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Zhou J, Wang Y, Li L. Regulating the Flow-Driven Translocation of Macromolecules through Nanochannels by Interfacial Physical Adsorption. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Jianing Zhou
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yiren Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Lianwei Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
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2
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Kang X, Elson C, Penfield J, Kirui A, Chen A, Zhang L, Wang T. Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human β-defensin analog. Commun Biol 2019; 2:402. [PMID: 31701030 PMCID: PMC6825183 DOI: 10.1038/s42003-019-0653-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/15/2019] [Indexed: 12/11/2022] Open
Abstract
Human β-defensins (hBD) play central roles in antimicrobial activities against various microorganisms and in immune-regulation. These peptides perturb phospholipid membranes for function, but it is not well understood how defensins approach, insert and finally disrupt membranes on the molecular level. Here we show that hBD-3 analogs interact with lipid bilayers through a conserved surface that is formed by two adjacent loops in the solution structure. By integrating a collection of 13C, 1H and 31P solid-state NMR methods with long-term molecular dynamic simulations, we reveal that membrane-binding rigidifies the peptide, enhances structural polymorphism, and promotes β-strand conformation. The peptide colocalizes with negatively charged lipids, confines the headgroup motion, and deforms membrane into smaller, ellipsoidal vesicles. This study designates the residue-specific, membrane-bound topology of hBD-3 analogs, serves as the basis for further elucidating the function-relevant structure and dynamics of other defensins, and facilitates the development of defensin-mimetic antibiotics, antifungals, and anti-inflammatories.
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Affiliation(s)
- Xue Kang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Christopher Elson
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Jackson Penfield
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Adrian Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505 USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 USA
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3
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Mordvinkin A, Saalwächter K. Microscopic observation of the segmental orientation autocorrelation function for entangled and constrained polymer chains. J Chem Phys 2017. [DOI: 10.1063/1.4977041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Anton Mordvinkin
- Institut für Physik – NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle,
Germany
| | - Kay Saalwächter
- Institut für Physik – NMR, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, D-06120 Halle,
Germany
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4
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Bärenwald R, Achilles A, Lange F, Ferreira TM, Saalwächter K. Applications of Solid-State NMR Spectroscopy for the Study of Lipid Membranes with Polyphilic Guest (Macro)Molecules. Polymers (Basel) 2016; 8:E439. [PMID: 30974716 PMCID: PMC6432237 DOI: 10.3390/polym8120439] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/01/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022] Open
Abstract
The incorporation of polymers or smaller complex molecules into lipid membranes allows for property modifications or the introduction of new functional elements. The corresponding molecular-scale details, such as changes in dynamics or features of potential supramolecular structures, can be studied by a variety of solid-state NMR techniques. Here, we review various approaches to characterizing the structure and dynamics of the guest molecules as well as the lipid phase structure and dynamics by different high-resolution magic-angle spinning proton and 13C NMR experiments as well as static 31P NMR experiments. Special emphasis is placed upon the incorporation of novel synthetic polyphilic molecules such as shape-persistent T- and X-shaped molecules as well as di- and tri-block copolymers. Most of the systems studied feature dynamic heterogeneities, for instance those arising from the coexistence of different phases; possibilities for a quantitative assessment are of particular concern.
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Affiliation(s)
- Ruth Bärenwald
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Anja Achilles
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Frank Lange
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Tiago Mendes Ferreira
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik-NMR, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle, Germany.
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5
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Jeschke G. Ensemble models of proteins and protein domains based on distance distribution restraints. Proteins 2016; 84:544-60. [PMID: 26994550 DOI: 10.1002/prot.25000] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
Conformational ensembles of intrinsically disordered peptide chains are not fully determined by experimental observations. Uncertainty due to lack of experimental restraints and due to intrinsic disorder can be distinguished if distance distributions restraints are available. Such restraints can be obtained from pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy applied to pairs of spin labels. Here, we introduce a Monte Carlo approach for generating conformational ensembles that are consistent with a set of distance distribution restraints, backbone dihedral angle statistics in known protein structures, and optionally, secondary structure propensities or membrane immersion depths. The approach is tested with simulated restraints for a terminal and an internal loop and for a protein with 69 residues by using sets of sparse restraints for underlying well-defined conformations and for published ensembles of a premolten globule-like and a coil-like intrinsically disordered protein.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Zürich, 8093, Switzerland
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6
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Achilles A, Bärenwald R, Lechner BD, Werner S, Ebert H, Tschierske C, Blume A, Bacia K, Saalwächter K. Self-Assembly of X-Shaped Bolapolyphiles in Lipid Membranes: Solid-State NMR Investigations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:673-682. [PMID: 26735449 DOI: 10.1021/acs.langmuir.5b03712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A novel class of rigid-rod bolapolyphilic molecules with three philicities (rigid aromatic core, mobile aliphatic side chains, polar end groups) has recently been demonstrated to incorporate into and span lipid membranes, and to exhibit a rich variety of self-organization modes, including macroscopically ordered snowflake structures with 6-fold symmetry. In order to support a structural model and to better understand the self-organization on a molecular scale, we here report on proton and carbon-13 high-resolution magic-angle spinning solid-state NMR investigations of two different bolapolyphiles (BPs) in model membranes of two different phospholipids (DPPC, DOPC). We elucidate the changes in molecular dynamics associated with three new phase transitions detected by calorimetry in composite membranes of different composition, namely, a change in π-π-packing, the melting of lipid tails associated with the superstructure, and the dissolution and onset of free rotation of the BPs. We derive dynamic order parameters associated with different H-H and C-H bond directions of the BPs, demonstrating that the aromatic cores are well packed below the final phase transition, showing only 180° flips of the phenyl ring, and that they perform free rotations with additional oscillations of the long axis when dissolved in the fluid membrane. Our data suggests that BPs not only form ordered superstructures, but also rather homogeneously dispersed π-packed filaments within the lipid gel phase, thus reducing the corrugation of large vesicles.
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Affiliation(s)
- Anja Achilles
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Ruth Bärenwald
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Bob-Dan Lechner
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Stefan Werner
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Helgard Ebert
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Carsten Tschierske
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Alfred Blume
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Kirsten Bacia
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik - NMR, ‡Institut für Chemie - Physikalische Chemie, §ZIK HALOmem, and ∥Institut für Chemie - Organische Chemie, Martin-Luther-Universität Halle-Wittenberg , D-06120 Halle, Germany
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7
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Zhao Y, Cho H, Widanapathirana L, Zhang S. Conformationally controlled oligocholate membrane transporters: learning through water play. Acc Chem Res 2013; 46:2763-72. [PMID: 23537285 DOI: 10.1021/ar300337f] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Controlled translocation of molecules and ions across lipid membranes is the basis of numerous biological functions. Because synthetic systems can help researchers understand the more complex biological ones, many chemists have developed synthetic mimics of biological transporters. Both systems need to deal with similar fundamental challenges. In addition to providing mechanistic insights into transport mechanisms, synthetic transporters are useful in a number of applications including separation, sensing, drug delivery, and catalysis. In this Account, we present several classes of membrane transporters constructed in our laboratory from a facially amphiphilic building block, cholic acid. Our "molecular baskets" can selectively shuttle glucose across lipid membranes without transporting smaller sodium ions. We have also built oligocholate foldamers that transiently fold into helices with internal hydrophilic binding pockets to transport polar guests. Lastly, we describe amphiphilic macrocycles, which form transmembrane nanopores in lipid bilayers through the strong associative interactions of encapsulated water molecules. In addition to presenting the different transport properties of these oligocholate transporters, we illustrate how fundamental studies of molecular behavior in solution facilitate the creation of new and useful membrane transporters, despite the large difference between the two environments. We highlight the strong conformational effect of transporters. Because the conformation of a molecule often alters its size and shape, and the distribution of functional groups, conformational control can be used rationally to tune the property of a transporter. Finally, we emphasize that, whenever water is the solvent, its unique properties--small size, strong solvation for ionic functionalities, and an extraordinary cohesive energy density (i.e., total intermolecular interactions per unit volume)--tend to become critical factors to be considered. Purposeful exploitation of these solvent properties may be essential to the success of the supramolecular process involved--this is also the reason for the "learning through water play" in the title of this Account.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Hongkwan Cho
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | | | - Shiyong Zhang
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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8
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Kel O, Tamimi A, Thielges MC, Fayer MD. Ultrafast Structural Dynamics Inside Planar Phospholipid Multibilayer Model Cell Membranes Measured with 2D IR Spectroscopy. J Am Chem Soc 2013; 135:11063-74. [DOI: 10.1021/ja403675x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oksana Kel
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Amr Tamimi
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Megan C. Thielges
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United
States
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9
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Widanapathirana L, Zhao Y. Tuning Nanopore Formation of Oligocholate Macrocycles by Carboxylic Acid Dimerization in Lipid Membranes. J Org Chem 2013; 78:4610-4. [DOI: 10.1021/jo400455x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United
States
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