1
|
He Q, Meneely J, Grant IR, Chin J, Fanning S, Situ C. Phytotherapeutic potential against MRSA: mechanisms, synergy, and therapeutic prospects. Chin Med 2024; 19:89. [PMID: 38909250 PMCID: PMC11193263 DOI: 10.1186/s13020-024-00960-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Rising resistance to antimicrobials, particularly in the case of methicillin-resistant Staphylococcus aureus (MRSA), represents a formidable global health challenge. Consequently, it is imperative to develop new antimicrobial solutions. This study evaluated 68 Chinese medicinal plants renowned for their historical applications in treating infectious diseases. METHODS The antimicrobial efficacy of medicinal plants were evaluated by determining their minimum inhibitory concentration (MIC) against MRSA. Safety profiles were assessed on human colorectal adenocarcinoma (Caco-2) and hepatocellular carcinoma (HepG2) cells. Mechanistic insights were obtained through fluorescence and transmission electron microscopy (FM and TEM). Synergistic effects with vancomycin were investigated using the Fractional Inhibitory Concentration Index (FICI). RESULTS Rheum palmatum L., Arctium lappa L. and Paeonia suffructicosaas Andr. have emerged as potential candidates with potent anti-MRSA properties, with an impressive low MIC of 7.8 µg/mL, comparable to the 2 µg/mL MIC of vancomycin served as the antibiotic control. Crucially, these candidates demonstrated significant safety profiles when evaluated on Caco-2 and HepG2 cells. Even at 16 times the MIC, the cell viability ranged from 83.3% to 95.7%, highlighting their potential safety. FM and TEM revealed a diverse array of actions against MRSA, such as disrupting the cell wall and membrane, interference with nucleoids, and inducing morphological alterations resembling pseudo-multicellular structures in MRSA. Additionally, the synergy between vancomycin and these three plant extracts was evident against MRSA (FICI < 0.5). Notably, aqueous extract of R. palmatum at 1/4 MIC significantly reduced the vancomycin MIC from 2 µg/mL to 0.03 µg/mL, making a remarkable 67-fold decrease. CONCLUSIONS This study unveil new insights into the mechanistic actions and pleiotropic antibacterial effectiveness of these medicinal plants against resistant bacteria, providing robust evidence for their potential use as standalone or in conjunction with antibiotics, to effectively combat antimicrobial resistance, particularly against MRSA.
Collapse
Affiliation(s)
- Qiqi He
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Julie Meneely
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Irene R Grant
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Jason Chin
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Séamus Fanning
- University College Dublin Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Dublin, Republic of Ireland
| | - Chen Situ
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK.
| |
Collapse
|
2
|
Sharma P, Vaiwala R, Gopinath AK, Chockalingam R, Ayappa KG. Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7791-7811. [PMID: 38451026 DOI: 10.1021/acs.langmuir.3c03474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.
Collapse
Affiliation(s)
- Pradyumn Sharma
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Amar Krishna Gopinath
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - Rajalakshmi Chockalingam
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka, India, 560012
| |
Collapse
|
3
|
Lee TH, Charchar P, Separovic F, Reid GE, Yarovsky I, Aguilar MI. The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes. Chem Sci 2024; 15:3408-3427. [PMID: 38455013 PMCID: PMC10915831 DOI: 10.1039/d3sc04523d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.
Collapse
Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| | - Patrick Charchar
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
| | - Gavin E Reid
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne VIC 3010 Australia
- Department of Biochemistry and Pharmacology, University of Melbourne Parkville VIC 3010 Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University Melbourne Victoria 3001 Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University Clayton VIC 3800 Australia
| |
Collapse
|
4
|
Li J, Monje-Galvan V. Effect of Glycone Diversity on the Interaction of Triterpenoid Saponins and Lipid Bilayers. ACS APPLIED BIO MATERIALS 2024; 7:553-563. [PMID: 36854194 DOI: 10.1021/acsabm.2c00928] [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] [Indexed: 03/02/2023]
Abstract
Triterpenoid saponins are organic compounds widely available in the plant kingdom. These molecules have received extensive attention due to their antibacterial activity against both Gram-negative and Gram-positive bacteria. Recent studies identified the antibacterial activity of saponins closely relates to their interaction with bacterial membrane lipids; however, molecular details of this interaction remain unclear. Increased understanding of the mechanisms to disrupt bacterial lipid bilayers can help to mitigate development of antibiotic resistance. Here, we examined the effect of chemical structure and deprotonation states of saponin on its interaction with a bacterial membrane model using molecular dynamics simulations. We run multiple simulations with a ternary lipid mixture of POPE/POPG/DPPG (80/15/5 mol %) and different saponin molecules. While all saponin structures can permanently bind the membrane, their location and orientation inside the bilayer depend on the sugar chains attached to their backbone. Similarly, cluster formation and stability also depend on the chemical structure of the saponin molecule. Deprotonation site affects interactions with the bilayer by modulating hydrophilicity of the molecules. At the low concentrations simulated in this work, there is no statistically significant change in the membrane properties upon saponin(s) binding, but the molecules do preferentially partition to POPE lipid environment.
Collapse
Affiliation(s)
- Jinhui Li
- Department of Chemical and Biomolecular Engineering, State University of New York (SUNY) at Buffalo, Buffalo, New York 14260, United States
| | - Viviana Monje-Galvan
- Department of Chemical and Biomolecular Engineering, State University of New York (SUNY) at Buffalo, Buffalo, New York 14260, United States
| |
Collapse
|
5
|
Linney JA, Routledge SJ, Connell SD, Larson TR, Pitt AR, Jenkinson ER, Goddard AD. Identification of membrane engineering targets for increased butanol tolerance in Clostridium saccharoperbutylacetonicum. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184217. [PMID: 37648011 DOI: 10.1016/j.bbamem.2023.184217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/17/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
There is a growing interest in the use of microbial cell factories to produce butanol, an industrial solvent and platform chemical. Biobutanol can also be used as a biofuel and represents a cleaner and more sustainable alternative to the use of conventional fossil fuels. Solventogenic Clostridia are the most popular microorganisms used due to the native expression of butanol synthesis pathways. A major drawback to the wide scale implementation and development of these technologies is the toxicity of butanol. Various membrane properties and related functions are perturbed by the interaction of butanol with the cell membrane, causing lower yields and higher purification costs. This is ultimately why the technology remains underemployed. This study aimed to develop a deeper understanding of butanol toxicity at the membrane to determine future targets for membrane engineering. Changes to the lipidome in Clostridium saccharoperbutylacetonicum N1-4 (HMT) throughout butanol fermentation were investigated with thin layer chromatography and mass spectrometry. By the end of fermentation, levels of phosphatidylglycerol lipids had increased significantly, suggesting an important role of these lipid species in tolerance to butanol. Using membrane models and in vitro assays to investigate characteristics such as permeability, fluidity, and swelling, it was found that altering the composition of membrane models can convey tolerance to butanol, and that modulating membrane fluidity appears to be a key factor. Data presented here will ultimately help to inform rational strain engineering efforts to produce more robust strains capable of producing higher butanol titres.
Collapse
Affiliation(s)
- John A Linney
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Sarah J Routledge
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Simon D Connell
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Tony R Larson
- Department of Biology, University of York, York YO10 5DD, UK
| | - Andrew R Pitt
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | | | - Alan D Goddard
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| |
Collapse
|
6
|
Lee HM, Thai TD, Lim W, Ren J, Na D. Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology. J Biotechnol 2023; 375:40-48. [PMID: 37652168 DOI: 10.1016/j.jbiotec.2023.08.008] [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: 02/21/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
Abstract
In microbial biotechnology, there is a constant demand for functional peptides to give new functionality to engineered proteins to address problems such as direct delivery of functional proteins into bacterial cells, enhanced protein solubility during the expression of recombinant proteins, and efficient protein secretion from bacteria. To tackle these critical issues, we selected three types of functional small peptides: cell-penetrating peptides (CPPs) enable the delivery of diverse cargoes into bacterial cytoplasm for a variety of purposes, protein-solubilizing peptide tags demonstrate remarkable efficiency in solubilizing recombinant proteins without folding interference, and signal peptides play a key role in enabling the secretion of recombinant proteins from bacterial cells. In this review, we introduced these three functional small peptides that offer effective solutions to address emerging problems in microbial biotechnology. Additionally, we summarized various engineering efforts aimed at enhancing the activity and performance of these peptides, thereby providing valuable insights into their potential for further applications.
Collapse
Affiliation(s)
- Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, the Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, the Republic of Korea
| | - Wonseop Lim
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, the Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, the Republic of Korea.
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, the Republic of Korea.
| |
Collapse
|
7
|
Zeng R, Cai L, Perez-Aguilar JM, Gu Z, Liu X. Robust Mechanical Destruction to the Cell Membrane of Carbon Nitride Polyaniline (C 3N): A Molecular Dynamics Simulation Study. J Chem Inf Model 2023. [PMID: 37319424 DOI: 10.1021/acs.jcim.3c00570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The drug-resistant bacteria, particularly multidrug-resistant bacteria, has emerged as a major global public health concern posing serious threats to human life and survival. Nanomaterials, including graphene, have shown promise as effective antibacterial agents owing to their unique antibacterial mechanism compared with traditional drugs. Despite the structural similarity to graphene, the potential antibacterial activity of carbon nitride polyaniline (C3N) remains unexplored. In this study, we employed molecular dynamics simulations to investigate the effects of the interaction between the C3N nanomaterial and the bacterial membrane to evaluate the potential antibacterial activity of C3N. Our results suggest that C3N is capable of inserting deep into the bacterial membrane interior, regardless of the presence or absence of positional restraints in the C3N. The insertion process also resulted in local lipid extraction by the C3N sheet. Additional structural analyses revealed that C3N induced significant changes in membrane parameters, including mean square displacement, deuterium order parameters, membrane thickness, and area per lipid. Docking simulations, where all the C3N are restraint to a specific positions, confirmed that C3N can extract lipids from the membrane, indicating the strong interaction between the C3N material and the membrane. Free-energy calculations further revealed that the insertion of the C3N sheet is energetically favorable and that C3N exhibits membrane insertion capacity comparable to that observed for graphene, suggesting their potential for similar antibacterial activity. This study provides the first evidence of the potential antibacterial properties of C3N nanomaterials via bacterial membrane damage and underscores the potential for its use as antibacterial agents in the future applications.
Collapse
Affiliation(s)
- Renqing Zeng
- First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Longxue Cai
- First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Zonglin Gu
- College of Physical Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xianfa Liu
- First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| |
Collapse
|
8
|
Poshvina DV, Dilbaryan DS, Vasilchenko AS. Gausemycin A-Resistant Staphylococcus aureus Demonstrates Affected Cell Membrane and Cell Wall Homeostasis. Microorganisms 2023; 11:1330. [PMID: 37317304 DOI: 10.3390/microorganisms11051330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
Antibiotic resistance is a significant and pressing issue in the medical field, as numerous strains of infectious bacteria have become resistant to commonly prescribed antibiotics. Staphylococcus aureus is a bacterium that poses a grave threat, as it is responsible for a large number of nosocomial infections and has high mortality rates worldwide. Gausemycin A is a new lipoglycopeptide antibiotic that has considerable efficacy against multidrug-resistant S. aureus strains. Although the cellular targets of gausemycin A have been previously identified, detailing the molecular processes of action is still needed. We performed gene expression analysis to identify molecular mechanisms that may be involved in bacterial resistance to gausemycin A. In the present study, we observed that gausemycin A-resistant S. aureus in the late-exponential phase showed an increased expression of genes involved in cell wall turnover (sceD), membrane charge (dltA), phospholipid metabolism (pgsA), the two-component stress-response system (vraS), and the Clp proteolytic system (clpX). The increased expression of these genes implies that changes in the cell wall and cell membrane are essential for the bacterial resistance to gausemycin A. In the stationary phase, we observed a decrease in the expression of genes involved in the phospholipid metabolism (mprF) and Clp proteolytic system (clpX).
Collapse
Affiliation(s)
- Darya V Poshvina
- Laboratory of Antimicrobial Resistance, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Diana S Dilbaryan
- Laboratory of Antimicrobial Resistance, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Alexey S Vasilchenko
- Laboratory of Antimicrobial Resistance, Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| |
Collapse
|
9
|
Pastuszak K, Chmiel E, Kowalczyk B, Tarasiuk J, Jurak M, Palusińska-Szysz M. Physicochemical Characteristics of Model Membranes Composed of Legionella gormanii Lipids. MEMBRANES 2023; 13:356. [PMID: 36984743 PMCID: PMC10058700 DOI: 10.3390/membranes13030356] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Legionella gormanii is one of the species belonging to the genus Legionella, which causes atypical community-acquired pneumonia. The most important virulence factors that enable the bacteria to colonize the host organism are associated with the cell surface. Lipids building the cell envelope are crucial not only for the membrane integrity of L. gormanii but also by virtue of being a dynamic site of interactions between the pathogen and the metabolites supplied by its host. The utilization of exogenous choline by the Legionella species results in changes in the lipids' composition, which influences the physicochemical properties of the cell surface. The aim of this study was to characterize the interfacial properties of the phospholipids extracted from L. gormanii cultured with (PL+choline) and without exogenous choline (PL-choline). The Langmuir monolayer technique coupled with the surface potential (SPOT) sensor and the Brewster angle microscope (BAM) made it possible to prepare the lipid monomolecular films (model membranes) and study their properties at the liquid/air interface at 20 °C and 37 °C. The results indicate the effect of the choline addition to the bacterial medium on the properties of the L. gormanii phospholipid membranes. The differences were revealed in the organization of monolayers, their molecular packing and ordering, degree of condensation and changes in the components' miscibility. These findings are the basis for further research on the mechanisms of adaptation of this pathogen, which by changing the native composition and properties of lipids, bypasses the action of antimicrobial compounds and avoids the host immune attack.
Collapse
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;
| | - Elżbieta Chmiel
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (E.C.); (B.K.); (J.T.); (M.P.-S.)
| | - Bożena Kowalczyk
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (E.C.); (B.K.); (J.T.); (M.P.-S.)
| | - Jacek Tarasiuk
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (E.C.); (B.K.); (J.T.); (M.P.-S.)
| | - 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;
| | - 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; (E.C.); (B.K.); (J.T.); (M.P.-S.)
| |
Collapse
|
10
|
Nikolic P, Mudgil P. The Cell Wall, Cell Membrane and Virulence Factors of Staphylococcus aureus and Their Role in Antibiotic Resistance. Microorganisms 2023; 11:microorganisms11020259. [PMID: 36838224 PMCID: PMC9965861 DOI: 10.3390/microorganisms11020259] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Antibiotic resistant strains of bacteria are a serious threat to human health. With increasing antibiotic resistance in common human pathogens, fewer antibiotics remain effective against infectious diseases. Staphylococcus aureus is a pathogenic bacterium of particular concern to human health as it has developed resistance to many of the currently used antibiotics leaving very few remaining as effective treatment. Alternatives to conventional antibiotics are needed for treating resistant bacterial infections. A deeper understanding of the cellular characteristics of resistant bacteria beyond well characterized resistance mechanisms can allow for increased ability to properly treat them and to potentially identify targetable changes. This review looks at antibiotic resistance in S aureus in relation to its cellular components, the cell wall, cell membrane and virulence factors. Methicillin resistant S aureus bacteria are resistant to most antibiotics and some strains have even developed resistance to the last resort antibiotics vancomycin and daptomycin. Modifications in cell wall peptidoglycan and teichoic acids are noted in antibiotic resistant bacteria. Alterations in cell membrane lipids affect susceptibility to antibiotics through surface charge, permeability, fluidity, and stability of the bacterial membrane. Virulence factors such as adhesins, toxins and immunomodulators serve versatile pathogenic functions in S aureus. New antimicrobial strategies can target cell membrane lipids and virulence factors including anti-virulence treatment as an adjuvant to traditional antibiotic therapy.
Collapse
|
11
|
Boopathi S, Garduño‐Juárez R. Calcium inhibits penetration of Alzheimer's Aβ 1 - 42 monomers into the membrane. Proteins 2022; 90:2124-2143. [PMID: 36321654 PMCID: PMC9804374 DOI: 10.1002/prot.26403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/08/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023]
Abstract
Calcium ion regulation plays a crucial role in maintaining neuronal functions such as neurotransmitter release and synaptic plasticity. Copper (Cu2+ ) coordination to amyloid-β (Aβ) has accelerated Aβ1-42 aggregation that can trigger calcium dysregulation by enhancing the influx of calcium ions by extensive perturbing integrity of the membranes. Aβ1-42 aggregation, calcium dysregulation, and membrane damage are Alzheimer disease (AD) implications. To gain a detail of calcium ions' role in the full-length Aβ1-42 and Aβ1-42 -Cu2+ monomers contact, the cellular membrane before their aggregation to elucidate the neurotoxicity mechanism, we carried out 2.5 μs extensive molecular dynamics simulation (MD) to rigorous explorations of the intriguing feature of the Aβ1-42 and Aβ1-42 -Cu2+ interaction with the dimyristoylphosphatidylcholine (DMPC) bilayer in the presence of calcium ions. The outcome of the results compared to the same simulations without calcium ions. We surprisingly noted robust binding energies between the Aβ1-42 and membrane observed in simulations containing without calcium ions and is two and a half fold lesser in the simulation with calcium ions. Therefore, in the case of the absence of calcium ions, N-terminal residues of Aβ1-42 deeply penetrate from the surface to the center of the bilayer; in contrast to calcium ions presence, the N- and C-terminal residues are involved only in surface contacts through binding phosphate moieties. On the other hand, Aβ1-42 -Cu2+ actively participated in surface bilayer contacts in the absence of calcium ions. These contacts are prevented by forming a calcium bridge between Aβ1-42 -Cu2+ and the DMPC bilayer in the case of calcium ions presence. In a nutshell, Calcium ions do not allow Aβ1-42 penetration into the membranes nor contact of Aβ1-42 -Cu2+ with the membranes. These pieces of information imply that the calcium ions mediate the membrane perturbation via the monomer interactions but do not damage the membrane; they agree with the western blot experimental results of a higher concentration of calcium ions inhibit the membrane pore formation by Aβ peptides.
Collapse
Affiliation(s)
- Subramanian Boopathi
- Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Ramón Garduño‐Juárez
- Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| |
Collapse
|
12
|
Growth Substrate and Prophage Induction Collectively Influence Metabolite and Lipid Profiles in a Marine Bacterium. mSystems 2022; 7:e0058522. [PMID: 35972149 PMCID: PMC9600351 DOI: 10.1128/msystems.00585-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacterial growth substrates influence a variety of biological functions, including the biosynthesis and regulation of lipid intermediates. The extent of this rewiring is not well understood nor has it been considered in the context of virally infected cells. Here, we used a one-host-two-temperate phage model system to probe the combined influence of growth substrate and phage infection on host carbon and lipid metabolism. Using untargeted metabolomics and lipidomics, we reported the detection of a suite of metabolites and lipid classes for two Sulfitobacter lysogens provided with three growth substrates of differing complexity and nutrient composition (yeast extract/tryptone [complex], glutamate and acetate). The growth medium led to dramatic differences in the detectable intracellular metabolites, with only 15% of 175 measured metabolites showing overlap across the three growth substrates. Between-strain differences were most evident in the cultures grown on acetate, followed by glutamate then complex medium. Lipid distribution profiles were also distinct between cultures grown on different substrates as well as between the two lysogens grown in the same medium. Five phospholipids, three aminolipid, and one class of unknown lipid-like features were identified. Most (≥94%) of these 75 lipids were quantifiable in all samples. Metabolite and lipid profiles were strongly determined by growth medium composition and modestly by strain type. Because fluctuations in availability and form of carbon substrates and nutrients, as well as virus pressure, are common features of natural systems, the influence of these intersecting factors will undoubtedly be imprinted in the metabolome and lipidome of resident bacteria. IMPORTANCE Community-level metabolomics approaches are increasingly used to characterize natural microbial populations. These approaches typically depend upon temporal snapshots from which the status and function of communities are often inferred. Such inferences are typically drawn from lab-based studies of select model organisms raised under limited growth conditions. To better interpret community-level data, the extent to which ecologically relevant bacteria demonstrate metabolic flexibility requires elucidation. Herein, we used an environmentally relevant model heterotrophic marine bacterium to assess the relationship between growth determinants and metabolome. We also aimed to assess the contribution of phage activity to the host metabolome. Striking differences in primary metabolite and lipid profiles appeared to be driven primarily by growth regime and, secondarily, by phage type. These findings demonstrated the malleable nature of metabolomes and lipidomes and lay the foundation for future studies that relate cellular composition with function in complex environmental microbial communities.
Collapse
|
13
|
Lyon R, Jones RA, Shropshire H, Aberdeen I, Scanlan DJ, Millard A, Chen Y. Membrane lipid renovation in Pseudomonas aeruginosa - implications for phage therapy? Environ Microbiol 2022; 24:4533-4546. [PMID: 35837865 PMCID: PMC9804370 DOI: 10.1111/1462-2920.16136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/05/2023]
Abstract
Pseudomonas aeruginosa is an important Gram-negative pathogen with intrinsic resistance to many clinically used antibiotics. It is particularly troublesome in nosocomial infections, immunocompromised patients, and individuals with cystic fibrosis. Antimicrobial resistance (AMR) is a huge threat to global health, with a predicted 10 million people dying from resistant infections by 2050. A promising therapy for combatting AMR infections is phage therapy. However, more research is required to investigate mechanisms that may influence the efficacy of phage therapy. An important overlooked aspect is the impact of membrane lipid remodelling on phage binding ability. P. aeruginosa undergoes changes in membrane lipids when it encounters phosphorus stress, an environmental perturbation that is likely to occur during infection. Lipid changes include the substitution of glycerophospholipids with surrogate glycolipids and the over-production of ornithine-containing aminolipids. Given that membrane lipids are known to influence the structure and function of membrane proteins, we propose that changes in the composition of membrane lipids during infection may alter phage binding and subsequent phage infection dynamics. Consideration of such effects needs to be urgently prioritised in order to develop the most effective phage therapy strategies for P. aeruginosa infections.
Collapse
Affiliation(s)
- Rhiannon Lyon
- BBSRC Midlands Integrative Biosciences Training PartnershipUniversity of WarwickCoventryUK,School of Life SciencesUniversity of WarwickCoventryUK
| | - Rebekah A. Jones
- School of Life SciencesUniversity of WarwickCoventryUK,MRC Doctoral Training PartnershipUniversity of WarwickCoventryUK
| | - Holly Shropshire
- BBSRC Midlands Integrative Biosciences Training PartnershipUniversity of WarwickCoventryUK,School of Life SciencesUniversity of WarwickCoventryUK
| | - Isabel Aberdeen
- BBSRC Midlands Integrative Biosciences Training PartnershipUniversity of WarwickCoventryUK,School of Life SciencesUniversity of WarwickCoventryUK
| | | | - Andrew Millard
- Department of Genetics and Genome BiologyUniversity of LeicesterUK
| | - Yin Chen
- School of Life SciencesUniversity of WarwickCoventryUK
| |
Collapse
|
14
|
Karathanou K, Bondar AN. Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183859. [PMID: 34999081 DOI: 10.1016/j.bbamem.2022.183859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.
Collapse
Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.
| |
Collapse
|
15
|
Tereshkin EV, Loiko NG, Tereshkina KB, Krupyanskii YF. Migration of 4-Hexylresorcinol Through Escherichia coli Cell Membranes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793121060099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Oliveira AA, Róg T, da Silva ABF, Amaro RE, Johnson MS, Postila PA. Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations. Biomolecules 2022; 12:biom12020183. [PMID: 35204684 PMCID: PMC8961577 DOI: 10.3390/biom12020183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/11/2022] Open
Abstract
The outer mitochondrial membrane (OMM) is involved in multiple cellular functions such as apoptosis, inflammation and signaling via its membrane-associated and -embedded proteins. Despite the central role of the OMM in these vital phenomena, the structure and dynamics of the membrane have regularly been investigated in silico using simple two-component models. Accordingly, the aim was to generate the realistic multi-component model of the OMM and inspect its properties using atomistic molecular dynamics (MD) simulations. All major lipid components, phosphatidylinositol (PI), phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS), were included in the probed OMM models. Because increased levels of anionic PS lipids have potential effects on schizophrenia and, more specifically, on monoamine oxidase B enzyme activity, the effect of varying the PS concentration was explored. The MD simulations indicate that the complex membrane lipid composition (MLC) behavior is notably different from the two-component PC-PE model. The MLC changes caused relatively minor effects on the membrane structural properties such as membrane thickness or area per lipid; however, notable effects could be seen with the dynamical parameters at the water-membrane interface. Increase of PS levels appears to slow down lateral diffusion of all lipids and, in general, the presence of anionic lipids reduced hydration and slowed down the PE headgroup rotation. In addition, sodium ions could neutralize the membrane surface, when PI was the main anionic component; however, a similar effect was not seen for high PS levels. Based on these results, it is advisable for future studies on the OMM and its protein or ligand partners, especially when wanting to replicate the correct properties on the water-membrane interface, to use models that are sufficiently complex, containing anionic lipid types, PI in particular.
Collapse
Affiliation(s)
- Aline A. Oliveira
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland;
| | - Albérico B. F. da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
| | - Pekka A. Postila
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
- Institute of Biomedicine, Kiinamyllynkatu 10, Integrative Physiology and Pharmacy, University of Turku, FI-20520 Turku, Finland
- Aurlide Ltd., FI-21420 Lieto, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20520 Turku, Finland
- Correspondence:
| |
Collapse
|
17
|
Hsieh MK, Yu Y, Klauda JB. All-Atom Modeling of Complex Cellular Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3-17. [PMID: 34962814 DOI: 10.1021/acs.langmuir.1c02084] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.
Collapse
|
18
|
Hsieh MK, Klauda JB. Leaflet Asymmetry Modeling in the Lipid Composition of Escherichia coli Cytoplasmic Membranes. J Phys Chem B 2021; 126:184-196. [PMID: 34962410 DOI: 10.1021/acs.jpcb.1c07332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Lipid composition asymmetry between leaflets is important to cell function and plays a key role in the "positive inside" rule in transmembrane proteins. In this work, Escherichia coli inner plasma membrane models reflecting this asymmetry have been investigated at the early-log and stationary stages during the bacterial lifecycle using all-atom molecular dynamics simulations. The CHARMM36 lipid force field is used, and selected membrane properties are tested for variations between two leaflets and whole membranes. Our models include bacterial lipids with a cyclopropane moiety on the sn-2 acyl chain in the stationary membrane model. The PE/PG ratio for two leaflets reflects the "positive inside" rule of membrane proteins, set to 6.8 and 2.8 for the inner and outer leaflets of the two models, respectively. We are the first to model leaflet asymmetry in the lipid composition of E. coli cytoplasmic membranes and observe the effect on membrane properties in leaflets and whole membranes. Specifically, our results show that for the stationary phase bilayer, the surface area per lipid (SA/lipid) is larger, the thickness (2DC and DB) is smaller, the tilt angle is larger, the tilt modulus is smaller, and the deuterium order parameters (SCD) of sn-1 and sn-2 tails are lower, compared to the early-log stage. Moreover, the stationary stage bilayer has a positive spontaneous curvature, while the early-log stage has a near flat spontaneous curvature. For leaflet asymmetry, the inner leaflet has a larger SA/lipid, a smaller thickness, a smaller elastic tilt modulus (a larger tilt angle), and lower SCD, compared to the outer leaflet in both stages. Moreover, an asymmetric membrane involves a lipid tilt and a lateral extension, varying from a reference state of a pre-equilibrium membrane. This work encourages a more profound exploration of leaflet asymmetry in various other membrane models and how this might affect the structure and function of membrane-associated peptides and proteins.
Collapse
Affiliation(s)
- Min-Kang Hsieh
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States.,Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
19
|
Changes in the distribution of membrane lipids during growth of Thermotoga maritima at different temperatures: Indications for the potential mechanism of biosynthesis of ether-bound diabolic acid (membrane-spanning) lipids. Appl Environ Microbiol 2021; 88:e0176321. [PMID: 34731048 PMCID: PMC8788747 DOI: 10.1128/aem.01763-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Membrane-spanning lipids are present in a wide variety of archaea but they are rarely in bacteria. Nevertheless, the (hyper)thermophilic members of the order Thermotogales harbor tetraester, tetraether, and mixed ether/ester membrane-spanning lipids mostly composed of core lipids derived from diabolic acids, C30, C32 and C34 dicarboxylic acids with two adjacent mid-chain methyl substituents. Lipid analysis of Thermotoga maritima across growth phases revealed a decrease of the relative abundance of fatty acids together with an increase of diabolic acids with independence of growth temperature. We also identified isomers of C30 and C32 diabolic acids, i.e. dicarboxylic acids with only one methyl group at C-15. Their distribution suggests they are products of the condensation reaction but preferably produced when the length of the acyl chains is not optimal. In comparison with growth at the optimal temperature of 80°C, an increase of glycerol ether-derived lipids was observed at 55°C. Besides, our analysis only detected diabolic acid-containing intact polar lipids with phosphoglycerol (PG) headgroups. Considering these findings, we hypothesize a biosynthetic pathway for the synthesis of membrane-spanning lipids based on PG polar lipid formation, suggesting that the protein catalyzing this process could be a membrane protein. We also identified, by genomic and protein domain analyses, a gene coding for a putative plasmalogen synthase homologue in T. maritima, which is also present in other bacteria producing sn1-alkyl ether lipids but not plasmalogens, suggesting it could be involved in the conversion of the ester to ether bond in the diabolic acids bound in membrane-spanning lipids. Importance Membrane-spanning lipids are unique compounds found in most archaeal membranes, but they are also present in specific bacterial groups like the Thermotogales. The synthesis and physiological role of membrane-spanning lipids in bacteria represent an evolutionary and biochemical open question that points to the differentiation of the membrane lipids composition. Understanding the formation of membrane-spanning lipids is crucial to solving this question and identifying the enzymatic and biochemical mechanism performing this procedure. In the present work, we found changes at the core lipid level, and we propose that the growth phase drives the biosynthesis of these lipids rather than temperature. Our results identified physiological conditions influencing the membrane-spanning lipids biosynthetic process which can further clarify the pathway leading to the biosynthesis of these compounds.
Collapse
|
20
|
Koneru JK, Prakashchand DD, Dube N, Ghosh P, Mondal J. Spontaneous transmembrane pore formation by short-chain synthetic peptide. Biophys J 2021; 120:4557-4574. [PMID: 34478698 DOI: 10.1016/j.bpj.2021.08.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022] Open
Abstract
Amphiphilic β-peptides, which are synthetically designed short-chain helical foldamers of β-amino acids, are established potent biomimetic alternatives of natural antimicrobial peptides. An intriguing question is how the distinct molecular architecture of these short-chain and rigid synthetic peptides translates to its potent membrane-disruption ability. Here, we address this question via a combination of all-atom and coarse-grained molecular dynamics simulations of the interaction of mixed phospholipid bilayer with an antimicrobial 10-residue globally amphiphilic helical β-peptide at a wide range of concentrations. The simulation demonstrates that multiple copies of this synthetic peptide, initially placed in aqueous solution, readily self-assemble and adsorb at membrane interface. Subsequently, beyond a threshold peptide/lipid ratio, the surface-adsorbed oligomeric aggregate moves inside the membrane and spontaneously forms stable water-filled transmembrane pores via a cooperative mechanism. The defects induced by these pores lead to the dislocation of interfacial lipid headgroups, membrane thinning, and substantial water leakage inside the hydrophobic core of the membrane. A molecular analysis reveals that despite having a short architecture, these synthetic peptides, once inside the membrane, would stretch themselves toward the distal leaflet in favor of potential contact with polar headgroups and interfacial water layer. The pore formed in coarse-grained simulation was found to be resilient upon structural refinement. Interestingly, the pore-inducing ability was found to be elusive in a non-globally amphiphilic sequence isomer of the same β-peptide, indicating strong sequence dependence. Taken together, this work puts forward key perspectives of membrane activity of minimally designed synthetic biomimetic oligomers relative to the natural antimicrobial peptides.
Collapse
Affiliation(s)
- Jaya Krishna Koneru
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Dube Dheeraj Prakashchand
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Namita Dube
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Pushpita Ghosh
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad, Telangana, India.
| |
Collapse
|
21
|
Zhang C, Guo J, Zou X, Guo S, Guo Y, Shi R, Yan F. Acridine-Based Covalent Organic Framework Photosensitizer with Broad-Spectrum Light Absorption for Antibacterial Photocatalytic Therapy. Adv Healthc Mater 2021; 10:e2100775. [PMID: 34165250 DOI: 10.1002/adhm.202100775] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/18/2021] [Indexed: 12/11/2022]
Abstract
Antibiotic resistance is considered as one of the serious public health issues. Antibacterial photocatalytic therapy, a clinically proven antibacterial therapy, is gaining increasing attention in recent years owing to its high efficacy. Here, an acridine-based covalent organic framework (COF) photosensitizer, named TPDA, with multiple active sites is synthesized via Schiff base condensation between 2,4,6-triformylphloroglucinol (TFP) and 3,6-diaminoacridine (DAA). Owing to the increased conjugation effect of the COF skeleton and outstanding light harvesting ability of DAA, TPDA exhibits a narrow optical band gap (1.6 eV), enhancing light energy transformation and conferring a wide optical absorption spectrum (intensity arbitrary unit > 0.8) ranging from the UV to near-infrared region. Moreover, TPDA shows high antibacterial activities against both gram-negative and gram-positive bacteria within a short time (10 min) of light irradiation and is found to efficiently protect fish from skin infections. Molecular dynamics simulation data show that the introduction of DAA and TFP facilitates the interaction between TPDA and bacteria and is conducive to reactive oxygen species migration, which further improves the antimicrobial performance. These findings indicate the potential of TPDA as a novel photosensitive material for photodynamic therapy.
Collapse
Affiliation(s)
- Cuiping Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Jiangna Guo
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Xiuyang Zou
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Siyu Guo
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Yu Guo
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Rongwei Shi
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| | - Feng Yan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, 215123, China
| |
Collapse
|
22
|
Dyett BP, Yu H, Lakic B, De Silva N, Dahdah A, Bao L, Blanch EW, Drummond CJ, Conn CE. Delivery of antimicrobial peptides to model membranes by cubosome nanocarriers. J Colloid Interface Sci 2021; 600:14-22. [PMID: 34000474 DOI: 10.1016/j.jcis.2021.03.161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/21/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022]
Abstract
Antimicrobial peptides (AMPs), which typically disrupt the bacterial wall prompting leakage or lysis of the cell, form a growing contingent in the arsenal against antibiotic resistant bacteria. The effectiveness of AMPs is, however, hampered by their low solubility, general chemical and physical instability, and short half-life in vivo. Lipid nanocarriers such as cubosomes are effective at encapsulating and protecting proteins while simultaneously showing promise in delivery applications. Here, the efficacy of cubosome mediated delivery of AMPs is evaluated by the in-situ surface characterization of model membranes with varying composition. The cubosomes were observed to initially fuse with the membranes, with subsequent membrane disruption observed after approximately 20 - 60 min. The time for the disruption was sensitive to the charge of the cubosome as well as the composition of the bilayer. More physiologically relevant bilayers including lipids with phospho-(1'-rac-glycerol) (PG) or phosphoethanolamine (PE) headgroups were more vulnerable than those of neat phosphocholine (PC). Notably, disruption to the bilayer occurred an order of magnitude faster for encapsulated AMP compared to free AMP.
Collapse
Affiliation(s)
- Brendan P Dyett
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Haitao Yu
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Biserka Lakic
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Nilamuni De Silva
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Anthony Dahdah
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Lei Bao
- School of Engineering, STEM College, RMIT University, Victoria, Australia
| | - Ewan W Blanch
- School of Science, STEM College, RMIT University, Victoria, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Victoria, Australia.
| | - Charlotte E Conn
- School of Science, STEM College, RMIT University, Victoria, Australia.
| |
Collapse
|
23
|
Rani G, Kuroda K, Vemparala S. Towards designing globular antimicrobial peptide mimics: role of polar functional groups in biomimetic ternary antimicrobial polymers. SOFT MATTER 2021; 17:2090-2103. [PMID: 33439212 DOI: 10.1039/d0sm01896a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Using atomistic molecular dynamics simulations, we study the interaction of ternary methacrylate polymers, composed of charged cationic, hydrophobic and neutral polar groups, with model bacterial membrane. Our simulation data shows that the random ternary polymers can penetrate deep into the membrane interior and partitioning of even a single polymer has a pronounced effect on the membrane structure. Lipid reorganization, on polymer binding, shows a strong affinity of the ternary polymer for anionic POPG lipids and the same is compared with the control case of binary polymers (only cationic and hydrophobic groups). While binary polymers exhibit strong propensity of acquired amphiphilic conformations upon membrane insertion, our results strongly suggest that such amphiphilic conformations are absent in the case of random ternary polymers. The ternary polymers adopt a more folded conformation, staying aligned in the direction of the membrane normal and subsequently penetrating deeper into the membrane interior suggesting a novel membrane partitioning mechanism without amphiphilic conformations. Finally, we also examine the interactions of ternary polymer aggregates with model bacterial membranes, which show that replacing some of the hydrophobic groups by polar groups leads to weakly held ternary aggregates enabling them to undergo rapid partitioning and insertion into membrane interior. Our work thus underscores the role of inclusion of polar groups into the framework of traditional binary biomimetic antimicrobial polymers and suggests different mode of partitioning into bacterial membranes, mimicking antimicrobial mechanism of globular antimicrobial peptides like Defensin.
Collapse
Affiliation(s)
- Garima Rani
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India. and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| |
Collapse
|
24
|
Aghazadeh H, Ganjali Koli M, Ranjbar R, Pooshang Bagheri K. Interactions of GF-17 derived from LL-37 antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study. J Comput Aided Mol Des 2020; 34:1261-1273. [DOI: 10.1007/s10822-020-00348-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/29/2020] [Indexed: 01/04/2023]
|
25
|
Sharma P, Parthasarathi S, Patil N, Waskar M, Raut JS, Puranik M, Ayappa KG, Basu JK. Assessing Barriers for Antimicrobial Penetration in Complex Asymmetric Bacterial Membranes: A Case Study with Thymol. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8800-8814. [PMID: 32609530 DOI: 10.1021/acs.langmuir.0c01124] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The bacterial cell envelope is a complex multilayered structure evolved to protect bacteria in hostile environments. An understanding of the molecular basis for the interaction and transport of antibacterial therapeutics with the bacterial cell envelope will enable the development of drug molecules to combat bacterial infections and suppress the emergence of drug-resistant strains. Here we report the successful creation of an in vitro supported lipid bilayer (SLB) platform of the outer membrane (OM) of E. coli, an archetypical Gram-negative bacterium, containing the full smooth lipopolysaccharide (S-LPS) architecture of the membrane. Using this platform, we performed fluorescence correlation spectroscopy (FCS) in combination with molecular dynamics (MD) simulations to measure lipid diffusivities and provide molecular insights into the transport of natural antimicrobial agent thymol. Lipid diffusivities measured on symmetric supported lipid bilayers made up of inner membrane lipids show a distinct increase in the presence of thymol as also corroborated by MD simulations. However, lipid diffusivities in the asymmetric OM consisting of only S-LPS are invariant upon exposure to thymol. Increasing the phospholipid content in the LPS-containing outer leaflet improved the penetration toward thymol as reflected in slightly higher relative diffusivity changes in the inner leaflet when compared with the outer leaflet. Free-energy computations reveal the presence of a barrier (∼6 kT) only in the core-saccharide region of the OM for the translocation of thymol while the external O-antigen part is easily traversed. In contrast, thymol spontaneously inserts into the inner membrane. In addition to providing leaflet-resolved penetration barriers in bacterial membranes, we also assess the ability of small molecules to penetrate various membrane components. With rising bacterial resistance, our study opens up the possibility of screening potential antimicrobial drug candidates using these realistic model platforms for Gram-negative bacteria.
Collapse
Affiliation(s)
| | | | - Nivedita Patil
- Unilever RD Bangalore, 64 Main Road, Whitefield, Bangalore 560066, India
| | - Morris Waskar
- Unilever RD Bangalore, 64 Main Road, Whitefield, Bangalore 560066, India
| | - Janhavi S Raut
- Unilever RD Bangalore, 64 Main Road, Whitefield, Bangalore 560066, India
| | - Mrinalini Puranik
- Unilever RD Bangalore, 64 Main Road, Whitefield, Bangalore 560066, India
| | | | | |
Collapse
|
26
|
Sowlati-Hashjin S, Carbone P, Karttunen M. Insights into the Polyhexamethylene Biguanide (PHMB) Mechanism of Action on Bacterial Membrane and DNA: A Molecular Dynamics Study. J Phys Chem B 2020; 124:4487-4497. [DOI: 10.1021/acs.jpcb.0c02609] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Paola Carbone
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| |
Collapse
|
27
|
Wang J, Jin H, Schlenke T, Yang Y, Wang F, Yao H, Fang Q, Ye G. Lipidomics reveals how the endoparasitoid wasp Pteromalus puparum manipulates host energy stores for its young. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158736. [PMID: 32438058 DOI: 10.1016/j.bbalip.2020.158736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 02/02/2023]
Abstract
Endoparasitoid wasps inject venom along with their eggs to adjust the physiological and nutritional environment inside their hosts to benefit the development of their offspring. In particular, wasp venoms are known to modify host lipid metabolism, lipid storage in the fat body, and release of lipids into the hemolymph, but how venoms accomplish these functions remains unclear. Here, we use an UPLC-MS-based lipidomics approach to analyze the identities and concentrations of lipids in both fat body and hemolymph of host cabbage butterfly (Pieris rapae) infected by the pupal endoparasitoid Pteromalus puparum. During infection, host fat body levels of highly unsaturated, soluble triacylglycerides (TAGs) increased while less unsaturated, less soluble forms decreased. Furthermore, in infected host hemolymph, overall levels of TAG and phospholipids (the major component of cell membranes) increased, suggesting that fat body cells are destroyed and their contents are dispersed. Altogether, these data suggest that wasp venom induces host fat body TAGs to be transformed into lower melting point (more liquid) forms and released into the host hemolymph following infection, allowing simple absorption and nutritional acquisition by wasp larvae. Finally, cholesteryl esters (CEs, a dietary lipid derived from cholesterol) increased in host hemolymph following infection with no concomitant decrease in host cholesterol, implying that the wasp may provide this necessary food resource to its offspring via its venom. This study provides novel insight into how parasitoid infection alters lipid metabolism in insect hosts, and begins to uncover the wasp venom proteins responsible for host physiological changes and offspring development.
Collapse
Affiliation(s)
- Jiale Wang
- State Key Laboratory of Rice Biology & Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Hongxia Jin
- State Key Laboratory of Rice Biology & Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Todd Schlenke
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Yi Yang
- State Key Laboratory of Rice Biology & Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fang Wang
- State Key Laboratory of Rice Biology & Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology & Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
28
|
Kunacheva C, Soh YNA, Stuckey DC. Identification of soluble microbial products (SMPs) from the fermentation and methanogenic phases of anaerobic digestion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134177. [PMID: 31783466 DOI: 10.1016/j.scitotenv.2019.134177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
The production and transformation of Soluble Microbial Products (SMPs) in biological treatment systems is complex, and their genesis and reasons for production are still unclear. SMPs are important since they constitute the main fraction of effluent COD (both aerobic and anaerobic), and hence are the main precursors for disinfection by-products (DBPs). In addition, they are a key component of fouling in membrane bioreactors. Hence, it is important to identify the chemical composition of SMPs, determine their origin, and understand what system parameters influence their production so we can possibly develop strategies to control their production. This study focuses on the production and identification of SMPs in an anaerobic batch process being fed a synthetic feed. To further understand the origins of SMPs, and how they are produced, we analysed the processes of fermentation and methanogenesis independently which has never been done in detail before. SMP concentration, molecular weight distribution and carbohydrate analyses were used to estimate the amount of SMPs in the supernatants. Gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-Time-of-Flight mass spectrometry (LC-ESI-Q-ToF) were used to identify many of the SMPs which have relative masses up to 2 kDa. Our results showed that fermentation released much higher SMP concentrations compared to methanogenesis, especially in the range of 70 k-1000 k Da and 106-1500 Da. Alkanes, alkenes, alcohols, acids, and nitrogen-compounds were the major group of compounds identified in the supernatant of both fermentation and methanogenesis, and 71% of the compounds identified were found in both phases of digestion. Results from LC-ESI-Q-ToF analysis identified components of the cell membrane, such as phosphatidylglycerol, phosphatidylethanolamine and phosphatidylserine, as well as other compounds such as flavonoids, acylglycerol, terpene and terpenoids, benzenoid, glyceride, steroid and steroid derivatives.
Collapse
Affiliation(s)
- C Kunacheva
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Clean Tech One, Singapore 637141, Singapore.
| | - Y N A Soh
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Clean Tech One, Singapore 637141, Singapore.
| | - D C Stuckey
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Clean Tech One, Singapore 637141, Singapore; Department of Chemical Engineering, Imperial College London, SW7 2AZ, UK.
| |
Collapse
|
29
|
Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
30
|
Klauda JB. Perspective: Computational modeling of accurate cellular membranes with molecular resolution. J Chem Phys 2018; 149:220901. [DOI: 10.1063/1.5055007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, USA
| |
Collapse
|
31
|
Juretić D, Sonavane Y, Ilić N, Gajski G, Goić-Barišić I, Tonkić M, Kozic M, Maravić A, Pellay FX, Zoranić L. Designed peptide with a flexible central motif from ranatuerins adapts its conformation to bacterial membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2655-2668. [DOI: 10.1016/j.bbamem.2018.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
|
32
|
Gurtovenko AA, Mukhamadiarov EI, Kostritskii AY, Karttunen M. Phospholipid–Cellulose Interactions: Insight from Atomistic Computer Simulations for Understanding the Impact of Cellulose-Based Materials on Plasma Membranes. J Phys Chem B 2018; 122:9973-9981. [DOI: 10.1021/acs.jpcb.8b07765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg, 199004 Russia
| | - Evgenii I. Mukhamadiarov
- Faculty of Physics, St. Petersburg State University, Ulyanovskaya str. 3, Petrodvorets, St. Petersburg, 198504 Russia
| | - Andrei Yu. Kostritskii
- Faculty of Physics, St. Petersburg State University, Ulyanovskaya str. 3, Petrodvorets, St. Petersburg, 198504 Russia
| | - Mikko Karttunen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg, 199004 Russia
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 3K7
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5B7
| |
Collapse
|
33
|
Lipopeptide daptomycin: Interactions with bacterial and phospholipid membranes, stability of membrane aggregates and micellation in solution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1949-1954. [DOI: 10.1016/j.bbamem.2018.03.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 11/17/2022]
|
34
|
Li J, Beuerman RW, Verma CS. Molecular Insights into the Membrane Affinities of Model Hydrophobes. ACS OMEGA 2018; 3:2498-2507. [PMID: 30023836 PMCID: PMC6044992 DOI: 10.1021/acsomega.7b01759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Membrane-active antibiotics are of great interest in fighting bacterial resistance. α-Mangostin is a membrane-active molecule, but there are no details of its mechanism of action at the atomistic level. We have employed free-energy simulations and microsecond-long conventional molecular dynamics simulations to study the mode of interaction of α-mangostin with a model bacterial membrane and compare it with the mechanisms of three hydrophobic molecules (ciprofloxacin, xanthone, and tetracycline). We find that α-mangostin is thermodynamically more favored to insert into the membrane compared to the other three molecules. Apart from tetracycline, which is largely hydrophilic, the other three molecules aggregate in water; however, only α-mangostin can penetrate into the lipid tail region of the membrane. When it reaches a high concentration in the lipid tail region, α-mangostin can form tubular clusters that span the two head group regions of the membrane, resulting in a large number of water translocations along the transmembrane aggregates. Structure-activity relationship analysis revealed two structural properties that characterize α-mangostin, namely, the two isoprenyl groups and the polar groups present in the aromatic rings, which result in "disruptive amphiphilicity" and hence its excellent membrane activity.
Collapse
Affiliation(s)
- Jianguo Li
- Singapore
Eye Research Institute, The Academia, 20 College Road, 169856, Singapore
- Bioinformatics
Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, 138671 Singapore
| | - Roger W. Beuerman
- Singapore
Eye Research Institute, The Academia, 20 College Road, 169856, Singapore
- Department
of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Road, 119074 Singapore
- Duke-NUS,
SRP Neuroscience & Behavioural Disorders, 8 College Road, 169857, Singapore
| | - Chandra S. Verma
- Singapore
Eye Research Institute, The Academia, 20 College Road, 169856, Singapore
- Bioinformatics
Institute (A*-STAR), 30 Biopolis Street, #07-01 Matrix, 138671 Singapore
- School
of Biological Sciences, Nanyang Technological
University, 60 Nanyang
Drive, 637551 Singapore
- Department
of Biological Sciences, National University
of Singapore, 14 Science
Drive 4, 117543 Singapore
| |
Collapse
|
35
|
Montemayor D, Rivera E, Jang SJ. Computational Modeling of Exciton-Bath Hamiltonians for Light Harvesting 2 and Light Harvesting 3 Complexes of Purple Photosynthetic Bacteria at Room Temperature. J Phys Chem B 2018. [PMID: 29533664 DOI: 10.1021/acs.jpcb.8b00358] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light harvesting 2 (LH2) complex is the primary component of the photosynthetic unit of purple bacteria that is responsible for harvesting and relaying excitons. The electronic absorption line shape of LH2 contains two major bands at 800 and 850 nm wavelength regions. Under low light conditions, some species of purple bacteria replace LH2 with light harvesting 3 (LH3), a variant form with almost the same structure as the former but with distinctively different spectral features. The major difference between the absorption line shapes of LH2 and LH3 is the shift of the 850 nm band of the former to a new 820 nm region. The microscopic origin of this difference has been the subject of some theoretical/computational investigations. However, the genuine molecular level source of such a difference is not clearly understood yet. This work reports a comprehensive computational study of LH2 and LH3 complexes so as to clarify different molecular level features of LH2 and LH3 complexes and to construct simple exciton-bath models with a common form. All-atomistic molecular dynamics simulations of both LH2 and LH3 complexes provide detailed molecular level structural differences of bacteriochlorophylls (BChls) in the two complexes, in particular, in their patterns of hydrogen bonding (HB) and torsional angles of the acetyl group. Time-dependent density functional theory calculation of the excitation energies of BChls for structures sampled from the MD simulations suggests that the observed differences in the HB and torsional angles cannot fully account for the experimentally observed spectral shift of LH3. Potential sources that can explain the actual spectral shift of LH3 are discussed, and their magnitudes are assessed through fitting of experimental line shapes. These results demonstrate the feasibility of developing simple exciton-bath models for both LH2 and LH3, which can be employed for large-scale exciton quantum dynamics in their aggregates.
Collapse
Affiliation(s)
- Daniel Montemayor
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Eva Rivera
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Seogjoo J Jang
- Department of Chemistry and Biochemistry, Queens College , City University of New York , 65-30 Kissena Boulevard , Queens , New York 11367 , United States.,PhD Programs in Chemistry and Physics, and Initiative for the Theoretical Sciences, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| |
Collapse
|
36
|
Fang G, Li W, Shen X, Perez-Aguilar JM, Chong Y, Gao X, Chai Z, Chen C, Ge C, Zhou R. Differential Pd-nanocrystal facets demonstrate distinct antibacterial activity against Gram-positive and Gram-negative bacteria. Nat Commun 2018; 9:129. [PMID: 29317632 PMCID: PMC5760645 DOI: 10.1038/s41467-017-02502-3] [Citation(s) in RCA: 261] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/05/2017] [Indexed: 02/08/2023] Open
Abstract
Noble metal-based nanomaterials have shown promise as potential enzyme mimetics, but the facet effect and underlying molecular mechanisms are largely unknown. Herein, with a combined experimental and theoretical approach, we unveil that palladium (Pd) nanocrystals exhibit facet-dependent oxidase and peroxidase-like activities that endow them with excellent antibacterial properties via generation of reactive oxygen species. The antibacterial efficiency of Pd nanocrystals against Gram-positive bacteria is consistent with the extent of their enzyme-like activity, that is {100}-faceted Pd cubes with higher activities kill bacteria more effectively than {111}-faceted Pd octahedrons. Surprisingly, a reverse trend of antibacterial activity is observed against Gram-negative bacteria, with Pd octahedrons displaying stronger penetration into bacterial membranes than Pd nanocubes, thereby exerting higher antibacterial activity than the latter. Our findings provide a deeper understanding of facet-dependent enzyme-like activities and might advance the development of noble metal-based nanomaterials with both enhanced and targeted antibacterial activities.
Collapse
Affiliation(s)
- Ge Fang
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Weifeng Li
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Xiaomei Shen
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | | | - Yu Chong
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Xingfa Gao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhifang Chai
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China
| | - Chunying Chen
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China and Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Cuicui Ge
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China.
| | - Ruhong Zhou
- School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, 215123, China.
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, 10598, USA.
- Department of Chemistry, Columbia University, New York, New York, 10027, USA.
| |
Collapse
|
37
|
Jafari M, Mehrnejad F, Doustdar F. Insight into the interactions, residue snorkeling, and membrane disordering potency of a single antimicrobial peptide into different lipid bilayers. PLoS One 2017; 12:e0187216. [PMID: 29125878 PMCID: PMC5695277 DOI: 10.1371/journal.pone.0187216] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Pardaxin, with a bend-helix-bend-helix structure, is a membrane-active antimicrobial peptide that its membrane activity depends on the lipid bilayer composition. Herein, all-atom molecular dynamics (MD) simulations were performed to provide further molecular insight into the interactions, structural dynamics, orientation behavior, and cationic residues snorkeling of pardaxin in the DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) lipid bilayers. The results showed that the C-terminal helix of the peptide was maintained in all six types of the model-bilayers and pardaxin was tilted into the DMPC, DPPC, and POPG/POPE mixed bilayers more than the POPC and POPG bilayers. As well as, the structure of zwitterionic membranes was more affected by the peptide than the anionic bilayers. Taken together, the study demonstrated that the cationic residues of pardaxin snorkeled toward the interface of lipid bilayers and all phenylalanine residues of the peptide played important roles in the peptide-membrane interactions. We hope that this work will provide a better understanding of the interactions of antimicrobial peptides with the membranes.
Collapse
Affiliation(s)
- Majid Jafari
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Farahnoosh Doustdar
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
38
|
Dugail I, Kayser BD, Lhomme M. Specific roles of phosphatidylglycerols in hosts and microbes. Biochimie 2017; 141:47-53. [DOI: 10.1016/j.biochi.2017.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/04/2017] [Indexed: 11/25/2022]
|
39
|
Varshney GK, Kintali SR, Das K. Effect of Curcumin Addition on the Adsorption and Transport of a Cationic Dye across DPPG-POPG Liposomes Probed by Second Harmonic Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8302-8310. [PMID: 28742369 DOI: 10.1021/acs.langmuir.7b01783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The effect of addition of curcumin on the adsorption and transport characteristics of a cationic dye, LDS+, across negatively charged bilayers composed of POPG and DPPG lipids were investigated by the interface selective second harmonic (SH) spectroscopic technique. Curcumin induced changes in the SH electric field signal of the LDS+ ions (E2ω (LDS+)) were observed to depend critically on the bilayer acyl chain saturation/unsaturation ratio (S/U). Following earlier works, the increase in the E2ω (LDS+) signal is attributed to the release of the Na+ counterions present in the head group region of the bilayer by curcumin and the decay of the E2ω (LDS+) signal is attributed to the bilayer intercalated state of curcumin. While the changes observed in the E2ω (LDS+) signal in the presence of POPG liposomes were consistent with our earlier study ( Varshney, G. K. et al. Langmuir , 2016 , 32 , 10415 - 10421 ), they were significantly different for DPPG liposomes, following curcumin addition. While the increase in the E2ω (LDS+) signal in the presence of POPG liposomes, is marginal (∼10-20%) and instantaneous (<1 s) followed by a rapid decay (completed within ∼100 s), in the presence of DPPG liposomes it was observed to increase slowly and at saturation shows a substantial increase (100-200%), following curcumin addition. When liposomes consisting of a mixture of POPG and DPPG lipids are used, curcumin induced kinetic characteristics of the E2ω (LDS+) signal showed a mixture of the individual kinetic characteristics observed for the unsaturated (POPG) and saturated (DPPG) liposomes. The observed kinetic trends of the E2ω (LDS+) signal following curcumin addition are explained on the basis of the relative strength of the Na+-POPG and Na+-DPPG interaction. Higher ordering of the lipid acyl chain region in DPPG liposome makes the Na+-DPPG interaction much stronger than the Na+-POPG interaction. Further, it is proposed that, in POPG-DPPG liposomes, individual domains of POPG and DPPG lipids exist at low temperature as suggested by the observed temperature dependent kinetic characteristics of the E2ω (LDS+) signal following curcumin addition. These domains are dependent on the S/U ratio and phase state of the bilayer. The gel phase was observed to be more conducive for individual domain formation. Results presented in this work not only support the notion that biological activity of curcumin is associated with its bilayer altering properties, but more interestingly it provides a qualitative insight about how bilayer phase separation can be achieved by modulating the hydrophobic interactions between the lipid acyl chains.
Collapse
Affiliation(s)
- G K Varshney
- Photochem. & Photophys. Appl. Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, M.P. India 452013
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - S R Kintali
- Photochem. & Photophys. Appl. Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, M.P. India 452013
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - K Das
- Photochem. & Photophys. Appl. Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, M.P. India 452013
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| |
Collapse
|
40
|
Mokkila S, Postila PA, Rissanen S, Juhola H, Vattulainen I, Róg T. Calcium Assists Dopamine Release by Preventing Aggregation on the Inner Leaflet of Presynaptic Vesicles. ACS Chem Neurosci 2017; 8:1242-1250. [PMID: 28165217 DOI: 10.1021/acschemneuro.6b00395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this study, the dopamine-lipid bilayer interactions were probed with three physiologically relevant ion compositions using atomistic molecular dynamics simulations and free energy calculations. The in silico results indicate that calcium is able to decrease significantly the binding of dopamine to a neutral (zwitterionic) phosphatidylcholine lipid bilayer model mimicking the inner leaflet of a presynaptic vesicle. We argue that the observed calcium-induced effect is likely in crucial role in the neurotransmitter release from the presynaptic vesicles docked in the active zone of nerve terminals. The inner leaflets of presynaptic vesicles, which are responsible for releasing neurotransmitters into the synaptic cleft, are mainly composed of neutral lipids such as phosphatidylcholine and phosphatidylethanolamine. The neutrality of the lipid head group region, enhanced by a low pH level, should limit membrane aggregation of transmitters. In addition, the simulations suggest that the high calcium levels inside presynaptic vesicles prevent even the most lipophilic transmitters such as dopamine from adhering to the inner leaflet surface, thus rendering unhindered neurotransmitter release feasible.
Collapse
Affiliation(s)
- Sini Mokkila
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Pekka A. Postila
- Structural Bioinformatics Laboratory, Biochemistry,
Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Sami Rissanen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Hanna Juhola
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- MEMPHYS − Center for Biomembrane
Physics, University of Southern Denmark, 5230 Odense, Denmark
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| |
Collapse
|
41
|
Oliveira M, Gomes-Alves AG, Sousa C, Mirta Marani M, Plácido A, Vale N, Delerue-Matos C, Gameiro P, Kückelhaus SAS, Tomas AM, S A Leite JR, Eaton P. Ocellatin-PT antimicrobial peptides: High-resolution microscopy studies in antileishmania models and interactions with mimetic membrane systems. Biopolymers 2017; 105:873-86. [PMID: 27463422 DOI: 10.1002/bip.22925] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 01/07/2023]
Abstract
Although the mechanism of action of antimicrobial peptides (AMPs) is not clear, they can interact electrostatically with the cell membranes of microorganisms. New ocellatin-PT peptides were recently isolated from the skin secretion of Leptodactylus pustulatus. The secondary structure of these AMPs and their effect on Leishmania infantum cells, and on different lipid surface models was characterized in this work. The results showed that all ocellatin-PT peptides have an α-helix structure and five of them (PT3, PT4, PT6 to PT8) have leishmanicidal activity; PT1 and PT2 affected the cellular morphology of the parasites and showed greater affinity for leishmania and bacteria-mimicking lipid membranes than for those of mammals. The results show selectivity of ocellatin-PTs to the membranes of microorganisms and the applicability of biophysical methods to clarify the interaction of AMPs with cell membranes.
Collapse
Affiliation(s)
- Mayara Oliveira
- Programa de Pós-Graduação em Medicina Tropical, Núcleo de Medicina Tropical, NMT, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brazil.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200, Portugal
| | - Ana Georgina Gomes-Alves
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CEB, Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, Braga, 4710-057, Portugal
| | - Carla Sousa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200, Portugal
| | - Mariela Mirta Marani
- PEEC ? CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Chubut, Argentina
| | - Alexandra Plácido
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Porto, Portugal
| | - Nuno Vale
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200, Portugal
| | - Cristina Delerue-Matos
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Porto, Portugal
| | - Paula Gameiro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200, Portugal
| | - Selma A S Kückelhaus
- Programa de Pós-Graduação em Medicina Tropical, Núcleo de Medicina Tropical, NMT, Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brazil.,Departmento de Morfologia, Faculdade de Medicina, Universidade de Brasília, Brasilia, Brazil
| | - Ana M Tomas
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,ICBAS, Instituto de Ciencias Biomedicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - José Roberto S A Leite
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200, Portugal.,Departmento de Morfologia, Faculdade de Medicina, Universidade de Brasília, Brasilia, Brazil.,Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Biotec, Campus Ministro Reis Velloso, Universidade Federal do Piauí, UFPI, Parnaiba, PI, Brazil
| | - Peter Eaton
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4200, Portugal. .,Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Biotec, Campus Ministro Reis Velloso, Universidade Federal do Piauí, UFPI, Parnaiba, PI, Brazil.
| |
Collapse
|
42
|
Screening for a Potent Antibacterial Peptide to Treat Mupirocin-Resistant MRSA Skin Infections. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9580-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
43
|
Murcar-Evans BI, Cabral AD, Toutah K, de Araujo ED, Lai A, Macdonald PM, Berger-Becvar A, Kraskouskaya D, Gunning PT. ProxyPhos sensors for the detection of negatively charged membranes. Analyst 2017; 142:4511-4521. [DOI: 10.1039/c7an00568g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
ProxyPhos sensors selectively detect negatively charged phospholipid membranes.
Collapse
Affiliation(s)
- Bronte I. Murcar-Evans
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Aaron D. Cabral
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Krimo Toutah
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Elvin D. de Araujo
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Angel Lai
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Peter M. Macdonald
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Angelika Berger-Becvar
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Dziyana Kraskouskaya
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| | - Patrick T. Gunning
- Department of Chemistry and Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Mississauga
- Canada L5L 1C6
| |
Collapse
|
44
|
Bondar AN. Biophysical mechanism of rhomboid proteolysis: Setting a foundation for therapeutics. Semin Cell Dev Biol 2016; 60:46-51. [DOI: 10.1016/j.semcdb.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 08/12/2016] [Accepted: 09/12/2016] [Indexed: 11/16/2022]
|
45
|
Pan X, Liu H, Liu J, Wang C, Wen J. Omics-based approaches reveal phospholipids remodeling of Rhizopus oryzae responding to furfural stress for fumaric acid-production from xylose. BIORESOURCE TECHNOLOGY 2016; 222:24-32. [PMID: 27697734 DOI: 10.1016/j.biortech.2016.09.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 06/06/2023]
Abstract
In order to relieve the toxicity of furfural on Rhizopus oryzae fermentation, the molecular mechanism of R. oryzae responding to furfural stress for fumaric acid-production was investigated by omics-based approaches. In metabolomics analysis, 29 metabolites including amino acid, sugars, polyols and fatty acids showed significant changes for maintaining the basic cell metabolism at the cost of lowering fumaric acid production. To further uncover the survival mechanism, lipidomics was carried out, revealing that phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and polyunsaturated acyl chains might be closely correlated with R. oryzae's adapting to furfural stress. Based on the above omics analysis, lecithin, inositol and soybean oil were exogenously supplemented separately with an optimized concentration in the presence of furfural, which increased fumaric acid titer from 5.78g/L to 10.03g/L, 10.05g/L and 12.13g/L (increased by 73.5%, 73.8% and 110%, respectively). These findings provide a methodological guidance for hemicellulose-fumaric acid development.
Collapse
Affiliation(s)
- Xinrong Pan
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Huanhuan Liu
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jiao Liu
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Cheng Wang
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jianping Wen
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, People's Republic of China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China.
| |
Collapse
|
46
|
Antimicrobial Peptide Potency is Facilitated by Greater Conformational Flexibility when Binding to Gram-negative Bacterial Inner Membranes. Sci Rep 2016; 6:37639. [PMID: 27874065 PMCID: PMC5118786 DOI: 10.1038/srep37639] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/28/2016] [Indexed: 11/24/2022] Open
Abstract
The interaction of antimicrobial peptides (AMPs) with the inner membrane of Gram-negative bacteria is a key determinant of their abilities to exert diverse bactericidal effects. Here we present a molecular level understanding of the initial target membrane interaction for two cationic α-helical AMPs that share structural similarities but have a ten-fold difference in antibacterial potency towards Gram-negative bacteria. The binding and insertion from solution of pleurocidin or magainin 2 to membranes representing the inner membrane of Gram-negative bacteria, comprising a mixture of 128 anionic and 384 zwitterionic lipids, is monitored over 100 ns in all atom molecular dynamics simulations. The effects of the membrane interaction on both the peptide and lipid constituents are considered and compared with new and published experimental data obtained in the steady state. While both magainin 2 and pleurocidin are capable of disrupting bacterial membranes, the greater potency of pleurocidin is linked to its ability to penetrate within the bacterial cell. We show that pleurocidin displays much greater conformational flexibility when compared with magainin 2, resists self-association at the membrane surface and penetrates further into the hydrophobic core of the lipid bilayer. Conformational flexibility is therefore revealed as a key feature required of apparently α-helical cationic AMPs for enhanced antibacterial potency.
Collapse
|
47
|
Duneau JP, Khao J, Sturgis JN. Lipid perturbation by membrane proteins and the lipophobic effect. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:126-134. [PMID: 27794424 DOI: 10.1016/j.bbamem.2016.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 11/26/2022]
Abstract
Understanding how membrane proteins interact with their environment is fundamental to the understanding of their structure, function and interactions. We have performed coarse-grained molecular dynamics simulations on a series of membrane proteins in a membrane environment to examine the perturbations of the lipids by the presence of protein. We analyze these perturbations in terms of elastic membrane deformations and local lipid protein interactions. However these two factors are insufficient to describe the variety of effects that we observe and the changes caused by membranes proteins to the structure and dynamics of their lipid environment. Other factors that change the conformation available to lipid molecules are evident and are able to modify lipid structure far from the protein surface, and thus mediate long-range interactions between membrane proteins. We suggest that these multiple modifications to lipid behavior are responsible, at the molecular level, for the lipophobic effect we have proposed to account for our observations of membrane protein organization.
Collapse
Affiliation(s)
- Jean-Pierre Duneau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
| | - Jonathan Khao
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France
| | - James N Sturgis
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, CNRS and Aix-Marseille Univ, Marseille 13402 cedex 20, France.
| |
Collapse
|
48
|
Kostritskii AY, Kondinskaia DA, Nesterenko AM, Gurtovenko AA. Adsorption of Synthetic Cationic Polymers on Model Phospholipid Membranes: Insight from Atomic-Scale Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10402-10414. [PMID: 27642663 DOI: 10.1021/acs.langmuir.6b02593] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Although synthetic cationic polymers represent a promising class of effective antibacterial agents, the molecular mechanisms behind their antimicrobial activity remain poorly understood. To this end, we employ atomic-scale molecular dynamics simulations to explore adsorption of several linear cationic polymers of different chemical structure and protonation (polyallylamine (PAA), polyethylenimine (PEI), polyvinylamine (PVA), and poly-l-lysine (PLL)) on model bacterial membranes (4:1 mixture of zwitterionic phosphatidylethanolamine (PE) and anionic phosphatidylglycerol (PG) lipids). Overall, our findings show that binding of polycations to the anionic membrane surface effectively neutralizes its charge, leading to the reorientation of water molecules close to the lipid/water interface and to the partial release of counterions to the water phase. In certain cases, one has even an overcharging of the membrane, which was shown to be a cooperative effect of polymer charges and lipid counterions. Protonated amine groups of polycations are found to interact preferably with head groups of anionic lipids, giving rise to formation of hydrogen bonds and to a noticeable lateral immobilization of the lipids. While all the above findings are mostly defined by the overall charge of a polymer, we found that the polymer architecture also matters. In particular, PVA and PEI are able to accumulate anionic PG lipids on the membrane surface, leading to lipid segregation. In turn, PLL whose charge twice exceeds charges of PVA/PEI does not induce such lipid segregation due to its considerably less compact architecture and relatively long side chains. We also show that partitioning of a polycation into the lipid/water interface is an interplay between its protonation level (the overall charge) and hydrophobicity of the backbone. Therefore, a possible strategy in creating highly efficient antimicrobial polymeric agents could be in tuning these polycation's properties through proper combination of protonated and hydrophobic blocks.
Collapse
Affiliation(s)
- Andrei Yu Kostritskii
- Faculty of Physics, St. Petersburg State University , Ulyanovskaya str. 3, Petrodvorets, St. Petersburg 198504 Russia
| | - Diana A Kondinskaia
- Faculty of Physics, St. Petersburg State University , Ulyanovskaya str. 3, Petrodvorets, St. Petersburg 198504 Russia
| | - Alexey M Nesterenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119991 Russia
| | - Andrey A Gurtovenko
- Faculty of Physics, St. Petersburg State University , Ulyanovskaya str. 3, Petrodvorets, St. Petersburg 198504 Russia
- Institute of Macromolecular Compounds, Russian Academy of Sciences , Bolshoi Prospect V.O. 31, St. Petersburg 199004 Russia
| |
Collapse
|
49
|
Varshney GK, Kintali SR, Gupta PK, Das K. Effect of Bilayer Partitioning of Curcumin on the Adsorption and Transport of a Cationic Dye Across POPG Liposomes Probed by Second-Harmonic Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10415-10421. [PMID: 27636651 DOI: 10.1021/acs.langmuir.6b02797] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The effect of Curcumin partitioning into the bilayer during the adsorption and transport of a cationic dye, LDS, across a negatively charged POPG bilayer was investigated by the interface-selective second-harmonic (SH) spectroscopic technique. The intensity of SH electric field (E2ω) arising due to LDS adsorbed on the outer bilayer of the POPG liposome was observed to increase instantaneously (<1 s) following the addition of Curcumin. The fractional increase in the SH electric field (Ef2ω) and the bilayer transport rates (kT) of LDS were studied with respect to the pH of the solution and also with the Curcumin content in the lipid bilayer. Results obtained indicate that compared with the anionic form of the drug, its neutral form is more conducive of increasing the Ef2ω of LDS. With increasing Curcumin content in the lipid bilayer, two distinct regimes could be observed in terms of Ef2ω and kT values of LDS. For Curcumin:Lipid (C/L) ratio ≤0.02, the Ef2ω of LDS increases rapidly, while kT remains unchanged; and for C/L ratio ≥0.02, the Ef2ω values remains more or less constant, while there is a significant (∼40 times) increase followed by a modest increase in the kT values of LDS. The observed results support an earlier two-state binding model of Curcumin with the POPG bilayer. In addition, it is further proposed that at low C/L ratio Curcumin binds to the surface of the bilayer replacing the counterions (Na+) bound to the lipid head groups, which changes the bilayer surface charge density, thereby causing more LDS cations to adsorb on the bilayer surface. At high C/L ratio, Curcumin intercalates within the hydrophobic domain of the bilayer, altering its hydrophobicity and inducing enhanced transport of the LDS cation. Results presented in this work provide further insights into how Curcumin alters bilayer properties when it partitions from the aqueous to the bilayer phase.
Collapse
Affiliation(s)
- G K Varshney
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - S R Kintali
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - P K Gupta
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - K Das
- Optical Spectroscopy & Diagnostic Lab, Laser Bio-Medical Applications Section, Raja Ramanna Center for Advanced Technology , Indore, Madhya Pradesh 452013, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| |
Collapse
|
50
|
Jiang Y, Tan H, Zheng J, Li X, Chen G, Jia Z. Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study. Phys Chem Chem Phys 2016; 17:25228-34. [PMID: 26352441 DOI: 10.1039/c5cp03342j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diacylglycerol kinase is an integral membrane protein which catalyzes phosphoryl transfer from ATP to diacylglycerol. As the smallest kinase known, it shares no sequence homology with conventional kinases and possesses a distinct trimer structure. Thus far, its catalytic mechanism remains elusive. Using molecular dynamics and quantum mechanics calculations, we investigated the co-factor and the substrate binding and phosphoryl transfer mechanism. Based on the analysis of density functional theory calculations, we reveal that the phosphorylation reaction of diacylglycerol kinase features the same phosphoryl transfer mechanism as other kinases, despite its unique structural properties. Our results further show that the active site is relatively open and able to accommodate ligands in multiple orientations, suggesting that the optimization of binding orientations and conformational changes would occur prior to actual phosphoryl transfer.
Collapse
Affiliation(s)
- Yafei Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | | | | | | | | | | |
Collapse
|