13 residue Host Defense Peptide (HDP) isolated from the skin of frogs. It has a strong affinity for lipopolysaccharides (LPS), which is related to its high activity against Gram-negative bacteria and also to its strong tendency to neutralize the pro-inflammatory response caused by LPS release from inactivated bacteria. A designed analog with the Q3K substitution shows an enhancement in both these activities. In the present paper, Molecular Dynamics (MD) simulations have been used to investigate the origin of these improved properties. To this end, we have studied the behavior of the peptides both in water solution and in the presence of LPS lipid-A bilayers, demonstrating that the main effect through which the Q3K substitution improves the peptide activities is the destabilization of peptide aggregates in water.
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Affiliation(s)
- Andrea Farrotti
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", Rome 00133, Italy.
| | - Paolo Conflitti
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", Rome 00133, Italy.
| | - Saurabh Srivastava
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India.
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India.
| | - Antonio Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", Rome 00133, Italy.
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", Rome 00133, Italy.
| | - Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", Rome 00133, Italy.
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20
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Triana-Vidal LE, Castro MS, Pires Júnior OR, Álvares ACM, de Freitas SM, Fontes W, Vargas JAG, Zúñiga-Baos JA, Correia Batista IDF, Grellier P, Charneau S. Dendropsophin 1, a novel antimicrobial peptide from the skin secretion of the endemic Colombian frog Dendropsophus columbianus. Nat Prod Res 2017; 32:1383-1389. [DOI: 10.1080/14786419.2017.1346646] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Luz Elena Triana-Vidal
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Mariana Souza Castro
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
- Laboratório de Toxinologia, Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Osmindo Rodrigues Pires Júnior
- Laboratório de Toxinologia, Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Alice Cunha Morales Álvares
- Laboratório de Biofísica, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Sonia Maria de Freitas
- Laboratório de Biofísica, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Wagner Fontes
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Jimmy Alexander Guerrero Vargas
- Departamento de Biología, Universidad del Cauca, Grupo de Investigaciones Herpetológicas y Toxinológicas (GIHT), Popayán, Colombia
| | - Jorge Alberto Zúñiga-Baos
- Departamento de Biología, Universidad del Cauca, Grupo de Investigaciones Herpetológicas y Toxinológicas (GIHT), Popayán, Colombia
| | | | - Philippe Grellier
- Muséum National d’Histoire Naturelle,UMR 7245 CNRS – Molécules de Communication et Adaptation des Micro-organismes, Paris, France
| | - Sébastien Charneau
- Laboratório de Bioquímica e Química de proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
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21
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Wu H, Liu S, Wiradharma N, Ong ZY, Li Y, Yang YY, Ying JY. Short Synthetic α-Helical-Forming Peptide Amphiphiles for Fungal Keratitis Treatment In Vivo. Adv Healthc Mater 2017; 6. [PMID: 28081296 DOI: 10.1002/adhm.201600777] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/26/2016] [Indexed: 12/28/2022]
Abstract
The emergence of fungal keratitis is on the rise globally. However, current antifungal therapeutics are ineffective in severe keratomycosis. Previously reported α-helical peptides comprising 8-14 amino acids demonstrate broad-spectrum antimicrobial activity both in vitro and in vivo. Here, α-helical peptides of the optimized sequences are investigated for antifungal biofilm in vitro and in vivo using a fungal biofilm-caused mouse keratitis model. The peptides with the optimal composition demonstrate higher α-helical propensity and improve antifungal activity in dispersing Candida albicans biofilm in vitro. Moreover, the optimized α-helical peptides are not only effective in treating C. albicans biofilm-induced keratitis in mice, they are also nontoxic to the mice eyes. These peptides have the potential to be developed as antifungal agents for the treatment of C. albicans biofilm-caused keratitis.
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Affiliation(s)
- Hong Wu
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Shaoqiong Liu
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Nikken Wiradharma
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Zhan Yuin Ong
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Yan Li
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Yi Yan Yang
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
| | - Jackie Y. Ying
- Institute of Bioengineering and Nanotechnology; 31 Biopolis Way The Nanos 138669 Singapore
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22
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Woo SY, Lee H. Aggregation and insertion of melittin and its analogue MelP5 into lipid bilayers at different concentrations: effects on pore size, bilayer thickness and dynamics. Phys Chem Chem Phys 2017; 19:7195-7203. [DOI: 10.1039/c6cp06834k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Melittin and its analogue MelP5 (five mutations T10A, R22A, K23A, R24Q, and Q26L of melittin) were simulated with lipid bilayers at different peptide/lipid molar ratios using all-atom and coarse-grained (CG) force fields.
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Affiliation(s)
- Sun Young Woo
- Department of Chemical Engineering
- Dankook University
- Yongin
- South Korea
| | - Hwankyu Lee
- Department of Chemical Engineering
- Dankook University
- Yongin
- South Korea
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23
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Prince A, Sandhu P, Ror P, Dash E, Sharma S, Arakha M, Jha S, Akhter Y, Saleem M. Lipid-II Independent Antimicrobial Mechanism of Nisin Depends On Its Crowding And Degree Of Oligomerization. Sci Rep 2016; 6:37908. [PMID: 27897200 PMCID: PMC5126574 DOI: 10.1038/srep37908] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/02/2016] [Indexed: 02/07/2023] Open
Abstract
Nisin inhibits bacterial growth by generating pores in cell membrane and interrupting cell-wall biosynthesis through specific lipid II interaction. However, the role of the hinge region and C-terminus residues of the peptide in antibacterial action of nisin is largely unknown. Here, using molecular dynamics simulations and experimental approach, we report that at high concentration regimes of nisin, interaction with phospholipids may equally deform the bacterial cell membranes even under significantly varying amounts of lipid-II. Membrane thinning, destabilization and decrease in lipid density depend on the degree of oligomerization of nisin. Growth kinetics of Bacillus subtilis and Escherichia coli interestingly show recovery by extended lag phase under low concentrations of nisin treatment while high concentrations of nisin caused decrease in cell viability as recorded by striking reduction in membrane potential and surface area. The significant changes in the dipole potential and fluorescence anisotropy were observed in negatively charged membranes in the absence of lipid-II with increasing concentration of nisin. The identical correlation of cell viability, membrane potential dissipation and morphology with the concentration regime of nisin, in both Bacillus subtilis (lipid II rich) and Escherichia coli (lipid II impoverished), hints at a non-specific physical mechanism where degree of membrane deformation depends on degree of crowding and oligomerization of nisin.
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Affiliation(s)
- Ashutosh Prince
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Padmani Sandhu
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, India
| | - Pankaj Ror
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Eva Dash
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Shingarika Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, India
| | - Manoranjan Arakha
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Suman Jha
- Department of Life Sciences, National Institute of Technology, Rourkela, India
| | - Yusuf Akhter
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, India
| | - Mohammed Saleem
- Department of Life Sciences, National Institute of Technology, Rourkela, India
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24
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Ponnappan N, Budagavi DP, Yadav BK, Chugh A. Membrane-active peptides from marine organisms--antimicrobials, cell-penetrating peptides and peptide toxins: applications and prospects. Probiotics Antimicrob Proteins 2016; 7:75-89. [PMID: 25559972 DOI: 10.1007/s12602-014-9182-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Marine organisms are known to be a rich and unique source of bioactive compounds as they are exposed to extreme conditions in the oceans. The present study is an attempt to briefly describe some of the important membrane-active peptides (MAPs) such as antimicrobial peptides (AMPs), cell-penetrating peptides (CPPs) and peptide toxins from marine organisms. Since both AMPs and CPPs play a role in membrane perturbation and exhibit interchangeable role, they can speculatively fall under the broad umbrella of MAPs. The study focuses on the structural and functional characteristics of different classes of marine MAPs. Further, AMPs are considered as a potential remedy to antibiotic resistance acquired by several pathogens. Peptides from marine organisms show novel post-translational modifications such as cysteine knots, halogenation and histidino-alanine bridge that enable these peptides to withstand harsh marine environmental conditions. These unusual modifications of AMPs from marine organisms are expected to increase their half-life in living systems, contributing to their increased bioavailability and stability when administered as drug in in vivo systems. Apart from AMPs, marine toxins with membrane-perturbing properties could be essentially investigated for their cytotoxic effect on various pathogens and their cell-penetrating activity across various mammalian cells. The current review will help in identifying the MAPs from marine organisms with crucial post-translational modifications that can be used as template for designing novel therapeutic agents and drug-delivery vehicles for treatment of human diseases.
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Affiliation(s)
- Nisha Ponnappan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
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25
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Faruck MO, Yusof F, Chowdhury S. An overview of antifungal peptides derived from insect. Peptides 2016; 80:80-88. [PMID: 26093218 DOI: 10.1016/j.peptides.2015.06.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 06/02/2015] [Accepted: 06/05/2015] [Indexed: 12/29/2022]
Abstract
Fungi are not classified as plants or animals. They resemble plants in many ways but do not produce chlorophyll or make their own food photosynthetically like plants. Fungi are useful for the production of beer, bread, medicine, etc. More complex than viruses or bacteria; fungi can be destructive human pathogens responsible for various diseases in humans. Most people have a strong natural immunity against fungal infection. However, fungi can cause diseases when this immunity breaks down. In the last few years, fungal infection has increased strikingly and has been accompanied by a rise in the number of deaths of cancer patients, transplant recipients, and acquired immunodeficiency syndrome (AIDS) patients owing to fungal infections. The growth rate of fungi is very slow and quite difficult to identify. A series of molecules with antifungal activity against different strains of fungi have been found in insects, which can be of great importance to tackle human diseases. Insects secrete such compounds, which can be peptides, as a part of their immune defense reactions. Active antifungal peptides developed by insects to rapidly eliminate infectious pathogens are considered a component of the defense munitions. This review focuses on naturally occurring antifungal peptides from insects and their challenges to be used as armaments against human diseases.
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Affiliation(s)
- Mohammad Omer Faruck
- Department of Biotechnology Engineering, Kulliyah of Engineering, International Islamic University Malaysia, P.O. Box 10, 50728 Kuala Lumpur, Malaysia
| | - Faridah Yusof
- Department of Biotechnology Engineering, Kulliyah of Engineering, International Islamic University Malaysia, P.O. Box 10, 50728 Kuala Lumpur, Malaysia.
| | - Silvia Chowdhury
- Department of Mechatronics Engineering, Kulliyah of Engineering, International Islamic University Malaysia, P.O. Box 10, 50728 Kuala Lumpur, Malaysia
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26
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Freeman EC, Farimani AB, Aluru NR, Philen MK. Multiscale modeling of droplet interface bilayer membrane networks. BIOMICROFLUIDICS 2015; 9:064101. [PMID: 26594262 PMCID: PMC4644148 DOI: 10.1063/1.4935382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/28/2015] [Indexed: 05/17/2023]
Abstract
Droplet interface bilayer (DIB) networks are considered for the development of stimuli-responsive membrane-based materials inspired by cellular mechanics. These DIB networks are often modeled as combinations of electrical circuit analogues, creating complex networks of capacitors and resistors that mimic the biomolecular structures. These empirical models are capable of replicating data from electrophysiology experiments, but these models do not accurately capture the underlying physical phenomena and consequently do not allow for simulations of material functionalities beyond the voltage-clamp or current-clamp conditions. The work presented here provides a more robust description of DIB network behavior through the development of a hierarchical multiscale model, recognizing that the macroscopic network properties are functions of their underlying molecular structure. The result of this research is a modeling methodology based on controlled exchanges across the interfaces of neighboring droplets. This methodology is validated against experimental data, and an extension case is provided to demonstrate possible future applications of droplet interface bilayer networks.
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Affiliation(s)
- Eric C Freeman
- College of Engineering, University of Georgia , Athens, Georgia 30602, USA
| | - Amir B Farimani
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, USA
| | - Michael K Philen
- Department of Aerospace and Ocean Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
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27
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Han E, Lee H. Structural effects of tachyplesin I and its linear derivative on their aggregation and mobility in lipid bilayers. J Mol Graph Model 2015; 59:123-8. [DOI: 10.1016/j.jmgm.2015.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
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28
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Berglund NA, Piggot TJ, Jefferies D, Sessions RB, Bond PJ, Khalid S. Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study. PLoS Comput Biol 2015; 11:e1004180. [PMID: 25885324 PMCID: PMC4401565 DOI: 10.1371/journal.pcbi.1004180] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/06/2015] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial peptides are small, cationic proteins that can induce lysis of bacterial cells through interaction with their membranes. Different mechanisms for cell lysis have been proposed, but these models tend to neglect the role of the chemical composition of the membrane, which differs between bacterial species and can be heterogeneous even within a single cell. Moreover, the cell envelope of Gram-negative bacteria such as E. coli contains two membranes with differing compositions. To this end, we report the first molecular dynamics simulation study of the interaction of the antimicrobial peptide, polymyxin B1 with complex models of both the inner and outer membranes of E. coli. The results of >16 microseconds of simulation predict that polymyxin B1 is likely to interact with the membranes via distinct mechanisms. The lipopeptides aggregate in the lipopolysaccharide headgroup region of the outer membrane with limited tendency for insertion within the lipid A tails. In contrast, the lipopeptides readily insert into the inner membrane core, and the concomitant increased hydration may be responsible for bilayer destabilization and antimicrobial function. Given the urgent need to develop novel, potent antibiotics, the results presented here reveal key mechanistic details that may be exploited for future rational drug development.
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Affiliation(s)
- Nils A Berglund
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom; Bioinformatics Institute (A*STAR), Singapore
| | - Thomas J Piggot
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | - Damien Jefferies
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
| | | | - Peter J Bond
- Bioinformatics Institute (A*STAR), Singapore; Department of Biological Sciences, National University of Singapore, Singapore
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton, United Kingdom
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29
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Zhang M, Zhao J, Zheng J. Molecular understanding of a potential functional link between antimicrobial and amyloid peptides. SOFT MATTER 2014; 10:7425-7451. [PMID: 25105988 DOI: 10.1039/c4sm00907j] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antimicrobial and amyloid peptides do not share common sequences, typical secondary structures, or normal biological activity but both the classes of peptides exhibit membrane-disruption ability to induce cell toxicity. Different membrane-disruption mechanisms have been proposed for antimicrobial and amyloid peptides, individually, some of which are not exclusive to either peptide type, implying that certain common principles may govern the folding and functions of different cytolytic peptides and associated membrane disruption mechanisms. Particularly, some antimicrobial and amyloid peptides have been identified to have dual complementary amyloid and antimicrobial properties, suggesting a potential functional link between amyloid and antimicrobial peptides. Given that some similar structural and membrane-disruption characteristics exist between the two classes of peptides, this review summarizes major findings, recent advances, and future challenges related to antimicrobial and amyloid peptides and strives to illustrate the similarities, differences, and relationships in the sequences, structures, and membrane interaction modes between amyloid and antimicrobial peptides, with a special focus on direct interactions of the peptides with the membranes. We hope that this review will stimulate further research at the interface of antimicrobial and amyloid peptides - which has been studied less intensively than either type of peptides - to decipher a possible link between both amyloid pathology and antimicrobial activity, which can guide drug design and peptide engineering to influence peptide-membrane interactions important in human health and diseases.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA.
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Carmona-Ribeiro AM, de Melo Carrasco LD. Novel formulations for antimicrobial peptides. Int J Mol Sci 2014; 15:18040-83. [PMID: 25302615 PMCID: PMC4227203 DOI: 10.3390/ijms151018040] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 08/30/2014] [Accepted: 09/16/2014] [Indexed: 12/22/2022] Open
Abstract
Peptides in general hold much promise as a major ingredient in novel supramolecular assemblies. They may become essential in vaccine design, antimicrobial chemotherapy, cancer immunotherapy, food preservation, organs transplants, design of novel materials for dentistry, formulations against diabetes and other important strategical applications. This review discusses how novel formulations may improve the therapeutic index of antimicrobial peptides by protecting their activity and improving their bioavailability. The diversity of novel formulations using lipids, liposomes, nanoparticles, polymers, micelles, etc., within the limits of nanotechnology may also provide novel applications going beyond antimicrobial chemotherapy.
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Affiliation(s)
- Ana Maria Carmona-Ribeiro
- Biocolloids Laboratory, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil.
| | - Letícia Dias de Melo Carrasco
- Biocolloids Laboratory, Instituto de Química, Universidade de São Paulo, Av. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil.
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31
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Ruiz J, Calderon J, Rondón-Villarreal P, Torres R. Analysis of Structure and Hemolytic Activity Relationships of Antimicrobial Peptides (AMPs). ADVANCES IN INTELLIGENT SYSTEMS AND COMPUTING 2014. [DOI: 10.1007/978-3-319-01568-2_36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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32
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Zhao J, Zhao C, Liang G, Zhang M, Zheng J. Engineering antimicrobial peptides with improved antimicrobial and hemolytic activities. J Chem Inf Model 2013; 53:3280-96. [PMID: 24279498 DOI: 10.1021/ci400477e] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The rapid rise of antibiotic resistance in pathogens becomes a serious and growing threat to medicine and public health. Naturally occurring antimicrobial peptides (AMPs) are an important line of defense in the immune system against invading bacteria and microbial infection. In this work, we present a combined computational and experimental study of the biological activity and membrane interaction of the computationally designed Bac2A-based peptide library. We used the MARTINI coarse-grained molecular dynamics with adaptive biasing force method and the umbrella sampling technique to investigate the translocation of a total of 91 peptides with different amino acid substitutions through a mixed anionic POPE/POPG (3:1) bilayer and a neutral POPC bilayer, which mimic the bacterial inner membrane and the human red blood cell (hRBC) membrane, respectively. Potential of mean force (PMF, free energy profile) was obtained to measure the free energy barrier required to transfer the peptides from the bulk water phase to the water-membrane interface and to the bilayer interior. Different PMF profiles can indeed identify different membrane insertion scenarios by mapping out peptide-lipid energy landscapes, which are correlated with antimicrobial activity and hemolytic activity. Computationally designed peptides were further tested experimentally for their antimicrobial and hemolytic activities using bacteria growth inhibition assay and hemolysis assay. Comparison of PMF data with cell assay results reveals a good correlation of the peptides between predictive transmembrane activity and antimicrobial/hemolytic activity. Moreover, the most active mutants with the balanced substitutions of positively charged Arg and hydrophobic Trp residues at specific positions were discovered to achieve the improved antimicrobial activity while minimizing red blood cell lysis. Such substitutions provide more effective and cooperative interactions to distinguish the peptide interaction with different lipid bilayers. This work provides a useful computational tool to better understand the mechanism and energetics of membrane insertion of AMPs and to rationally design more effective AMPs.
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Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, The University of Akron , Akron, Ohio 44325, United States
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Han E, Lee H. Effects of PEGylation on the binding interaction of magainin 2 and tachyplesin I with lipid bilayer surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14214-14221. [PMID: 24160865 DOI: 10.1021/la4036985] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Poly(ethylene glycol) (PEG)-grafted magainin 2 and tachyplesin I were simulated with lipid bilayers. In the simulations of PEGylated magainin 2 and tachyplesin I in water, both peptides are wrapped by PEG chains. The α-helical structure of PEGylated magainin 2 is broken in water, while the β-sheet of PEGylated tachyplesin I keeps stable, similar to the structural behavior of unPEGylated peptides, in agreement with experiments. Simulations of PEGylated peptides with lipid bilayers show that PEG chains block the electrostatic interaction between cationic residues of peptides and anionic phosphates of lipids, leading to the less binding of the peptide to the bilayer surface, which is observed more significantly for magainin 2 than for tachyplesin I. Since the random-coiled magainin 2 can be more completely covered by PEGs than does the β-sheet tachyplesin I, the PEGylation effect on the decreased binding is larger for magainin 2, showing the dependence of PEGylation on the peptide structure. These simulation findings qualitatively support the experimental observation of the different extents of the reduced membrane-permeabilizing activity for PEGylated magainin 2 and tachyplesin I.
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Affiliation(s)
- Eol Han
- Department of Chemical Engineering, Dankook University , Yongin 448-701, South Korea
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34
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Bacteriocin AS-48 binding to model membranes and pore formation as revealed by coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2524-31. [DOI: 10.1016/j.bbamem.2013.05.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 05/24/2013] [Accepted: 05/31/2013] [Indexed: 02/05/2023]
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35
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Bortolus M, De Zotti M, Formaggio F, Maniero AL. Alamethicin in bicelles: Orientation, aggregation, and bilayer modification as a function of peptide concentration. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2620-7. [DOI: 10.1016/j.bbamem.2013.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/24/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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36
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Peptide-lipid interactions: experiments and applications. Int J Mol Sci 2013; 14:18758-89. [PMID: 24036440 PMCID: PMC3794806 DOI: 10.3390/ijms140918758] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 02/06/2023] Open
Abstract
The interactions between peptides and lipids are of fundamental importance in the functioning of numerous membrane-mediated cellular processes including antimicrobial peptide action, hormone-receptor interactions, drug bioavailability across the blood-brain barrier and viral fusion processes. Moreover, a major goal of modern biotechnology is obtaining new potent pharmaceutical agents whose biological action is dependent on the binding of peptides to lipid-bilayers. Several issues need to be addressed such as secondary structure, orientation, oligomerization and localization inside the membrane. At the same time, the structural effects which the peptides cause on the lipid bilayer are important for the interactions and need to be elucidated. The structural characterization of membrane active peptides in membranes is a harsh experimental challenge. It is in fact accepted that no single experimental technique can give a complete structural picture of the interaction, but rather a combination of different techniques is necessary.
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Lim K, Chua RRY, Saravanan R, Basu A, Mishra B, Tambyah PA, Ho B, Leong SSJ. Immobilization studies of an engineered arginine-tryptophan-rich peptide on a silicone surface with antimicrobial and antibiofilm activity. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6412-22. [PMID: 23758173 DOI: 10.1021/am401629p] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the rapid rise of antibiotic-resistant-device-associated infections, there has been increasing demand for an antimicrobial biomedical surface. Synthetic antimicrobial peptides that have excellent bactericidal potency and negligible cytotoxicity are promising targets for immobilization on these target surfaces. An engineered arginine-tryptophan-rich peptide (CWR11) was developed, which displayed potent antimicrobial activity against a broad spectrum of microbes via membrane disruption, and possessed excellent salt resistance properties. A tethering platform was subsequently developed to tether CWR11 onto a model polymethylsiloxane (PDMS) surface using a simple and robust strategy. Surface characterization assays such as attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), and energy-dispersive X-ray spectroscopy (EDX) confirmed the successful grafting of CWR11 onto the chemically treated PDMS surface. The immobilized peptide concentration was 0.8 ± 0.2 μg/cm(2) as quantitated by sulfosuccinimidyl-4-o-(4,4-dimethoxytrityl) butyrate (sulfo-SDTB) assay. Antimicrobial assay and cytotoxic investigation confirmed that the peptide-immobilized surface has good bactericidal and antibiofilm properties, and is also noncytotoxic to mammalian cells. Tryptophan-arginine-rich antimicrobial peptides have the potential for antimicrobial protection of biomedical surfaces and may have important clinical applications in patients.
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Affiliation(s)
- Kaiyang Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
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38
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Abstract
The time and length scales accessible by biomolecular simulations continue to increase. This is in part due to improvements in algorithms and computing performance, but is also the result of the emergence of coarse-grained (CG) potentials, which complement and extend the information obtainable from fully detailed models. CG methods have already proven successful for a range of applications that benefit from the ability to rapidly simulate spontaneous self-assembly within a lipid membrane environment, including the insertion and/or oligomerization of a range of "toy models," transmembrane peptides, and single- and multi-domain proteins. While these simplified approaches sacrifice atomistic level detail, it is now straightforward to "reverse map" from CG to atomistic descriptions, providing a strategy to assemble membrane proteins within a lipid environment, prior to all-atom simulation. Moreover, recent developments have been made in "dual resolution" techniques, allowing different molecules in the system to be modeled with atomistic or CG resolution simultaneously.
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Affiliation(s)
- Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
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Salay LC, Ferreira M, Oliveira ON, Nakaie CR, Schreier S. Headgroup specificity for the interaction of the antimicrobial peptide tritrpticin with phospholipid Langmuir monolayers. Colloids Surf B Biointerfaces 2012; 100:95-102. [DOI: 10.1016/j.colsurfb.2012.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 04/23/2012] [Accepted: 05/01/2012] [Indexed: 11/16/2022]
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40
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Hong GS, Chen CP, Lin MH, Krüger J, Becker CFW, Fink RHA, Fischer WB. Molecular dynamics simulations and conductance studies of the interaction of VP1 N-terminus from Polio virus and gp41 fusion peptide from HIV-1 with lipid membranes. Mol Membr Biol 2012; 29:9-25. [PMID: 22276694 DOI: 10.3109/09687688.2011.644589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The icosahedral Polio virus capsid consists of 60 copies of each of the coat proteins VP1, VP2, VP3 and myristolyated VP4 (myrVP4). Catalyzed by the host cell receptor the Polio virus enters the host cell via externalization of myrVP4 and the N terminal part of VP1. There are several assumptions about the individual role of both of the proteins in the mechanism of membrane attachment and genome injection. We use the first 32 N terminal amino acids of VP1 and applied molecular dynamics simulations to assess its mechanism of function when attached and inserted into hydrated lipid membranes (POPC). Helical models are placed in various positions in regard to the lipid membrane to start with. As a comparison, the first 33 amino acids of the fusion peptide of gp41 of HIV-1 are simulated under identical conditions. Computational data support the idea that VP1 is not penetrating into the membrane to form a pore; it rather lays on the membrane surface and only perturbs the membrane. Furthermore, this idea is strengthened by channel recordings of both peptides showing irregular openings.
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Affiliation(s)
- Guo-Sheng Hong
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, 155 Li-Non Street, Taipei, Taiwan
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41
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Development of Bioactive Peptides from Fish Proteins and Their Health Promoting Ability. MARINE MEDICINAL FOODS - IMPLICATIONS AND APPLICATIONS - ANIMALS AND MICROBES 2012; 65:235-48. [DOI: 10.1016/b978-0-12-416003-3.00015-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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42
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Bocchinfuso G, Bobone S, Mazzuca C, Palleschi A, Stella L. Fluorescence spectroscopy and molecular dynamics simulations in studies on the mechanism of membrane destabilization by antimicrobial peptides. Cell Mol Life Sci 2011; 68:2281-301. [PMID: 21584808 PMCID: PMC11114703 DOI: 10.1007/s00018-011-0719-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022]
Abstract
Since their initial discovery, 30 years ago, antimicrobial peptides (AMPs) have been intensely investigated as a possible solution to the increasing problem of drug-resistant bacteria. The interaction of antimicrobial peptides with the cellular membrane of bacteria is the key step of their mechanism of action. Fluorescence spectroscopy can provide several structural details on peptide-membrane systems, such as partition free energy, aggregation state, peptide position and orientation in the bilayer, and the effects of the peptides on the membrane order. However, these "low-resolution" structural data are hardly sufficient to define the structural requirements for the pore formation process. Molecular dynamics simulations, on the other hand, provide atomic-level information on the structure and dynamics of the peptide-membrane system, but they need to be validated experimentally. In this review we summarize the information that can be obtained by both approaches, highlighting their versatility and complementarity, suggesting that their synergistic application could lead to a new level of insight into the mechanism of membrane destabilization by AMPs.
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Affiliation(s)
- Gianfranco Bocchinfuso
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Sara Bobone
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Claudia Mazzuca
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Antonio Palleschi
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- IRCCS Neuromed, 86077 Pozzilli, IS Italy
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- IRCCS Neuromed, 86077 Pozzilli, IS Italy
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43
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Kawamoto S, Takasu M, Miyakawa T, Morikawa R, Oda T, Futaki S, Nagao H. Inverted micelle formation of cell-penetrating peptide studied by coarse-grained simulation: Importance of attractive force between cell-penetrating peptides and lipid head group. J Chem Phys 2011; 134:095103. [DOI: 10.1063/1.3555531] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Wang Q, Hong G, Johnson GR, Pachter R, Cheung MS. Biophysical properties of membrane-active peptides based on micelle modeling: a case study of cell-penetrating and antimicrobial peptides. J Phys Chem B 2011; 114:13726-35. [PMID: 20939546 DOI: 10.1021/jp1069362] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the molecular mechanisms of short peptides interacting with membrane-mimetic systems. Three short peptides were selected for this study: penetratin as a cell-penetrating peptide (CPP), and temporin A and KSL as antimicrobial peptides (AMP). We investigated the detailed interactions of the peptides with dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles, and the subsequent peptide insertion based on free energy calculations by using all-atomistic molecular dynamics simulations with the united atom force field and explicit solvent models. First, we found that the free energy barrier to insertion for the three peptides is dependent on the chemical composition of the micelles. Because of the favorable electrostatic interactions between the peptides and the headgroups of lipids, the insertion barrier into an SDS micelle is less than a DPC micelle. Second, the peptides' secondary structures may play a key role in their binding and insertion ability, particularly for amphiphilic peptides such as penetratin and KSL. The secondary structures with a stronger ability to bind with and insert into micelles are the ones that account for a smaller surface area of hydrophobic core, thus offering a possible criterion for peptide design with specific functionalities.
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Affiliation(s)
- Qian Wang
- Department of Physics, University of Houston, Houston, Texas, USA
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45
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Knowledge-based computational methods for identifying or designing novel, non-homologous antimicrobial peptides. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:371-85. [DOI: 10.1007/s00249-011-0674-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 12/16/2010] [Accepted: 01/04/2011] [Indexed: 02/07/2023]
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46
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Fuzo CA, Degrève L. Study of the antimicrobial peptide indolicidin and mutants in eukaryotic modelled membrane by molecular dynamics simulations. Mol Phys 2011. [DOI: 10.1080/00268976.2010.520753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Eby DM, Johnson GR, Farmer BL, Pandey RB. Supramolecular assembly of a biomineralizing antimicrobial peptide in coarse-grained Monte Carlo simulations. Phys Chem Chem Phys 2011; 13:1123-30. [PMID: 21072418 DOI: 10.1039/c0cp01364a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- D Matthew Eby
- Universal Technology Corporation, 139 Barnes Dr., Suite 2, Tyndall Air Force Base, FL 32403, USA.
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48
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Wiradharma N, Khoe U, Hauser CAE, Seow SV, Zhang S, Yang YY. Synthetic cationic amphiphilic α-helical peptides as antimicrobial agents. Biomaterials 2010; 32:2204-12. [PMID: 21168911 DOI: 10.1016/j.biomaterials.2010.11.054] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 11/19/2010] [Indexed: 10/18/2022]
Abstract
Antimicrobial peptides (AMPs) secreted by the innate immune system are prevalent as the effective first-line of defense to overcome recurring microbial invasions. They have been widely accepted as the blueprints for the development of new antimicrobial agents for the treatment of drug resistant infections. However, there is also a growing concern that AMPs with a sequence that is too close to the host organism's AMP may inevitably compromise its own natural defense. In this study, we design a series of synthetic (non-natural) short α-helical AMPs to expand the arsenal of the AMP families and to gain further insights on their antimicrobial activities. These cationic and amphiphilic peptides have a general sequence of (XXYY)(n) (X: hydrophobic residue, Y: cationic residue, and n: the number of repeat units), and are designed to mimic the folding behavior of the naturally-occurring α-helical AMPs. The synthetic α-helical AMPs with 3 repeat units, (FFRR)(3), (LLRR)(3), and (LLKK)(3), are found to be more selective towards microbial cells than rat red blood cells, with minimum inhibitory concentration (MIC) values that are more than 10 times lower than their 50% hemolytic concentrations (HC(50)). They are effective against Gram-positive B. subtilis and yeast C. albicans; and the studies using scanning electron microscopy (SEM) have elucidated that these peptides possess membrane-lytic activities against microbial cells. Furthermore, non-specific immune stimulation assays of a typical peptide shows negligible IFN-α, IFN-γ, and TNF-α inductions in human peripheral blood mononuclear cells, which implies additional safety aspects of the peptide for both systemic and topical use. Therefore, the peptides designed in this study can be promising antimicrobial agents against the frequently-encountered Gram-positive bacteria- or yeast-induced infections.
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Affiliation(s)
- Nikken Wiradharma
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Singapore 138669, Singapore
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49
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Gofman Y, Linser S, Rzeszutek A, Shental-Bechor D, Funari SS, Ben-Tal N, Willumeit R. Interaction of an antimicrobial peptide with membranes: experiments and simulations with NKCS. J Phys Chem B 2010; 114:4230-7. [PMID: 20201501 DOI: 10.1021/jp909154y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used Monte Carlo simulations and biophysical measurements to study the interaction of NKCS, a derivative of the antimicrobial peptide NK-2, with a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) membrane. The simulations showed that NKCS adsorbed on the membrane surface and the dominant conformation featured two amphipathic helices connected by a hinge region. We designed two mutants in the hinge to investigate the interplay between helicity and membrane affinity. Simulations with a Leu-to-Pro substitution showed that the helicity and membrane affinity of the mutant (NKCS-[LP]) decreased. Two Ala residues were added to NKCS to produce a sequence that is compatible with a continuous amphipathic helix structure (NKCS-[AA]), and the simulations showed that the mutant adsorbed on the membrane surface with a particularly high affinity. The circular dichroism spectra of the three peptides also showed that NKCS-[LP] is the least helical and NKCS-[AA] is the most. However, the activity of the peptides, determined in terms of their antimicrobial potency and influence on the temperature of the transition of the lipid to hexagonal phase, displayed a complex behavior: NKCS-[LP] was the least potent and had the smallest influence on the transition temperature, and NKCS was the most potent and had the largest effect on the temperature.
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Affiliation(s)
- Yana Gofman
- GKSS Research Center, 21502 Geesthacht, Germany
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50
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Matejuk A, Leng Q, Begum MD, Woodle MC, Scaria P, Chou ST, Mixson AJ. Peptide-based Antifungal Therapies against Emerging Infections. DRUG FUTURE 2010; 35:197. [PMID: 20495663 DOI: 10.1358/dof.2010.035.03.1452077] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acquired drug resistance to mycotic infections is rapidly emerging as a major medical problem. Opportunistic fungal infections create therapeutic challenges, particularly in high risk immunocompromised patients with AIDS, cancer, and those undergoing transplantation. Higher mortality and/or morbidity rates due to invasive mycosis have been increasing over the last 20 years, and in light of growing resistance to commonly used antibiotics, novel antifungal drugs and approaches are required. Currently there is considerable interest in antifungal peptides that are ubiquitous in plant and animal kingdoms. These small cationic peptides may have specific targets or may be multifunctional in their mechanism of action. On the basis of recent advances in protein engineering and solid phase syntheses, the utility and potential of selected peptides as efficient antifungal drugs with acceptable toxicity profiles are being realized. This review will discuss recent advances in peptide therapy for opportunistic fungal infections.
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Affiliation(s)
- A Matejuk
- Department of Pathology, University of Maryland Baltimore, MSTF Building, 10 South Pine Street, Baltimore, MD 21201, USA
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