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Vo ATN, Murphy MA, Phan PK, Prabhu RK, Stone TW. Effect of Force Field Resolution on Membrane Mechanical Response and Mechanoporation Damage under Deformation Simulations. Mol Biotechnol 2024; 66:865-875. [PMID: 37016179 DOI: 10.1007/s12033-023-00726-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/19/2023] [Indexed: 04/06/2023]
Abstract
Damage induced by transient disruption and mechanoporation in an intact cell membrane is a vital nanoscale biomechanical mechanism that critically affects cell viability. To complement experimental studies of mechanical membrane damage and disruption, molecular dynamics (MD) simulations have been performed at different force field resolutions, each of which follows different parameterization strategies and thus may influence the properties and dynamics of membrane systems. Therefore, the current study performed tensile deformation MD simulations of bilayer membranes using all-atom (AA), united-atom (UA), and coarse-grained Martini (CG-M) models to investigate how the damage biomechanics differs across atomistic and coarse-grained (CG) simulations. The mechanical response and mechanoporation damage were qualitatively similar but quantitatively different in the three models, including some progressive changes based on the coarse-graining level. The membranes yielded and reached ultimate strength at similar strains; however, the coarser systems exhibited lower average yield stresses and failure strains. The average failure strain in the UA model was approximately 7% lower than the AA, and the CG-M was 20% lower than UA and 27% lower than AA. The CG systems also nucleated a higher number of pores and larger pores, which resulted in higher damage during the deformation process. Overall, the study provides insight on the impact of force field-a critical factor in modeling biomolecular systems and their interactions-in inspecting membrane mechanosensitive responses and serves as a reference for justifying the appropriate force field for future studies of more complex membranes and more diverse biomolecular assemblies.
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Affiliation(s)
- Anh T N Vo
- Center for Advanced Vehicular Systems (CAVS), Mississippi State University, 200 Research Blvd, Starkville, MS, 39759, USA.
- Department of Agricultural and Biological Engineering, Mississippi State University, Mississippi State, Starkville, MS, 39762, USA.
| | - Michael A Murphy
- Center for Advanced Vehicular Systems (CAVS), Mississippi State University, 200 Research Blvd, Starkville, MS, 39759, USA
| | - Phong K Phan
- Center for Advanced Vehicular Systems (CAVS), Mississippi State University, 200 Research Blvd, Starkville, MS, 39759, USA
- Department of Agricultural and Biological Engineering, Mississippi State University, Mississippi State, Starkville, MS, 39762, USA
| | - Raj K Prabhu
- NASA Johnson Space Center, 2101 NASA Parkway, Houston, TX, 77058, USA
| | - Tonya W Stone
- Center for Advanced Vehicular Systems (CAVS), Mississippi State University, 200 Research Blvd, Starkville, MS, 39759, USA
- Department of Mechanical Engineering, Mississippi State University, Mississippi State, Starkville, MS, 39762, USA
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Abdel-Gawad WM, Abdelmohsen M, Gaber MH, Khalil WMA, Abu-Elmagd MSM. Molecular dynamics simulation of phosphatidylcholine membrane in low ionic strengths of sodium chloride. J Biomol Struct Dyn 2023; 41:13891-13901. [PMID: 36812302 DOI: 10.1080/07391102.2023.2183040] [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: 08/16/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
The one-microsecond molecular dynamics simulations of a membrane-protein complex investigate the influence of the aqueous sodium chloride solutions on the structure and dynamics of a palmitoyl-oleoyl-phosphatidylcholine bilayer membrane. The simulations were performed on five different concentrations (40, 150, 200, 300, and 400 mM) in addition to a salt-free system by using the charmm36 force field for all atoms. Four biophysical parameters, (membrane thicknesses of annular and bulk lipids, and the area per lipid of both leaflets), were computed separately. Nevertheless, the area per lipid was expressed by using the Voronoi algorithm. All time-independent analyses were carried out for the last 400 ns trajectories. Different concentrations revealed dissimilar membrane dynamics before equilibration. The biophysical properties of the membrane (thickness, area-per-lipid, and order parameter) have non-significant changes with increasing ionic strength, however, the 150 mM system had exceptional behavior. Sodium cations were dynamically penetrating the membrane forming weak coordinate bonds with single or multiple lipids. Nevertheless, the binding constant was unaffected by the cation concentration. The electrostatic and Van der Waals energies of lipid-lipid interactions were influenced by the ionic strength. On the other hand, the Fast Fourier Transform was performed to figure out the dynamics at the membrane-protein interface. The nonbonding energies of membrane-protein interactions and order parameters explained the differences in the synchronization pattern. All results were consensus with experimental and theoretical works.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mahmoud Abdelmohsen
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Mathematics and Engineering Physics Department, The Higher Institute of Engineering, Shorouk Academy, El-Shorouk City, Cairo, Egypt
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Bakhtiarydavijani A, Khalid G, Murphy MA, Johnson KL, Peterson LE, Jones M, Horstemeyer MF, Dobbins AC, Prabhu RK. A mesoscale finite element modeling approach for understanding brain morphology and material heterogeneity effects in chronic traumatic encephalopathy. Comput Methods Biomech Biomed Engin 2021; 24:1169-1183. [PMID: 33635182 DOI: 10.1080/10255842.2020.1867851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Chronic Traumatic Encephalopathy (CTE) affects a significant portion of athletes in contact sports but is difficult to quantify using clinical examinations and modeling approaches. We use an in silico approach to quantify CTE biomechanics using mesoscale Finite Element (FE) analysis that bridges with macroscale whole head FE analysis. The sulci geometry produces complex stress waves that interact with one another to create increased shear stresses at the sulci depth that are significantly larger than in analyses without sulci (from 0.5 to 18.0 kPa). Sulci peak stress concentration regions coincide with experimentally observed CTE sites documented in the literature. HighlightsSulci introduce stress localizations at their depth in the gray matterSulci stress fields interact to produce stress concentration sites in white matterDifferentiating brain tissue properties did not significantly affect peak stresses.
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Affiliation(s)
- A Bakhtiarydavijani
- Center for Advanced Vehicular Systems, Mississippi State University, Starkville, MS, USA
| | - G Khalid
- Middle Technical University, Baghdad, Iraq
| | - M A Murphy
- Center for Advanced Vehicular Systems, Mississippi State University, Starkville, MS, USA
| | | | - L E Peterson
- Center for Advanced Vehicular Systems, Mississippi State University, Starkville, MS, USA
| | - M Jones
- Institute of Medical Engineering & Medical Physics, Cardiff University, Cardiff, Wales, UK
| | | | - A C Dobbins
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, USA
| | - R K Prabhu
- Center for Advanced Vehicular Systems, Mississippi State University, Starkville, MS, USA.,Department of Agricultural and Biological Engineering, Mississippi State University, MS, USA
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