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Banyikwa A, Goos A, Kiemle DJ, Foulkes MAC, Braiman MS. Experimental and Computational Modeling of H-Bonded Arginine-Tyrosine Groupings in Aprotic Environments. ACS Omega 2017; 2:5641-5659. [PMID: 31457828 PMCID: PMC6644469 DOI: 10.1021/acsomega.7b00282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/28/2017] [Indexed: 06/08/2023]
Abstract
H-bonds between neutral tyrosine and arginine in nonpolar environments are modeled by small-molecule phenol/guanidine complexes. From the temperature and concentration dependence of UV spectra, a value of ΔH° = -74 ± 4 kJ mol-1 is deduced for the formation of H-bonded p-cresol/dodecylguanidine in hexane. ΔE = -71 kJ mol-1 is computed with density functional theory (in vacuo). In dimethyl sulfoxide or crystals, (p-phenolyl)alkylguanidines form head-to-tail homodimers with two strong H-bonding interactions, as evidenced by UV, IR, and NMR spectral shifts, strong IR continuum absorbance bands, and short O···N distances in X-ray crystal structures. Phenol/alkylguanidine H-bonded complexes consist of polarizable rapidly interconverting tautomers, with the proton shift from phenol to guanidine increasing with increase in the polarity of the aprotic solvent. As measured by NMR, both groups in these strongly H-bonded neutral complexes can simultaneously appear to be predominantly protonated. These systems serve as models for the hypothetical hydrogen-Bonded Uncharged (aRginine + tYrosine), or "BU(RY)", motifs in membrane proteins.
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Affiliation(s)
- Andrew
Toyi Banyikwa
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
| | - Alan Goos
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
| | - David J. Kiemle
- Analytical
and Technical Services, SUNY College of
Environmental Science and Forestry, 123 Jahn Laboratory, Syracuse, New York 13210, United
States
| | - Michael A. C. Foulkes
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
| | - Mark S. Braiman
- Chemistry
Department, Center for Science & Technology, Syracuse University, Room 1-014, Syracuse, New
York 13244, United
States
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2
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Abstract
The sugar subunits of natural glycosides can be conveniently determined by acid hydrolysis and (1)H NMR spectroscopy without isolation or derivatization. The chemical shifts, coupling constants, and integral ratios of the anomeric signals allow each monosaccharide to be identified and its molar ratio to other monosaccharides to be quantified. The NMR data for the anomeric signals of 28 monosaccharides and three disaccharides are reported. Application of the method is demonstrated with the flavonoid glycoside naringin (1), the aminoglycoside antibiotics kanamycin (2) and tobramycin (3), and the saponin digitonin (4).
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Affiliation(s)
- José-Luis Giner
- Department of Chemistry, State University of New York-ESF , Syracuse, New York 13210, United States
| | - Ju Feng
- Department of Chemistry, State University of New York-ESF , Syracuse, New York 13210, United States
| | - David J Kiemle
- Department of Chemistry, State University of New York-ESF , Syracuse, New York 13210, United States
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3
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Gitsov I, Wang L, Vladimirov N, Simonyan A, Kiemle DJ, Schutz A. “Green” Synthesis of Unnatural Poly(Amino Acid)s with Zwitterionic Character and pH-Responsive Solution Behavior, Mediated by Linear–Dendritic Laccase Complexes. Biomacromolecules 2014; 15:4082-95. [DOI: 10.1021/bm501126a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | | | | | | | - Andri Schutz
- Department
of Materials Science, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland
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4
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Wang L, Kiemle DJ, Boyle CJ, Connors EL, Gitsov I. “Click” Synthesis of Intrinsically Hydrophilic Dendrons and Dendrimers Containing Metal Binding Moieties at Each Branching Unit. Macromolecules 2014. [DOI: 10.1021/ma500126f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lili Wang
- Department of Chemistry and ‡The Michael M. Szwarc Polymer Research Institute, State University of New York-ESF, Syracuse, New York 13210, United States
| | - David J. Kiemle
- Department of Chemistry and ‡The Michael M. Szwarc Polymer Research Institute, State University of New York-ESF, Syracuse, New York 13210, United States
| | - Connor J. Boyle
- Department of Chemistry and ‡The Michael M. Szwarc Polymer Research Institute, State University of New York-ESF, Syracuse, New York 13210, United States
| | - Eoghan L. Connors
- Department of Chemistry and ‡The Michael M. Szwarc Polymer Research Institute, State University of New York-ESF, Syracuse, New York 13210, United States
| | - Ivan Gitsov
- Department of Chemistry and ‡The Michael M. Szwarc Polymer Research Institute, State University of New York-ESF, Syracuse, New York 13210, United States
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Sallans L, Giner JL, Kiemle DJ, Custer JE, Kaneshiro ES. Structural identities of four glycosylated lipids in the oral bacterium Streptococcus mutans UA159. Biochim Biophys Acta 2013; 1831:1239-1249. [PMID: 24046864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The cariogenic bacterium Streptococcus mutans is an important dental pathogen that forms biofilms on tooth surfaces, which provide a protective niche for the bacterium where it secretes organic acids leading to the demineralization of tooth enamel. Lipids, especially glycolipids are likely to be key components of these biofilm matrices. The UA159 strain of S. mutans was among the earliest microorganisms to have its genome sequenced. While the lipids of other S. mutans strains have been identified and characterized, lipid analyses of UA159 have been limited to a few studies on its fatty acids. Here we report the structures of the four major glycolipids from stationary-phase S. mutans UA159 cells grown in standing cultures. These were shown to be monoglucosyldiacylglycerol (MGDAG), diglucosyldiacylglycerol (DGDAG), diglucosylmonoacylglycerol (DGMAG) and, glycerophosphoryldiglucosyldiacylglycerol (GPDGDAG). The structures were determined by high performance thin-layer chromatography, mass spectrometry and nuclear magnetic resonance spectroscopy. The glycolipids were identified by accurate, high resolution, and tandem mass spectrometry. The identities of the sugar units in the glycolipids were determined by a novel and highly efficient NMR method. All sugars were shown to have alpha-glycosidic linkages and DGMAG was shown to be acylated in the sn-1 position by NMR. This is the first observation of unsubstituted DGMAG in any organism and the first mass spectrometry data for GPDGDAG.
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Affiliation(s)
- Larry Sallans
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA.
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6
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Shupe AM, Kiemle DJ, Liu S. Quantitative 2D HSQC NMR Analysis of Mixed Wood Sugars in Hemicellulosic Hydrolysate Fermentation Broth. ACTA ACUST UNITED AC 2012. [DOI: 10.1166/jbeb.2012.1007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Barnhart D, Kaplan DL, Winter WT, Panilaitis BJ, Kiemle DJ. Structural details of the Polyelectrolytic Exopolysaccharide (APE), the stabilizing component of the Acinetobacter venetianus RAG-1 emulsan complex. Carbohydr Polym 2012. [DOI: 10.1016/j.carbpol.2011.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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8
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Mittal A, Scott GM, Amidon TE, Kiemle DJ, Stipanovic AJ. Quantitative analysis of sugars in wood hydrolyzates with 1H NMR during the autohydrolysis of hardwoods. Bioresour Technol 2009; 100:6398-406. [PMID: 19674893 DOI: 10.1016/j.biortech.2009.06.107] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 06/18/2009] [Accepted: 06/27/2009] [Indexed: 05/16/2023]
Abstract
The focus of this work was to determine the utility of (1)H NMR spectroscopy in the quantification of sugars resulting from the solubilization of hemicelluloses during the autohydrolysis of hardwoods and the use of this technique to evaluate the kinetics of this process over a range of temperatures and times. Yields of residual xylan, xylooligomers, xylose, glucose, and the degraded products of sugars, i.e., furfural and HMF (5-hydroxymethyl furfural), were determined. The monosaccharide and oligomer contents were quantified with a recently developed high resolution (1)H NMR spectroscopic analysis. This method provided precise measurement of the residual xylan and cellulose remaining in the extracted wood samples and xylose and glucose in the hydrolyzates. NMR was found to exhibit good repeatability and provided carbohydrate compositional results comparable to published methods for sugar maple and aspen woods.
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Affiliation(s)
- Ashutosh Mittal
- Department of Paper and Bioprocess Engineering, SUNY College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210, United States.
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Affiliation(s)
- John E. Baldwin
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - David J. Kiemle
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210
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Baldwin JE, Kiemle DJ, Kostikov AP. Quantitative Analyses of Stereoisomeric 3,4-d2-Cyclohexenes in the Presence of 3,6-d2-Cyclohexenes. J Org Chem 2009; 74:3866-74. [DOI: 10.1021/jo900430w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John E. Baldwin
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, and Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210
| | - David J. Kiemle
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, and Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210
| | - Alexey P. Kostikov
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, and Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York 13210
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Abstract
The complete assignments of the (1)H and (13)C NMR spectra of the hallucinogenic neoclerodane diterpenoid salvinorin A were determined in three different NMR solvents using HSQC, HMBC and COSY. Solvent systems are described that allow the resolution of all (1)H signals. Virtual coupling was observed for the protons at C-2, C-3 and C-4 in the 600 MHz (1)H spectrum in CDCl(3). The complete assignments of the (1)H and (13)C NMR spectra of salvinorin B are also reported.
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Affiliation(s)
- José-Luis Giner
- Department of Chemistry, State University of New York ESF, Syracuse, NY 13210, USA.
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12
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Abstract
A simple, inexpensive, and highly efficient NMR sample preparation technique for volatile chemicals has been devised using a micropreparative GC system. The recovery efficiency of a volatile chemical using this technique was >80% with sample sizes of 0.05 to 0.5 microg. The purity of the acquired NMR samples was sufficient for high sensitive NMR analyses including two dimensional experiments.
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Affiliation(s)
- Satoshi Nojima
- Department of Entomology, NYS Agricultural Experiment Station, Cornell University Geneva, New York, USA.
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13
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Affiliation(s)
- David J. Kiemle
- Faculty of Chemistry, College of Environmental Science and Forestry (SUNY-ESF), E. C. Jahn Chemistry Laboratory, State University of New York, One Forestry Drive, Syracuse, NY 13210
| | - Arthur J. Stipanovic
- Faculty of Chemistry, College of Environmental Science and Forestry (SUNY-ESF), E. C. Jahn Chemistry Laboratory, State University of New York, One Forestry Drive, Syracuse, NY 13210
| | - Kelly E. Mayo
- Faculty of Chemistry, College of Environmental Science and Forestry (SUNY-ESF), E. C. Jahn Chemistry Laboratory, State University of New York, One Forestry Drive, Syracuse, NY 13210
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Abstract
Tunicamycin is a reversible inhibitor of polyprenol-phosphate: N-acetylhexosamine-1-phosphate translocases and is produced by several Streptomyces species. We have examined tunicamycin biosynthesis, an important but poorly characterized biosynthetic pathway. Biosynthetic precursors have been identified by incorporating radioactive and stable isotopes, and by determining the labeling pattern using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS), and proton, deuterium, and C-13 nuclear magnetic resonance (NMR) spectroscopy. Preparation and analysis of [uracil-5-(2)H]-labeled tunicamycin established the complete ESI-CID-MS fragmentation pathway for the major components of the tunicamycin complex. Competitive metabolic experiments indicate that 7 deuteriums incorporate into tunicamycin from [6,6'-(2)H,(2)H]-labeled D-glucose, 6 of which arise from D-GlcNAc and 1 from uridine and/or D-ribose. Inverse correlation NMR experiments (heteronuclear single-quantum coherence (HSQC)) of (13)C-labeled tunicamycin enriched from D-[1-(13)C]glucose suggest that the unique tunicamine 11-carbon dialdose sugar backbone arises from a 5-carbon furanose precursor derived from uridine and a 6-carbon N-acetylamino-pyranose precursor derived from UDP-D-N-acetylglucosamine. The equivalent incorporation of (13)C into both the alpha-1" and beta-11' anomeric carbons of tunicamycin supports a direct biosynthesis via 6-carbon metabolism. It also indicates that the tunicamine motif and the alpha-1"-linked GlcNAc residue are both derived from the same metabolic pool of UDP-GlcNAc, without significant differential metabolic processing. A biosynthetic pathway is therefore proposed for tunicamycin for the first time: an initial formation of the 11-carbon tunicamine sugar motif from uridine and UDP-GlcNAc via uridine-5'-aldehyde and UDP-4-keto-6-ene-N-acetylhexosamine, respectively, and subsequent formation of the anomeric-to-anomeric alpha, beta-1",11'-glycosidic bond.
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Affiliation(s)
- Billyana C Tsvetanova
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, New York 13210, USA
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15
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Abstract
Positional preferences for para benzylic oxygenation of tetrahydronaphthalenes by 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ)-aqueous dioxane were investigated by comparing the tetralone products from 6-hydroxy-7-methoxy- and 6-acetoxy-7-methoxy-1,2,3,4-tetrahydronaphthalene. The directing influence by an aromatic substituent on para benzylic oxygenation was in the order OH > OMe > OAc. Consistent with this finding were results obtained from lignan analogues. Treatment of (+)-beta-conidendryl alcohol with DDQ in dry dioxane resulted in the intramolecular bridging by one of two primary hydroxy groups to the benzylic position, giving an oxabicyclo[3.2.1]octane. Similar treatment of (+)-dimethyl-beta-conidendryl alcohol resulted in bridging by the alternate primary hydroxyl group to the benzhydrylic carbon giving an isomeric oxabicyclo[3.2.1]octane.
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Affiliation(s)
- Frank D. Ramdayal
- Department of Chemistry, Jahn Laboratory, State University of New York, College of Environmental Science and Forestry, Syracuse, New York 13210
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