1
|
Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
Collapse
Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| |
Collapse
|
2
|
Nakatani Y, Ribeiro N, Streiff S, Gotoh M, Pozzi G, Désaubry L, Milon A. Search for the most 'primitive' membranes and their reinforcers: a review of the polyprenyl phosphates theory. ORIGINS LIFE EVOL B 2014; 44:197-208. [PMID: 25351682 PMCID: PMC4669544 DOI: 10.1007/s11084-014-9365-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 09/17/2014] [Indexed: 11/26/2022]
Abstract
Terpenoids have an essential function in present-day cellular membranes, either as membrane reinforcers in Eucarya and Bacteria or as principal membrane constituents in Archaea. We have shown that some terpenoids, such as cholesterol and α, ω-dipolar carotenoids reinforce lipid membranes by measuring the water permeability of unilamellar vesicles. It was possible to arrange the known membrane terpenoids in a ‘phylogenetic’ sequence, and a retrograde analysis led us to conceive that single-chain polyprenyl phosphates might have been ‘primitive’ membrane constituents. By using an optical microscopy, we have observed that polyprenyl phosphates containing 15 to 30 C-atoms form giant vesicles in water in a wide pH range. The addition of 10 % molar of some polyprenols to polyprenyl phosphate vesicles have been shown to reduce the water permeability of membranes even more efficiently than the equimolecular addition of cholesterol. A ‘prebiotic’ synthesis of C10 and C15 prenols from C5 monoprenols was achieved in the presence of a montmorillonite clay. Hypothetical pathway from C1 or C2 units to ‘primitive’ membranes and that from ‘primitive’ membranes to archaeal lipids are presented.
Collapse
Affiliation(s)
- Yoichi Nakatani
- Institute of Chemistry, University of Strasbourg - CNRS, 67000, Strasbourg, France,
| | | | | | | | | | | | | |
Collapse
|
3
|
Bulacu M, Périole X, Marrink SJ. In Silico Design of Robust Bolalipid Membranes. Biomacromolecules 2011; 13:196-205. [DOI: 10.1021/bm201454j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Monica Bulacu
- Groningen
Biomolecular Sciences and Biotechnology Institute
and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Xavier Périole
- Groningen
Biomolecular Sciences and Biotechnology Institute
and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute
and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| |
Collapse
|
4
|
Rosenbaum AI, Maxfield FR. Niemann-Pick type C disease: molecular mechanisms and potential therapeutic approaches. J Neurochem 2011; 116:789-95. [PMID: 20807315 DOI: 10.1111/j.1471-4159.2010.06976.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cholesterol is an important lipid of mammalian cells. Its unique physicochemical properties modulate membrane behavior and it serves as the precursor for steroid hormones, oxysterols and vitamin D. Cholesterol is effluxed from the late endosomes/lysosomes via the concerted action of at least two distinct proteins: Niemann-Pick C (NPC)1 and NPC2. Mutations in these two proteins manifest as NPC disease - a very rare, usually fatal, autosomal, recessive, neurovisceral, lysosomal storage disorder. In this review, we discuss the possible mechanisms of action for NPC1 and NPC2 in mediating cholesterol efflux, as well as the different therapeutic approaches being pursued for the treatment of this lipid storage disorder.
Collapse
Affiliation(s)
- Anton I Rosenbaum
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, USA
| | | |
Collapse
|
5
|
Murcia M, Faráldo-Gómez JD, Maxfield FR, Roux B. Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. J Lipid Res 2006; 47:2614-30. [PMID: 16990645 DOI: 10.1194/jlr.m600232-jlr200] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Steroidogenic acute regulatory protein-related lipid transfer (StART) domains are ubiquitously involved in intracellular lipid transport and metabolism and other cell-signaling events. In this work, we use a flexible docking algorithm, comparative modeling, and molecular dynamics (MD) simulations to generate plausible three-dimensional atomic models of the StART domains of human metastatic lymph node 64 (MLN64) and steroidogenic acute regulatory protein (StAR) proteins in complex with cholesterol. Our results show that cholesterol can adopt a similar conformation in the binding cavity in both cases and that the main contribution to the protein-ligand interaction energy derives from hydrophobic contacts. However, hydrogen-bonding and water-mediated interactions appear to be important in the fine-tuning of the binding affinity and the position of the ligand. To gain insights into the mechanism of binding, we carried out steered MD simulations in which cholesterol was gradually extracted from within the StAR model. These simulations indicate that a transient opening of loop Omega1 may be sufficient for uptake and release, and they also reveal a pathway of intermediate states involving residues known to be crucial for StAR activity. Based on these observations, we suggest specific mutagenesis targets for binding studies of cholesterol and its derivatives that could improve our understanding of the structural determinants for ligand binding by sterol carrier proteins.
Collapse
Affiliation(s)
- Marta Murcia
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
| | | | | | | |
Collapse
|
6
|
Abstract
Syntheses of new benzophenone-containing fatty acids (FABPs) 1, 5, and 6 and a new route to FABP 3 are described. Combined with the known 2 and 4, these FABPs comprise a set of photoactivatable fatty acid analogues with the crosslinking site at defined distances from the carboxylic acid hydroxyl group oxygen atoms ranging from 7.9 to 25.0 A.
Collapse
Affiliation(s)
- Yonghong Gan
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA
| | | | | |
Collapse
|
7
|
Gotoh M, Ribeiro N, Michels B, Elhabiri M, Albrecht-Gary AM, Yamashita J, Hato M, Ourisson G, Nakatani Y. A Novel Type of Membrane Based on Cholesteryl Phosphocholine, Cholesteryl Phosphate, or Sitosteryl Phosphate, and Dimyristoylglycerol. Chem Biodivers 2006; 3:198-209. [PMID: 17193258 DOI: 10.1002/cbdv.200690023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mixtures of amphiphilic cholesteryl phosphate (CP), sitosteryl phosphate (SP), or cholesteryl phosphocholine (CPC) with the nonphosphoryl diacyl lipid dimyristoylglycerol (DMG) or with cholesterol give self-organized systems (giant vesicles) in a wide range of pH, as demonstrated by fluorescence microscopy, differential scanning calorimetry, and small-angle X-ray scattering. The water permeability of a 1 : 1 molar mixture of CPC and DMG was also measured by a stopped-flow/light-scattering method. The novel self-organized systems are akin to natural eukaryotic ones, the only difference being the site of the phosphate-containing head-group, located on cholesterol instead of DMG. They might be present in some organisms not yet studied for the composition of their membranes.
Collapse
Affiliation(s)
- Mari Gotoh
- Centre de Neurochimie, 5, rue Blaise Pascal, F-67084-Strasbourg
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Peng Q, Xia Y, Qu F, Wu X, Campese D, Peng L. Synthesis of a photoactivatable phospholipidic probe containing tetrafluorophenylazide. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.06.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Spencer TA, Wang P, Li D, Russel JS, Blank DH, Huuskonen J, Fielding PE, Fielding CJ. Benzophenone-containing cholesterol surrogates: synthesis and biological evaluation. J Lipid Res 2004; 45:1510-8. [PMID: 15175357 DOI: 10.1194/jlr.m400081-jlr200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Eight analogs of cholesterol (1) containing a benzophenone group have been synthesized as prospective photoaffinity labels for studies in cellular sterol efflux and HDL formation. Six of these compounds (4-9) have the photophore replacing different portions of the cholesterol alkyl side chain, and two (10 and 11) have it attached via nitrogen at carbon 3. The suitability of these analogs as cholesterol surrogates was determined by examining their ability to replace [3H]1 in fibroblasts preequilibrated with [3H]1. All eight analogs were effective in replacing natural 1 in competition with [3H]1 for apolipoprotein A-I-induced efflux. These are the first compounds shown to replace cholesterol successfully in a complex pathway of multiple intracellular steps. The results suggest an unexpected tolerance of biological membranes regarding the incorporation of sterols of differing chemical structure.
Collapse
Affiliation(s)
- Thomas A Spencer
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA.
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Wang P, Blank DH, Spencer TA. Synthesis of Benzophenone-Containing Analogues of Phosphatidylcholine. J Org Chem 2004; 69:2693-702. [PMID: 15074915 DOI: 10.1021/jo030329d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of a collaborative study of cellular efflux of cholesterol and phospholipids, photoactivable analogues 4-8 of phosphatidylcholine (PC) having benzophenone groups in the choline moiety and at the end of the C2 and C1 alkyl chains have been synthesized. The efficient preparation via Suzuki coupling of the appropriate long-chain benzophenone-containing carboxylic acid and alcohol and their incorporation by adaptation of known approaches into the acyl- and ether-linked PC analogues 6-8 are described. Development of a method for radiolabeling these PC analogues, via hydrogenation of a double bond in modified side chains, is also described.
Collapse
Affiliation(s)
- Pingzhen Wang
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA
| | | | | |
Collapse
|
11
|
|
12
|
Quesada E, Acuña AU, Amat-Guerri F. New Transmembrane Polyene Bolaamphiphiles as Fluorescent Probes in Lipid Bilayers. Angew Chem Int Ed Engl 2001; 40:2095-2097. [DOI: 10.1002/1521-3773(20010601)40:11<2095::aid-anie2095>3.0.co;2-i] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2000] [Revised: 02/26/2001] [Indexed: 11/07/2022]
|
13
|
|
14
|
Ogawa Y, Hahn W, Garnier P, Higashi N, Massotte D, Metz-Boutigue MH, Rousseau B, Sunamoto J, Ourisson G, Nakatani Y. Mid-Membrane Photolabeling of the Transmembrane Domain of Glycophorin A in Phospholipid Vesicles. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010302)113:5<970::aid-ange970>3.0.co;2-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
15
|
Ogawa Y, Hahn W, Garnier P, Higashi N, Massotte D, Metz-Boutigue MH, Rousseau B, Sunamoto J, Ourisson G, Nakatani Y. Mid-Membrane Photolabeling of the Transmembrane Domain of Glycophorin A in Phospholipid Vesicles. Angew Chem Int Ed Engl 2001; 40:944-946. [DOI: 10.1002/1521-3773(20010302)40:5<944::aid-anie944>3.0.co;2-o] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2000] [Indexed: 01/05/2023]
|
16
|
Arakawa K, Eguchi T, Kakinuma K. 36-Membered Macrocyclic Diether Lipid is Advantageous for Archaea to Thrive under the Extreme Thermal Environments. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.347] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
17
|
Ourisson G, Nakatani Y. Addendum: Origins of cellular life: Molecular foundations and new approaches. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00116-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
18
|
Arakawa K, Eguchi T, Kakinuma K. Specific Deuterium Labeling of Archaeal 36-Membered Macrocyclic Diether Lipid. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1998. [DOI: 10.1246/bcsj.71.2419] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
19
|
Ueda T, Lee SJ, Nakatani Y, Ourisson G, Sunamoto J. Coating of POPC Giant Liposomes with Hydrophobized Polysaccharide. CHEM LETT 1998. [DOI: 10.1246/cl.1998.417] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
20
|
Deseke E, Nakatani Y, Ourisson G. Intrinsic Reactivities of Amino Acids towards Photoalkylation with Benzophenone − A Study Preliminary to Photolabelling of the Transmembrane Protein Glycophorin A. European J Org Chem 1998. [DOI: 10.1002/(sici)1099-0690(199802)1998:2<243::aid-ejoc243>3.0.co;2-i] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
21
|
Otsuki J, Ogawa H, Okuda N, Araki K, Seno M. Behavior of Ruthenium Trisbipyridine–Anthraquinone Conjugates Connected with Alkyl Spacers in Homogeneous and Microheterogeneous Media. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1997. [DOI: 10.1246/bcsj.70.2077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|