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Kligman A, Dastmalchi K, Smith S, John G, Stark RE. Building Blocks of the Protective Suberin Plant Polymer Self-Assemble into Lamellar Structures with Antibacterial Potential. ACS OMEGA 2022; 7:3978-3989. [PMID: 35155893 PMCID: PMC8829861 DOI: 10.1021/acsomega.1c04709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/06/2022] [Indexed: 05/20/2023]
Abstract
The protection of terrestrial plants from desiccation, mechanical injury, and pathogenic invasion is achieved by waxes and cutin polyesters on leaf and fruit surfaces as well as suberin polymers that are embedded in the cell walls of roots, but the physicochemical principles governing the organization of these biological composites remain incompletely understood. Despite the well-established enzymatic mediation of suberin formation in the skins of potato tubers, cork oak trees, and internal plant tissues, the additional possibility of self-assembly in this system was suggested by our serendipitous finding that solvent extracts from potato phellem tissues form suspended fibers and needles in the absence of such catalysts over a period of several weeks. In the current study, we investigated self-assembly for three-component model chemical mixtures comprised of a hydroxyfatty acid, glycerol, and either of two hydroxycinnamic acids that together typify the building blocks of potato suberin biopolymers. We demonstrate that these mixtures spontaneously form lamellar structures that are reminiscent of suberized plant tissues, incorporate all constituents into self-assemblies, can form covalently bound ester structures, and display antibacterial activity. These findings provide new perspectives on the self-association and reactivity of these classes of organic compounds, insights into agriculturally important suberin formation in food crops, and a starting point for engineering sustainable materials with antimicrobial capabilities.
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Affiliation(s)
- Arina Kligman
- Department
of Chemistry and Biochemistry, The City
College of New York, City University of New York and CUNY Institute
for Macromolecular Assemblies, 160 Convent Avenue, New
York, New York 10031, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
| | - Keyvan Dastmalchi
- Department
of Chemistry and Biochemistry, The City
College of New York, City University of New York and CUNY Institute
for Macromolecular Assemblies, 160 Convent Avenue, New
York, New York 10031, United States
| | - Stephan Smith
- Department
of Chemistry and Biochemistry, The City
College of New York, City University of New York and CUNY Institute
for Macromolecular Assemblies, 160 Convent Avenue, New
York, New York 10031, United States
| | - George John
- Department
of Chemistry and Biochemistry, The City
College of New York, City University of New York and CUNY Institute
for Macromolecular Assemblies, 160 Convent Avenue, New
York, New York 10031, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
| | - Ruth E. Stark
- Department
of Chemistry and Biochemistry, The City
College of New York, City University of New York and CUNY Institute
for Macromolecular Assemblies, 160 Convent Avenue, New
York, New York 10031, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- . Phone: +1-212-650-8916. Fax: +1-212-650-6107
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Hsieh MK, Yu Y, Klauda JB. All-Atom Modeling of Complex Cellular Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3-17. [PMID: 34962814 DOI: 10.1021/acs.langmuir.1c02084] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.
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Wei C, Pohorille A. Fast bilayer-micelle fusion mediated by hydrophobic dipeptides. Biophys J 2021; 120:2330-2342. [PMID: 33887225 DOI: 10.1016/j.bpj.2021.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/15/2021] [Accepted: 04/02/2021] [Indexed: 11/30/2022] Open
Abstract
To understand the transition from inanimate matter to life, we studied a process that directly couples simple metabolism to evolution via natural selection, demonstrated experimentally by Adamala and Szostak. In this process, dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles, inducing their preferential growth and division at the expense of other vesicles. The process is explained on the basis of coarse-grained molecular dynamics simulations, each extending for tens of microseconds, carried out to model fusion between a micelle and a membrane, both made of fatty acids in the absence and presence of hydrophobic dipeptides. In all systems with dipeptides, but not in their absence, fusion events were observed. They involve the formation of a stalk made by hydrophobic chains from the micelle and the membrane, similar to that postulated for vesicle-vesicle fusion. The emergence of a stalk is facilitated by transient clusters of dipeptides, side chains of which form hydrophobic patches at the membrane surface. Committor probability calculations indicate that the size of a patch is a suitable reaction coordinate and allows for identifying the transition state for fusion. Free-energy barrier to fusion is greatly reduced in the presence of dipeptides to only 4-5 kcal/mol, depending on the hydrophobicity of side chains. The mechanism of mediated fusion, which is expected to apply to other small peptides and hydrophobic molecules, provides a robust means by which a nascent metabolism can confer evolutionary advantage to precursors of cells.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Andrew Pohorille
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.
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Wang E, Klauda JB. Molecular Structure of the Long Periodicity Phase in the Stratum Corneum. J Am Chem Soc 2019; 141:16930-16943. [DOI: 10.1021/jacs.9b08995] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Tascini AS, Noro MG, Seddon JM, Chen R, Bresme F. Mechanisms of lipid extraction from skin lipid bilayers by sebum triglycerides. Phys Chem Chem Phys 2019; 21:1471-1477. [DOI: 10.1039/c8cp05706k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Microsecond computations identify the pathways leading to the extraction of skin lipids by sebum triglycerides and the associated energetic costs.
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Affiliation(s)
| | | | | | - Rongjun Chen
- Department of Chemical Engineering
- Imperial College London
- UK
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6
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Wang E, Klauda JB. Models for the Stratum Corneum Lipid Matrix: Effects of Ceramide Concentration, Ceramide Hydroxylation, and Free Fatty Acid Protonation. J Phys Chem B 2018; 122:11996-12008. [DOI: 10.1021/acs.jpcb.8b06188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Remsing RC, Weeks JD. Alchemical free energy calculations and umbrella sampling with local molecular field theory. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618400035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Understanding the thermodynamic driving forces underlying any chemical process requires a description of the underlying free energy surface. However, computation of free energies is difficult, often requiring advanced sampling techniques. Moreover, these computations can be further complicated by the evaluation of any long-ranged interactions in the system of interest, such as Coulomb interactions in charged and polar media. Local molecular field theory is a promising approach to avoid many of the conceptual and computational difficulties associated with long-ranged interactions. We present frameworks for performing alchemical free energy calculations and non-Boltzmann sampling with local molecular field theory. We demonstrate that local molecular field theory can be used to perform these free energy calculations with accuracy comparable to traditional methodologies while eliminating the need for explicit treatment of long-ranged interactions in simulations.
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Affiliation(s)
- Richard C. Remsing
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - John D. Weeks
- Institute for Physical Science and Technology, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Del Regno A, Notman R. Permeation pathways through lateral domains in model membranes of skin lipids. Phys Chem Chem Phys 2018; 20:2162-2174. [DOI: 10.1039/c7cp03258g] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lateral organisation of skin lipids in membranes produces regions with different permeability; water permeation is favoured through cholesterol-rich regions.
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Affiliation(s)
| | - Rebecca Notman
- Department of Chemistry, University of Warwick
- Coventry
- UK
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Paloncýová M, Vávrová K, Sovová Ž, DeVane R, Otyepka M, Berka K. Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails. J Phys Chem B 2015; 119:9811-9. [DOI: 10.1021/acs.jpcb.5b05522] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Markéta Paloncýová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Kateřina Vávrová
- Skin
Barrier Research Group, Faculty of Pharmacy in Hradec Králové, Charles University in Prague, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Žofie Sovová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Russell DeVane
- Corporate Modeling & Simulation, Procter & Gamble, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Karel Berka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17. listopadu 12, 771 46 Olomouc, Czech Republic
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