1
|
Sedano LF, Blazquez S, Vega C. Accuracy limit of non-polarizable four-point water models: TIP4P/2005 vs OPC. Should water models reproduce the experimental dielectric constant? J Chem Phys 2024; 161:044505. [PMID: 39046346 DOI: 10.1063/5.0211871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/30/2024] [Indexed: 07/25/2024] Open
Abstract
The last generation of four center non-polarizable models of water can be divided into two groups: those reproducing the dielectric constant of water, as OPC, and those significantly underestimating its value, as TIP4P/2005. To evaluate the global performance of OPC and TIP4P/2005, we shall follow the test proposed by Vega and Abascal in 2011 evaluating about 40 properties to fairly address this comparison. The liquid-vapor and liquid-solid equilibria are computed, as well as the heat capacities, isothermal compressibilities, surface tensions, densities of different ice polymorphs, the density maximum, equations of state at high pressures, and transport properties. General aspects of the phase diagram are considered by comparing the ratios of different temperatures (namely, the temperature of maximum density, the melting temperature of hexagonal ice, and the critical temperature). The final scores are 7.2 for TIP4P/2005 and 6.3 for OPC. The results of this work strongly suggest that we have reached the limit of what can be achieved with non-polarizable models of water and that the attempt to reproduce the experimental dielectric constant deteriorates the global performance of the water force field. The reason is that the dielectric constant depends on two surfaces (potential energy and dipole moment surfaces), whereas in the absence of an electric field, all properties can be determined simply from just one surface (the potential energy surface). The consequences of the choice of the water model in the modeling of electrolytes in water are also discussed.
Collapse
Affiliation(s)
- L F Sedano
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - S Blazquez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - C Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| |
Collapse
|
2
|
Ingram S, Reischl B, Vesala T, Vehkamäki H. Ruptures of mixed lipid monolayers under tension and supercooling: implications for nanobubbles in plants. NANOSCALE ADVANCES 2024; 6:3775-3784. [PMID: 39050947 PMCID: PMC11265596 DOI: 10.1039/d4na00316k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/10/2024] [Indexed: 07/27/2024]
Abstract
Mixed phospholipid and glycolipid monolayers likely coat the surfaces of pressurised gas nanobubbles within the hydraulic systems of plants. The lipid coatings bond to water under negative pressure and are thus stretched out of equilibrium. In this work, we have used molecular dynamics simulations to produce trajectories of a biologically relevant mixed monolayer, pulled at mild negative pressures (-1.5 to -4.5 MPa). Pore formation within the monolayer is observed at both 270 and 310 K, and proceeds as an activated process once the lipid tails fully transition from the two dimensional liquid condensed to liquid expanded phase. Pressure:area isotherms showed reduced surface pressure under slight supercooling (T = 270 K) at all observed areas per lipid. Finally, Rayleigh-Plesset simulations were used to predict evolving nanobubble size using the calculated pressure:area isotherms as dynamic surface tensions. We confirm the existence of a second critical radius with respect to runaway growth, above the homogeneous cavitation radius.
Collapse
Affiliation(s)
- Stephen Ingram
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki P.O. Box 64 Helsinki FI-00014 Finland
| | - Bernhard Reischl
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki P.O. Box 64 Helsinki FI-00014 Finland
| | - Timo Vesala
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki P.O. Box 64 Helsinki FI-00014 Finland
- Institute for Atmospheric and Earth System Research/Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki P.O. Box 27 Helsinki FI-00014 Finland
| | - Hanna Vehkamäki
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki P.O. Box 64 Helsinki FI-00014 Finland
| |
Collapse
|
3
|
Chen X, Al-Mualem ZA, Baiz CR. Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity. Annu Rev Phys Chem 2024; 75:283-305. [PMID: 38382566 DOI: 10.1146/annurev-physchem-090722-010230] [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: 02/23/2024]
Abstract
Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation spectroscopy, and two-dimensional infrared spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale molecular dynamics (MD) simulations, focusing on recently developed simulation algorithms, which have emerged as a powerful approach to interpret complex spectra. We highlight the ongoing challenges in studying heterogeneous environments in multicomponent membranes via current vibrational spectroscopic techniques and MD simulations. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations, which has great potential to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes.
Collapse
Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA;
| | | | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA;
| |
Collapse
|
4
|
Antila HS, Dixit S, Kav B, Madsen JJ, Miettinen MS, Ollila OHS. Evaluating Polarizable Biomembrane Simulations against Experiments. J Chem Theory Comput 2024; 20:4325-4337. [PMID: 38718349 PMCID: PMC11137822 DOI: 10.1021/acs.jctc.3c01333] [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: 12/06/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/29/2024]
Abstract
Owing to the increase of available computational capabilities and the potential for providing a more accurate description, polarizable molecular dynamics force fields are gaining popularity in modeling biomolecular systems. It is, however, crucial to evaluate how much precision is truly gained with increasing cost and complexity of the simulation. Here, we leverage the NMRlipids open collaboration and Databank to assess the performance of available polarizable lipid models─the CHARMM-Drude and the AMOEBA-based parameters─against high-fidelity experimental data and compare them to the top-performing nonpolarizable models. While some improvement in the description of ion binding to membranes is observed in the most recent CHARMM-Drude parameters, and the conformational dynamics of AMOEBA-based parameters are excellent, the best nonpolarizable models tend to outperform their polarizable counterparts for each property we explored. The identified shortcomings range from inaccuracies in describing the conformational space of lipids to excessively slow conformational dynamics. Our results provide valuable insights for the further refinement of polarizable lipid force fields and for selecting the best simulation parameters for specific applications.
Collapse
Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Department
of Biomedicine, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Sneha Dixit
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
| | - Batuhan Kav
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jïulich 52428, Germany
| | - Jesper J. Madsen
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Center
for Global Health and Infectious Diseases Research, Global and Planetary
Health, College of Public Health, University
of South Florida, Tampa, Florida 33612, United States of America
| | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
- Department
of Chemistry, University of Bergen, Bergen 5007, Norway
| | - O. H. Samuli Ollila
- VTT Technical
Research Centre of Finland, Espoo 02044, Finland
- Institute
of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
5
|
Cruces Chamorro V, Jungwirth P, Martinez-Seara H. Building Water Models Compatible with Charge Scaling Molecular Dynamics. J Phys Chem Lett 2024; 15:2922-2928. [PMID: 38451169 PMCID: PMC10945568 DOI: 10.1021/acs.jpclett.4c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Charge scaling has proven to be an efficient way to account in a mean-field manner for electronic polarization by aqueous ions in force field molecular dynamics simulations. However, commonly used water models with dielectric constants over 50 are not consistent with this approach leading to "overscaling", i.e., generally too weak ion-ion interactions. Here, we build water models fully compatible with charge scaling, i.e., having the correct low-frequency dielectric constant of about 45. To this end, we employ advanced optimization and machine learning schemes in order to explore the vast parameter space of four-site water models efficiently. As an a priori unwarranted positive result, we find a sizable range of force field parameters that satisfy the above dielectric constant constraint providing at the same time accuracy with respect to experimental data comparable with the best existing four-site water models such as TIP4P/2005, TIP4P-FB, or OPC. The present results thus open the way to the development of a consistent charge scaling force field for modeling ions in aqueous solutions.
Collapse
Affiliation(s)
- Victor Cruces Chamorro
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and
Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| |
Collapse
|
6
|
Nencini R, Regnier MLG, Backlund SM, Mantzari E, Dunn CD, Ollila OHS. Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations. Commun Chem 2024; 7:28. [PMID: 38351219 PMCID: PMC10864328 DOI: 10.1038/s42004-024-01115-4] [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: 08/24/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not straightforward. Here we show that the dynamic landscape of peptide-containing molecular assemblies can be determined by a synergistic combination of solution state NMR experiments and molecular dynamics (MD) simulations. Solution state NMR experiments are straightforward to implement without an excessive amount of sample, while direct combination of spin relaxation data to MD simulations enables interpretation of dynamic landscapes of peptides and other aggregated molecules. To demonstrate this, we interpret NMR data from transmembrane, peripheral, and tail anchored peptides embedded in micelles. Our results indicate that peptides and detergent molecules do not rotate together as a rigid body, but peptides rotate in a viscous medium composed of detergent micelle. Spin relaxation times also provide indirect information on peptide conformational ensembles. This work gives new perspectives on peptide dynamics in complex biomolecular assemblies.
Collapse
Affiliation(s)
- Ricky Nencini
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Cory D Dunn
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- VTT Technical Research Centre of Finland, Espoo, Finland.
| |
Collapse
|
7
|
Martin A, Tempra C, Yu Y, Liekkinen J, Thakker R, Lee H, de Santos Moreno B, Vattulainen I, Rossios C, Javanainen M, Bernardino de la Serna J. Exposure to Aldehyde Cherry e-Liquid Flavoring and Its Vaping Byproduct Disrupt Pulmonary Surfactant Biophysical Function. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1495-1508. [PMID: 38186267 PMCID: PMC10809783 DOI: 10.1021/acs.est.3c07874] [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: 09/26/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Over the past decade, there has been a significant rise in the use of vaping devices, particularly among adolescents, raising concerns for effects on respiratory health. Pressingly, many recent vaping-related lung injuries are unexplained by current knowledge, and the overall implications of vaping for respiratory health are poorly understood. This study investigates the effect of hydrophobic vaping liquid chemicals on the pulmonary surfactant biophysical function. We focus on the commonly used flavoring benzaldehyde and its vaping byproduct, benzaldehyde propylene glycol acetal. The study involves rigorous testing of the surfactant biophysical function in Langmuir trough and constrained sessile drop surfactometer experiments with both protein-free synthetic surfactant and hydrophobic protein-containing clinical surfactant models. The study reveals that exposure to these vaping chemicals significantly interferes with the synthetic and clinical surfactant biophysical function. Further atomistic simulations reveal preferential interactions with SP-B and SP-C surfactant proteins. Additionally, data show surfactant lipid-vaping chemical interactions and suggest significant transfer of vaping chemicals to the experimental subphase, indicating a toxicological mechanism for the alveolar epithelium. Our study, therefore, reveals novel mechanisms for the inhalational toxicity of vaping. This highlights the need to reassess the safety of vaping liquids for respiratory health, particularly the use of aldehyde chemicals as vaping flavorings.
Collapse
Affiliation(s)
- Alexia Martin
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Carmelo Tempra
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6 160 00, Czech Republic
| | - Yuefan Yu
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Juho Liekkinen
- Department
of Physics, University of Helsinki, Helsinki 00560, Finland
| | - Roma Thakker
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Hayoung Lee
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Berta de Santos Moreno
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Ilpo Vattulainen
- Department
of Physics, University of Helsinki, Helsinki 00560, Finland
| | - Christos Rossios
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| | - Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6 160 00, Czech Republic
- Institute
of Biotechnology, University of Helsinki, Helsinki 00790, Finland
| | - Jorge Bernardino de la Serna
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
| |
Collapse
|
8
|
Perrone M, Capelli R, Empereur-mot C, Hassanali A, Pavan GM. Lessons Learned from Multiobjective Automatic Optimizations of Classical Three-Site Rigid Water Models Using Microscopic and Macroscopic Target Experimental Observables. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2023; 68:3228-3241. [PMID: 38115916 PMCID: PMC10726314 DOI: 10.1021/acs.jced.3c00538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
The development of accurate water models is of primary importance for molecular simulations. Despite their intrinsic approximations, three-site rigid water models are still ubiquitously used to simulate a variety of molecular systems. Automatic optimization approaches have been recently used to iteratively refine three-site water models to fit macroscopic (average) thermodynamic properties, providing state-of-the-art three-site models that still present some deviations from the liquid water properties. Here, we show the results obtained by automatically optimizing three-site rigid water models to fit a combination of microscopic and macroscopic experimental observables. We use Swarm-CG, a multiobjective particle-swarm-optimization algorithm, for training the models to reproduce the experimental radial distribution functions of liquid water at various temperatures (rich in microscopic-level information on, e.g., the local orientation and interactions of the water molecules). We systematically analyze the agreement of these models with experimental observables and the effect of adding macroscopic information to the training set. Our results demonstrate how adding microscopic-rich information in the training of water models allows one to achieve state-of-the-art accuracy in an efficient way. Limitations in the approach and in the approximated description of water in these three-site models are also discussed, providing a demonstrative case useful for the optimization of approximated molecular models, in general.
Collapse
Affiliation(s)
- Mattia Perrone
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, Torino I-10129, Italy
| | - Riccardo Capelli
- Department
of Biosciences, Università degli
Studi di Milano, Via Celoria 26, Milano I-20133, Italy
| | - Charly Empereur-mot
- Department
of Innovative Technologies, University of Applied Sciences and Arts
of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, Lugano-Viganello CH-6962, Switzerland
| | - Ali Hassanali
- The
Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - Giovanni M. Pavan
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, Torino I-10129, Italy
- Department
of Innovative Technologies, University of Applied Sciences and Arts
of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, Lugano-Viganello CH-6962, Switzerland
| |
Collapse
|
9
|
Sharma T, Erimban S, Azad R, Nam Y, Raj R, Daschakraborty S. Investigating the Vapor-Phase Adsorption of Aroma Molecules on the Water-Vapor Interface using Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 38032075 DOI: 10.1021/acs.langmuir.3c02531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Surfactants are amphiphilic additives primarily used to reduce the surface tension of water and manipulate its wettability on various surfaces. Recent reports suggest that volatile surfactants, such as aroma molecules, diffuse more quickly to the interface from the vapor-phase than conventional surfactants typically used in the aqueous phase. The ability to adsorb from the vapor phase, in addition to their use as cosurfactants, expands the potential applications of volatile surfactants, particularly in situations where adding surfactants from the liquid phase is difficult. Here, we present a molecular level understanding of the adsorption kinetics of linalool, a common aroma molecule, on the water interface using molecular dynamics simulations. We note that the value of surface tension while adsorption from vapor and liquid phases is dependent only on the surface coverage. A minimum surface tension of 32 ± 1.8 mN/m is obtained in both cases at a maximum surface coverage of 4.88 μmol/m2 at 300 K. We observe the extent of decrease of the H-bonds between linalool-water and linalool-linalool molecules at various surface coverages to explain the mechanism of surface tension reduction. We solve Gibb's adsorption equation to establish a correlation between the surface coverage of linalool and the corresponding bulk concentration in experiments. We investigate the free energy profile of linalool's adsorption behavior at different surface coverages and temperatures. Our report suggests that linalool adsorption onto the water interface is an enthalpy-driven process primarily dependent on the strength of the interaction between the hydroxyl group of linalool and water molecules. These insights are crucial for selecting a suitable aroma molecule for various applications that target the vapor-phase adsorption mechanism.
Collapse
Affiliation(s)
- Tonmoy Sharma
- Thermal and Fluid Transport Laboratory, Department of Mechanical Engineering, Indian Institute of Technology, Patna, Bihar 801106, India
| | - Shakkira Erimban
- Department of Chemistry, Indian Institute of Technology, Patna, Bihar 801106, India
| | - Rajnish Azad
- Thermal and Fluid Transport Laboratory, Department of Mechanical Engineering, Indian Institute of Technology, Patna, Bihar 801106, India
| | - Youngsuk Nam
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Rishi Raj
- Thermal and Fluid Transport Laboratory, Department of Mechanical Engineering, Indian Institute of Technology, Patna, Bihar 801106, India
| | | |
Collapse
|
10
|
Grava M, Ibrahim M, Sudarsan A, Pusterla J, Philipp J, Rädler JO, Schwierz N, Schneck E. Combining molecular dynamics simulations and x-ray scattering techniques for the accurate treatment of protonation degree and packing of ionizable lipids in monolayers. J Chem Phys 2023; 159:154706. [PMID: 37861119 DOI: 10.1063/5.0172552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
The pH-dependent change in protonation of ionizable lipids is crucial for the success of lipid-based nanoparticles as mRNA delivery systems. Despite their widespread application in vaccines, the structural changes upon acidification are not well understood. Molecular dynamics simulations support structure prediction but require an a priori knowledge of the lipid packing and protonation degree. The presetting of the protonation degree is a challenging task in the case of ionizable lipids since it depends on pH and on the local lipid environment and often lacks experimental validation. Here, we introduce a methodology of combining all-atom molecular dynamics simulations with experimental total-reflection x-ray fluorescence and scattering measurements for the ionizable lipid Dlin-MC3-DMA (MC3) in POPC monolayers. This joint approach allows us to simultaneously determine the lipid packing and the protonation degree of MC3. The consistent parameterization is expected to be useful for further predictive modeling of the action of MC3-based lipid nanoparticles.
Collapse
Affiliation(s)
- Miriam Grava
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
| | - Mohd Ibrahim
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Akhil Sudarsan
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Julio Pusterla
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
| | - Julian Philipp
- Fakultät für Physik, Ludwig-Maximilians-Universität München (LMU), München, Germany
| | - Joachim O Rädler
- Fakultät für Physik, Ludwig-Maximilians-Universität München (LMU), München, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Augsburg, Germany
| | - Emanuel Schneck
- Institute for Condensed Matter Physics, TU Darmstadt, Hochschulstraße 8, 64289 Darmstadt, Germany
| |
Collapse
|
11
|
Prabhu J, Singh AP, Vanni S. An in silico osmotic pressure approach allows characterization of pressure-area isotherms of lipid monolayers at low molecular areas. SOFT MATTER 2023; 19:3377-3385. [PMID: 37102755 PMCID: PMC10170484 DOI: 10.1039/d2sm01419j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Surface pressure-area isotherms of lipid monolayers at the air-water interface provide essential information about the structure and mechanical behaviour of lipid membranes. These curves can be readily obtained through Langmuir trough measurements and, as such, have been collected for decades in the field of membrane biochemistry. However, it is still challenging to directly observe and understand nanoscopic features of monolayers through such experiments, and molecular dynamics (MD) simulations are generally used to provide a molecular view of such interfaces. In MD simulations, the surface pressure-area (Π-A) isotherms are generally computed using the Kirkwood-Irving formula, that relies on the evaluation of the pressure tensor. This approach, however, has intrinsic limitations when the molecular area in the monolayer is low (typically < 60 Å2 per lipid). Recently, an alternative method to compute Π-A isotherms of surfactants, based on the calculation of the three-dimensional osmotic pressure via the implementation of semipermeable barriers was proposed. In this work, we investigate the feasibility of this approach for long-chain surfactants such as phospholipids. We identify some discrepancies between the computed values and experimental results, and we propose a semi-empirical correction based on the molecular structure of the surfactants at the monolayer interface. To validate the potential of this new approach, we simulate several phosphatidylcholine and phosphatidylethanolamine lipids at various temperatures using all-atom and coarse-grained force fields, and we compute the corresponding Π-A isotherms. Our results show that the Π-A isotherms obtained using the new method are in very good agreement with experiments and far superior to the canonical pressure tensor-based method at low molecular areas. This corrected osmotic pressure method allows for accurate characterization of the molecular packing in monolayers in various physical phases.
Collapse
Affiliation(s)
- Janak Prabhu
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Akhil Pratap Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| |
Collapse
|
12
|
Liekkinen J, Olżyńska A, Cwiklik L, Bernardino de la Serna J, Vattulainen I, Javanainen M. Surfactant Proteins SP-B and SP-C in Pulmonary Surfactant Monolayers: Physical Properties Controlled by Specific Protein-Lipid Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4338-4350. [PMID: 36917773 PMCID: PMC10061932 DOI: 10.1021/acs.langmuir.2c03349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The lining of the alveoli is covered by pulmonary surfactant, a complex mixture of surface-active lipids and proteins that enables efficient gas exchange between inhaled air and the circulation. Despite decades of advancements in the study of the pulmonary surfactant, the molecular scale behavior of the surfactant and the inherent role of the number of different lipids and proteins in surfactant behavior are not fully understood. The most important proteins in this complex system are the surfactant proteins SP-B and SP-C. Given this, in this work we performed nonequilibrium all-atom molecular dynamics simulations to study the interplay of SP-B and SP-C with multicomponent lipid monolayers mimicking the pulmonary surfactant in composition. The simulations were complemented by z-scan fluorescence correlation spectroscopy and atomic force microscopy measurements. Our state-of-the-art simulation model reproduces experimental pressure-area isotherms and lateral diffusion coefficients. In agreement with previous research, the inclusion of either SP-B and SP-C increases surface pressure, and our simulations provide a molecular scale explanation for this effect: The proteins display preferential lipid interactions with phosphatidylglycerol, they reside predominantly in the lipid acyl chain region, and they partition into the liquid expanded phase or even induce it in an otherwise packed monolayer. The latter effect is also visible in our atomic force microscopy images. The research done contributes to a better understanding of the roles of specific lipids and proteins in surfactant function, thus helping to develop better synthetic products for surfactant replacement therapy used in the treatment of many fatal lung-related injuries and diseases.
Collapse
Affiliation(s)
- Juho Liekkinen
- Department
of Physics, University of Helsinki, FI-00560 Helsinki, Finland
| | - Agnieszka Olżyńska
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, CZ-18223 Prague, Czech Republic
| | - Lukasz Cwiklik
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, CZ-18223 Prague, Czech Republic
| | - Jorge Bernardino de la Serna
- National
Heart and Lung Institute, Imperial College
London, Sir Alexander Fleming Building, London SW7 2AZ, U.K.
- NIHR
Imperial Biomedical Research Centre, London SW7 2AZ, U.K.
| | - Ilpo Vattulainen
- Department
of Physics, University of Helsinki, FI-00560 Helsinki, Finland
| | - Matti Javanainen
- Institute
of Biotechnology, University of Helsinki, FI-00790 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, CZ-16100 Prague 6, Czech Republic
| |
Collapse
|
13
|
Towards predicting shear-banding instabilities in lipid monolayers. J Mech Behav Biomed Mater 2023; 141:105743. [PMID: 36893685 DOI: 10.1016/j.jmbbm.2023.105743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/16/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023]
Abstract
Langmuir monolayers are advantageous systems used to investigate how lipid membranes get involved in the physiology of many living structures, such as collapse phenomena in alveolar structures. Much work focuses on characterizing the pressure-bearing capacity of Langmuir films, expressed in the form of isotherm curves. These show that monolayers experience different phases during compression with an according evolution of their mechanical response, incurring into instability events when a critical stress threshold is overcome. Although well-known state equations, which establish an inverse relationship between surface pressure and area change, are able to properly describe monolayer behaviour during liquid expanded phase, the modelling of their nonlinear behaviour in the subsequent condensed region is still an open issue. In this regard, most efforts are addressed to explain out-of-plane collapse by modelling buckling and wrinkling mainly resorting to linearly elastic plate theory. However, some experiments on Langmuir monolayers also show in-plane instability phenomena leading to the formation of the so-called shear bands and, to date, no theoretical description of the onset of shear banding bifurcation in monolayers has been yet provided. For this reason, by adopting a macroscopic description, we here study material stability of the lipid monolayers and exploit an incremental approach to find the conditions that kindle shear bands. In particular, by starting from the widely assumed hypothesis that monolayers behave elastically in the solid-like region, in this work a hyperfoam hyperelastic potential is introduced as a new constitutive strategy to trace back the nonlinear response of monolayer response during densification. In this way, the obtained mechanical properties together with the adopted strain energy are successfully employed to reproduce the onset of shear banding exhibited by some lipid systems under different chemical and thermal conditions.
Collapse
|
14
|
Costa RKM, Souza LMP, Silva RS, Souza FR, Pimentel AS. The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question. J Biomol Struct Dyn 2023; 41:11510-11517. [PMID: 36715129 DOI: 10.1080/07391102.2023.2173298] [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: 11/09/2022] [Accepted: 12/26/2022] [Indexed: 01/31/2023]
Abstract
The octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was investigated using atomistic molecular dynamics simulations via thermodynamic integration and multistate Bennett acceptance ratio methods. The GAFF and CHARMM36 force fields were used with six water models widely used in molecular dynamics simulations. The OPC4 water model provided the best agreement with the experimental octanol-water partition coefficient of DPPC using the two force fields. However, there is still plenty of room for improvement in water models with correct estimation of surface tension that uses better and suitable non-bonded interaction parameters between water-water and water-DPPC. The Gibbs free energy of transferring DPPC from octanol to water phase was calculated to be 19.8 ± 0.3 and 20.2 ± 0.3 kcal mol-1, giving a partition coefficient of 14.5 ± 0.4 and 14.8 ± 0.3 for the GAFF and CHARMM36 force fields, respectively. This study reinforces the importance of developing new water models that reproduce experimental surface tensions to reconcile the water-water and water-DPPC non-bonded interactions and the existing discrepancy between experimental measurements of amphiphilic molecules that are important in many areas of scientific applications and industry such as biophysics, surfactant, colloids, membranes, medicine, nanotechnology, and food and pharmaceutical industries, and so on. It raises two important open questions: Is the experimental octanol-water partition coefficient of DPPC reliable? Or is its calculation accurate using the OPC4 water model? With respect to the experimental measurements, there may be non-treated aspects such as the formation of aggregates in aqueous phase and limit of detection of the applied method. And, in the calculation, some effects are not possible to be considered in a correct way or viable time such as calculating quantum effects, sampling all conformations, considering phase transitions, and correctly evaluating the intermolecular forces to estimate an accurate surface tension.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | | | - Rudielson Santos Silva
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Felipe Rodrigues Souza
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - André Silva Pimentel
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
15
|
Modulation of Anionic Lipid Bilayers by Specific Interplay of Protons and Calcium Ions. Biomolecules 2022; 12:biom12121894. [PMID: 36551322 PMCID: PMC9775051 DOI: 10.3390/biom12121894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Biomembranes, important building blocks of living organisms, are often exposed to large local fluctuations of pH and ionic strength. To capture changes in the membrane organization under such harsh conditions, we investigated the mobility and hydration of zwitterionic and anionic lipid bilayers upon elevated H3O+ and Ca2+ content by the time-dependent fluorescence shift (TDFS) technique. While the zwitterionic bilayers remain inert to lower pH and increased calcium concentrations, anionic membranes are responsive. Specifically, both bilayers enriched in phosphatidylserine (PS) and phosphatidylglycerol (PG) become dehydrated and rigidified at pH 4.0 compared to at pH 7.0. However, their reaction to the gradual Ca2+ increase in the acidic environment differs. While the PG bilayers exhibit strong rehydration and mild loosening of the carbonyl region, restoring membrane properties to those observed at pH 7.0, the PS bilayers remain dehydrated with minor bilayer stiffening. Molecular dynamics (MD) simulations support the strong binding of H3O+ to both PS and PG. Compared to PS, PG exhibits a weaker binding of Ca2+ also at a low pH.
Collapse
|
16
|
Hao X, Li C, Liu C, Meng Q, Sun J. The performance of OPC water model in prediction of the phase equilibria of methane hydrate. J Chem Phys 2022; 157:014504. [DOI: 10.1063/5.0093659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics (MD) simulations were performed to determine the three-phase coexistence line of sI methane hydrates. The MD simulations were carried out at four different pressures (4, 10, 40 and 100 MPa) by using direct phase coexistence method. In current simulations, water was described by either TIP4P/Ice or OPC models and methane was described as a simple Lennard-Jones (LJ) interaction site. Lorentz-Berthelot combining rules were used to calculate the parameters of the cross interactions. For OPC model, positive deviations from the energetic Lorentz-Berthelot rule were also considered based on the solubility of methane in water. For TIP4P/Ice water model, the obtained three phase coexistence temperatures showed good agreement with experiment data at higher pressures, which is consistent with previous predictions. For OPC water model, simulations using the classic and the modified LB parameters both showed negative deviations to the experimental values. Our results also indicated that the deviation of the T3 prediction by OPC model not much correlated with the predicted melting point of ice. At 4 MPa, the modified OPC model showed outstanding prediction of hydrate equilibrium temperature, even better than the prediction by TIP4P/Ice. The relative higher accuracy in biomolecular MD of OPC model suggests that this model may have a better performance in hydrate MD simulations of biomolecule-based additives.
Collapse
Affiliation(s)
- Xiluo Hao
- Qingdao Institute of Marine Geology, China
| | | | | | | | - Jianye Sun
- Qingdao Institute of Marine Geology, China
| |
Collapse
|
17
|
Antila HS, Kav B, Miettinen MS, Martinez-Seara H, Jungwirth P, Ollila OHS. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J Phys Chem B 2022. [DOI: 10.1021/acs.jpcb.2c01954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne S. Antila
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum
Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Markus S. Miettinen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Biotechonology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|