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Gligonov IA, Bagaeva DI, Demina GR, Vostroknutova GN, Vorozhtsov DS, Kaprelyants AS, Savitsky AP, Shleeva MO. The accumulation of methylated porphyrins in dormant cells of Mycolicibacterium smegmatis is accompanied by a decrease in membrane fluidity and an impede of the functioning of the respiratory chain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184270. [PMID: 38211647 DOI: 10.1016/j.bbamem.2024.184270] [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: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
Transition of Mycolicibacterium smegmatis (Msm) and Mycobacterium tuberculosis to dormancy in vitro is accompanied by an accumulation of free methylated forms of porphyrins (tetramethyl coproporphyrin - TMC) localized in the cell wall of dormant bacteria. A study of the fluorescence anisotropy of BODIPY based fluorescent probes on individual cell level using confocal microscope revealed significant changes in this parameter for BODIPY FL C16 from 0.05 to 0.22 for vegetative and dormant Msm cells correspondingly. Similarly, the increase of TMC concentration in vegetative Msm cells grown in the presence of 5-aminolevulinic acid (a known inducer of porphyrin synthesis) resulted in an increase of BODIPY FL C16 anisotropy. These changes in TMC concentration and membrane fluidity were accompanied by an inhibition of the activity of the respiratory chain measured by oxygen consumption and a reduction of the DCPIP redox acceptor. During the first 8 h of the reactivation of the dormant Msm cells, the porphyrin content and probe fluorescent anisotropy returned to the level for vegetative bacteria. We suggested that upon transition to dormancy, an accumulation of TMC in membranes leads to a decrease in membrane fluidity, resulting in an inhibition of the respiratory chain activity. However, direct interactions of TMC with membrane bound enzymes cannot also be excluded. This, in turn, may result in the down regulation of many metabolic energy-dependent reactions as a part of mechanisms accompanying the transition to a hypometabolic state of mycobacteria.
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Affiliation(s)
- Ivan A Gligonov
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daria I Bagaeva
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Galina R Demina
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Galina N Vostroknutova
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Dmitriy S Vorozhtsov
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Arseny S Kaprelyants
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexander P Savitsky
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Margarita O Shleeva
- A.N. Bach Institute of Biochemistry, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow 119071, Russia.
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Islam MZ, Hossain SI, Deplazes E, Luo Z, Saha SC. The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach. RSC Adv 2022; 12:33313-33328. [PMID: 36506480 PMCID: PMC9680622 DOI: 10.1039/d2ra05268g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022] Open
Abstract
Understanding the adsorption mechanism of corticosteroids in the lung surfactant requires the knowledge of corticosteroid molecular interactions with lung surfactant monolayer (LSM). We employed coarse-grained molecular dynamics simulation to explore the action of hydrocortisone on an LSM comprised of a phospholipid, cholesterol and surfactant protein. The structural and dynamical morphology of the lung surfactant monolayer at different surface tensions were investigated to assess the monolayer compressibility. The simulations were also conducted at the two extreme ends of breathing cycles: exhalation (0 mN m-1 surface tension) and inhalation (20 mN m-1 surface tension). The impact of surface tension and hydrocortisone concentration on the monolayer compressibility and stability are significant, resulting the monolayer expansion at higher surface tension. However, at low surface tension, the highly compressed monolayer induces monolayer instability in the presence of the drug due to the accumulation of surfactant protein and drug. The constant area per lipid simulation results demonstrate that the surface pressure-area isotherms show a decrease in area-per-lipid with increased drug concentration. The drug-induced expansion causes considerable instability in the monolayer after a specific drug concentration is attained at inhalation breathing condition, whereas, for exhalation breathing, the monolayer gets more compressed, causing the LSM to collapse. The monolayer collapse occurs for inhalation due to the higher drug concentration, whereas for exhalation due to the accumulation of surfactant proteins and drugs. The findings from this study will aid in enhancing the knowledge of molecular interactions of corticosteroid drugs with lung surfactants to treat respiratory diseases.
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Affiliation(s)
- Mohammad Zohurul Islam
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney15 BroadwayUltimo 2007NSWAustralia
| | - Sheikh I. Hossain
- School of Life Sciences, University of Technology Sydney15 BroadwayUltimo 2007NSWAustralia
| | - E. Deplazes
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney15 BroadwayUltimo 2007NSWAustralia,School of Life Sciences, University of Technology Sydney15 BroadwayUltimo 2007NSWAustralia
| | - Zhen Luo
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney15 BroadwayUltimo 2007NSWAustralia
| | - Suvash C. Saha
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney15 BroadwayUltimo 2007NSWAustralia
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The lung surfactant activity probed with molecular dynamics simulations. Adv Colloid Interface Sci 2022; 304:102659. [PMID: 35421637 DOI: 10.1016/j.cis.2022.102659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 01/17/2023]
Abstract
The surface of pulmonary alveolar subphase is covered with a mixture of lipids and proteins. This lung surfactant plays a crucial role in lung functioning. It shows a complex phase behavior which can be altered by the interaction with third molecules such as drugs or pollutants. For studying multicomponent biological systems, it is of interest to couple experimental approach with computational modelling yielding atomic-scale information. Simple two, three, or four-component model systems showed to be useful for getting more insight in the interaction between lipids, lipids and proteins or lipids and proteins with drugs and impurities. These systems were studied theoretically using molecular dynamic simulations and experimentally by means of the Langmuir technique. A better understanding of the structure and behavior of lung surfactants obtained from this research is relevant for developing new synthetic surfactants for efficient therapies, and may contribute to public health protection.
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Hossain SI, Islam MZ, Saha SC, Deplazes E. Drug Meets Monolayer: Understanding the Interactions of Sterol Drugs with Models of the Lung Surfactant Monolayer Using Molecular Dynamics Simulations. Methods Mol Biol 2022; 2402:103-121. [PMID: 34854039 DOI: 10.1007/978-1-0716-1843-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The lung surfactant monolayer (LSM) is a thin layer of lipids and proteins that forms the air/water interface of the alveoli. The primary function of the LSM is to reduce the surface tension at the air/water interface during breathing. The LSM also forms the main biological barrier for any inhaled particles, including drugs, to treat lung diseases. Elucidating the mechanism by which these drugs bind to and absorb into the LSM requires a molecular-level understanding of any drug-induced changes to the morphology, structure, and phase changes of the LSM.Molecular dynamics simulations have been used extensively to study the structure and dynamics of the LSM. The monolayer is usually simulated in at least two states: the compressed state, mimicking exhalation, and the expanded state, mimicking inhalation. In this chapter, we provide detailed instructions on how to set up, run, and analyze coarse-grained MD simulations to study the concentration-dependent effect of a sterol drug on the LSM, both in the expanded and compressed state.
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Affiliation(s)
- Sheikh I Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mohammad Z Islam
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW, Australia
- Department of Mathematics, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Suvash C Saha
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.
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Souza FR, Souza LMP, Pimentel AS. Recent Open Issues in Coarse Grained Force Fields. J Chem Inf Model 2020; 60:5881-5884. [PMID: 33231448 DOI: 10.1021/acs.jcim.0c01265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This viewpoint intends to show recent open issues of using coarse grained models in molecular dynamics simulation. It reviews the current knowledge of the comparison between experimental and simulation data of structural and physical chemical properties that depend on the hydrophilic and hydrophobic behavior of the molecule.
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Affiliation(s)
- Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
| | - Lucas Miguel Pereira Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
| | - Andre Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ 22453-900 Brazil
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Ludwig J, Maibaum L. Effect of alcohol on the phase separation in model membranes. Chem Phys Lipids 2020; 233:104986. [PMID: 33080278 DOI: 10.1016/j.chemphyslip.2020.104986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022]
Abstract
The discovery of coexisting liquid-ordered and liquid-disordered phases in multicomponent lipid bilayers has received widespread attention due to its potential relevance for biological systems. One of the many open questions is how the presence of additional components affects the nature of the coexisting phases. Of particular interest is the addition of alcohols because their anesthetic properties may arise from modulating bilayer behavior. We use coarse-grained Molecular Dynamics simulations to gain insight into the partitioning preferences of linear n-alcohols into ordered and disordered bilayers alongside their effects on local membrane structure. We find that alcohols cause only small changes to membrane composition alongside a lack of significant effects on membrane thickness and lipid tail order. Cholesterol and n-alcohol trans-bilayer motion is measured and found to be near or within the range of previous atomistic results. The cholesterol flip-flop rates increase with both n-alcohol length and concentration for octanol, dodecanol, and hexadecanol, indicating a decrease in lipid order. Umbrella sampling simulations of removing cholesterol from tertiary membranes find no significant difference with or without n-alcohols at various concentrations. Simulations of a phase-separated bilayer show that octanol preferentially partitions into the liquid-disordered phase in a ratio of approximately 3:1 over the liquid-ordered phase. Furthermore, partition coefficients of alcohol in single-phase membranes show a preference for longer alcohols (dodecanol and hexadecanol) to partition preferentially into the liquid-ordered phase, while decreasing the length of the alcohol reverses this trend. Our work tests experimental results while also investigating the ability for coarse-grained MARTINI simulations to capture minute differences in model membrane spatial arrangements on the nanoscale level.
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Affiliation(s)
- James Ludwig
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States.
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Javanainen M, Lamberg A, Cwiklik L, Vattulainen I, Ollila OHS. Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2565-2572. [PMID: 28945973 DOI: 10.1021/acs.langmuir.7b02855] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lung surfactant and a tear film lipid layer are examples of biologically relevant macromolecular structures found at the air-water interface. Because of their complexity, they are often studied in terms of simplified lipid layers, the simplest example being a Langmuir monolayer. Given the profound biological significance of these lipid assemblies, there is a need to understand their structure and dynamics on the nanoscale, yet there are not many techniques able to provide this information. Atomistic molecular dynamics simulations would be a tool fit for this purpose; however, the simulation models suggested until now have been qualitative instead of quantitative. This limitation has mainly stemmed from the challenge to correctly describe the surface tension of water with simulation parameters compatible with other biomolecules. In this work, we show that this limitation can be overcome by using the recently introduced four-point OPC water model, whose surface tension for water is demonstrated to be quantitatively consistent with experimental data and which is also shown to be compatible with the commonly employed lipid models. We further establish that the approach of combining the OPC four-point water model with the CHARMM36 lipid force field provides nearly quantitative agreement with experiments for the surface pressure-area isotherm for POPC and DPPC monolayers, also including the experimentally observed phase coexistence in a DPPC monolayer. The simulation models reported in this work pave the way for nearly quantitative atomistic studies of lipid-rich biological structures at air-water interfaces.
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Affiliation(s)
- Matti Javanainen
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
| | | | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , 182 23 Prague 8, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , 166 10 Prague 6, Czech Republic
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
- MEMPHYS - Center for Biomembrane Physics, www.memphys.dk
| | - O H Samuli Ollila
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , 166 10 Prague 6, Czech Republic
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Lovrić J, Duflot D, Monnerville M, Toubin C, Briquez S. Water-Induced Organization of Palmitic Acid at the Surface of a Model Sea Salt Particle: A Molecular Dynamics Study. J Phys Chem A 2016; 120:10141-10149. [DOI: 10.1021/acs.jpca.6b07792] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josip Lovrić
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Denis Duflot
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Maurice Monnerville
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Céline Toubin
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
| | - Stéphane Briquez
- Laboratoire de
Physique des Lasers, Atomes et Molécules (PhLAM) CNRS, UMR
8523, Univ. Lille, F-59000 Lille, France
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Miguel V, Perillo MA, Villarreal MA. Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2903-2910. [DOI: 10.1016/j.bbamem.2016.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/11/2016] [Accepted: 08/30/2016] [Indexed: 02/04/2023]
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Korchowiec B, Gorczyca M, Rogalska E, Regnouf-de-Vains JB, Mourer M, Korchowiec J. The selective interactions of cationic tetra-p-guanidinoethylcalix[4]arene with lipid membranes: theoretical and experimental model studies. SOFT MATTER 2016; 12:181-190. [PMID: 26451711 DOI: 10.1039/c5sm01891a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Behavior of cationic tetra-p-guanidinoethylcalix[4]arene (CX1) and its building block, p-guanidinoethylphenol (mCX1) in model monolayer lipid membranes was investigated using all atom molecular dynamics simulations and surface pressure measurements. Members of two classes of lipids were taken into account: zwitterionic 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and anionic 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine sodium salt (DMPS) as models of eukaryotic and bacterial cell membranes, respectively. It was demonstrated that CX1 and mCX1 accumulate near the negatively charged DMPS monolayers. The adsorption to neutral monolayers was negligible. In contrast to mCX1, CX1 penetrated into the hydrophobic part of the monolayer. The latter effect, which is possible due to a flip-flop inversion of the CX1 orientation in the lipid layer compared to the aqueous phase, may be responsible for its antibacterial activity.
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Affiliation(s)
- Beata Korchowiec
- Department of Physical Chemistry and Electrochemistry, Faculty of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland.
| | - Marcelina Gorczyca
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland.
| | - Ewa Rogalska
- Structure et Réactivité des Systèmes Moléculaires Complexes, BP 239, CNRS/Université de Lorraine, 54506 Vandoeuvre-lès-Nancy cedex, France
| | - Jean-Bernard Regnouf-de-Vains
- Structure et Réactivité des Systèmes Moléculaires Complexes, BP 239, CNRS/Université de Lorraine, 54506 Vandoeuvre-lès-Nancy cedex, France
| | - Maxime Mourer
- Structure et Réactivité des Systèmes Moléculaires Complexes, BP 239, CNRS/Université de Lorraine, 54506 Vandoeuvre-lès-Nancy cedex, France
| | - Jacek Korchowiec
- Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, ul. R. Ingardena 3, 30-060 Krakow, Poland.
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