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Angles G, Hail A, Dotson RJ, Pias SC. Atomistic simulations modify interpretation of spin-label oximetry data. Part 1: intensified water-lipid interfacial resistances. APPLIED MAGNETIC RESONANCE 2021; 52:1261-1289. [PMID: 37292189 PMCID: PMC10249954 DOI: 10.1007/s00723-021-01398-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 06/10/2023]
Abstract
The role of membrane cholesterol in cellular function and dysfunction has been the subject of much inquiry. A few studies have suggested that cholesterol may slow oxygen diffusive transport, altering membrane physical properties and reducing oxygen permeability. The primary experimental technique used in recent years to study membrane oxygen transport is saturation-recovery electron paramagnetic resonance (EPR) oximetry, using spin-label probes targeted to specific regions of a lipid bilayer. The technique has been used, in particular, to assess the influence of cholesterol on oxygen transport and membrane permeability. The reliability of such EPR recordings at the water-lipid interface near the phospholipid headgroups has been challenged by all-atom molecular dynamics (MD) simulation data that show substantive agreement with spin-label probe measurements throughout much of the bilayer. This work uses further MD simulations, with an updated oxygen model, to determine the location of the maximum resistance to permeation and the rate-limiting barrier to oxygen permeation in 1-palmitoyl,2-oleoylphosphatidylcholine (POPC) and POPC/cholesterol bilayers at 25 and 35°C. The current simulations show a spike of resistance to permeation in the headgroup region that was not detected by EPR but was predicted in early theoretical work by Diamond and Katz. Published experimental nuclear magnetic resonance (NMR) oxygen measurements provide key validation of the MD models and indicate that the positions and relative magnitudes of the phosphatidylcholine resistance peaks are accurate. Consideration of the headgroup-region resistances predicts bilayer permeability coefficients lower than estimated in EPR studies, giving permeabilities lower than the permeability of unstirred water layers of the same thickness. Here, the permeability of POPC at 35°C is estimated to be 13 cm/s, compared with 10 cm/s for POPC/cholesterol and 118 cm/s for simulation water layers of similar thickness. The value for POPC is 12 times lower than estimated from EPR measurements, while the value for POPC/cholesterol is 5 times lower. These findings underscore the value of atomic resolution models for guiding the interpretation of experimental probe-based measurements.
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Affiliation(s)
| | | | | | - Sally C. Pias
- Corresponding author: , Department of Chemistry, New Mexico Institute of Mining and Technology (New Mexico Tech), 801 Leroy Place, Socorro, NM 87801, USA
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Liu J, Shadpour S, Prévôt ME, Chirgwin M, Nemati A, Hegmann E, Lemieux RP, Hegmann T. Molecular Conformation of Bent-Core Molecules Affected by Chiral Side Chains Dictates Polymorphism and Chirality in Organic Nano- and Microfilaments. ACS NANO 2021; 15:7249-7270. [PMID: 33734664 DOI: 10.1021/acsnano.1c00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The coupling between molecular conformation and chirality is a cornerstone in the construction of supramolecular helical structures of small molecules across various length scales. Inspired by biological systems, conformational preselection and control in artificial helical molecules, polymers, and aggregates has guided various applications in optics, photonics, and chiral sorting among others, which are frequently based on an inherent chirality amplification through processes such as templating and self-assembly. The so-called B4 nano- or microfilament phase formed by some bent-shaped molecules is an exemplary case for such chirality amplification across length scales, best illustrated by the formation of distinct nano- or microscopic chiral morphologies controlled by molecular conformation. Introduction of one or more chiral centers in the aliphatic side chains led to the discovery of homochiral helical nanofilament, helical microfilament, and heliconical-layered nanocylinder morphologies. Herein, we demonstrate how a priori calculations of the molecular conformation affected by chiral side chains are used to design bent-shaped molecules that self-assemble into chiral nano- and microfilament as well as nanocylinder conglomerates despite the homochiral nature of the molecules. Furthermore, relocation of the chiral center leads to formation of helical as well as flat nanoribbons. Self-consistent data sets from polarized optical as well as scanning and transmission electron microscopy, thin-film and solution circular dichroism spectropolarimetry, and synchrotron-based X-ray diffraction experiments support the progressive and predictable change in morphology controlled by structural changes in the chiral side chains. The formation of these morphologies is discussed in light of the diminishing effects of molecular chirality as the chain length increases or as the chiral center is moved away from the core-chain juncture. The type of phase (B1-columnar or B4) and morphology of the nano- or microfilaments generated can further be controlled by sample treatment conditions such as by the cooling rate from the isotropic melt or by the presence of an organic solvent in the ensuing colloidal dispersions. We show that these nanoscale morphologies can then organize into a wealth of two- and three-dimensional shapes and structures ranging from flower blossoms to fiber mats formed by intersecting flat nanoribbons.
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Affiliation(s)
- Jiao Liu
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Sasan Shadpour
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Marianne E Prévôt
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Michael Chirgwin
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Ahlam Nemati
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
| | - Elda Hegmann
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242-0001, United States
- Brain Health Research Institute, Kent State University, Kent, Ohio 44242-0001, United States
| | - Robert P Lemieux
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Torsten Hegmann
- Materials Science Graduate Program, Kent State University, Kent (Ohio) 44242-0001, United States
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent (Ohio) 44242-0001, United States
- Department of Biological Sciences, Kent State University, Kent, Ohio 44242-0001, United States
- Brain Health Research Institute, Kent State University, Kent, Ohio 44242-0001, United States
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242-0001, United States
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Xue Z, Tan Z, Huang A, Zhou Y, Sun J, Wang X, Thimmappa RB, Stephenson MJ, Osbourn A, Qi X. Identification of key amino acid residues determining product specificity of 2,3-oxidosqualene cyclase in Oryza species. THE NEW PHYTOLOGIST 2018; 218:1076-1088. [PMID: 29528490 DOI: 10.1111/nph.15080] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/05/2018] [Indexed: 05/27/2023]
Abstract
Triterpene synthases, also known as 2,3-oxidosqualene cyclases (OSCs), synthesize diverse triterpene skeletons that form the basis of an array of functionally divergent steroids and triterpenoids. Tetracyclic and pentacyclic triterpene skeletons are synthesized via protosteryl and dammarenyl cations, respectively. The mechanism of conversion between two scaffolds is not well understood. Here, we report a promiscuous OSC from rice (Oryza sativa) (OsOS) that synthesizes a novel pentacyclic triterpene orysatinol as its main product. The OsOS gene is widely distributed in indica subspecies of cultivated rice and in wild rice accessions. Previously, we have characterized a different OSC, OsPS, a tetracyclic parkeol synthase found in japonica subspecies. Phylogenetic and protein structural analyses identified three key amino acid residues (#732, #365, #124) amongst 46 polymorphic sites that determine functional conversion between OsPS and OsOS, specifically, the chair-semi(chair)-chair and chair-boat-chair interconversions. The different orientation of a fourth amino acid residue Y257 was shown to be important for functional conversion The discovery of orysatinol unlocks a new path to triterpene diversity in nature. Our findings also reveal mechanistic insights into the cyclization of oxidosqualene into tetra- and pentacyclic skeletons, and provide a new strategy to identify key residues determining OSC specificity.
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Affiliation(s)
- Zheyong Xue
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zhengwei Tan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Ancheng Huang
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yuan Zhou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juncong Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoning Wang
- Department of Natural Product Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Ramesha B Thimmappa
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Michael J Stephenson
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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Torday JS. Pleiotropy as the Mechanism for Evolving Novelty: Same Signal, Different Result. BIOLOGY 2015; 4:443-59. [PMID: 26103090 PMCID: PMC4498309 DOI: 10.3390/biology4020443] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 06/02/2015] [Accepted: 06/10/2015] [Indexed: 11/22/2022]
Abstract
In contrast to the probabilistic way of thinking about pleiotropy as the random expression of a single gene that generates two or more distinct phenotypic traits, it is actually a deterministic consequence of the evolution of complex physiology from the unicellular state. Pleiotropic novelties emerge through recombinations and permutations of cell-cell signaling exercised during reproduction based on both past and present physical and physiologic conditions, in service to the future needs of the organism for its continued survival. Functional homologies ranging from the lung to the kidney, skin, brain, thyroid and pituitary exemplify the evolutionary mechanistic strategy of pleiotropy. The power of this perspective is exemplified by the resolution of evolutionary gradualism and punctuated equilibrium in much the same way that Niels Bohr resolved the paradoxical duality of light as Complementarity.
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Affiliation(s)
- John S Torday
- Harbor-UCLA Medical Center, 1124 West Carson Street, Torrance, CA 90502-2006, USA.
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Roberts JB, Stevens R. COMPOSITION AND BIOGENESIS OF ESSENTIAL OIL OF HOPS. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1962.tb01884.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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An inborn error of cholesterol biosynthesis. Nutr Rev 1986; 44:334-6. [PMID: 3025784 DOI: 10.1111/j.1753-4887.1986.tb07562.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Goad LJ, Goodwin TW. Studies on phytosterol biosynthesis: the sterols of Larix decidua leaves. EUROPEAN JOURNAL OF BIOCHEMISTRY 1967; 1:357-362. [PMID: 6060188 DOI: 10.1007/978-3-662-25813-2_49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Goad LJ, Goodwin TW. Studies on Phytosterol Biosynthesis: the Sterols of Larix decidua Leaves. ACTA ACUST UNITED AC 1967. [DOI: 10.1111/j.1432-1033.1967.tb00082.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dempsey ME. Pathways of Enzymic Synthesis and Conversion to Cholesterol of Δ5,7,24-Cholestatrien-3β-ol and Other Naturally Occurring Sterols. J Biol Chem 1965. [DOI: 10.1016/s0021-9258(18)97043-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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GARA A, ESTRADA E, ROTHMAN S, LORINCZ AL. Deficient Cholesterol Esterifying Ability of Lesion-Free Skin Surfaces in Psoriatic Individuals*. J Invest Dermatol 1964; 43:559-64. [PMID: 14234862 DOI: 10.1038/jid.1964.198] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Lederer E. The origin and function of some methyl groups in branched-chain fatty acids, plant sterols and quinones. Biochem J 1964; 93:449-68. [PMID: 5320419 PMCID: PMC1213993 DOI: 10.1042/bj0930449] [Citation(s) in RCA: 81] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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SIEGELMAN HW, HENDRICKS SB. PHYTOCHROME AND ITS CONTROL OF PLANT GROWTH AND DEVELOPMENT. ADVANCES IN ENZYMOLOGY AND RELATED SUBJECTS OF BIOCHEMISTRY 1964; 26:1-33. [PMID: 14150646 DOI: 10.1002/9780470122716.ch1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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MARTIN-SMITH M, KHATOON T. BIOLOGICAL ACTIVITY OF THE TERPENOIDS AND THEIR DERIVATIVES. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRESS IN DRUG RESEARCH. PROGRES DES RECHERCHES PHARMACEUTIQUES 1963; 5:279-346. [PMID: 14287132 DOI: 10.1007/978-3-0348-7050-4_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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16
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Ubiquinones (Coenzymes Q), Ubichromenols, and Related Substances. VITAMINS AND HORMONES 1962. [DOI: 10.1016/s0083-6729(08)61052-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Steinberg D. Chemotherapeutic Approaches to the Problem of Hyperlipidemia. ADVANCES IN PHARMACOLOGY 1962. [DOI: 10.1016/s1054-3589(08)60508-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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NEIDERHISER DH, WELLS WW. The structure of methostenol and its distribution in rat tissues. Arch Biochem Biophys 1959; 81:300-8. [PMID: 13637991 DOI: 10.1016/0003-9861(59)90207-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Hutner S, Nathan HA, Baker H. Metabolism of Folic Acid and Other Pterin-Pteridine Vitamins. VITAMINS AND HORMONES 1959. [DOI: 10.1016/s0083-6729(08)60267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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BIOSYNTHESIS OF CHOLESTEROL. CHOLESTEROL 1958. [DOI: 10.1016/b978-1-4832-2772-6.50011-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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