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Paratore TA, Schmidt GE, Ross AH, Gericke A. Thermal stability of bivalent cation/phosphoinositide domains in model membranes. Chem Phys Lipids 2024; 264:105424. [PMID: 39098579 DOI: 10.1016/j.chemphyslip.2024.105424] [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: 06/19/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
As key mediators in a wide array of signaling events, phosphoinositides (PIPs) orchestrate the recruitment of proteins to specific cellular locations at precise moments. This intricate spatiotemporal regulation of protein activity often necessitates the localized enrichment of the corresponding PIP. We investigate the extent and thermal stabilities of phosphatidylinositol-4-phosphate (PI(4)P), phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2 and phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3) clusters with calcium and magnesium ions. We observe negligible or minimal clustering of all examined PIPs in the presence of Mg2+ ions. While PI(4)P shows in the presence of Ca2+ no clustering, PI(4,5)P2 forms with Ca2+ strong clusters that exhibit stablity up to at least 80°C. The extent of cluster formation for the interaction of PI(3,4,5)P3 with Ca2+ is less than what was observed for PI(4,5)P2, yet we still observe some clustering up to 80°C. Given that cholesterol has been demonstrated to enhance PIP clustering, we examined whether bivalent cations and cholesterol synergistically promote PIP clustering. We found that the interaction of Mg2+ or Ca2+ with PI(4)P remains extraordinarily weak, even in the presence of cholesterol. In contrast, we observe synergistic interaction of cholesterol and Ca2+ with PI(4,5)P2. Also, in the presence of cholesterol, the interaction of Mg2+ with PI(4,5)P2 remains weak. PI(3,4,5)P3 does not show strong clustering with cholesterol for the experimental conditions of our study and the interaction with Ca2+ and Mg2+ was not influenced by the presence of cholesterol.
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Affiliation(s)
- Trevor A Paratore
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01609, USA
| | - Greta E Schmidt
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01609, USA
| | - Alonzo H Ross
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01609, USA
| | - Arne Gericke
- Worcester Polytechnic Institute, Department of Chemistry and Biochemistry, Worcester, MA 01609, USA.
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Beiter J, Voth GA. Making the cut: Multiscale simulation of membrane remodeling. Curr Opin Struct Biol 2024; 87:102831. [PMID: 38740001 PMCID: PMC11283976 DOI: 10.1016/j.sbi.2024.102831] [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: 02/19/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Biological membranes are dynamic heterogeneous materials, and their shape and organization are tightly coupled to the properties of the proteins in and around them. However, the length scales of lipid and protein dynamics are far below the size of membrane-bound organelles, much less an entire cell. Therefore, multiscale modeling approaches are often necessary to build a comprehensive picture of the interplay of these factors, and have provided critical insights into our understanding of membrane dynamics. Here, we review computational methods for studying membrane remodeling, as well as passive and active examples of protein-driven membrane remodeling. As the field advances towards the modeling of key aspects of organelles and whole cells - an increasingly accessible regime of study - we summarize here recent successes and offer comments on future trends.
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Affiliation(s)
- Jeriann Beiter
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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3
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Rice A, Prasad S, Brooks BR, Pastor RW. Simulating asymmetric membranes using P2 1 periodic boundary conditions. Methods Enzymol 2024; 701:309-358. [PMID: 39025575 DOI: 10.1016/bs.mie.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Molecular dynamics (MD) simulations of symmetric lipid bilayers are now well established, while those of asymmetric ones are considerably less developed. This disjunction arises in part because the surface tensions of leaflets in asymmetric bilayers can differ (unlike those of symmetric ones), and there is no simple way to determine them without assumptions. This chapter describes the use of P21 periodic boundary conditions (PBC), which allow lipids to switch leaflets, to generate asymmetric bilayers under the assumption of equal chemical potentials of lipids in opposing leaflets. A series of examples, ranging from bilayers with one lipid type to those with peptides and proteins, provides a guide for the use of P21 PBC. Critical properties of asymmetric membranes, such as spontaneous curvature, are highly sensitive to differences in the leaflet surface tensions (or differential stress), and equilibration with P21 PBC substantially reduces differential stress of asymmetric bilayers assembled with surface area-based methods. Limitations of the method are discussed. Technically, the nonstandard unit cell is difficult to parallelize and to incorporate restraints. Inherently, the assumption of equal chemical potentials, and therefore the method itself, is not applicable to all target systems. Despite these limitations, it is argued that P21 simulations should be considered when designing equilibration protocols for MD studies of most asymmetric membranes.
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Affiliation(s)
- Amy Rice
- Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Samarjeet Prasad
- Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, Blood Institute, National Institutes of Health, Bethesda, MD, United States.
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Jarin Z, Venable RM, Han K, Pastor RW. Ion-Induced PIP2 Clustering with Martini3: Modification of Phosphate-Ion Interactions and Comparison with CHARMM36. J Phys Chem B 2024; 128:2134-2143. [PMID: 38393820 DOI: 10.1021/acs.jpcb.3c06523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) is a critical lipid for cellular signaling. The specific phosphorylation of the inositol ring controls protein binding as well as clustering behavior. Two popular models to describe ion-mediated clustering of PIP2 are Martini3 (M3) and CHARMM36 (C36). Molecular dynamics simulations of PIP2-containing bilayers in solutions of potassium chloride, sodium chloride, and calcium chloride, and at two different resolutions are performed to understand the aggregation and the model parameters that drive it. The average M3 clusters of PIP2 in bilayers of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine and PIP2 bilayers in the presence of K+, Na+, or Ca2+ contained 2.2, 2.6, and 6.4 times more PIP2 than C36 clusters, respectively. Indeed, the Ca2+-containing systems often formed a single large aggregate. Reparametrization of the M3 ion-phosphate Lennard-Jones interaction energies to reproduce experimental osmotic pressure of sodium dimethyl phosphate (DMP), K[DMP], and Ca[DMP]2 solutions, the same experimental target as C36, yielded comparably sized PIP2 clusters for the two models. Furthermore, C36 and the modified M3 predict similar saturation of the phosphate groups with increasing Ca2+, although the coarse-grained model does not capture the cooperativity between K+ and Ca2+. This characterization of the M3 behavior in the presence of monovalent and divalent ions lays a foundation to study cation/protein/PIP2 clustering.
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Affiliation(s)
- Zack Jarin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Kyungreem Han
- Laboratory of Computational Neurophysics, Center for Brain Technology, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892, United States
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Nguyen ATP, Weigle AT, Shukla D. Functional regulation of aquaporin dynamics by lipid bilayer composition. Nat Commun 2024; 15:1848. [PMID: 38418487 PMCID: PMC10901782 DOI: 10.1038/s41467-024-46027-y] [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: 07/21/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics are examined. We demonstrate that SoPIP2;1's structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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Jain H, Karathanou K, Bondar AN. Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes. Biomolecules 2023; 13:1238. [PMID: 37627303 PMCID: PMC10452392 DOI: 10.3390/biom13081238] [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: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers.
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Affiliation(s)
- Honey Jain
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Atomiștilor 405, 077125 Măgurele, Romania
- IAS-5/INM-9, Forschungszentrum Jülich, Institute of Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany
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Yuan Z, Hansen SB. Cholesterol Regulation of Membrane Proteins Revealed by Two-Color Super-Resolution Imaging. MEMBRANES 2023; 13:membranes13020250. [PMID: 36837753 PMCID: PMC9966874 DOI: 10.3390/membranes13020250] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 05/15/2023]
Abstract
Cholesterol and phosphatidyl inositol 4,5-bisphosphate (PIP2) are hydrophobic molecules that regulate protein function in the plasma membrane of all cells. In this review, we discuss how changes in cholesterol concentration cause nanoscopic (<200 nm) movements of membrane proteins to regulate their function. Cholesterol is known to cluster many membrane proteins (often palmitoylated proteins) with long-chain saturated lipids. Although PIP2 is better known for gating ion channels, in this review, we will discuss a second independent function as a regulator of nanoscopic protein movement that opposes cholesterol clustering. The understanding of the movement of proteins between nanoscopic lipid domains emerged largely through the recent advent of super-resolution imaging and the establishment of two-color techniques to label lipids separate from proteins. We discuss the labeling techniques for imaging, their strengths and weakness, and how they are used to reveal novel mechanisms for an ion channel, transporter, and enzyme function. Among the mechanisms, we describe substrate and ligand presentation and their ability to activate enzymes, gate channels, and transporters rapidly and potently. Finally, we define cholesterol-regulated proteins (CRP) and discuss the role of PIP2 in opposing the regulation of cholesterol, as seen through super-resolution imaging.
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Affiliation(s)
- Zixuan Yuan
- Department of Molecular Medicine, Department of Neuroscience, UF Scripps, Jupiter, FL 33458, USA
- Department of Neuroscience UF Scripps, Jupiter, FL 33458, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Scott B. Hansen
- Department of Molecular Medicine, Department of Neuroscience, UF Scripps, Jupiter, FL 33458, USA
- Department of Neuroscience UF Scripps, Jupiter, FL 33458, USA
- Correspondence:
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Liang Q, Ofosuhene AP, Kiessling V, Liang B, Kreutzberger AJB, Tamm LK, Cafiso DS. Complexin-1 and synaptotagmin-1 compete for binding sites on membranes containing PtdInsP 2. Biophys J 2022; 121:3370-3380. [PMID: 36016497 PMCID: PMC9515229 DOI: 10.1016/j.bpj.2022.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/28/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
Complexin-1 is an essential protein for neuronal exocytosis that acts to depress spontaneous fusion events while enhancing evoked neurotransmitter release. In addition to binding soluble N-ethylmaleimide-sensitive factor attachment protein receptors, it is well established that complexin associates with membranes in a manner that depends upon membrane curvature. In the present work, we examine the membrane binding of complexin using electron paramagnetic resonance spectroscopy, fluorescence anisotropy, and total internal reflection fluorescence microscopy. The apparent membrane affinity of complexin is found to strongly depend upon the concentration of protein used in the binding assay, and this is a result of a limited number of binding sites for complexin on the membrane interface. Although both the N- and C-terminal regions of complexin associate with the membrane interface, membrane affinity is driven by its C-terminus. Complexin prefers to bind liquid-disordered membrane phases and shows an enhanced affinity toward membranes containing phosphatidylinositol 4-5-bisphosphate (PI(4,5)P2). In the presence of PI(4,5)P2, complexin is displaced from the membrane surface by proteins that bind to or sequester PI(4,5)P2. In particular, the neuronal calcium sensor synaptotagmin-1 displaces complexin from the membrane but only when PI(4,5)P2 is present. Complexin and synaptotagmin compete on the membrane interface in the presence of PI(4,5)P2, and this interaction may play a role in calcium-triggered exocytosis by displacing complexin from its fusion-inhibiting state.
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Affiliation(s)
- Qian Liang
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Akosua P Ofosuhene
- Department of Chemistry, University of Virginia, Charlottesville, Virginia
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics University of Virginia, Charlottesville, Virginia; Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics University of Virginia, Charlottesville, Virginia; Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Alex J B Kreutzberger
- Department of Molecular Physiology and Biological Physics University of Virginia, Charlottesville, Virginia; Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics University of Virginia, Charlottesville, Virginia; Center for Membrane Biology, University of Virginia, Charlottesville, Virginia
| | - David S Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, Virginia; Center for Membrane Biology, University of Virginia, Charlottesville, Virginia.
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