1
|
Gholizadeh A, Amjad-Iranagh S, Halladj R. Assessing the Interaction between Dodecylphosphocholine and Dodecylmaltoside Mixed Micelles as Drug Carriers with Lipid Membrane: A Coarse-Grained Molecular Dynamics Simulation. ACS OMEGA 2024; 9:40433-40445. [PMID: 39372004 PMCID: PMC11447843 DOI: 10.1021/acsomega.4c02551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 08/30/2024] [Accepted: 09/04/2024] [Indexed: 10/08/2024]
Abstract
Integrating drugs into cellular membranes efficiently is a significant challenge in drug delivery systems. This study aimed to overcome these barriers by utilizing mixed micelles to enhance drug incorporation into cell membranes. We employed coarse-grained molecular dynamics (MD) simulations to investigate the stability and efficacy of micelles composed of dodecylphosphocholine (DPC), a zwitterionic surfactant, and dodecylmaltoside (DDM), a nonionic surfactant, at various mixing ratios. Additionally, we examined the incorporation of a mutated form of Indolicidin (IND) (CP10A), an anti-HIV peptide, into these micelles. This study provides valuable insights for the development of more effective drug delivery systems by optimizing the mixing ratios of DPC and DDM. By balancing stability and penetration efficiency, these mixed micelles can improve the delivery of drugs that face challenges crossing lipid membranes. Such advancements can enhance the efficacy of treatments for various conditions, including viral infections and cancer, by ensuring that therapeutic agents reach their intended cellular targets more effectively.
Collapse
Affiliation(s)
- Atefeh Gholizadeh
- Department
of Chemical Engineering, Amirkabir University
of Technology (Tehran Polytechnic), Tehran 15875-4313, Iran
| | - Sepideh Amjad-Iranagh
- Department
of Materials and Metallurgical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran 15875-4313, Iran
| | - Rouein Halladj
- Department
of Chemical Engineering, Amirkabir University
of Technology (Tehran Polytechnic), Tehran 15875-4313, Iran
| |
Collapse
|
2
|
Vo ATN, Murphy MA, Prabhu RK, Stone TW. Influence of phospholipid head and tail molecular structures on cell membrane mechanical response under tension. J Chem Phys 2024; 161:085103. [PMID: 39177086 DOI: 10.1063/5.0214893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/02/2024] [Indexed: 08/24/2024] Open
Abstract
Biological cell membranes are primarily comprised of a diverse lipid bilayer with multiple phospholipid (lipid) types, each of which is comprised of a hydrophilic headgroup and two hydrophobic hydrocarbon tails. The lipid type determines the molecular structure of head and tail groups, which can affect membrane mechanics at nanoscale and subsequently cell viability under mechanical loading. Hence, using molecular dynamics simulations, the current study investigated seven membrane phospholipids and the effect of their structural differences on physical deformation, mechanoporation damage, and mechanical failure of the membranes under tension. The inspected phospholipids showed similar yield stresses and strains, as well as pore evolution and damage, but significantly different failure strains. In general, failure occurred at a lower strain for lipids with a larger equilibrium area per lipid. The obtained results suggest that larger headgroup structure, greater degree of unsaturation, and tail-length asymmetry influenced the phospholipids' ability to pack against each other, increased the fluidity and equilibrium area per lipid of the membrane, and resulted in lower failure strain. Overall, this study provides insights on how different phospholipid structures affect membrane physical responses at the molecular level and serves as a reference for future studies of more complex membrane systems with intricate biophysical properties.
Collapse
Affiliation(s)
- Anh T N Vo
- Center for Advanced Vehicular Systems (CAVS), Mississippi State University, Starkville, Mississippi 39759, USA
- Department of Agricultural and Biological Engineering, Mississippi State University, Mississippi State, Mississippi 39762, USA
- Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Michael A Murphy
- Center for Advanced Vehicular Systems (CAVS), Mississippi State University, Starkville, Mississippi 39759, USA
| | - Raj K Prabhu
- NASA Johnson Space Center, 2101 NASA Parkway, Houston, Texas 77058, USA
| | - Tonya W Stone
- Center for Advanced Vehicular Systems (CAVS), Mississippi State University, Starkville, Mississippi 39759, USA
- Department of Mechanical Engineering, Mississippi State University, Mississippi State, Mississippi 39762, USA
| |
Collapse
|
3
|
Needham D. Niclosamide: A career builder. J Control Release 2024; 369:786-856. [PMID: 37544514 DOI: 10.1016/j.jconrel.2023.07.016] [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: 03/19/2023] [Revised: 06/24/2023] [Accepted: 07/08/2023] [Indexed: 08/08/2023]
Abstract
My contribution to honoring Professor Kinam Park celebrates and resonates with his scholarly career in drug delivery, his commitment to encouraging the next generation(s), and his efforts to keep us focused on clinically effective formulations. To do this I take as my example, niclosamide, a small molecule protonophore that, uniquely, can "target" all cell membranes, both plasma and organelle. As such, it acts upstream of many cell pathways and so has the potential to affect many of the essential events that a cell, and particularly a diseased cell or other entities like a virus, use to stay alive and prosper. Literature shows that it has so far been discovered to positively influence (at least): cancer, bacterial and viral infection, metabolic diseases such as Type II diabetes, NASH and NAFLD, artery constriction, endometriosis, neuropathic pain, rheumatoid arthritis, sclerodermatous graft-versus-host disease, systemic sclerosis, Parkinson's, and COPD. With such a fundamental action and broad-spectrum activity, I believe that studying niclosamide in all its manifestations, discovering if and to what extent it can contribute positively to disease control (and also where it can't), formulating it as effective therapeutics, and testing them in preclinical and clinical trials is a career builder for our next generation(s). The article is divided into two parts: Part I introduces niclosamide and other proton shunts mainly in cancer and viral infections and reviews an exponentially growing literature with some concepts and physicochemical properties that lead to its proton shunt mechanism. Part II focuses on repurposing by reformulation of niclosamide. I give two examples of "carrier-free formulations", - one for cancer (as a prodrug therapeutic of niclosamide stearate for i.v. and other administration routes, exemplified by our recent work on Osteosarcoma in mice and canine patients), and the other as a niclosamide solution formulation (that could provide the basis for a preventative nasal spray and early treatment option for COVID19 and other respiratory virus infections). My goal is to excite and enthuse, encourage, and motivate all involved in the drug development and testing process in academia, institutes, and industry, to learn more about this interesting molecule and others like it. To enable such endeavors, I give many proposed ideas throughout the document, that have been stimulated and inspired by gaps in the literature, urgent needs in disease, and new studies arising from our own work. The hope is that, by reading through this document and studying the suggested topics and references, the drug delivery and development community will continue our lineage and benefit from our legacy to achieve niclosamide's potential as an effective contributor to the treatment and control of many diseases and conditions.
Collapse
Affiliation(s)
- David Needham
- Department of Mechanical Engineering and Material Science, Duke University, Durham, NC 27708, USA; Translational Therapeutics, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK.
| |
Collapse
|
4
|
Vasyankin AV, Panteleev SV, Steshin IS, Shirokova EA, Rozhkov AV, Livshits GD, Radchenko EV, Ignatov SK, Palyulin VA. Temperature-Induced Restructuring of Mycolic Acid Bilayers Modeling the Mycobacterium tuberculosis Outer Membrane: A Molecular Dynamics Study. Molecules 2024; 29:696. [PMID: 38338443 PMCID: PMC10856651 DOI: 10.3390/molecules29030696] [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: 01/02/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The emergence of new drug-resistant strains of the tuberculosis pathogen Mycobacterium tuberculosis (Mtb) is a new challenge for modern medicine. Its resistance capacity is closely related to the properties of the outer membrane of the Mtb cell wall, which is a bilayer membrane formed by mycolic acids (MAs) and their derivatives. To date, the molecular mechanisms of the response of the Mtb outer membrane to external factors and, in particular, elevated temperatures have not been sufficiently studied. In this work, we consider the temperature-induced changes in the structure, ordering, and molecular mobility of bilayer MA membranes of various chemical and conformational compositions. Using all-atom long-term molecular dynamics simulations of various MA membranes, we report the kinetic parameters of temperature-dependent changes in the MA self-diffusion coefficients and conformational compositions, including the apparent activation energies of these processes, as well as the characteristic times of ordering changes and the features of phase transitions occurring over a wide range of elevated temperatures. Understanding these effects could be useful for the prevention of drug resistance and the development of membrane-targeting pharmaceuticals, as well as in the design of membrane-based materials.
Collapse
Affiliation(s)
- Alexander V. Vasyankin
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
| | - Sergey V. Panteleev
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
| | - Ilya S. Steshin
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
| | - Ekaterina A. Shirokova
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
| | - Alexey V. Rozhkov
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
| | - Grigory D. Livshits
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
| | - Eugene V. Radchenko
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Stanislav K. Ignatov
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
| | - Vladimir A. Palyulin
- Department of Chemistry, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603022, Russia; (A.V.V.); (S.V.P.); (I.S.S.); (E.A.S.); (A.V.R.); (G.D.L.); (E.V.R.)
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
5
|
Blazhynska M, Gumbart JC, Chen H, Tajkhorshid E, Roux B, Chipot C. A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes. J Chem Theory Comput 2023; 19:9077-9092. [PMID: 38091976 PMCID: PMC11145395 DOI: 10.1021/acs.jctc.3c00941] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for understanding the mechanisms by which they recognize one another and reversibly associate. The glycophorin A (GpA) homodimer, composed of two α-helical segments, has long served as a model system for studying TM protein reversible association. The present work establishes a methodological framework for calculating the binding affinity of the GpA homodimer in the heterogeneous environment of a membrane. Our investigation carefully considered a variety of protocols, including the appropriate choice of the force field, rigorous standardization reflecting the experimental conditions, sampling algorithm, anisotropic environment, and collective variables, to accurately describe GpA dimerization via molecular dynamics-based approaches. Specifically, two strategies were explored: (i) an unrestrained potential mean force (PMF) calculation, which merely enhances sampling along the separation of the two binding partners without any restraint, and (ii) a so-called "geometrical route", whereby the α-helices are progressively separated with imposed restraints on their orientational, positional, and conformational degrees of freedom to accelerate convergence. Our simulations reveal that the simplified, unrestrained PMF approach is inadequate for the description of GpA dimerization. Instead, the geometrical route, tailored specifically to GpA in a membrane environment, yields excellent agreement with experimental data within a reasonable computational time. A dimerization free energy of -10.7 kcal/mol is obtained, in fairly good agreement with available experimental data. The geometrical route further helps elucidate how environmental forces drive association before helical interactions stabilize it. Our simulations also brought to light a distinct, long-lived spatial arrangement that potentially serves as an intermediate state during dimer formation. The methodological advances in the generalized geometrical route provide a powerful tool for accurate and efficient binding-affinity calculations of intricate TM protein complexes in inhomogeneous environments.
Collapse
Affiliation(s)
- Marharyta Blazhynska
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332, United States
| | - Haochuan Chen
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n°7019, Université de Lorraine, B.P. 70239, Vandœuvre-lès-Nancy cedex 54506, France
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57th Street W225, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Hawai'i at Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| |
Collapse
|
6
|
Kumar A, Daschakraborty S. Anomalous lateral diffusion of lipids during the fluid/gel phase transition of a lipid membrane. Phys Chem Chem Phys 2023; 25:31431-31443. [PMID: 37962400 DOI: 10.1039/d3cp04081j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A lipid membrane undergoes a phase transition from fluid to gel phase upon changing external thermodynamic conditions, such as decreasing temperature and increasing pressure. Extremophilic organisms face the challenge of preventing this deleterious phase transition. The main focus of their adaptive strategy is to facilitate effective temperature sensing through sensor proteins, relying on the drastic changes in packing density and membrane fluidity during the phase transition. Although the changes in packing density parameters due to the fluid/gel phase transition are studied in detail, the impact on membrane fluidity is less explored in the literature. Understanding the lateral diffusive dynamics of lipids in response to temperature, particularly during the fluid/gel phase transition, is albeit crucial. Here we have simulated the phase transition of a single component lipid membrane composed of dipalmitoylphosphatidylcholine (DPPC) lipids using a coarse-grained (CG) model and studied the changes of the structural and dynamical properties. It is observed that near the phase transition point, both fluid and gel phase domains coexist together. The dynamics remains highly non-Gaussian for a long time even when the mean square displacement reaches the Fickian regime at a much earlier time. This Fickian yet non-Gaussian diffusion (FnGD) is a characteristic of a highly heterogeneous system, previously observed for the lateral diffusion of lipids in raft mimetic membranes having liquid-ordered and liquid-disordered phases co-existing together. We have analyzed the molecular trajectories and calculated the jump-diffusion of the lipids, stemming from sudden jump translations, using a translational jump-diffusion (TJD) approach. An overwhelming contribution of the jump-diffusion of the lipids is observed suggesting anomalous diffusion of lipids during fluid/gel phase transition of the membrane. These results are important in unravelling the intricate nature of lipid diffusion during the phase transition of the membrane and open up a new possibility of investigating the most significant change of membrane properties during phase transition, which can be effectively sensed by proteins.
Collapse
Affiliation(s)
- Abhay Kumar
- Department of Chemistry, Indian Institute of Technology Patna, Bihar 801106, India.
| | | |
Collapse
|
7
|
Odenkirk MT, Zhang G, Marty MT. Do Nanodisc Assembly Conditions Affect Natural Lipid Uptake? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2006-2015. [PMID: 37524089 PMCID: PMC10528108 DOI: 10.1021/jasms.3c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Lipids play critical roles in modulating membrane protein structure, interactions, and activity. Nanodiscs provide a tunable membrane mimetic that can model these endogenous protein-lipid interactions in a nanoscale lipid bilayer. However, most studies of membrane proteins with nanodiscs use simple synthetic lipids that lack the headgroup and fatty acyl diversity of natural extracts. Prior research has successfully used natural lipid extracts in nanodiscs that more accurately mimic natural environments, but it is not clear how nanodisc assembly may bias the incorporated lipid profiles. Here, we applied lipidomics to investigate how nanodisc assembly conditions affect the profile of natural lipids in nanodiscs. Specifically, we tested the effects of assembly temperature, nanodisc size, and lipidome extract complexity. Globally, our analysis demonstrates that the lipids profiles are largely unaffected by nanodisc assembly conditions. However, a few notable changes emerged within individual lipids and lipid classes, such as a differential incorporation of cardiolipin and phosphatidylglycerol lipids from the E. coli polar lipid extract at different temperatures. Conversely, some classes of brain lipids were affected by nanodisc size at higher temperatures. Collectively, these data enable the application of nanodiscs to study protein-lipid interactions in complex lipid environments.
Collapse
Affiliation(s)
- Melanie T. Odenkirk
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
- Bio5 Institute, University of Arizona, Tucson, AZ
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ
- Bio5 Institute, University of Arizona, Tucson, AZ
| |
Collapse
|
8
|
Ugarte La Torre D, Takada S, Sugita Y. Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers. J Chem Phys 2023; 159:075101. [PMID: 37581417 DOI: 10.1063/5.0160417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
iSoLF is a coarse-grained (CG) model for lipid molecules with the implicit-solvent approximation used in molecular dynamics (MD) simulations of biological membranes. Using the original iSoLF (iSoLFv1), MD simulations of lipid bilayers consisting of either POPC or DPPC and these bilayers, including membrane proteins, can be performed. Here, we improve the original model, explicitly treating the electrostatic interactions between different lipid molecules and adding CG particle types. As a result, the available lipid types increase to 30. To parameterize the potential functions of the new model, we performed all-atom MD simulations of each lipid at three different temperatures using the CHARMM36 force field and the modified TIP3P model. Then, we parameterized both the bonded and non-bonded interactions to fit the area per lipid and the membrane thickness of each lipid bilayer by using the multistate Boltzmann Inversion method. The final model reproduces the area per lipid and the membrane thickness of each lipid bilayer at the three temperatures. We also examined the applicability of the new model, iSoLFv2, to simulate the phase behaviors of mixtures of DOPC and DPPC at different concentrations. The simulation results with iSoLFv2 are consistent with those using Dry Martini and Martini 3, although iSoLFv2 requires much fewer computations. iSoLFv2 has been implemented in the GENESIS MD software and is publicly available.
Collapse
Affiliation(s)
- Diego Ugarte La Torre
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| |
Collapse
|
9
|
Aghaaminiha M, Farnoud AM, Sharma S. Interdependence of cholesterol distribution and conformational order in lipid bilayers. Biointerphases 2023; 18:2887740. [PMID: 37125848 DOI: 10.1116/6.0002489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
We show, via molecular simulations, that not only does cholesterol induce a lipid order, but the lipid order also enhances cholesterol localization within the lipid leaflets. Therefore, there is a strong interdependence between these two phenomena. In the ordered phase, cholesterol molecules are predominantly present in the bilayer leaflets and orient themselves parallel to the bilayer normal. In the disordered phase, cholesterol molecules are mainly present near the center of the bilayer at the midplane region and are oriented orthogonal to the bilayer normal. At the melting temperature of the lipid bilayers, cholesterol concentration in the leaflets and the bilayer midplane is equal. This result suggests that the localization of cholesterol in the lipid bilayers is mainly dictated by the degree of ordering of the lipid bilayer. We validate our findings on 18 different lipid bilayer systems, obtained from three different phospholipid bilayers with varying concentrations of cholesterol. To cover a large temperature range in simulations, we employ the Dry Martini force field. We demonstrate that the Dry and the Wet Martini (with polarizable water) force fields produce comparable results.
Collapse
Affiliation(s)
| | - Amir M Farnoud
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, Ohio 45701
| | - Sumit Sharma
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, Ohio 45701
| |
Collapse
|
10
|
Malik S, Karmakar S, Debnath A. Relaxation time scales of interfacial water upon fluid to ripple to gel phase transitions of bilayers. J Chem Phys 2023; 158:114503. [PMID: 36948835 DOI: 10.1063/5.0138681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The slow relaxation of interface water (IW) across three primary phases of membranes is relevant to understand the influence of IW on membrane functions at supercooled conditions. To this objective, a total of ∼16.26μs all-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes are carried out. A supercooling-driven drastic slow-down in heterogeneity time scales of the IW is found at the fluid to the ripple to the gel phase transitions of the membranes. At both fluid-to-ripple-to-gel phase transitions, the IW undergoes two dynamic crossovers in Arrhenius behavior with the highest activation energy at the gel phase due to the highest number of hydrogen bonds. Interestingly, the Stokes-Einstein (SE) relation is conserved for the IW near all three phases of the membranes for the time scales derived from the diffusion exponents and the non-Gaussian parameters. However, the SE relation breaks for the time scale obtained from the self-intermediate scattering functions. The behavioral difference in different time scales is universal and found to be an intrinsic property of glass. The first dynamical transition in the α relaxation time of the IW is associated with an increase in the Gibbs energy of activation of hydrogen bond breaking with locally distorted tetrahedral structures, unlike the bulk water. Thus, our analyses unveil the nature of the relaxation time scales of the IW across membrane phase transitions in comparison with the bulk water. The results will be useful to understand the activities and survival of complex biomembranes under supercooled conditions in the future.
Collapse
Affiliation(s)
- Sheeba Malik
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Ananya Debnath
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
| |
Collapse
|
11
|
Nagle JF, Jennings N, Qin W, Yan D, Tristram-Nagle S, Heinrich F. Structure of the gel phase of diC22:1PC lipid bilayers determined by x-ray diffraction. Biophys J 2023; 122:1033-1042. [PMID: 36566351 PMCID: PMC10111270 DOI: 10.1016/j.bpj.2022.12.030] [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: 09/13/2022] [Revised: 11/21/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
High-resolution x-ray data are reported for the ordered phases of long-chain di-monounsaturated C22:1 phosphocholine lipid bilayers. Similar to PC lipids that have saturated chains, diC22:1PC has a subgel phase and a gel phase, but dissimilarly, we find no ripple phase. Our quantitative focus is on the structure of the gel phase. We have recorded 17 lamellar orders, indicating a very well-ordered structure. Fitting to a model provides the phases of the orders. The Fourier construction of the electron density profile has two well-defined headgroup peaks and a very sharp and deep methyl trough. The wide-angle scattering exhibits two Bragg rods that provide the area per molecule. They have an intensity pattern quite different than that of lipids with saturated chains. Models of chain packing indicate that ground state chain configurations are tilted primarily toward next nearest neighbors with an angle that is also consistent with the modeling of the electron density profile. Wide-angle modeling also indicates broken mirror symmetry between the monolayers. Our wide-angle results and our electron density profile together leads to the hypothesis that the sn-1 and sn-2 chains have equivalent penetration depths in contrast to the gel phase structure of lipids with saturated hydrocarbon chains.
Collapse
Affiliation(s)
- John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
| | - Nathaniel Jennings
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Weiheng Qin
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Daniel Yan
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | | | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
| |
Collapse
|
12
|
Malik S, Karmakar S, Debnath A. Quantifying dynamical heterogeneity length scales of interface water across model membrane phase transitions. J Chem Phys 2023; 158:091103. [PMID: 36889951 DOI: 10.1063/5.0137727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
All-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes reveal a drastic growth in the heterogeneity length scales of interface water (IW) across fluid to ripple to gel phase transitions. It acts as an alternate probe to capture the ripple size of the membrane and follows an activated dynamical scaling with the relaxation time scale solely within the gel phase. The results quantify the mostly unknown correlations between the spatiotemporal scales of the IW and membranes at various phases under physiological and supercooled conditions.
Collapse
Affiliation(s)
- Sheeba Malik
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Ananya Debnath
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
| |
Collapse
|
13
|
Ivanova N, Chamati H. The Effect of Cholesterol in SOPC Lipid Bilayers at Low Temperatures. MEMBRANES 2023; 13:275. [PMID: 36984662 PMCID: PMC10058253 DOI: 10.3390/membranes13030275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
We study the behavior of lipid bilayers composed of SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) with different concentrations of cholesterol, ranging from 10 mol% to 50 mol% at 273 K. To this end, we carry out extensive atomistic molecular dynamic simulations with the aid of the Slipid force field aiming at computing basic bilayer parameters, as well as thermodynamic properties and structural characteristics. The obtained results are compared to available relevant experimental data and the outcome of atomistic simulations performed on bilayers composed of analogous phospholipids. Our results show a good quantitative, as well as qualitative, agreement with the main trends associated with the concentration increase in cholesterol. Moreover, it comes out that a change in the behavior of the bilayer is brought about at a concentration of about 30 mol% cholesterol. At this very concentration, some of the bilayer properties are found to exhibit a saturation and a significant long-range ordering of the lipid molecules in the membrane shows up.
Collapse
Affiliation(s)
- Nikoleta Ivanova
- Department of Physical Chemistry, University of Chemical Technology and Metallurgy, 8 Kliment Ohridski Blvd., 1756 Sofia, Bulgaria
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., 1784 Sofia, Bulgaria
| | - Hassan Chamati
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussee Blvd., 1784 Sofia, Bulgaria
| |
Collapse
|
14
|
Bringas M, Luck M, Müller P, Scheidt HA, Di Lella S. Effects of the RNA-Polymerase Inhibitors Remdesivir and Favipiravir on the Structure of Lipid Bilayers-An MD Study. MEMBRANES 2022; 12:941. [PMID: 36295700 PMCID: PMC9608901 DOI: 10.3390/membranes12100941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The structure and dynamics of membranes are crucial to ensure the proper functioning of cells. There are some compounds used in therapeutics that show nonspecific interactions with membranes in addition to their specific molecular target. Among them, two compounds recently used in therapeutics against COVID-19, remdesivir and favipiravir, were subjected to molecular dynamics simulation assays. In these, we demonstrated that the compounds can spontaneously bind to model lipid membranes in the presence or absence of cholesterol. These findings correlate with the corresponding experimental results recently reported by our group. In conclusion, insertion of the compounds into the membrane is observed, with a mean position close to the phospholipid head groups.
Collapse
Affiliation(s)
- Mauro Bringas
- Instituto de Química Biológica—Ciencias Exactas y Naturales (IQUIBICEN)—CONICET and Departamento de Química Biológica FCEN, Universidad de Buenos Aires, Int. Güiraldes 2160, Buenos Aires C1428EGA, Argentina
| | - Meike Luck
- Department of Biology, Humboldt Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Peter Müller
- Department of Biology, Humboldt Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Holger A. Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16–18, D-04107 Leipzig, Germany
| | - Santiago Di Lella
- Instituto de Química Biológica—Ciencias Exactas y Naturales (IQUIBICEN)—CONICET and Departamento de Química Biológica FCEN, Universidad de Buenos Aires, Int. Güiraldes 2160, Buenos Aires C1428EGA, Argentina
| |
Collapse
|
15
|
Kurniawan J, Ishida T. Protein Model Quality Estimation Using Molecular Dynamics Simulation. ACS OMEGA 2022; 7:24274-24281. [PMID: 35874260 PMCID: PMC9301944 DOI: 10.1021/acsomega.2c01475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The estimation of protein model quality remains a challenging task and is important for protein structural model utilization. In the last decade, existing methods that rely on machine learning to deep learning have been developed and shown progressive improvement. Despite utilizing more sophisticated techniques and introducing new features, none of these methods employ explicit protein structure stability information. Hypothetically, protein model quality might be indicated by its structural stability in an in silico system disclosed by the structural difference from its initial structure. One of the possible methods to exploit such information is by implementing molecular dynamics simulations that have shown successful applications in many research fields. We present a novel approach by introducing explicit protein structure stability information using molecular dynamics simulation. Despite using only simple features, small data with no training process required, and a short molecular dynamics simulation time, our method shows comparable performance to the state-of-the-art deep learning-based method.
Collapse
|
16
|
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
|
17
|
Zizzi EA, Cavaglià M, Tuszynski JA, Deriu MA. Alteration of lipid bilayer mechanics by volatile anesthetics: Insights from μs-long molecular dynamics simulations. iScience 2022; 25:103946. [PMID: 35265816 PMCID: PMC8898909 DOI: 10.1016/j.isci.2022.103946] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 11/24/2022] Open
Abstract
Very few drugs in clinical practice feature the chemical diversity, narrow therapeutic window, unique route of administration, and reversible cognitive effects of volatile anesthetics. The correlation between their hydrophobicity and their potency and the increasing amount of evidence suggesting that anesthetics exert their action on transmembrane proteins, justifies the investigation of their effects on phospholipid bilayers at the molecular level, given the strong functional and structural link between transmembrane proteins and the surrounding lipid matrix. Molecular dynamics simulations of a model lipid bilayer in the presence of ethylene, desflurane, methoxyflurane, and the nonimmobilizer 1,2-dichlorohexafluorocyclobutane (also called F6 or 2N) at different concentrations highlight the structural consequences of VA partitioning in the lipid phase, with a decrease of lipid order and bilayer thickness, an increase in overall lipid lateral mobility and area-per-lipid, and a marked reduction in the mechanical stiffness of the membrane, that strongly correlates with the compounds' hydrophobicity.
Collapse
Affiliation(s)
- Eric A. Zizzi
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Turin, Italy
| | - Marco Cavaglià
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Turin, Italy
| | - Jack A. Tuszynski
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Turin, Italy
- Department of Physics, University of Alberta, Edmonton, AB, Canada
| | - Marco A. Deriu
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Turin, Italy
| |
Collapse
|
18
|
Adams WR, Gautam R, Locke A, Masson LE, Borrachero-Conejo AI, Dollinger B, Throckmorton GA, Duvall C, Jansen ED, Mahadevan-Jansen A. Visualizing Lipid Dynamics Role in Infrared Neural Stimulation using Stimulated Raman Scattering. Biophys J 2022; 121:1525-1540. [PMID: 35276133 PMCID: PMC9072573 DOI: 10.1016/j.bpj.2022.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/14/2021] [Accepted: 03/04/2022] [Indexed: 11/02/2022] Open
Abstract
Infrared neural stimulation, or INS, uses pulsed infrared light to yield label-free neural stimulation with broad experimental and translational utility. Despite its robust demonstration, INS's mechanistic and biophysical underpinnings have been the subject of debate for more than a decade. The role of lipid membrane thermodynamics appears to play an important role in how fast IR-mediated heating nonspecifically drives action potential generation. Direct observation of lipid membrane dynamics during INS remains to be shown in a live neural model system. We used hyperspectral stimulated Raman scattering (hsSRS) microscopy to study biochemical signatures of high-speed vibrational dynamics underlying INS in a live neural cell culture model. Findings suggest that lipid bilayer structural changes are occurring during INS in vitro in NG108-15 neuroglioma cells. Lipid-specific signatures of cell SRS spectra varied with stimulation energy and radiant exposure. Spectroscopic observations agree with high-speed ratiometric fluorescence imaging of a conventional lipophilic membrane structure reporter, di-4-ANNEPS. Overall, the presented findings support the hypothesis that INS causes changes in the lipid membrane of neural cells by changing lipid membrane packing order. Furthermore, this work highlights the potential of hsSRS as a method to study biophysical and biochemical dynamics safely in live cells.
Collapse
Affiliation(s)
- Wilson R Adams
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Rekha Gautam
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Andrea Locke
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Laura E Masson
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Bryan Dollinger
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Craig Duvall
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - E Duco Jansen
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Dept. of Neurosurgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anita Mahadevan-Jansen
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Dept. of Neurosurgery, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
19
|
Järvenpää J, Perkkiö M, Laitinen R, Lahtela-Kakkonen M. PE and PET oligomers' interplay with membrane bilayers. Sci Rep 2022; 12:2234. [PMID: 35140293 PMCID: PMC8828856 DOI: 10.1038/s41598-022-06217-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022] Open
Abstract
The prevalence of microplastic pollution in nature and foodstuffs is fairly well identified. However, studies of micro- or nanoplastics' cell membrane permeation and health effects in humans are lacking. Our study focuses on examining the interactions of polyethylene (PE) and polyethylene terephthalate (PET) with bilayer membranes. We have performed molecular dynamics simulations to study how plastic oligomers behave in bilayers. In addition, we have studied membrane permeation of PE and Bis(2-hydroxyethyl) terephthalate (BHET), a type of PET monomer, with Parallel Artificial Membrane Permeability Assay (PAMPA). As a result, in simulations the molecules exhibited different movements and preferred locations in membrane. PAMPA studies suggested similar preferences in membrane, especially for PE plastic. Our results suggest that passive diffusion could be an important transport mechanism into cells for some small plastic oligomers. Both molecular dynamics simulations and PAMPA have potential for micro- and nanoplastics research.
Collapse
Affiliation(s)
- Joni Järvenpää
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210, Kuopio, Finland.
| | - Milla Perkkiö
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Riikka Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210, Kuopio, Finland
| | - Maija Lahtela-Kakkonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210, Kuopio, Finland.
| |
Collapse
|
20
|
Shobhna, Kumari M, Kashyap HK. Mechanistic Insight on BioIL-Induced Structural Alterations in DMPC Lipid Bilayer. J Phys Chem B 2021; 125:11955-11966. [PMID: 34672578 DOI: 10.1021/acs.jpcb.1c06218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The emerging application risks of traditional ionic liquids (ILs) toward the ecosystem have changed the perception regarding their greenness. This resulted in the exploration of their more biocompatible alternatives known as biocompatible ILs (BioILs). Here, we have investigated the impact of two such biocompatible cholinium amino acid-based ILs on the structural behavior of model homogeneous DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) lipid bilayer using all-atom molecular dynamics simulation technique. Two classic cholinium-amino acid-based ILs, cholinium glycinate ([Ch][Gly]) and cholinium phenylalaninate ([Ch][Phe]), which differ only by the side chain lengths and hydrophobicity of the anions, have been utilized in the present work. Simultaneous analysis of the bilayer structural properties reveals that the existence of [Ch][Gly] BioIL above a particular concentration induces phase transition from fluid phase to gel phase in the DMPC lipid bilayer. Such a freezing of lipid bilayer upon the exposure to concentrated aqueous solution of [Ch][Gly] BioIL indicates the harmfulness of this BioIL toward the cell membranes majorly containing DMPC lipids, as the cell freezing can negatively affect its stability and functionality. Despite having a more hydrophobic amino acid side chain of [Phe]- anion in [Ch][Phe], in the case of bilayer-[Ch][Phe] systems we observe the minimal impact of [Ch][Phe] BioIL on the DMPC bilayer properties up to 10 mol % concentration. In the presence of these BioIL, we observe the thickening of the bilayer and accumulation of the cations and anions of the BioILs at the interface of DMPC lipid heads and tails. The transfer free-energy profile of a [Phe]- anion from aqueous phase to membrane center also indicates the anion partitioning at lipid head-tail interface and its inability to penetrate in the lipid membrane tail region. In contrast, the free-energy profile for a [Gly]- anion offers a very high energy barrier to the insertion of [Gly]- into the membrane interior, leading to accumulation of [Gly]- anions at the lipid head-water region.
Collapse
Affiliation(s)
- Shobhna
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| |
Collapse
|
21
|
Sikdar S, Banerjee M, Vemparala S. Effect of cholesterol on the membrane partitioning dynamics of hepatitis A virus-2B peptide. SOFT MATTER 2021; 17:7963-7977. [PMID: 34378608 DOI: 10.1039/d1sm01019k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding viral peptide detection and partitioning and the subsequent host membrane composition-based response is essential for gaining insights into the viral mechanism. Here, we probe the crucial role of the presence of membrane lipid packing defects, depending on the membrane composition, in allowing the viral peptide belonging to C-terminal Hepatitis A Virus-2B (HAV-2B) to detect, attach and subsequently partition into host cell membrane mimics. Using molecular dynamics simulations, we conclusively show that the hydrophobic residues in the viral peptide detect transiently present lipid packing defects, insert themselves into such defects, form anchor points and facilitate the partitioning of the peptide, thereby inducing membrane disruption. We also show that the presence of cholesterol significantly alters such lipid packing defects, both in size and in number, thus mitigating the partitioning of the membrane active viral peptide into cholesterol-rich membranes. Our results are in excellent agreement with previously published experimental data and further explain the role of lipid defects in understanding such data. These results show differential ways in which the presence and absence of cholesterol can alter the permeability of the host membranes to the membrane active peptide component of HAV-2B virus, via lipid packing defects, and can possibly be a part of the general membrane detection mechanism for viroporins.
Collapse
Affiliation(s)
- Samapan Sikdar
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India.
| | | | | |
Collapse
|
22
|
Sui N, Huang K. Study on the interfacial behaviors for extraction of heavy rare earths with PC-88A: A new strategy of thin oil film extraction. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
23
|
Malik S, Debnath A. Dehydration induced dynamical heterogeneity and ordering mechanism of lipid bilayers. J Chem Phys 2021; 154:174904. [PMID: 34241050 DOI: 10.1063/5.0044614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα -1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα -0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
Collapse
Affiliation(s)
- Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| |
Collapse
|
24
|
Abstract
Molecular simulations of biological molecules require an accurate description of molecular interactions through a force field (FF). The focus of this Perspective is on all-atom lipid FFs. Recent additions to the CHARMM36 lipid FF continue to expand a researcher's ability to probe membrane structure and function with a wide variety of biologically important lipids. Currently, there is an effort to reduce the assumptions in all-atom lipid FFs. The inclusion of long-range dispersion interaction through particle-mesh Ewald is allowing for more accurate descriptions of lipid bilayer and monolayer properties without additional computational cost. Soon, simulations with lipid FFs will no longer depend on short-range cutoffs and will accurately represent long-range dispersion. This requires efficient FF parametrization with an automated approach due to FF complexity. In addition, polarizable FFs for lipids will be important for the next generation of simulations that accurately represent how molecule interactions respond to a varied environment.
Collapse
|
25
|
Rasouli A, Jamali Y, Tajkhorshid E, Bavi O, Pishkenari HN. Mechanical properties of ester- and ether-DPhPC bilayers: A molecular dynamics study. J Mech Behav Biomed Mater 2021; 117:104386. [PMID: 33588213 PMCID: PMC8009841 DOI: 10.1016/j.jmbbm.2021.104386] [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: 07/11/2020] [Revised: 01/03/2021] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Abstract
In addition to its biological importance, DPhPC lipid bilayers are widely used in droplet bilayers, study of integral membrane proteins, drug delivery systems as well as patch-clamp electrophysiology of ion channels, yet their mechanical properties are not fully measured. Herein, we examined the effect of the ether linkage on the mechanical properties of ester- and ether-DPhPC lipid bilayers using all-atom molecular dynamics simulation. The values of area per lipid, thickness, intrinsic lateral pressure profile, order parameter, and elasticity moduli were estimated using various computational frameworks and were compared with available experimental values. Overall, a good agreement was observed between the two. The global properties of the two lipid bilayers are vastly different, with ether bilayer being stiffer, less ordered, and thicker than ester bilayer. Moreover, ether linkage decreased the area per lipid in the ether lipid bilayer. Our computational framework and output demonstrate how ether modification changes the mechano-chemical properties of DPhPC bilayers.
Collapse
Affiliation(s)
- Ali Rasouli
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, And Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yousef Jamali
- School of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, And Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, Iran.
| | | |
Collapse
|
26
|
Ebtehaj Z, Malekmohammad M, Hatef A, Soltanolkotabi M. Direct and Plasmonic Nanoparticle‐Mediated Infrared Neural Stimulation: Comprehensive Computational Modeling and Validation. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zahra Ebtehaj
- Department of Physics, Faculty of Science University of Isfahan Isfahan 81746‐73441 Iran
| | - Mohammad Malekmohammad
- Department of Physics, Faculty of Science University of Isfahan Isfahan 81746‐73441 Iran
| | - Ali Hatef
- Nipissing Computational Physics Laboratory, Department of Computer Science and Mathematics Nipissing University North Bay Ontario P1B 8L7 Canada
| | - Mahmood Soltanolkotabi
- Department of Physics, Faculty of Science University of Isfahan Isfahan 81746‐73441 Iran
| |
Collapse
|
27
|
Yu Y, Krämer A, Venable RM, Brooks BR, Klauda JB, Pastor RW. CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids. J Chem Theory Comput 2021; 17:1581-1595. [PMID: 33620194 PMCID: PMC8130185 DOI: 10.1021/acs.jctc.0c01327] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Long-range Lennard-Jones (LJ) interactions have been incorporated into the CHARMM36 (C36) lipid force field (FF) using the LJ particle-mesh Ewald (LJ-PME) method in order to remove the inconsistency of bilayer and monolayer properties arising from the exclusion of long-range dispersion [Yu, Y.; Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. J. Chem. Theory Comput. 2021, 10.1021/acs.jctc.0c01326. (preceding article in this issue)]. The new FF is denoted C36/LJ-PME. While the first optimization was based on three phosphatidylcholines (PCs), this work extends the validation and parametrization to more lipids including PC, phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and ether lipids. The agreement with experimental structure data is excellent for PC, PE, and ether lipids. C36/LJ-PME also compares favorably with scattering data of PG bilayers but less so with NMR deuterium order parameters of 1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DMPG) at 303.15 K, indicating a need for future optimization regarding PG-specific parameters. Frequency dependence of NMR T1 spin-lattice relaxation times is well-described by C36/LJ-PME, and the overall agreement with experiment is comparable to C36. Lipid diffusion is slower than C36 due to the added long-range dispersion causing a higher viscosity, although it is still too fast compared to experiment after correction for periodic boundary conditions. When using a 10 Å real-space cutoff, the simulation speed of C36/LJ-PME is roughly equal to C36. While more lipids will be incorporated into the FF in the future, C36/LJ-PME can be readily used for common lipids and extends the capability of the CHARMM FF by supporting monolayers and eliminating the cutoff dependence.
Collapse
Affiliation(s)
- Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jeffery B Klauda
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
28
|
Yu Y, Krämer A, Venable RM, Simmonett AC, MacKerell AD, Klauda JB, Pastor RW, Brooks BR. Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. J Chem Theory Comput 2021; 17:1562-1580. [PMID: 33620214 PMCID: PMC8059446 DOI: 10.1021/acs.jctc.0c01326] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of the CHARMM lipid force field (FF) can be traced back to the early 1990s with its current version denoted CHARMM36 (C36). The parametrization of C36 utilized high-level quantum mechanical data and free energy calculations of model compounds before parameters were manually adjusted to yield agreement with experimental properties of lipid bilayers. While such manual fine-tuning of FF parameters is based on intuition and trial-and-error, automated methods can identify beneficial modifications of the parameters via their sensitivities and thereby guide the optimization process. This work introduces a semi-automated approach to reparametrize the CHARMM lipid FF with consistent inclusion of long-range dispersion through the Lennard-Jones particle-mesh Ewald (LJ-PME) approach. The optimization method is based on thermodynamic reweighting with regularization with respect to the C36 set. Two independent optimizations with different topology restrictions are presented. Targets of the optimizations are primarily liquid crystalline phase properties of lipid bilayers and the compression isotherm of monolayers. Pair correlation functions between water and lipid functional groups in aqueous solution are also included to address headgroup hydration. While the physics of the reweighting strategy itself is well-understood, applying it to heterogeneous, complex anisotropic systems poses additional challenges. These were overcome through careful selection of target properties and reweighting settings allowing for the successful incorporation of the explicit treatment of long-range dispersion, and we denote the newly optimized lipid force field as C36/LJ-PME. The current implementation of the optimization protocol will facilitate the future development of the CHARMM and related lipid force fields.
Collapse
Affiliation(s)
- Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Jeffery B Klauda
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| |
Collapse
|
29
|
Pluhackova K, Horner A. Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity. BMC Biol 2021; 19:4. [PMID: 33441107 PMCID: PMC7807449 DOI: 10.1186/s12915-020-00936-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high spatio-temporal resolution, molecular dynamics simulations have to be performed in natural(-like) lipid environments. RESULTS To enable more accurate MD simulations, we have prepared four membrane models of E. coli polar lipid extract, a typical model organism, each at all-atom (CHARMM36) and coarse-grained (Martini3) representations. These models contain all main lipid headgroup types of the E. coli inner membrane, i.e., phosphatidylethanolamines, phosphatidylglycerols, and cardiolipins, symmetrically distributed between the membrane leaflets. The lipid tail (un)saturation and propanylation stereochemistry represent the bacterial lipid tail composition of E. coli grown at 37∘C until 3/4 of the log growth phase. The comparison of the Simple three lipid component models to the complex 14-lipid component model Avanti over a broad range of physiologically relevant temperatures revealed that the balance of lipid tail unsaturation and propanylation in different positions and inclusion of lipid tails of various length maintain realistic values for lipid mobility, membrane area compressibility, lipid ordering, lipid volume and area, and the bilayer thickness. The only Simple model that was able to satisfactory reproduce most of the structural properties of the complex Avanti model showed worse agreement of the activation energy of basal water permeation with the here performed measurements. The Martini3 models reflect extremely well both experimental and atomistic behavior of the E. coli polar lipid extract membranes. Aquaporin-1 embedded in our native(-like) membranes causes partial lipid ordering and membrane thinning in its vicinity. Moreover, aquaporin-1 attracts and temporarily binds negatively charged lipids, mainly cardiolipins, with a distinct cardiolipin binding site in the crevice at the contact site between two monomers, most probably stabilizing the tetrameric protein assembly. CONCLUSIONS The here prepared and validated membrane models of E. coli polar lipids extract revealed that lipid tail complexity, in terms of double bond and cyclopropane location and varying lipid tail length, is key to stabilize membrane properties over a broad temperature range. In addition, they build a solid basis for manifold future simulation studies on more realistic lipid membranes bridging the gap between simulations and experiments.
Collapse
Affiliation(s)
- Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössiche Technische Hochschule (ETH) Zürich, Mattenstr. 26, Basel, 4058, Switzerland.
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| |
Collapse
|
30
|
Ramos-Martín F, Herrera-León C, Antonietti V, Sonnet P, Sarazin C, D’Amelio N. Antimicrobial Peptide K11 Selectively Recognizes Bacterial Biomimetic Membranes and Acts by Twisting Their Bilayers. Pharmaceuticals (Basel) 2020; 14:1. [PMID: 33374932 PMCID: PMC7821925 DOI: 10.3390/ph14010001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 12/14/2022] Open
Abstract
K11 is a synthetic peptide originating from the introduction of a lysine residue in position 11 within the sequence of a rationally designed antibacterial scaffold. Despite its remarkable antibacterial properties towards many ESKAPE bacteria and its optimal therapeutic index (320), a detailed description of its mechanism of action is missing. As most antimicrobial peptides act by destabilizing the membranes of the target organisms, we investigated the interaction of K11 with biomimetic membranes of various phospholipid compositions by liquid and solid-state NMR. Our data show that K11 can selectively destabilize bacterial biomimetic membranes and torque the surface of their bilayers. The same is observed for membranes containing other negatively charged phospholipids which might suggest additional biological activities. Molecular dynamic simulations reveal that K11 can penetrate the membrane in four steps: after binding to phosphate groups by means of the lysine residue at the N-terminus (anchoring), three couples of lysine residues act subsequently to exert a torque in the membrane (twisting) which allows the insertion of aromatic side chains at both termini (insertion) eventually leading to the flip of the amphipathic helix inside the bilayer core (helix flip and internalization).
Collapse
Affiliation(s)
- Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (C.S.)
| | - Claudia Herrera-León
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (C.S.)
| | - Viviane Antonietti
- Agents Infectieux, Résistance et Chimiothérapie, AGIR UR 4294, Université de Picardie Jules Verne, UFR de Pharmacie, 80037 Amiens, France; (V.A.); (P.S.)
| | - Pascal Sonnet
- Agents Infectieux, Résistance et Chimiothérapie, AGIR UR 4294, Université de Picardie Jules Verne, UFR de Pharmacie, 80037 Amiens, France; (V.A.); (P.S.)
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (C.S.)
| | - Nicola D’Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (C.S.)
| |
Collapse
|
31
|
Mondal D, Malik S, Banerjee P, Kundu N, Debnath A, Sarkar N. Modulation of Membrane Fluidity to Control Interfacial Water Structure and Dynamics in Saturated and Unsaturated Phospholipid Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12423-12434. [PMID: 33035065 DOI: 10.1021/acs.langmuir.0c02736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.
Collapse
Affiliation(s)
- Dipankar Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Niloy Kundu
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
- Environment Research Group, R&D and Scientific Services Department, Tata Steel Ltd., Jamshedpur 831007, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| |
Collapse
|
32
|
Dehury B, Kepp KP. Membrane dynamics of γ-secretase with the anterior pharynx-defective 1B subunit. J Cell Biochem 2020; 122:69-85. [PMID: 32830360 DOI: 10.1002/jcb.29832] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/13/2020] [Indexed: 01/12/2023]
Abstract
The four-subunit protease complex γ-secretase cleaves many single-pass transmembrane (TM) substrates, including Notch and β-amyloid precursor protein to generate amyloid-β (Aβ), central to Alzheimer's disease. Two of the subunits anterior pharynx-defective 1 (APH-1) and presenilin (PS) exist in two homologous forms APH1-A and APH1-B, and PS1 and PS2. The consequences of these variations are poorly understood and could affect Aβ production and γ-secretase medicine. Here, we developed the first complete structural model of the APH-1B subunit using the published cryo-electron microscopy (cryo-EM) structures of APH1-A (Protein Data Bank: 5FN2, 5A63, and 6IYC). We then performed all-atom molecular dynamics simulations at 303 K in a realistic bilayer system to understand both APH-1B alone and in γ-secretase without and with substrate C83-bound. We show that APH-1B adopts a 7TM topology with a water channel topology similar to APH-1A. We demonstrate direct transport of water through this channel, mainly via Glu84, Arg87, His170, and His196. The apo and holo states closely resemble the experimental cryo-EM structures with APH-1A, however with subtle differences: The substrate-bound APH-1B γ-secretase was quite stable, but some TM helices of PS1 and APH-1B rearranged in the membrane consistent with the disorder seen in the cryo-EM data. This produces different accessibility of water molecules for the catalytic aspartates of PS1, critical for Aβ production. In particular, we find that the typical distance between the catalytic aspartates of PS1 and the C83 cleavage sites are shorter in APH-1B, that is, it represents a more closed state, due to interactions with the C-terminal fragment of PS1. Our structural-dynamic model of APH-1B alone and in γ-secretase suggests generally similar topology but some notable differences in water accessibility which may be relevant to the protein's existence in two forms and their specific function and location.
Collapse
Affiliation(s)
- Budheswar Dehury
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
33
|
Martyna A, Bahsoun B, Madsen JJ, Jackson FSJS, Badham MD, Voth GA, Rossman JS. Cholesterol Alters the Orientation and Activity of the Influenza Virus M2 Amphipathic Helix in the Membrane. J Phys Chem B 2020; 124:6738-6747. [PMID: 32644803 PMCID: PMC7515559 DOI: 10.1021/acs.jpcb.0c03331] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The
influenza virus M2 amphipathic helix (M2AH) alters membrane
curvature in a cholesterol-dependent manner, mediating viral membrane
scission during influenza virus budding. Here, we have investigated
the biophysical effects of cholesterol on the ability of an M2AH peptide
to manipulate membrane properties. We see that the ability of the
M2AH to interact with membranes and form an α-helix is independent
of membrane cholesterol concentration; however, cholesterol affects
the angle of the M2AH peptide within the membrane. This change in
membrane orientation affects the ability of the M2AH to alter lipid
order. In low-cholesterol membranes, the M2AH is inserted near the
level of the lipid head groups, increasing lipid order, which may
contribute to generation of the membrane curvature. As the cholesterol
content increases, the M2AH insertion becomes flatter and slightly
deeper in the membrane below the lipid headgroups, where the polar
face can continue to interact with the headgroups while the hydrophobic
face binds cholesterol. This changed orientation minimizes lipid packing
defects and lipid order changes, likely reducing the generation of
membrane curvature. Thus, cholesterol regulates M2 membrane scission
by precisely modulating M2AH positioning within the membrane. This
has implications for the understanding of many of amphipathic-helix-driven
cellular budding processes that occur in specific lipid environments.
Collapse
Affiliation(s)
- Agnieszka Martyna
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Basma Bahsoun
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Jesper J Madsen
- Department of Chemistry and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | | | - Matthew D Badham
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Gregory A Voth
- Department of Chemistry and Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jeremy S Rossman
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| |
Collapse
|
34
|
Yu Y, Klauda JB. Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids. J Phys Chem B 2020; 124:6797-6812. [PMID: 32639155 DOI: 10.1021/acs.jpcb.0c04795] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate lipid force field (FF) parameters used in molecular dynamics (MD) simulations are crucial for understanding the properties of lipid-containing systems and biological processes related to lipids. The last update of the CHARMM36 united atom chain model (C36UA) was in 2013 [Lee, S. J. Phys. Chem. B 2014, 118, 547 556]; it utilized CHARMM36 (C36) lipid FF parameters for headgroups and OPLS-UA Lennard-Jones (LJ) parameters for tails. Simulations with the FF were able to reproduce many experimental observables of lipid bilayers accurately, but to be more applicable for a wide range of lipids, additional FF parameter optimization was needed. In this work, we present an update of the model, named C36UAr. The parameterization included the LJ parameters for hydrocarbons and related dihedrals. Bulk liquid properties (density, heat of vaporization, isothermal compressibility, and diffusion constant) of model compounds were used as targets for the LJ parameter fitting, and dihedrals were fit to either quantum mechanical (QM) or potential of mean force (PMF) calculations using C36. Thermodynamic reweighting was used to further improve the parameters. Bilayer simulations of various lipid headgroups (phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol) and tails (saturated, monounsaturated, and polyunsaturated) were performed to validate the model, and significant improvements were seen in bilayer properties, including surface area, membrane thicknesses, NMR deuterium order parameters, and density profiles. C36UAr was also compared to the hydrogen mass repartitioning (HMR) method. The high accuracy and competitive efficiency shown in this study make C36UAr one of the best choices for studies of membrane structure and membrane-associated proteins.
Collapse
|
35
|
Callahan KM, Mondou B, Sasseville L, Schwartz JL, D'Avanzo N. The influence of membrane bilayer thickness on KcsA channel activity. Channels (Austin) 2020; 13:424-439. [PMID: 31608774 PMCID: PMC6802934 DOI: 10.1080/19336950.2019.1676367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Atomic resolution structures have provided significant insight into the gating and permeation mechanisms of various ion channels, including potassium channels. However, ion channels may also be regulated by numerous factors, including the physiochemical properties of the membrane in which they are embedded. For example, the matching of the bilayer's hydrophobic region to the hydrophobic external surface of the ion channel is thought to minimize the energetic penalty needed to solvate hydrophobic residues or exposed lipid tails. To understand the molecular basis of such regulation by hydrophobic matching requires examining channels in the presence of the lipid membrane. Here we examine the role of hydrophobic matching in regulating the activity of the model potassium channel, KcsA. 86Rb+ influx assays and single-channel recordings indicate that the non-inactivating E71A KcsA channel is most active in thin bilayers (<diC18:1PC). Bilayer thickness affects the open probability of KcsA and not its unitary conductance. Molecular dynamics simulations indicate that the bilayer can sufficiently modify its dimensions to accommodate KcsA channels without major perturbations in the protein helical packing within the nanosecond timescale. Based on experimental results and MD simulations, we present a model in which bilayer thickness influences the stability of the open and closed conformations of the intracellular gate of KcsA, with minimal impact on the stability of the selectivity filter of the non-inactivating mutant, E71A.
Collapse
Affiliation(s)
- Karen M Callahan
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada
| | - Benoit Mondou
- Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada
| | - Louis Sasseville
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada
| | - Jean-Louis Schwartz
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada.,Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada.,Centre SÈVE, Université de Sherbrooke , Sherbrooke , Canada
| | - Nazzareno D'Avanzo
- From the Département de pharmacologie et physiologie, Faculté de médecine, Université de Montréal , Montréal , Canada.,Département de biochimie et médecine moléculaire, Université de Montréal , Montréal , Canada
| |
Collapse
|
36
|
Ramezanpour M, Schmidt ML, Bashe BYM, Pruim JR, Link ML, Cullis PR, Harper PE, Thewalt JL, Tieleman DP. Structural Properties of Inverted Hexagonal Phase: A Hybrid Computational and Experimental Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6668-6680. [PMID: 32437159 DOI: 10.1021/acs.langmuir.0c00600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inverted/reverse hexagonal (HII) phases are of special interest in several fields of research, including nanomedicine. We used molecular dynamics (MD) simulation to study HII systems composed of dioleoylphosphatidylethanolamine (DOPE) and palmitoyloleoylphosphatidylethanolamine (POPE) at several hydration levels and temperatures. The effect of the hydration level on several HII structural parameters, including deuterium order parameters, was investigated. We further used MD simulations to estimate the maximum hydrations of DOPE and POPE HII lattices at several given temperatures. Finally, the effect of acyl chain unsaturation degree on the HII structure was studied via comparing the DOPE with POPE HII systems. In addition to MD simulations, we used deuterium nuclear magnetic resonance (2H NMR) and small-angle X-ray scattering (SAXS) experiments to measure the DOPE acyl chain order parameters, lattice plane distances, and the water core radius in HII phase DOPE samples at several temperatures in the presence of excess water. Structural parameters calculated from MD simulations are in excellent agreement with the experimental data. Dehydration decreases the radius of the water core. An increase in hydration level slightly increased the deuterium order parameter of lipids acyl chains, whereas an increase in temperature decreased it. Lipid cylinders undulated along the cylinder axis as a function of hydration level. The maximum hydration levels of PE HII phases at different temperatures were successfully predicted by MD simulations based on a single experimental measurement for the lattice plane distance in the presence of excess water. An increase in temperature decreases the maximum hydration and consequently the radius of the water core and lattice plane distances. Finally, DOPE formed HII structures with a higher curvature compared to POPE, as expected. We propose a general protocol for constructing computational HII systems that correspond to the experimental systems. This protocol could be used to study HII systems composed of molecules other than the PE systems used here and to improve and validate force field parameters by using the target data in the HII phase.
Collapse
Affiliation(s)
- M Ramezanpour
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - M L Schmidt
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - B Y M Bashe
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - J R Pruim
- Department of Physics and Astronomy, Calvin University, Grand Rapids, Michigan 49546, United States
| | - M L Link
- Department of Physics and Astronomy, Calvin University, Grand Rapids, Michigan 49546, United States
| | - P R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - P E Harper
- Department of Physics and Astronomy, Calvin University, Grand Rapids, Michigan 49546, United States
| | - J L Thewalt
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - D P Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| |
Collapse
|
37
|
Doktorova M, Kučerka N, Kinnun JJ, Pan J, Marquardt D, Scott HL, Venable RM, Pastor RW, Wassall SR, Katsaras J, Heberle FA. Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data. J Phys Chem B 2020; 124:5186-5200. [PMID: 32468822 DOI: 10.1021/acs.jpcb.0c03389] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.
Collapse
Affiliation(s)
- Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.,Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 814 99 Bratislava, Slovakia
| | - Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen R Wassall
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
38
|
de Lichtervelde ACL, de Souza JP, Bazant MZ. Heat of nervous conduction: A thermodynamic framework. Phys Rev E 2020; 101:022406. [PMID: 32168602 DOI: 10.1103/physreve.101.022406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/04/2019] [Indexed: 01/08/2023]
Abstract
Early recordings of nervous conduction revealed a notable thermal signature associated with the electrical signal. The observed production and subsequent absorption of heat arise from physicochemical processes that occur at the cell membrane level during the conduction of the action potential. In particular, the reversible release of electrostatic energy stored as a difference of potential across the cell membrane appears as a simple yet consistent explanation for the heat production, as proposed in the "Condenser Theory." However, the Condenser Theory has not been analyzed beyond the analogy between the cell membrane and a parallel-plate capacitor, i.e., a condenser, and cannot account for the magnitude of the heat signature. In this work, we use a detailed electrostatic model of the cell membrane to revisit the Condenser Theory. We derive expressions for free energy and entropy changes associated with the depolarization of the membrane by the action potential, which give a direct measure of the heat produced and absorbed by neurons. We show how the density of surface charges on both sides of the membrane impacts the energy changes. Finally, considering a typical action potential, we show that if the membrane holds a bias of surface charges, such that the internal side of the membrane is 0.05Cm^{-2} more negative than the external side, the size of the heat predicted by the model reaches the range of experimental values. Based on our study, we identify the release of electrostatic energy by the membrane as the primary mechanism of heat production and absorption by neurons during nervous conduction.
Collapse
Affiliation(s)
- Aymar C L de Lichtervelde
- Department of Physical Chemistry & Soft Matter, Wageningen University, 6708 WG Wageningen, the Netherlands
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
39
|
West A, Zoni V, Teague WE, Leonard AN, Vanni S, Gawrisch K, Tristram-Nagle S, Sachs JN, Klauda JB. How Do Ethanolamine Plasmalogens Contribute to Order and Structure of Neurological Membranes? J Phys Chem B 2020; 124:828-839. [PMID: 31916765 PMCID: PMC8157475 DOI: 10.1021/acs.jpcb.9b08850] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ethanolamine plasmalogen (EtnPLA) is a conical-shaped ether lipid and an essential component of neurological membranes. Low stability against oxidation limits its study in experiments. The concentration of EtnPLA in the bilayer varies depending on cell type and disease progression. Here we report on mixed bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-(1Z-octadecenyl)-2-oleoyl-sn-glycero-3-phosphoethanolamine (C18(Plasm)-18:1PE, PLAPE), an EtnPLA lipid subtype, at mole ratios of 2:1, 1:1, and 1:2. We present X-ray diffuse scattering (XDS) form factors F(qz) from oriented stacks of bilayers, related electron-density profiles, and hydrocarbon chain NMR order parameters. To aid future research on EtnPLA lipids and associated proteins, we have also extended the CHARMM36 all-atom force field to include the PLAPE lipid. The ability of the new force-field parameters to reproduce both X-ray and NMR structural properties of the mixed bilayer is remarkable. Our results indicate a thickening of the bilayer upon incorporation of increasing amounts of PLAPE into mixed bilayers, a reduction of lateral area per molecule, and an increase in lipid tail-ordering. The lateral compressibility modulus (KA) calculated from simulations yielded values for PLAPE similar to POPC.
Collapse
Affiliation(s)
- Ana West
- Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Valeria Zoni
- Department of Biology , University of Fribourg , 1700 Fribourg , Switzerland
| | - Walter E Teague
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism , NIH , Bethesda , Maryland 20892 , United States
| | - Alison N Leonard
- Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Stefano Vanni
- Department of Biology , University of Fribourg , 1700 Fribourg , Switzerland
| | - Klaus Gawrisch
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism , NIH , Bethesda , Maryland 20892 , United States
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Physics Department , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Jonathan N Sachs
- Department of Biomedical Engineering , University of Minnesota , Twin Cities , Minnesota 55455 , United States
| | - Jeffery B Klauda
- Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
- Department of Chemical and Biomolecular Engineering , University of Maryland , College Park , Maryland 20742 , United States
| |
Collapse
|
40
|
Dehury B, Tang N, Kepp KP. Insights into membrane-bound presenilin 2 from all-atom molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:3196-3210. [PMID: 31405326 DOI: 10.1080/07391102.2019.1655481] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Presenilins 1 and 2 (PS1 or PS2) are main genetic risk factors of familial Alzheimer's disease (AD) that produce the β-amyloid (Aβ) peptides and also have important stand-alone functions related to, e.g. calcium signaling. Most work so far has focused on PS1, but humans carry both PS1 and PS2, and mutations in both cause AD. Here, we develop a computational model of PS2 in the membrane to address the question how pathogenic PS2 mutations affect the membrane-embedded protein. The models are based on cryo-electron microscopy structures of PS1 translated to PS2, augmented with missing residues and a complete all-atom membrane-water system, and equilibrated using three independent 500-ns simulations of molecular dynamics with a structure-balanced force field. We show that the nine-transmembrane channel structure is substantially controlled by major dynamics in the hydrophilic loop bridging TM6 and TM7, which functions as a 'plug' in the PS2 membrane channel. TM2, TM6, TM7 and TM9 flexibility controls the size of this channel. We find that most pathogenic PS2 mutations significantly reduce stability relative to random mutations, using a statistical ANOVA test with all possible mutations in the affected sites as a control. The associated loss of compactness may also impair calcium affinity. Remarkably, similar properties of the open state are known to impair the binding of substrates to γ-secretase, and we thus argue that the two mechanisms could be functionally related.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Budheswar Dehury
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ning Tang
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
41
|
Balusek C, Hwang H, Lau CH, Lundquist K, Hazel A, Pavlova A, Lynch DL, Reggio PH, Wang Y, Gumbart JC. Accelerating Membrane Simulations with Hydrogen Mass Repartitioning. J Chem Theory Comput 2019; 15:4673-4686. [PMID: 31265271 PMCID: PMC7271963 DOI: 10.1021/acs.jctc.9b00160] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest motions in the system and is typically limited to 2 fs. An increasingly popular approach is to increase the mass of the hydrogen atoms to ∼3 amu and decrease the mass of the parent atom by an equivalent amount. This approach, known as hydrogen-mass repartitioning (HMR), permits time steps up to 4 fs with reasonable simulation stability. While HMR has been applied in many published studies to date, it has not been extensively tested for membrane-containing systems. Here, we compare the results of simulations of a variety of membranes and membrane-protein systems run using a 2 fs time step and a 4 fs time step with HMR. For pure membrane systems, we find almost no difference in structural properties, such as area-per-lipid, electron density profiles, and order parameters, although there are differences in kinetic properties such as the diffusion constant. Conductance through a porin in an applied field, partitioning of a small peptide, hydrogen-bond dynamics, and membrane mixing show very little dependence on HMR and the time step. We also tested a 9 Å cutoff as compared to the standard CHARMM cutoff of 12 Å, finding significant deviations in many properties tested. We conclude that HMR is a valid approach for membrane systems, but a 9 Å cutoff is not.
Collapse
Affiliation(s)
| | | | - Chun Hon Lau
- Department of Physics , The Chinese University of Hong Kong , Shatin, NT, Hong Kong , People's Republic of China
| | | | | | | | - Diane L Lynch
- Department of Chemistry and Biochemistry , University of North Carolina , Greensboro , North Carolina 27402 , United States
| | - Patricia H Reggio
- Department of Chemistry and Biochemistry , University of North Carolina , Greensboro , North Carolina 27402 , United States
| | - Yi Wang
- Department of Physics , The Chinese University of Hong Kong , Shatin, NT, Hong Kong , People's Republic of China
| | | |
Collapse
|
42
|
Leonard AN, Wang E, Monje-Galvan V, Klauda JB. Developing and Testing of Lipid Force Fields with Applications to Modeling Cellular Membranes. Chem Rev 2019; 119:6227-6269. [DOI: 10.1021/acs.chemrev.8b00384] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
43
|
Klauda JB. Perspective: Computational modeling of accurate cellular membranes with molecular resolution. J Chem Phys 2018; 149:220901. [DOI: 10.1063/1.5055007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, USA
| |
Collapse
|
44
|
The Role of Lipid Interactions in Simulations of the α-Hemolysin Ion-Channel-Forming Toxin. Biophys J 2018; 115:1720-1730. [PMID: 30287110 DOI: 10.1016/j.bpj.2018.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 01/25/2023] Open
Abstract
Molecular dynamics simulations were performed to describe the function of the ion-channel-forming toxin α-hemolysin (αHL) in lipid membranes that were composed of either 1,2-diphytanoyl-sn-glycero-3-phospho-choline or 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline. The simulations highlight the importance of lipid type in maintaining αHL structure and function, enabling direct comparison to experiments for biosensing applications. We determined that although the two lipids studied are similar in structure, 1,2-diphytanoyl-sn-glycero-3-phospho-choline membranes better match the hydrophobic thickness of αHL compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline membranes. This hydrophobic match is essential to maintaining proper alignment of β-sheet loops at the trans entrance of αHL, which, when disrupted, creates an additional constriction to ion flow that decreases the channel current below experimental values and creates greater variability in channel conductance. Agreement with experiments was further improved with sufficient lipid membrane equilibration and allowed the discrimination of subtle αHL conduction states with lipid type. Finally, we explore the effects of truncating the extramembrane cap of αHL and its role in maintaining proper alignment of αHL in the membrane and channel conductance. Our results demonstrate the essential role of lipid type and lipid-protein interactions in simulations of αHL and will considerably improve the interpretation of experimental data.
Collapse
|
45
|
Khakbaz P, Klauda JB. Investigation of phase transitions of saturated phosphocholine lipid bilayers via molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1489-1501. [DOI: 10.1016/j.bbamem.2018.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/01/2022]
|
46
|
Ebtehaj Z, Hatef A, Malekmohammad M, Soltanolkotabi M. Computational Modeling and Validation of Thermally Induced Electrical Capacitance Changes for Lipid Bilayer Membranes Irradiated by Pulsed Lasers. J Phys Chem B 2018; 122:7319-7331. [PMID: 29912560 DOI: 10.1021/acs.jpcb.8b02616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neural stimulation has widespread applications in investigating brain functions, restoring impaired neural functions, and treating numerous neurological/psychiatric diseases. Use of infrared pulses to stimulate neurons (infrared neural stimulation) offers a direct and non-invasive technique. Recent research has demonstrated that transient heating associated with the absorption of infrared light by the local aqueous medium around the cell membrane can stimulate nerves. One mechanism for this stimulation is due to a thermally induced increase in the membrane electrical capacitance, which causes cell depolarization as well as action potential production under certain physiological conditions. A theoretical and computational model helps better understand the mechanism of thermally induced electrical capacitance changes and optimize the stimulus parameters. In this article, we develop the existing theoretical models for membrane electrical capacitance and its thermally induced changes. We improve the formulation of Gouy-Chapman-Stern theory by Genet et al. and Shapiro et al. with the addition of a diffuse layer to the electrical double layer and by modifying the relation of Stern layer capacitance, to calculate the membrane capacitive charge and capacitive current. We also present a new method to calculate the membrane electrical capacitance and the rate of its thermally induced changes. In our calculations, two new factors are considered including the temperature dependence of the surface charge density and the hydrophobic core dielectric constant of the lipid bilayer. Our developed model predicts rates of 0.3 and 0.26%/°C for the thermally induced capacitance changes of the artificial lipid bilayer under two different sets of conditions previously reported by Shapiro et al. and Carvalho-de-Souza et al., respectively. Our model is in very good agreement with the corresponding experimental values given by these groups. The presented model is also able to calculate the membrane capacitive currents and investigate the voltage dependence of this current.
Collapse
Affiliation(s)
- Z Ebtehaj
- Department of Physics, Faculty of science , University of Isfahan , Isfahan 81746-73441 , Iran
| | - A Hatef
- Nipissing Computational Physics Laboratory, Department of Computer Science and Mathematics , Nipissing University , North Bay , Ontario P1B 8L7 , Canada
| | - M Malekmohammad
- Department of Physics, Faculty of science , University of Isfahan , Isfahan 81746-73441 , Iran
| | - M Soltanolkotabi
- Department of Physics, Faculty of science , University of Isfahan , Isfahan 81746-73441 , Iran
| |
Collapse
|
47
|
Wang E, Klauda JB. Simulations of Pure Ceramide and Ternary Lipid Mixtures as Simple Interior Stratum Corneum Models. J Phys Chem B 2018; 122:2757-2768. [DOI: 10.1021/acs.jpcb.8b00348] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
48
|
Leonard AN, Simmonett AC, Pickard FC, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW. Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations. J Chem Theory Comput 2018; 14:948-958. [PMID: 29268012 DOI: 10.1021/acs.jctc.7b00948] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Long-range Lennard-Jones (LJ) interactions have a significant impact on the structural and thermodynamic properties of nonpolar systems. While several methods have been introduced for the treatment of long-range LJ interactions in molecular dynamics (MD) simulations, increased accuracy and extended applicability is required for anisotropic systems such as lipid bilayers. The recently refined Lennard-Jones particle-mesh Ewald (LJ-PME) method extends the particle-mesh Ewald (PME) method to long-range LJ interactions and is suitable for use with anisotropic systems. Implementation of LJ-PME with the CHARMM36 (C36) additive and CHARMM Drude polarizable force fields improves agreement with experiment for density, isothermal compressibility, surface tension, viscosity, translational diffusion, and 13C T1 relaxation times of pure alkanes. Trends in the temperature dependence of the density and isothermal compressibility of hexadecane are also improved. While the C36 additive force field with LJ-PME remains a useful model for liquid alkanes, the Drude polarizable force field with LJ-PME is more accurate for nearly all quantities considered. LJ-PME is also preferable to the isotropic long-range correction for hexadecane because the molecular order extends to nearly 20 Å, well beyond the usual 10-12 Å cutoffs used in most simulations.
Collapse
Affiliation(s)
- Alison N Leonard
- Biophysics Program, University of Maryland , College Park, Maryland 20742, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.,Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Jeffery B Klauda
- Biophysics Program, University of Maryland , College Park, Maryland 20742, United States.,Department of Chemical and Biomolecular Engineering, University of Maryland , College Park, Maryland 20742, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| |
Collapse
|
49
|
|
50
|
Haynes CJE, Zhu J, Chimerel C, Hernández-Ainsa S, Riddell IA, Ronson TK, Keyser UF, Nitschke JR. Blockable Zn10
L15
Ion Channels through Subcomponent Self-Assembly. Angew Chem Int Ed Engl 2017; 56:15388-15392. [DOI: 10.1002/anie.201709544] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Cally J. E. Haynes
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Jinbo Zhu
- Cavendish Laboratory; University of Cambridge; JJ Thompson Avenue Cambridge CB3 0HE UK
| | - Catalin Chimerel
- Cavendish Laboratory; University of Cambridge; JJ Thompson Avenue Cambridge CB3 0HE UK
| | | | - Imogen A. Riddell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Current address: School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Tanya K. Ronson
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Ulrich F. Keyser
- Cavendish Laboratory; University of Cambridge; JJ Thompson Avenue Cambridge CB3 0HE UK
| | - Jonathan R. Nitschke
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|