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Brown TP, Santa DE, Berger BA, Kong L, Wittenberg NJ, Im W. CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation. Curr Opin Struct Biol 2024; 86:102813. [PMID: 38598982 PMCID: PMC11102286 DOI: 10.1016/j.sbi.2024.102813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/12/2024]
Abstract
Oxidative stress leads to the production of oxidized phospholipids (oxPLs) that modulate the biophysical properties of phospholipid monolayers and bilayers. As many immune cells are responsible for surveilling cells and tissues for the presence of oxPLs, oxPL-dependent mechanisms have been suggested as targets for treating chronic kidney disease, atherosclerosis, diabetes, and cancer metastasis. This review details recent experimental and computational studies that characterize oxPLs' behaviors in various monolayers and bilayers. These studies investigate how the tail length and polar functional groups of OxPLs impact membrane properties, how oxidized membranes can be stabilized, and how membrane integrity is generally affected by oxidized lipids. In addition, for oxPL-containing membrane modeling and simulation, CHARMM-GUI Membrane Builder has been extended to support a variety of oxPLs, accelerating the simulation system building process for these biologically relevant lipid bilayers.
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Affiliation(s)
- Turner P Brown
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Dane E Santa
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Brett A Berger
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Lingyang Kong
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | | | - Wonpil Im
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA; Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA; Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA.
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2
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Rzycki M, Drabik D. Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models. J Chem Inf Model 2024; 64:4204-4217. [PMID: 38733348 PMCID: PMC11134499 DOI: 10.1021/acs.jcim.4c00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Membranes─cells' essential scaffolds─are valid molecular targets for substances with an antimicrobial effect. While certain substances, such as octenidine, have been developed to target membranes for antimicrobial purposes, the recently reported molecule, fabimycin (F2B)─a novel agent targeting drug-resistant Gram-negative bacteria─has not received adequate attention regarding its activity on membranes in the literature. The following study aims to investigate the effects of F2B on different bacterial membrane models, including simple planar bilayers and more complex bilayer systems that mimic the Escherichia coli shell equipped with double inner and outer bilayers. Our results show that F2B exhibited more pronounced interactions with bacterial membrane systems compared to the control PC system. Furthermore, we observed significant changes in local membrane property homeostasis in both the inner and outer membrane models, specifically in the case of lateral diffusion, membrane thickness, and membrane resilience (compressibility, tilt). Finally, our results showed that the effect of F2B differed in a complex system and a single membrane system. Our study provides new insights into the multifaceted activity of F2B, demonstrating its potential to disrupt bacterial membrane homeostasis, indicating that its activity extends the currently known mechanism of FabI enzyme inhibition. This disruption, coupled with the ability of F2B to penetrate the outer membrane layers, sheds new light on the behavior of this antimicrobial molecule. This highlights the importance of the interaction with the membrane, crucial in combating bacterial infections, particularly those caused by drug-resistant strains.
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Affiliation(s)
- Mateusz Rzycki
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
| | - Dominik Drabik
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wroclaw 50-370, Poland
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3
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Pfeffer ME, DiFrancesco ML, Marchesi A, Galluzzi F, Moschetta M, Rossini A, Francia S, Franz CM, Fok Y, Valotteau C, Paternò GM, Redondo Morata L, Vacca F, Mattiello S, Magni A, Maragliano L, Beverina L, Mattioli G, Lanzani G, Baldelli P, Colombo E, Benfenati F. Nanoactuator for Neuronal Optoporation. ACS NANO 2024; 18:12427-12452. [PMID: 38687909 DOI: 10.1021/acsnano.4c01672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Light-driven modulation of neuronal activity at high spatial-temporal resolution is becoming of high interest in neuroscience. In addition to optogenetics, nongenetic membrane-targeted nanomachines that alter the electrical state of the neuronal membranes are in demand. Here, we engineered and characterized a photoswitchable conjugated compound (BV-1) that spontaneously partitions into the neuronal membrane and undergoes a charge transfer upon light stimulation. The activity of primary neurons is not affected in the dark, whereas millisecond light pulses of cyan light induce a progressive decrease in membrane resistance and an increase in inward current matched to a progressive depolarization and action potential firing. We found that illumination of BV-1 induces oxidation of membrane phospholipids, which is necessary for the electrophysiological effects and is associated with decreased membrane tension and increased membrane fluidity. Time-resolved atomic force microscopy and molecular dynamics simulations performed on planar lipid bilayers revealed that the underlying mechanism is a light-driven formation of pore-like structures across the plasma membrane. Such a phenomenon decreases membrane resistance and increases permeability to monovalent cations, namely, Na+, mimicking the effects of antifungal polyenes. The same effect on membrane resistance was also observed in nonexcitable cells. When sustained light stimulations are applied, neuronal swelling and death occur. The light-controlled pore-forming properties of BV-1 allow performing "on-demand" light-induced membrane poration to rapidly shift from cell-attached to perforated whole-cell patch-clamp configuration. Administration of BV-1 to ex vivo retinal explants or in vivo primary visual cortex elicited neuronal firing in response to short trains of light stimuli, followed by activity silencing upon prolonged light stimulations. BV-1 represents a versatile molecular nanomachine whose properties can be exploited to induce either photostimulation or space-specific cell death, depending on the pattern and duration of light stimulation.
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Affiliation(s)
- Marlene E Pfeffer
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department of Experimental Medicine, University of Genova, Viale Benedetto XV 3, 16132 Genova, Italy
| | | | - Arin Marchesi
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Torrette di Ancona, Italy
| | - Filippo Galluzzi
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- The Open University Affiliated Research Centre at Istituto Italiano di Tecnologia (ARC@IIT), Via Morego 30, 16163 Genova, Italy
| | - Matteo Moschetta
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Raffaele Rubattino 81, 20134 Milano, Italy
| | - Andrea Rossini
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Raffaele Rubattino 81, 20134 Milano, Italy
| | - Simona Francia
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Clemens M Franz
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yulia Fok
- Aix-Marseille University, INSERM, DyNaMo, Turing Centre for Living Systems, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Claire Valotteau
- Aix-Marseille University, INSERM, DyNaMo, Turing Centre for Living Systems, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Giuseppe Maria Paternò
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Raffaele Rubattino 81, 20134 Milano, Italy
- Department of Physics, Politecnico di Milano, Piazza Leonardo Da Vinci, 32, 20133 Milan, Italy
| | - Lorena Redondo Morata
- Aix-Marseille University, INSERM, DyNaMo, Turing Centre for Living Systems, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Francesca Vacca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Sara Mattiello
- Department of Material Science, Bicocca University, Via Roberto Cozzi 55, 20126 Milano, Italy
| | - Arianna Magni
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Raffaele Rubattino 81, 20134 Milano, Italy
- Department of Physics, Politecnico di Milano, Piazza Leonardo Da Vinci, 32, 20133 Milan, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Luca Beverina
- Department of Material Science, Bicocca University, Via Roberto Cozzi 55, 20126 Milano, Italy
| | - Giuseppe Mattioli
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche (CNR-ISM), Via Salaria km 29.300, 00015 Monterotondo (RM), Italy
| | - Guglielmo Lanzani
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Raffaele Rubattino 81, 20134 Milano, Italy
- Department of Physics, Politecnico di Milano, Piazza Leonardo Da Vinci, 32, 20133 Milan, Italy
| | - Pietro Baldelli
- Department of Experimental Medicine, University of Genova, Viale Benedetto XV 3, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Elisabetta Colombo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
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Vaiwala R, Ayappa KG. Martini-3 Coarse-Grained Models for the Bacterial Lipopolysaccharide Outer Membrane of Escherichia coli. J Chem Theory Comput 2024; 20:1704-1716. [PMID: 37676287 DOI: 10.1021/acs.jctc.3c00471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
The outer lipopolysaccharide (LPS) membrane of Gram-negative bacteria forms the main barrier for transport of antimicrobial molecules into the bacterial cell. In this study we develop coarse-grained models for the outer membrane of Escherichia coli in the Martini-3 framework. The coarse-grained model force field was parametrized and validated using all-atom simulations of symmetric membranes of lipid A and rough LPS as well as a complete asymmetric membrane of LPS with the O-antigen. The bonded parameters were obtained using an iterative refinement procedure with target bonded distributions obtained from all-atom simulations. The membrane thickness, area of the LPS, and density distributions for the different regions as well as the water and ion densities in Martini-3 simulations show excellent agreement with the all-atom data. Additionally the solvent accessible surface area for individual molecules in water was found to be in good agreement. The binding of calcium ions with phosphate and carboxylate moieties of LPS is accurately captured in the Martini-3 model, indicative of the integrity of the highly negatively charged LPS molecules in the outer membranes of Gram-negative bacteria. The melting transition of the coarse-grained lipid A membrane model was found to occur between 300 and 310 K, and the model captured variations in area per LPS, order parameter, and membrane thickness across the melting transition. Our study reveals that the proposed Martini-3 models for LPS are able to capture the physicochemical balance of the complex sugar architecture of the outer membrane of Escherichia coli. The coarse-grained models developed in this study would be useful for determining membrane protein interactions and permeation of potential antimicrobials through bacterial membranes at mesoscopic spatial and temporal scales.
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Affiliation(s)
- Rakesh Vaiwala
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
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Brown T, Chavent M, Im W. Molecular Modeling and Simulation of the Mycobacterial Cell Envelope: From Individual Components to Cell Envelope Assemblies. J Phys Chem B 2023; 127:10941-10949. [PMID: 38091517 PMCID: PMC10758119 DOI: 10.1021/acs.jpcb.3c06136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023]
Abstract
Unlike typical Gram-positive bacteria, the cell envelope of mycobacteria is unique and composed of a mycobacterial outer membrane, also known as the mycomembrane, a peptidoglycan layer, and a mycobacterial inner membrane, which is analogous to that of Gram-negative bacteria. Despite its importance, however, our understanding of this complex cell envelope is rudimentary at best. Thus, molecular modeling and simulation of such an envelope can benefit the scientific community by proposing new hypotheses about the biophysical properties of its different layers. In this Perspective, we present recent advances in molecular modeling and simulation of the mycobacterial cell envelope from individual components to cell envelope assemblies. We also show how modeling other types of cell envelopes, such as that of Escherichia coli, may help modeling part of the mycobacterial envelopes. We hope that the studies presented here are just the beginning of the road and more and more new modeling and simulation studies help us to understand crucial questions related to mycobacteria such as antibiotic resistance or bacterial survival in the host.
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Affiliation(s)
- Turner Brown
- Department
of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Matthieu Chavent
- Institut
de Pharmacologie et Biologie Structurale, CNRS, Université
de Toulouse, 205 Route de Narbonne, 31400 Toulouse, France
| | - Wonpil Im
- Department
of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
- Departments
of Biological Sciences and Chemistry, Lehigh
University, Bethlehem, Pennsylvania 18015, United States
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