1
|
Doktorova M, Khelashvili G, Ashkar R, Brown MF. Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics. Biophys J 2023; 122:984-1002. [PMID: 36474442 PMCID: PMC10111610 DOI: 10.1016/j.bpj.2022.12.007] [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: 09/03/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent κC modulus for bilayer bending. Our results show a strong correlation with κC values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.
Collapse
Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona; Program in Applied Mathematics, University of Arizona, Tucson, Arizona.
| |
Collapse
|
2
|
Castillo SR, Rickeard BW, DiPasquale M, Nguyen MHL, Lewis-Laurent A, Doktorova M, Kav B, Miettinen MS, Nagao M, Kelley EG, Marquardt D. Probing the Link between Pancratistatin and Mitochondrial Apoptosis through Changes in the Membrane Dynamics on the Nanoscale. Mol Pharm 2022; 19:1839-1852. [PMID: 35559658 DOI: 10.1021/acs.molpharmaceut.1c00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pancratistatin (PST) is a natural antiviral alkaloid that has demonstrated specificity toward cancerous cells and explicitly targets the mitochondria. PST initiates apoptosis while leaving healthy, noncancerous cells unscathed. However, the manner by which PST induces apoptosis remains elusive and impedes the advancement of PST as a natural anticancer therapeutic agent. Herein, we use neutron spin-echo (NSE) spectroscopy, molecular dynamics (MD) simulations, and supporting small angle scattering techniques to study PST's effect on membrane dynamics using biologically representative model membranes. Our data suggests that PST stiffens the inner mitochondrial membrane (IMM) by being preferentially associated with cardiolipin, which would lead to the relocation and release of cytochrome c. Second, PST has an ordering effect on the lipids and disrupts their distribution within the IMM, which would interfere with the maintenance and functionality of the active forms of proteins in the electron transport chain. These previously unreported findings implicate PST's effect on mitochondrial apoptosis.
Collapse
Affiliation(s)
- Stuart R Castillo
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Brett W Rickeard
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Mitchell DiPasquale
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Michael H L Nguyen
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Aislyn Lewis-Laurent
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States
| | - Batuhan Kav
- Max-Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany.,Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Julich, Julich 52428, Germany
| | | | - Michihiro Nagao
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States.,Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States.,Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| | - Elizabeth G Kelley
- National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada.,Department of Physics, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| |
Collapse
|
3
|
Doktorova M, Harries D, Khelashvili G. Determination of bending rigidity and tilt modulus of lipid membranes from real-space fluctuation analysis of molecular dynamics simulations. Phys Chem Chem Phys 2018. [PMID: 28627570 DOI: 10.1039/c7cp01921a] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have recently developed a novel computational methodology (termed RSF for Real-Space Fluctuations) to quantify the bending rigidity and tilt modulus of lipid membranes from real-space analysis of fluctuations in the tilt and splay degrees of freedom as sampled in molecular dynamics (MD) simulations. In this article, we present a comprehensive study that combines results from the application of the RSF method to a wide range of lipid bilayer systems that encompass membranes of different fluidities and sizes, including lipids with saturated and unsaturated lipid tails, single and multi-component lipid systems, as well as non-standard lipids such as the four-tailed cardiolipin. By comparing the material properties calculated with the RSF method to those obtained from experimental data and from other computational methodologies, we rigorously demonstrate the validity of our approach and show its robustness. This should allow for future applications of even more complex lipidic assemblies, whose material properties are not tractable by other computational techniques. In addition, we discuss the relationship between different definitions of the tilt modulus appearing in current literature to address some important unresolved discrepancies in the field.
Collapse
Affiliation(s)
- M Doktorova
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | | | | |
Collapse
|