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Hryc J, Markiewicz M, Pasenkiewicz-Gierula M. Stacks of monogalactolipid bilayers can transform into a lattice of water channels. iScience 2023; 26:107863. [PMID: 37766978 PMCID: PMC10520361 DOI: 10.1016/j.isci.2023.107863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/17/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The lipid matrix of thylakoid membranes is a lamellar bilayer, but under a certain condition it can convert locally into a nonlamellar structure. This is possible because one of the main membrane lipids, MGDG, promotes the formation of an inverse hexagonal phase. Here, the spontaneous transformation of aligned hydrated MGDG bilayers into nonlamellar structures is investigated using all-atom molecular dynamics simulation. Previous studies have demonstrated that MGDG polar head groups connect vertically across the interface. In this study, the evolution of the system's initial structure into a lattice of water channels and contacted surfaces created by numerous vertical MGDG connections depended on the width of the hydrating water layers. These widths controlled the bilayers' ability to bend, which was a prerequisite for channel formation. Locally, an intensive exchange of MGDG molecules between apposing bilayer leaflets occurred, although a stable semi-toroidal stalk did not develop.
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Affiliation(s)
- Jakub Hryc
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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Sauvola CW, Littleton JT. SNARE Regulatory Proteins in Synaptic Vesicle Fusion and Recycling. Front Mol Neurosci 2021; 14:733138. [PMID: 34421538 PMCID: PMC8377282 DOI: 10.3389/fnmol.2021.733138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/20/2021] [Indexed: 01/01/2023] Open
Abstract
Membrane fusion is a universal feature of eukaryotic protein trafficking and is mediated by the soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) family. SNARE proteins embedded in opposing membranes spontaneously assemble to drive membrane fusion and cargo exchange in vitro. Evolution has generated a diverse complement of SNARE regulatory proteins (SRPs) that ensure membrane fusion occurs at the right time and place in vivo. While a core set of SNAREs and SRPs are common to all eukaryotic cells, a specialized set of SRPs within neurons confer additional regulation to synaptic vesicle (SV) fusion. Neuronal communication is characterized by precise spatial and temporal control of SNARE dynamics within presynaptic subdomains specialized for neurotransmitter release. Action potential-elicited Ca2+ influx at these release sites triggers zippering of SNAREs embedded in the SV and plasma membrane to drive bilayer fusion and release of neurotransmitters that activate downstream targets. Here we discuss current models for how SRPs regulate SNARE dynamics and presynaptic output, emphasizing invertebrate genetic findings that advanced our understanding of SRP regulation of SV cycling.
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Affiliation(s)
- Chad W Sauvola
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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Nian B, Xu YJ, Liu Y. Molecular dynamics simulation for mechanism revelation of the safety and nutrition of lipids and derivatives in food: State of the art. Food Res Int 2021; 145:110399. [PMID: 34112402 DOI: 10.1016/j.foodres.2021.110399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/26/2021] [Accepted: 05/06/2021] [Indexed: 11/29/2022]
Abstract
Molecular dynamics (MD) simulation has proved to be a powerful tool in the study of proteins, nucleic acids, lipids, and carbohydrates et al. in fields of health, nutrition, and food science. In particular, MD simulation has been employed in the investigation of various lipid systems such as triglycerides, phospholipid membranes, etc. Due to the continuous updating of computing resources and the development of new MD simulation methods and force field parameters, the simulation's time and size scale of lipids system has increased by several orders of magnitude. However, MD simulation cannot be used for systems invovle chemical reactions. These greatly limit its further application in the field of lipid research. This paper reviews the progress and development of MD simulation, especially for the application of MD simulation in different lipid systems. In this paper, MD simulation and its general workflow was briefly introduced firstly. Subsequently, the application of MD simulation in various lipid systems was reviewed in-depth. Finally, the limitation and future prospects of MD simulation in lipid research were also discussed. This review provided new insights into the investigation of MD simulation, and a novel thought for lipid study. We believe that MD simulation will exhibit more and more great advantages in the investigation of lipids in the future due to the development of novlel methods.
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Affiliation(s)
- Binbin Nian
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
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A stalk fluid forming above the transition from the lamellar to the rhombohedral phase of lipid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:265-278. [PMID: 33590276 PMCID: PMC8071804 DOI: 10.1007/s00249-020-01493-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/21/2020] [Accepted: 12/31/2020] [Indexed: 02/01/2023]
Abstract
In this work, we present evidence for the formation of transient stalks in aligned multilamellar stacks of lipid membranes. Just above the phase transition from the fluid ([Formula: see text]) lamellar phase to the rhombohedral phase (R), where lipid stalks crystallize on a super-lattice within the lipid bilayer stack, we observe a characteristic scattering pattern, which can be attributed to a correlated fluid of transient stalks. Excess (off-axis) diffuse scattering with a broad modulation around the position which later transforms to a sharp peak of the rhombohedral lattice, gives evidence for the stalk fluid forming as a pre-critical effect, reminiscent of critical phenomena in the vicinity of second-order phase transitions. Using high-resolution off-specular X-ray scattering and lineshape analysis we show that this pre-critical regime is accompanied by an anomalous elasticity behavior of the membrane stack, in particular an increase in inter-bilayer compressibility, i.e., a decrease in the compression modulus.
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Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
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Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
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Komorowski K, Salditt A, Xu Y, Yavuz H, Brennich M, Jahn R, Salditt T. Vesicle Adhesion and Fusion Studied by Small-Angle X-Ray Scattering. Biophys J 2019; 114:1908-1920. [PMID: 29694868 PMCID: PMC5936998 DOI: 10.1016/j.bpj.2018.02.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 02/19/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
We have studied the adhesion state (also denoted by docking state) of lipid vesicles as induced by the divalent ions Ca2+ or Mg2+ at well-controlled ion concentration, lipid composition, and charge density. The bilayer structure and the interbilayer distance in the docking state were analyzed by small-angle x-ray scattering. A strong adhesion state was observed for DOPC:DOPS vesicles, indicating like-charge attraction resulting from ion correlations. The observed interbilayer separations of ∼1.6 nm agree quantitatively with the predictions of electrostatics in the strong coupling regime. Although this phenomenon was observed when mixing anionic and zwitterionic (or neutral) lipids, pure anionic membranes (DOPS) with highest charge density σ resulted in a direct phase transition to a multilamellar state, which must be accompanied by rupture and fusion of vesicles. To extend the structural assay toward protein-controlled docking and fusion, we have characterized reconstituted N-ethylmaleimide-sensitive factor attachment protein receptors in controlled proteoliposome suspensions by small-angle x-ray scattering.
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Affiliation(s)
- Karlo Komorowski
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany; Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Annalena Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Yihui Xu
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Halenur Yavuz
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Martha Brennich
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany.
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