1
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Morgan JM, Jelenska J, Hensley DK, Li P, Srijanto BR, Retterer ST, Standaert RF, Morrell-Falvey JL, Greenberg JT. Using Vertically Aligned Carbon Nanofiber Arrays on Rigid or Flexible Substrates for Delivery of Biomolecules and Dyes to Plants. J Vis Exp 2023. [PMID: 37677009 DOI: 10.3791/65602] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Abstract
The delivery of biomolecules and impermeable dyes to intact plants is a major challenge. Nanomaterials are up-and-coming tools for the delivery of DNA to plants. As exciting as these new tools are, they have yet to be widely applied. Nanomaterials fabricated on rigid substrate (backing) are particularly difficult to successfully apply to curved plant structures. This study describes the process for microfabricating vertically aligned carbon nanofiber arrays and transferring them from a rigid to a flexible substrate. We detail and demonstrate how these fibers (on either rigid or flexible substrates) can be used for transient transformation or dye (e.g., fluorescein) delivery to plants. We show how VACNFs can be transferred from rigid silicon substrate to a flexible SU-8 epoxy substrate to form flexible VACNF arrays. To overcome the hydrophobic nature of SU-8, fibers in the flexible film were coated with a thin silicon oxide layer (2-3 nm). To use these fibers for delivery to curved plant organs, we deposit a 1 µL droplet of dye or DNA solution on the fiber side of VACNF films, wait 10 min, place the films on the plant organ and employ a swab with a rolling motion to drive fibers into plant cells. With this method, we have achieved dye and DNA delivery in plant organs with curved surfaces.
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Affiliation(s)
| | - Joanna Jelenska
- Molecular Genetics and Cell Biology, The University of Chicago
| | - Dale K Hensley
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory
| | - Pengju Li
- Pritzker School of Molecular Engineering, The University of Chicago
| | | | - Scott T Retterer
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory; Biosciences Division, Oak Ridge National Laboratory
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2
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Morgan JM, Jelenska J, Hensley D, Retterer ST, Morrell-Falvey JL, Standaert RF, Greenberg JT. An efficient and broadly applicable method for transient transformation of plants using vertically aligned carbon nanofiber arrays. Front Plant Sci 2022; 13:1051340. [PMID: 36507425 PMCID: PMC9728956 DOI: 10.3389/fpls.2022.1051340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Transient transformation in plants is a useful process for evaluating gene function. However, there is a scarcity of minimally perturbing methods for gene delivery that can be used on multiple organs, plant species, and non-excised tissues. We pioneered and demonstrated the use of vertically aligned carbon nanofiber (VACNF) arrays to efficiently perform transient transformation of different tissues with DNA constructs in multiple plant species. The VACNFs permeabilize plant tissue transiently to allow molecules into cells without causing a detectable stress response. We successfully delivered DNA into leaves, roots and fruit of five plant species (Arabidopsis, poplar, lettuce, Nicotiana benthamiana, and tomato) and confirmed accumulation of the encoded fluorescent proteins by confocal microscopy. Using this system, it is possible to transiently transform plant cells with both small and large plasmids. The method is successful for species recalcitrant to Agrobacterium-mediated transformation. VACNFs provide simple, reliable means of DNA delivery into a variety of plant organs and species.
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Affiliation(s)
- Jessica M Morgan
- Biophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Joanna Jelenska
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
| | - Dale Hensley
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Scott T Retterer
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Robert F Standaert
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States
| | - Jean T Greenberg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, United States
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3
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Mou Z, Eakes J, Cooper CJ, Foster CM, Standaert RF, Podar M, Doktycz MJ, Parks JM. Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases. Proteins 2020; 89:336-347. [DOI: 10.1002/prot.26019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/02/2020] [Accepted: 10/17/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Zhongyu Mou
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Jason Eakes
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology University of TennesseeWalters Life Science Knoxville Tennessee USA
| | - Carmen M. Foster
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | | | - Mircea Podar
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Mitchel J. Doktycz
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
- Graduate School of Genome Science and Technology University of TennesseeWalters Life Science Knoxville Tennessee USA
| | - Jerry M. Parks
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
- Graduate School of Genome Science and Technology University of TennesseeWalters Life Science Knoxville Tennessee USA
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4
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Nickels JD, Poudel S, Chatterjee S, Farmer A, Cordner D, Campagna SR, Giannone RJ, Hettich RL, Myles DAA, Standaert RF, Katsaras J, Elkins JG. Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome. Front Microbiol 2020; 11:914. [PMID: 32499768 PMCID: PMC7243436 DOI: 10.3389/fmicb.2020.00914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/17/2020] [Indexed: 12/22/2022] Open
Abstract
Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells – as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins.
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Affiliation(s)
- Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, United States
| | - Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sneha Chatterjee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Abigail Farmer
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Destini Cordner
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, United States
| | - Shawn R Campagna
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert F Standaert
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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5
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Garcia DC, Cheng X, Land ML, Standaert RF, Morrell-Falvey JL, Doktycz MJ. Computationally Guided Discovery and Experimental Validation of Indole-3-acetic Acid Synthesis Pathways. ACS Chem Biol 2019; 14:2867-2875. [PMID: 31693336 DOI: 10.1021/acschembio.9b00725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Elucidating the interaction networks associated with secondary metabolite production in microorganisms is an ongoing challenge made all the more daunting by the rate at which DNA sequencing technology reveals new genes and potential pathways. Developing the culturing methods, expression conditions, and genetic systems needed for validating pathways in newly discovered microorganisms is often not possible. Therefore, new tools and techniques are needed for defining complex metabolic pathways. Here, we describe an in vitro computationally assisted pathway description approach that employs bioinformatic searches of genome databases, protein structural modeling, and protein-ligand-docking simulations to predict the gene products most likely to be involved in a particular secondary metabolite production pathway. This information is then used to direct in vitro reconstructions of the pathway and subsequent confirmation of pathway activity using crude enzyme preparations. As a test system, we elucidated the pathway for biosynthesis of indole-3-acetic acid (IAA) in the plant-associated microbe Pantoea sp. YR343. This organism is capable of metabolizing tryptophan into the plant phytohormone IAA. BLAST analyses identified a likely three-step pathway involving an amino transferase, an indole pyruvate decarboxylase, and a dehydrogenase. However, multiple candidate enzymes were identified at each step, resulting in a large number of potential pathway reconstructions (32 different enzyme combinations). Our approach shows the effectiveness of crude extracts to rapidly elucidate enzymes leading to functional pathways. Results are compared to affinity purified enzymes for select combinations and found to yield similar relative activities. Further, in vitro testing of the pathway reconstructions revealed the "underground" nature of IAA metabolism in Pantoea sp. YR343 and the various mechanisms used to produce IAA. Importantly, our experiments illustrate the scalable integration of computational tools and cell-free enzymatic reactions to identify and validate metabolic pathways in a broadly applicable manner.
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Affiliation(s)
- David C. Garcia
- Biological and Nanoscale Systems Group, Biosciences Division Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996-4519, United States
| | - Xiaolin Cheng
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Miriam L. Land
- Computational Biology and Bioinformatics Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert F. Standaert
- Biological and Nanoscale Systems Group, Biosciences Division Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, East Tennessee State University, Johnson City, Tennessee 37604, United States
| | - Jennifer L. Morrell-Falvey
- Biological and Nanoscale Systems Group, Biosciences Division Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Mitchel J. Doktycz
- Biological and Nanoscale Systems Group, Biosciences Division Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996-4519, United States
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6
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Scott HL, Ashkar R, Heberle FA, Standaert RF, Katsaras J, Barrera FN. Neutron spin–echo detects effects of the pH-low insertion peptide on membrane thickness fluctuations. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318097040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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7
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Garcia DC, Mohr BP, Dovgan JT, Hurst GB, Standaert RF, Doktycz MJ. Elucidating the potential of crude cell extracts for producing pyruvate from glucose. Synth Biol (Oxf) 2018; 3:ysy006. [PMID: 32995514 PMCID: PMC7445776 DOI: 10.1093/synbio/ysy006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/23/2018] [Accepted: 04/19/2018] [Indexed: 01/05/2023] Open
Abstract
Living systems possess a rich biochemistry that can be harnessed through metabolic engineering to produce valuable therapeutics, fuels and fine chemicals. In spite of the tools created for this purpose, many organisms tend to be recalcitrant to modification or difficult to optimize. Crude cellular extracts, made by lysis of cells, possess much of the same biochemical capability, but in an easier to manipulate context. Metabolic engineering in crude extracts, or cell-free metabolic engineering, can harness these capabilities to feed heterologous pathways for metabolite production and serve as a platform for pathway optimization. However, the inherent biochemical potential of a crude extract remains ill-defined, and consequently, the use of such extracts can result in inefficient processes and unintended side products. Herein, we show that changes in cell growth conditions lead to changes in the enzymatic activity of crude cell extracts and result in different abilities to produce the central biochemical precursor pyruvate when fed glucose. Proteomic analyses coupled with metabolite measurements uncover the diverse biochemical capabilities of these different crude extract preparations and provide a framework for how analytical measurements can be used to inform and improve crude extract performance. Such informed developments can allow enrichment of crude extracts with pathways that promote or deplete particular metabolic processes and aid in the metabolic engineering of defined products.
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Affiliation(s)
- David C Garcia
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Benjamin P Mohr
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jakob T Dovgan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gregory B Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Mitchel J Doktycz
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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8
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Standaert RF, Giannone RJ, Michener JK. Identification of parallel and divergent optimization solutions for homologous metabolic enzymes. Metab Eng Commun 2018; 6:56-62. [PMID: 29896448 PMCID: PMC5994803 DOI: 10.1016/j.meteno.2018.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/02/2018] [Accepted: 04/16/2018] [Indexed: 11/02/2022] Open
Abstract
Metabolic pathway assembly typically involves the expression of enzymes from multiple organisms in a single heterologous host. Ensuring that each enzyme functions effectively can be challenging, since many potential factors can disrupt proper pathway flux. Here, we compared the performance of two enzyme homologs in a pathway engineered to allow Escherichia coli to grow on 4-hydroxybenzoate (4-HB), a byproduct of lignocellulosic biomass deconstruction. Single chromosomal copies of the 4-HB 3-monooxygenase genes pobA and praI, from Pseudomonas putida KT2440 and Paenibacillus sp. JJ-1B, respectively, were introduced into a strain able to metabolize protocatechuate (PCA), the oxidation product of 4-HB. Neither enzyme initially supported consistent growth on 4-HB. Experimental evolution was used to identify mutations that improved pathway activity. For both enzymes, silent mRNA mutations were identified that increased enzyme expression. With pobA, duplication of the genes for PCA metabolism allowed growth on 4-HB. However, with praI, growth required a mutation in the 4-HB/PCA transporter pcaK that increased intracellular concentrations of 4-HB, suggesting that flux through PraI was limiting. These findings demonstrate the value of directed evolution strategies to rapidly identify and overcome diverse factors limiting enzyme activity.
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Affiliation(s)
- Robert F Standaert
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA.,Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA.,Shull Wollan Center - A Joint Institute for Neutron Sciences, Oak Ridge, TN 37831, USA.,Department of Biochemistry&Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37830, USA
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9
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Estenson K, Hurst GB, Standaert RF, Bible AN, Garcia D, Chourey K, Doktycz MJ, Morrell-Falvey JL. Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343. J Proteome Res 2018; 17:1361-1374. [PMID: 29464956 DOI: 10.1021/acs.jproteome.7b00708] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indole-3-acetic acid (IAA) plays a central role in plant growth and development, and many plant-associated microbes produce IAA using tryptophan as the precursor. Using genomic analyses, we predicted that Pantoea sp. YR343, a microbe isolated from Populus deltoides, synthesizes IAA using the indole-3-pyruvate (IPA) pathway. To better understand IAA biosynthesis and the effects of IAA exposure on cell physiology, we characterized proteomes of Pantoea sp. YR343 grown in the presence of tryptophan or IAA. Exposure to IAA resulted in upregulation of proteins predicted to function in carbohydrate and amino acid transport and exopolysaccharide (EPS) biosynthesis. Metabolite profiles of wild-type cells showed the production of IPA, IAA, and tryptophol, consistent with an active IPA pathway. Finally, we constructed an Δ ipdC mutant that showed the elimination of tryptophol, consistent with a loss of IpdC activity, but was still able to produce IAA (20% of wild-type levels). Although we failed to detect intermediates from other known IAA biosynthetic pathways, this result suggests the possibility of an alternate pathway or the production of IAA by a nonenzymatic route in Pantoea sp. YR343. The Δ ipdC mutant was able to efficiently colonize poplar, suggesting that an active IPA pathway is not required for plant association.
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Affiliation(s)
- Kasey Estenson
- UT-ORNL Graduate School of Genome Science and Technology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | | | - Robert F Standaert
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Shull Wollan Center - a Joint Institute for Neutron Sciences , Oak Ridge , Tennessee 37831 , United States
| | - Amber N Bible
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - David Garcia
- Bredesen Center , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | | | - Mitchel J Doktycz
- UT-ORNL Graduate School of Genome Science and Technology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Bredesen Center , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Jennifer L Morrell-Falvey
- UT-ORNL Graduate School of Genome Science and Technology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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10
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Scott HL, Ashkar R, Heberle FA, Standaert RF, Katsaras J, Barrera FN. Neutron Spin Echo Detects Effects of the pH-Low Insertion Peptide on Membrane Thickness Fluctuations. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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11
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Holfeltz VE, Campbell EL, Peterman DR, Standaert RF, Paulenova A, Lumetta GJ, Levitskaia TG. Effect of HEH[EHP] impurities on the ALSEP solvent extraction process. Solvent Extraction and Ion Exchange 2017. [DOI: 10.1080/07366299.2017.1412111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Vanessa E Holfeltz
- Nuclear Chemistry and Engineering Group, Pacific Northwest National Laboratory, Richland, WA, USA
- School of Nuclear Science and Engineering, Oregon State University, Corvallis, OR, USA
| | - Emily L. Campbell
- Nuclear Chemistry and Engineering Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dean R. Peterman
- Aqueous Separations and Radiochemistry Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Robert F. Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
- Biology & Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Shull Wollan Center — a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alena Paulenova
- School of Nuclear Science and Engineering, Oregon State University, Corvallis, OR, USA
| | - Gregg J. Lumetta
- Nuclear Chemistry and Engineering Group, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tatiana G Levitskaia
- Nuclear Chemistry and Engineering Group, Pacific Northwest National Laboratory, Richland, WA, USA
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12
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Hurst GB, Asano KG, Doktycz CJ, Consoli EJ, Doktycz WL, Foster CM, Morrell-Falvey JL, Standaert RF, Doktycz MJ. Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis. Anal Chem 2017; 89:11443-11451. [DOI: 10.1021/acs.analchem.7b02555] [Citation(s) in RCA: 15] [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: 12/16/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Robert F. Standaert
- University of Tennessee, Department of Biochemistry & Cellular and Molecular Biology, Knoxville, Tennessee 37996, United States
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13
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Nickels JD, Chatterjee S, Mostofian B, Stanley CB, Ohl M, Zolnierczuk P, Schulz R, Myles DAA, Standaert RF, Elkins JG, Cheng X, Katsaras J. Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane. J Phys Chem Lett 2017; 8:4214-4217. [PMID: 28825491 DOI: 10.1021/acs.jpclett.7b01877] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Lipid extracts are an excellent choice of model biomembrane; however at present, there are no commercially available lipid extracts or computational models that mimic microbial membranes containing the branched-chain fatty acids found in many pathogenic and industrially relevant bacteria. We advance the extract of Bacillus subtilis as a standard model for these diverse systems, providing a detailed experimental description and equilibrated atomistic bilayer model included as Supporting Information to this Letter and at ( http://cmb.ornl.gov/members/cheng ). The development and validation of this model represents an advance that enables more realistic simulations and experiments on bacterial membranes and reconstituted bacterial membrane proteins.
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Affiliation(s)
| | | | | | | | - Michael Ohl
- Jülich Center for Neutron Science, Forschungszentrum Juelich GmbH , Outstation at SNS, Oak Ridge, Tennessee 37831, United States
| | - Piotr Zolnierczuk
- Jülich Center for Neutron Science, Forschungszentrum Juelich GmbH , Outstation at SNS, Oak Ridge, Tennessee 37831, United States
| | - Roland Schulz
- Intel Corporation , Hillsboro, Oregon 97124, United States of America
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14
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Li L, Shukla S, Meilleur F, Standaert RF, Pierce J, Myles DAA, Cuneo MJ. Neutron crystallographic studies of T4 lysozyme at cryogenic temperature. Protein Sci 2017; 26:2098-2104. [PMID: 28707382 DOI: 10.1002/pro.3231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022]
Abstract
Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics, and stability. Approximately 700 mutants of this protein and their respective complexes have been characterized by X-ray crystallography; however, despite the high resolution diffraction limits attained in several studies, no hydrogen atoms were reported being visualized in the electron density maps. To address this, a 2.2 Å-resolution neutron data set was collected at 80 K from a crystal of perdeuterated T4L pseudo-wild type. We describe a near complete atomic structure of T4L, which includes the positions of 1737 hydrogen atoms determined by neutron crystallography. The cryogenic neutron model reveals explicit detail of the hydrogen bonding interactions in the protein, in addition to the protonation states of several important residues.
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Affiliation(s)
- Le Li
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
| | - Shantanu Shukla
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Flora Meilleur
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Robert F Standaert
- Energy and Environmental Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Josh Pierce
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
| | - Dean A A Myles
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Matthew J Cuneo
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
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15
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Nickels JD, Chatterjee S, Stanley CB, Qian S, Cheng X, Myles DAA, Standaert RF, Elkins JG, Katsaras J. The in vivo structure of biological membranes and evidence for lipid domains. PLoS Biol 2017; 15:e2002214. [PMID: 28542493 PMCID: PMC5441578 DOI: 10.1371/journal.pbio.2002214] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/11/2017] [Indexed: 12/19/2022] Open
Abstract
Examining the fundamental structure and processes of living cells at the nanoscale poses a unique analytical challenge, as cells are dynamic, chemically diverse, and fragile. A case in point is the cell membrane, which is too small to be seen directly with optical microscopy and provides little observational contrast for other methods. As a consequence, nanoscale characterization of the membrane has been performed ex vivo or in the presence of exogenous labels used to enhance contrast and impart specificity. Here, we introduce an isotopic labeling strategy in the gram-positive bacterium Bacillus subtilis to investigate the nanoscale structure and organization of its plasma membrane in vivo. Through genetic and chemical manipulation of the organism, we labeled the cell and its membrane independently with specific amounts of hydrogen (H) and deuterium (D). These isotopes have different neutron scattering properties without altering the chemical composition of the cells. From neutron scattering spectra, we confirmed that the B. subtilis cell membrane is lamellar and determined that its average hydrophobic thickness is 24.3 ± 0.9 Ångstroms (Å). Furthermore, by creating neutron contrast within the plane of the membrane using a mixture of H- and D-fatty acids, we detected lateral features smaller than 40 nm that are consistent with the notion of lipid rafts. These experiments-performed under biologically relevant conditions-answer long-standing questions in membrane biology and illustrate a fundamentally new approach for systematic in vivo investigations of cell membrane structure.
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Affiliation(s)
- Jonathan D. Nickels
- Shull Wollan Center—A Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sneha Chatterjee
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Christopher B. Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Shuo Qian
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Xiaolin Cheng
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Dean A. A. Myles
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert F. Standaert
- Shull Wollan Center—A Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RFS); (JGE); (JK)
| | - James G. Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RFS); (JGE); (JK)
| | - John Katsaras
- Shull Wollan Center—A Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RFS); (JGE); (JK)
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16
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Jelenska J, Davern SM, Standaert RF, Mirzadeh S, Greenberg JT. Flagellin peptide flg22 gains access to long-distance trafficking in Arabidopsis via its receptor, FLS2. J Exp Bot 2017; 68:1769-1783. [PMID: 28521013 PMCID: PMC5444442 DOI: 10.1093/jxb/erx060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Diverse pathogen-derived molecules, such as bacterial flagellin and its conserved peptide flg22, are recognized in plants via plasma membrane receptors and induce both local and systemic immune responses. The fate of such ligands was unknown: whether and by what mechanism(s) they enter plant cells and whether they are transported to distal tissues. We used biologically active fluorophore and radiolabeled peptides to establish that flg22 moves to distal organs with the closest vascular connections. Remarkably, entry into the plant cell via endocytosis together with the FLS2 receptor is needed for delivery to vascular tissue and long-distance transport of flg22. This contrasts with known routes of long distance transport of other non-cell-permeant molecules in plants, which require membrane-localized transporters for entry to vascular tissue. Thus, a plasma membrane receptor acts as a transporter to enable access of its ligand to distal trafficking routes.
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Affiliation(s)
- Joanna Jelenska
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Sandra M Davern
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Nuclear Security and Isotope Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert F Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Saed Mirzadeh
- Nuclear Security and Isotope Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jean T Greenberg
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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17
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Marquardt D, Heberle FA, Greathouse DV, Koeppe RE, Standaert RF, Van Oosten BJ, Harroun TA, Kinnun JJ, Williams JA, Wassall SR, Katsaras J. Lipid bilayer thickness determines cholesterol's location in model membranes. Soft Matter 2016; 12:9417-9428. [PMID: 27801465 DOI: 10.1039/c6sm01777k] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cholesterol is an essential biomolecule of animal cell membranes, and an important precursor for the biosynthesis of certain hormones and vitamins. It is also thought to play a key role in cell signaling processes associated with functional plasma membrane microdomains (domains enriched in cholesterol), commonly referred to as rafts. In all of these diverse biological phenomena, the transverse location of cholesterol in the membrane is almost certainly an important structural feature. Using a combination of neutron scattering and solid-state 2H NMR, we have determined the location and orientation of cholesterol in phosphatidylcholine (PC) model membranes having fatty acids of different lengths and degrees of unsaturation. The data establish that cholesterol reorients rapidly about the bilayer normal in all the membranes studied, but is tilted and forced to span the bilayer midplane in the very thin bilayers. The possibility that cholesterol lies flat in the middle of bilayers, including those made from PC lipids containing polyunsaturated fatty acids (PUFAs), is ruled out. These results support the notion that hydrophobic thickness is the primary determinant of cholesterol's location in membranes.
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Affiliation(s)
- Drew Marquardt
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada and Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Frederick A Heberle
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA and Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
| | - Denise V Greathouse
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Roger E Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Robert F Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Brad J Van Oosten
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Jacob J Kinnun
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Justin A Williams
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Stephen R Wassall
- Department of Physics, Indiana University - Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - John Katsaras
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada and The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA and Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Shull Wollan Center-a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA and Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
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18
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Affiliation(s)
- Sarwat Chowdhury
- Department
of Chemistry, The University of Illinois at Chicago, 845 West
Taylor Street, Chicago, Illinois 60304, United States
| | - Robert F. Standaert
- Biosciences
Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, Tennessee 37831-6445, United States
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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19
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Heberle FA, Marquardt D, Doktorova M, Geier B, Standaert RF, Heftberger P, Kollmitzer B, Nickels JD, Dick R, Feigenson GW, Katsaras J, London E, Pabst G. Subnanometer Structure of an Asymmetric Model Membrane: Interleaflet Coupling Influences Domain Properties. Langmuir 2016; 32:5195-200. [PMID: 27128636 PMCID: PMC4910133 DOI: 10.1021/acs.langmuir.5b04562] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cell membranes possess a complex three-dimensional architecture, including nonrandom lipid lateral organization within the plane of a bilayer leaflet, and compositional asymmetry between the two leaflets. As a result, delineating the membrane structure-function relationship has been a highly challenging task. Even in simplified model systems, the interactions between bilayer leaflets are poorly understood, due in part to the difficulty of preparing asymmetric model membranes that are free from the effects of residual organic solvent or osmotic stress. To address these problems, we have modified a technique for preparing asymmetric large unilamellar vesicles (aLUVs) via cyclodextrin-mediated lipid exchange in order to produce tensionless, solvent-free aLUVs suitable for a range of biophysical studies. Leaflet composition and structure were characterized using isotopic labeling strategies, which allowed us to avoid the use of bulky labels. NMR and gas chromatography provided precise quantification of the extent of lipid exchange and bilayer asymmetry, while small-angle neutron scattering (SANS) was used to resolve bilayer structural features with subnanometer resolution. Isotopically asymmetric POPC vesicles were found to have the same bilayer thickness and area per lipid as symmetric POPC vesicles, demonstrating that the modified exchange protocol preserves native bilayer structure. Partial exchange of DPPC into the outer leaflet of POPC vesicles produced chemically asymmetric vesicles with a gel/fluid phase-separated outer leaflet and a uniform, POPC-rich inner leaflet. SANS was able to separately resolve the thicknesses and areas per lipid of coexisting domains, revealing reduced lipid packing density of the outer leaflet DPPC-rich phase compared to typical gel phases. Our finding that a disordered inner leaflet can partially fluidize ordered outer leaflet domains indicates some degree of interleaflet coupling, and invites speculation on a role for bilayer asymmetry in modulating membrane lateral organization.
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Affiliation(s)
- Frederick A. Heberle
- Biology and Soft Matter Division, Joint Institute for
Neutron Sciences, and Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
- E-mail:
| | - Drew Marquardt
- Institute
of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
- E-mail:
| | - Milka Doktorova
- Tri-Institutional
PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York 10065, United States
- Department
of Molecular Biology and Genetics, Cornell
University, Ithaca, New York 14853, United
States
| | - Barbara Geier
- Institute
of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Robert F. Standaert
- Biology and Soft Matter Division, Joint Institute for
Neutron Sciences, and Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
& Molecular Biology, and Department of
Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Peter Heftberger
- Institute
of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Benjamin Kollmitzer
- Institute
of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Jonathan D. Nickels
- Biology and Soft Matter Division, Joint Institute for
Neutron Sciences, and Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert
A. Dick
- Department
of Molecular Biology and Genetics, Cornell
University, Ithaca, New York 14853, United
States
| | - Gerald W. Feigenson
- Department
of Molecular Biology and Genetics, Cornell
University, Ithaca, New York 14853, United
States
| | - John Katsaras
- Biology and Soft Matter Division, Joint Institute for
Neutron Sciences, and Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular
& Molecular Biology, and Department of
Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Erwin London
- Department
of Biochemistry and Cell Biology, Stony
Brook University, Stony Brook, New York 11794, United States
| | - Georg Pabst
- Institute
of Molecular Biosciences, Biophysics Division, NAWI Graz, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
- E-mail:
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20
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Davern SM, McKnight TE, Standaert RF, Morrell-Falvey JL, Shpak ED, Kalluri UC, Jelenska J, Greenberg JT, Mirzadeh S. Carbon Nanofiber Arrays: A Novel Tool for Microdelivery of Biomolecules to Plants. PLoS One 2016; 11:e0153621. [PMID: 27119338 PMCID: PMC4847769 DOI: 10.1371/journal.pone.0153621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/31/2016] [Indexed: 11/19/2022] Open
Abstract
Effective methods for delivering bioprobes into the cells of intact plants are essential for investigating diverse biological processes. Increasing research on trees, such as Populus spp., for bioenergy applications is driving the need for techniques that work well with tree species. This report introduces vertically aligned carbon nanofiber (VACNF) arrays as a new tool for microdelivery of labeled molecules to Populus leaf tissue and whole plants. We demonstrated that VACNFs penetrate the leaf surface to deliver sub-microliter quantities of solution containing fluorescent or radiolabeled molecules into Populus leaf cells. Importantly, VACNFs proved to be gentler than abrasion with carborundum, a common way to introduce material into leaves. Unlike carborundum, VACNFs did not disrupt cell or tissue integrity, nor did they induce production of hydrogen peroxide, a typical wound response. We show that femtomole to picomole quantities of labeled molecules (fluorescent dyes, small proteins and dextran), ranging from 0.5-500 kDa, can be introduced by VACNFs, and we demonstrate the use of the approach to track delivered probes from their site of introduction on the leaf to distal plant regions. VACNF arrays thus offer an attractive microdelivery method for the introduction of biomolecules and other probes into trees and potentially other types of plants.
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Affiliation(s)
- Sandra M. Davern
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Timothy E. McKnight
- Electrical & Electronics Systems Research Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert F. Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Biology & Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jennifer L. Morrell-Falvey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Elena D. Shpak
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Joanna Jelenska
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Jean T. Greenberg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Saed Mirzadeh
- Nuclear Security & Isotope Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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21
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Whited AM, Heberle FA, Standaert RF, Nickels JD, Cheng X, Katsaras J, Johs A. Translocase Activity and Asymmetric Model Membranes Probed by Neutron Scattering. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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22
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Nickels JD, Cheng X, Mostofian B, Stanley C, Lindner B, Heberle FA, Perticaroli S, Feygenson M, Egami T, Standaert RF, Smith JC, Myles DAA, Ohl M, Katsaras J. Mechanical Properties of Nanoscopic Lipid Domains. J Am Chem Soc 2015; 137:15772-80. [DOI: 10.1021/jacs.5b08894] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan D. Nickels
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Department
of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Xiaolin Cheng
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Barmak Mostofian
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | | | - Benjamin Lindner
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frederick A. Heberle
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Stefania Perticaroli
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Mikhail Feygenson
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Takeshi Egami
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
| | - Robert F. Standaert
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dean A. A. Myles
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Michael Ohl
- Jülich Center for Neutron Science, Oak
Ridge, Tennessee 37831, United States
| | - John Katsaras
- Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
- Department
of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, United States
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23
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Abstract
Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured to suit a variety of fluidic operations or biochemical processes. We demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.
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Affiliation(s)
- L J Millet
- Biological and Nanoscale Systems Group, Biosciences Division, Oak Ridge National Laboratory, PO Box 2008 MS 6445, Oak Ridge, TN 37831-6445, USA.
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24
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Doktorova M, Heberle FA, Goh SL, Standaert RF, Katsaras J, Feigenson GW. Hybrid and Nonhybrid Lipids Exert Common Effects on Membrane Raft Size and Morphology. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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25
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Heberle FA, Petruzielo RS, Pan J, Drazba P, Kucerka N, Standaert RF, Feigenson GW, Katsaras J. Bilayer Thickness Mismatch Controls Domain Size in Model Membranes. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1686] [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: 11/26/2022] Open
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26
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Affiliation(s)
- Amandeep K. Sangha
- UT/ORNL Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | | | - Robert F. Standaert
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Mark F. Davis
- National
Bioenergy Center and Bioenergy Science Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jeremy C. Smith
- UT/ORNL Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jerry M. Parks
- UT/ORNL Center
for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
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27
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Heberle FA, Doktorova M, Goh SL, Standaert RF, Katsaras J, Feigenson GW. Hybrid and nonhybrid lipids exert common effects on membrane raft size and morphology. J Am Chem Soc 2013; 135:14932-5. [PMID: 24041024 DOI: 10.1021/ja407624c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nanometer-scale domains in cholesterol-rich model membranes emulate lipid rafts in cell plasma membranes (PMs). The physicochemical mechanisms that maintain a finite, small domain size are, however, not well understood. A special role has been postulated for chain-asymmetric or hybrid lipids having a saturated sn-1 chain and an unsaturated sn-2 chain. Hybrid lipids generate nanodomains in some model membranes and are also abundant in the PM. It was proposed that they align in a preferred orientation at the boundary of ordered and disordered phases, lowering the interfacial energy and thus reducing domain size. We used small-angle neutron scattering and fluorescence techniques to detect nanoscopic and modulated liquid phase domains in a mixture composed entirely of nonhybrid lipids and cholesterol. Our results are indistinguishable from those obtained previously for mixtures containing hybrid lipids, conclusively showing that hybrid lipids are not required for the formation of nanoscopic liquid domains and strongly implying a common mechanism for the overall control of raft size and morphology. We discuss implications of these findings for theoretical descriptions of nanodomains.
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Affiliation(s)
- Frederick A Heberle
- Biology and Soft Matter and §Biosciences Divisions, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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28
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Heberle FA, Petruzielo RS, Pan J, Drazba P, Kučerka N, Standaert RF, Feigenson GW, Katsaras J. Bilayer thickness mismatch controls domain size in model membranes. J Am Chem Soc 2013; 135:6853-9. [PMID: 23391155 DOI: 10.1021/ja3113615] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The observation of lateral phase separation in lipid bilayers has received considerable attention, especially in connection to lipid raft phenomena in cells. It is widely accepted that rafts play a central role in cellular processes, notably signal transduction. While micrometer-sized domains are observed with some model membrane mixtures, rafts much smaller than 100 nm-beyond the reach of optical microscopy-are now thought to exist, both in vitro and in vivo. We have used small-angle neutron scattering, a probe free technique, to measure the size of nanoscopic membrane domains in unilamellar vesicles with unprecedented accuracy. These experiments were performed using a four-component model system containing fixed proportions of cholesterol and the saturated phospholipid 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), mixed with varying amounts of the unsaturated phospholipids 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). We find that liquid domain size increases with the extent of acyl chain unsaturation (DOPC:POPC ratio). Furthermore, we find a direct correlation between domain size and the mismatch in bilayer thickness of the coexisting liquid-ordered and liquid-disordered phases, suggesting a dominant role for line tension in controlling domain size. While this result is expected from line tension theories, we provide the first experimental verification in free-floating bilayers. Importantly, we also find that changes in bilayer thickness, which accompany changes in the degree of lipid chain unsaturation, are entirely confined to the disordered phase. Together, these results suggest how the size of functional domains in homeothermic cells may be regulated through changes in lipid composition.
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Affiliation(s)
- Frederick A Heberle
- Biology & Soft Matter, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Tomanicek SJ, Standaert RF, Weiss KL, Ostermann A, Schrader TE, Ng JD, Coates L. Neutron and X-ray crystal structures of a perdeuterated enzyme inhibitor complex reveal the catalytic proton network of the Toho-1 β-lactamase for the acylation reaction. J Biol Chem 2012; 288:4715-22. [PMID: 23255594 DOI: 10.1074/jbc.m112.436238] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism by which class A β-lactamases hydrolyze β-lactam antibiotics has been the subject of intensive investigation using many different experimental techniques. Here, we report on the novel use of both neutron and high resolution x-ray diffraction to help elucidate the identity of the catalytic base in the acylation part of the catalytic cycle, wherein the β-lactam ring is opened and an acyl-enzyme intermediate forms. To generate protein crystals optimized for neutron diffraction, we produced a perdeuterated form of the Toho-1 β-lactamase R274N/R276N mutant. Protein perdeuteration, which involves replacing all of the hydrogen atoms in a protein with deuterium, gives a much stronger signal in neutron diffraction and enables the positions of individual deuterium atoms to be located. We also synthesized a perdeuterated acylation transition state analog, benzothiophene-2-boronic acid, which was also isotopically enriched with (11)B, as (10)B is a known neutron absorber. Using the neutron diffraction data from the perdeuterated enzyme-inhibitor complex, we were able to determine the positions of deuterium atoms in the active site directly rather than by inference. The neutron diffraction results, along with supporting bond-length analysis from high resolution x-ray diffraction, strongly suggest that Glu-166 acts as the general base during the acylation reaction.
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Tschaplinski TJ, Standaert RF, Engle NL, Martin MZ, Sangha AK, Parks JM, Smith JC, Samuel R, Jiang N, Pu Y, Ragauskas AJ, Hamilton CY, Fu C, Wang ZY, Davison BH, Dixon RA, Mielenz JR. Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog. Biotechnol Biofuels 2012; 5:71. [PMID: 22998926 PMCID: PMC3524654 DOI: 10.1186/1754-6834-5-71] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 09/05/2012] [Indexed: 05/02/2023]
Abstract
UNLABELLED BACKGROUND Down-regulation of the caffeic acid 3-O-methyltransferase EC 2.1.1.68 (COMT) gene in the lignin biosynthetic pathway of switchgrass (Panicum virgatum) resulted in cell walls of transgenic plants releasing more constituent sugars after pretreatment by dilute acid and treatment with glycosyl hydrolases from an added enzyme preparation and from Clostridium thermocellum. Fermentation of both wild-type and transgenic switchgrass after milder hot water pretreatment with no water washing showed that only the transgenic switchgrass inhibited C. thermocellum. Gas chromatography-mass spectrometry (GCMS)-based metabolomics were undertaken on cell wall aqueous extracts to determine the nature of the microbial inhibitors. RESULTS GCMS confirmed the increased concentration of a number of phenolic acids and aldehydes that are known inhibitors of microbial fermentation. Metabolomic analyses of the transgenic biomass additionally revealed the presence of a novel monolignol-like metabolite, identified as trans-3, 4-dimethoxy-5-hydroxycinnamyl alcohol (iso-sinapyl alcohol) in both non-pretreated, as well as hot water pretreated samples. iso-Sinapyl alcohol and its glucoside were subsequently generated by organic synthesis and the identity of natural and synthetic materials were confirmed by mass spectrometric and NMR analyses. The additional novel presence of iso-sinapic acid, iso-sinapyl aldehyde, and iso-syringin suggest the increased activity of a para-methyltransferase, concomitant with the reduced COMT activity, a strict meta-methyltransferase. Quantum chemical calculations were used to predict the most likely homodimeric lignans generated from dehydration reactions, but these products were not evident in plant samples. CONCLUSIONS Down-regulation of COMT activity in switchgrass resulted in the accumulation of previously undetected metabolites resembling sinapyl alcohol and its related metabolites, but that are derived from para-methylation of 5-hydroxyconiferyl alcohol, and related precursors and products; the accumulation of which suggests altered metabolism of 5-hydroxyconiferyl alcohol in switchgrass. Given that there was no indication that iso-sinapyl alcohol was integrated in cell walls, it is considered a monolignol analog. Diversion of substrates from sinapyl alcohol to free iso-sinapyl alcohol, its glucoside, and associated upstream lignin pathway changes, including increased phenolic aldehydes and acids, are together associated with more facile cell wall deconstruction, and to the observed inhibitory effect on microbial growth. However, iso-sinapyl alcohol and iso-sinapic acid, added separately to media, were not inhibitory to C. thermocellum cultures.
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Affiliation(s)
- Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Robert F Standaert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
- Department of Biochemistry and Molecular & Cellular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Madhavi Z Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Amandeep K Sangha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
- Department of Biochemistry and Molecular & Cellular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Jeremy C Smith
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
- Department of Biochemistry and Molecular & Cellular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Reichel Samuel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Nan Jiang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Yunqiao Pu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Arthur J Ragauskas
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Choo Y Hamilton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Chunxiang Fu
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Zeng-Yu Wang
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Richard A Dixon
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
| | - Jonathan R Mielenz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6341, USA
- BioEnergy Science Center, Oak Ridge, TN 38731, USA
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Heberle FA, Pan J, Standaert RF, Drazba P, Kučerka N, Katsaras J. Model-based approaches for the determination of lipid bilayer structure from small-angle neutron and X-ray scattering data. Eur Biophys J 2012; 41:875-90. [PMID: 22588484 DOI: 10.1007/s00249-012-0817-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/29/2012] [Accepted: 04/15/2012] [Indexed: 10/28/2022]
Abstract
Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Kučerka et al. (Biophys J 95:2356-2367, 2008; J Phys Chem B 116:232-239, 2012). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent to these models. In particular, it is recognized that standalone data do not contain enough information to fully resolve the structure of naturally disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structure parameters, including the much-sought-after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data, as well as the implementation of local volume conservation within the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.
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Affiliation(s)
- Frederick A Heberle
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6100, USA.
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Sangha AK, Parks JM, Standaert RF, Ziebell A, Davis M, Smith JC. Radical Coupling Reactions in Lignin Synthesis: A Density Functional Theory Study. J Phys Chem B 2012; 116:4760-8. [DOI: 10.1021/jp2122449] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amandeep K. Sangha
- UT/ORNL Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United
States
| | - Jerry M. Parks
- UT/ORNL Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United
States
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee 37831, United States
| | - Robert F. Standaert
- Department of Biochemistry
and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee 37831, United States
- Biology and Soft
Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Angela Ziebell
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Mark Davis
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado
80401, United States
| | - Jeremy C. Smith
- UT/ORNL Center for
Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United
States
- Department of Biochemistry
and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Bioenergy Science
Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee 37831, United States
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33
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Xie A, Yan J, Yue L, Feng F, Mir F, Abdel-Halim H, Chebib M, Le Breton GC, Standaert RF, Qian H, Pepperberg DR. 2-Aminoethyl methylphosphonate, a potent and rapidly acting antagonist of GABA(A)-ρ1 receptors. Mol Pharmacol 2011; 80:965-78. [PMID: 21810922 DOI: 10.1124/mol.111.071225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
2-Aminoethyl methylphosphonate (2-AEMP), an analog of GABA, has been found to exhibit antagonist activity at GABA(A)-ρ1 (also known as ρ1 GABA(C)) receptors. The present study was undertaken to elucidate 2-AEMP's action and to test the activities of 2-AEMP analogs. Whole-cell patch-clamp techniques were used to record membrane currents in neuroblastoma cells stably transfected with human GABA(A)-ρ1 receptors. The action of 2-AEMP was compared with that of 1,2,5,6-tetrahydropyridin-4-yl methylphosphinic acid (TPMPA), a commonly used GABA(A)-ρ1 antagonist. With 10 μM GABA, 2-AEMP's IC(50) (18 μM) differed by less than 2.5-fold from that of TPMPA (7 μM), and results obtained were consistent with a primarily competitive mode of inhibition by 2-AEMP. Terminating the presentation of 2-AEMP or TPMPA in the presence of GABA produced a release from inhibition. However, the rate of inhibition release upon the termination of 2-AEMP considerably exceeded that determined with termination of TPMPA. Moreover, when presented at concentrations near their respective IC(50) values, the preincubation period associated with 2-AEMP's onset of inhibition was much shorter than that for TPMPA. Analogs of 2-AEMP possessing a benzyl or n-butyl rather than a methyl substituent at the phosphorus atom, as well as analogs bearing a C-methyl substituent on the aminoethyl side chain, exhibited reduced potency relative to 2-AEMP. Of these analogs, only (R)-2-aminopropyl methylphosphonate significantly diminished the response to 10 μM GABA. Structure-activity relationships are discussed in the context of molecular modeling of ligand binding to the antagonist binding site of the GABA(A)-ρ1 receptor.
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Affiliation(s)
- An Xie
- Lions of Illinois Eye Research Institute, Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, College of Medicine, Chicago, Illinois 60612, USA
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Woodward J, Kennel SJ, Stuckey A, Osborne D, Wall J, Rondinone AJ, Standaert RF, Mirzadeh S. LaPO4 Nanoparticles Doped with Actinium-225 that Partially Sequester Daughter Radionuclides. Bioconjug Chem 2011; 22:766-76. [DOI: 10.1021/bc100574f] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jonathan Woodward
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephen J. Kennel
- Graduate School of Medicine, University of Tennessee, Knoxville, Tennessee 37920, United States
| | - Alan Stuckey
- Graduate School of Medicine, University of Tennessee, Knoxville, Tennessee 37920, United States
| | - Dustin Osborne
- Graduate School of Medicine, University of Tennessee, Knoxville, Tennessee 37920, United States
| | - Jonathan Wall
- Graduate School of Medicine, University of Tennessee, Knoxville, Tennessee 37920, United States
| | - Adam J. Rondinone
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | | | - Saed Mirzadeh
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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35
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Edwards AN, Fowlkes JD, Owens ET, Standaert RF, Pelletier DA, Hurst GB, Doktycz MJ, Morrell-Falvey JL. An in vivo imaging-based assay for detecting protein interactions over a wide range of binding affinities. Anal Biochem 2009; 395:166-77. [PMID: 19698693 DOI: 10.1016/j.ab.2009.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 08/13/2009] [Accepted: 08/17/2009] [Indexed: 11/28/2022]
Abstract
Identifying and characterizing protein interactions are fundamental steps toward understanding and modeling biological networks. Methods that detect protein interactions in intact cells rather than buffered solutions are likely more relevant to natural systems since molecular crowding events in the cytosol can influence the diffusion and reactivity of individual proteins. One in vivo, imaging-based method relies on the colocalization of two proteins of interest fused to DivIVA, a cell division protein from Bacillus subtilis, and green fluorescent protein (GFP). We have modified this imaging-based assay to facilitate rapid cloning by constructing new vectors encoding N- and C-terminal DivIVA or GFP molecular tag fusions based on site-specific recombination technology. The sensitivity of the assay was defined using a well-characterized protein interaction system involving the eukaryotic nuclear import receptor subunit, Importin alpha (Imp alpha), and variant nuclear localization signals (NLS) representing a range of binding affinities. These data demonstrate that the modified colocalization assay is sensitive enough to detect protein interactions with K(d) values that span over four orders of magnitude (1 nM to 15 microM). Lastly, this assay was used to confirm numerous protein interactions identified from mass spectrometry-based analyses of affinity isolates as part of an interactome mapping project in Rhodopseudomonas palustris.
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Affiliation(s)
- A Nicole Edwards
- University of Tennessee-Oak Ridge National Laboratory, Graduate School of Genome Science and Technology, Knoxville, TN 37996, USA
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36
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Chowdhury S, Muni NJ, Greenwood NP, Pepperberg DR, Standaert RF. Phosphonic acid analogs of GABA through reductive dealkylation of phosphonic diesters with lithium trialkylborohydrides. Bioorg Med Chem Lett 2007; 17:3745-8. [PMID: 17467985 DOI: 10.1016/j.bmcl.2007.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 04/04/2007] [Accepted: 04/05/2007] [Indexed: 10/23/2022]
Abstract
Lithium trialkylborohydrides were found to effect rapid monodealkylation of phosphonic diesters, and this reaction was applied to the synthesis of alkylphosphonic acid 2-aminoethyl esters [H(2)N(CH(2))(2)OP(OH)R, 4], a little-explored class of analogs of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA). Compound 4a (R=Me) proved to be a potent antagonist at human rho1 GABA(C) receptors (expressed in Xenopus laevis oocytes), with an IC(50) of 11.1 microM, but is inactive at alpha(1)beta(2)gamma(2) GABA(A) receptors.
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Affiliation(s)
- Sarwat Chowdhury
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607-7056, USA
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Abstract
Photoisomerizable amino acids provide a direct avenue to the experimental manipulation of bioactive polypeptides, potentially allowing real-time, remote control of biological systems and enabling useful applications in nanobiotechnology. Herein, we report a new class of photoisomerizable amino acids intended to cause pronounced expansion and contraction in the polypeptide backbone, i.e., to be photoelastic. These compounds, termed Abc amino acids, employ a photoisomerizable azobiphenyl chromophore to control the relative disposition of aminomethyl and carboxyl substituents. Molecular modeling of nine Abc isomers led to the identification of one with particularly attractive properties, including the ability to induce contractions up to 13 A in the backbone upon trans --> cis photoisomerization. This isomer, designated mpAbc, has substituents at meta and para positions on the inner (azo-linked) and outer rings, respectively. An efficient synthesis of Fmoc-protected mpAbc was executed in which the biaryl components were formed via Suzuki couplings and the azo linkage was formed via amine/nitroso condensation; protected forms of three other Abc isomers were prepared similarly. An undecapeptide incorporating mpAbc was synthesized by conventional solid-phase methods and displayed characteristic azobenzene photochemical behavior with optimal conversion to the cis isomer at 360 nm and a thermal cis --> trans half-life of 100 min at 80 degrees C.
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Affiliation(s)
- Robert F Standaert
- Life Sciences Division, Oak Ridge National Laboratory, PO Box 2008 MS 6123, Oak Ridge, Tennessee 37831-6123, USA.
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38
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Fontes MRM, Teh T, Riell RD, Park SB, Standaert RF, Kobe B. Crystallization and preliminary X-ray diffraction analysis of importin-alpha complexed with NLS peptidomimetics. Biochim Biophys Acta 2005; 1750:9-13. [PMID: 15878698 DOI: 10.1016/j.bbapap.2005.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 03/30/2005] [Accepted: 03/31/2005] [Indexed: 11/16/2022]
Abstract
Importin-alpha is the nuclear import receptor that recognizes cargo proteins with nuclear localization sequences (NLSs). The study of NLS peptidomimetics can provide a better understanding of the requirements for the molecular recognition of cargo proteins by importin-alpha, and potentially engender a large number of applications in medicine. Importin-alpha was crystallized with a set of six NLS peptidomimetics, and X-ray diffraction data were collected in the range 2.1-2.5 A resolution. Preliminary electron density calculations show that the ligands are present in the crystals.
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Affiliation(s)
- Marcos R M Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, UNESP, C. P. 510, CEP 18618-000, Botucatu-SP, Brazil.
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Vu TQ, Chowdhury S, Muni NJ, Qian H, Standaert RF, Pepperberg DR. Activation of membrane receptors by a neurotransmitter conjugate designed for surface attachment. Biomaterials 2005; 26:1895-903. [PMID: 15576163 DOI: 10.1016/j.biomaterials.2004.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2004] [Accepted: 06/01/2004] [Indexed: 10/26/2022]
Abstract
The derivatization of surfaces with bioactive molecules is a research area of growing importance for cell and tissue engineering. Tetherable molecules used in such applications must contain an anchoring moiety as well as the biofunctional group, typically along with a spacer to prevent steric clashes between the target molecule and the tethering surface. Post-synaptic membrane receptors at chemical synapses in neural tissue mediate signaling to the post-synaptic neuron and are activated by the binding of diffusible neurotransmitter molecules released by the pre-synaptic neuron. However, little attention has been directed at developing neurotransmitter analogs that might retain functionality when tethered to a surface that could be interfaced with post-synaptic receptor proteins. Muscimol (5-aminomethyl-3-hydroxyisoxazole), an analog of GABA (gamma-aminobutryic acid), is a known potent agonist of GABA(A) and GABA(C) post-synaptic receptors found in retina and other central nervous system tissue. The present paper reports experiments testing the electrophysiological activity of "muscimol-biotin" on cloned GABA receptors expressed in Xenopus oocytes. This compound, which is potentially suitable for tethering at avidin-coated surfaces, consists of muscimol conjugated through an N-acyl linkage to a 6-aminohexanoyl chain that is distally terminated by biotin. We find that muscimol-biotin, as well as a structurally similar compound (muscimol-BODIPY) containing a bulky fluorophore at the distal end of the aminohexanoyl chain, exhibits substantial agonist activity at GABA(A) and GABA(C) receptors. Muscimol-biotin and other similarly biotinylated neurotransmitter analogs, in combination with surface functionalization using avidin-biotin technology, may be useful in applications involving the controlled activation of neuronal post-synaptic receptors by surface-attached molecules.
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Affiliation(s)
- Tania Q Vu
- Department of Ophthalmology and Visual Sciences, Lions of Illinois Eye Research Institute, University of Illinois at Chicago, 1855 W. Taylor St., Chicago, IL 60612, USA.
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Abstract
[reaction: see text] L-alpha-(1-Cyclobutenyl)glycine (1-Cbg) was targeted as a potentially translatable analogue of isoleucine and valine and as a useful building block for peptides. An enantioselective synthesis was executed in which the key step was diastereoselective addition of 1-cyclobutenylmagnesium bromide to the sulfinimine 2b derived from (S)-t-butanesulfinimide and tert-butyl glyoxylate. 1-Cbg was found to substitute efficiently for isoleucine and valine, but not leucine, in the translation of green fluorescent protein in vitro.
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Affiliation(s)
- Lasanthi P Jayathilaka
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 West Taylor Street, Room 4500 Chicago, Illinois 60607, USA
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Nehilla BJ, Popat KC, Vu TQ, Chowdhury S, Standaert RF, Pepperberg DR, Desai TA. Neurotransmitter analog tethered to a silicon platform for neuro-bioMEMS applications. Biotechnol Bioeng 2004; 87:669-74. [PMID: 15352065 DOI: 10.1002/bit.20171] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The design of chemically well-defined, machinable surfaces containing neuroactive molecules offers potential for fundamental neuroscience and clinical neural engineering applications. Here we report the assembly and characterization of silicon platforms containing a tethered form of muscimol. Muscimol, an analog of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA), is a potent agonist at postsynaptic GABA(A) and GABA(C) receptors. Surfaces were assembled using covalent avidin conjugation to silanized silicon followed by high-affinity avidin-biotin binding of a biotinylated derivative of muscimol (muscimol-biotin). Contact angle measurements, ellipsometry, and X-ray photoelectron spectroscopy (XPS) were conducted to characterize the wettability, thickness, and chemical composition of progressively deposited surface layers. The data demonstrate successful incorporation of a neurotransmitter analog as part of a layered, silicon-based structure possessing robust and specific biomolecular composition. These findings represent a step toward the design of platforms for applications involving control and modulation of neural signaling.
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Affiliation(s)
- Barrett J Nehilla
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston University, Boston, Massachusetts 02118, USA
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Abstract
[reaction: see text] Molecular modeling was used to design mimetics of the HIV-1 matrix protein nuclear localization signal (NLS) in which a scaffold of two resorcinol units joined by a diamide linker presents 3-aminopropyl ethers in place of lysine side chains. Prospective mimetics with linkers of 6, 8, 10, or 12 atoms were synthesized and compared in a competition assay for binding to the nuclear import receptor subunit karyopherin alpha, showing the 10-atom linker to be best and shorter ones ineffective.
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Affiliation(s)
- Seung Bum Park
- University of Illinois at Chicago, Department of Chemistry (M/C 111), 845 West Taylor Street, Room 4500, Chicago, Illinois 60607, USA
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Abstract
FKBP25, a previously uncharacterized 25-kDa FK506- and rapamycin-binding protein, was purified to homogeneity from calf thymus, brain, and spleen, and the sequence of a 215 amino acid (aa) 24-kDa C-terminal peptide was established. The N-terminal domain (101 aa) is unrelated to any known protein, is hydrophilic, and is predicted by circular dichroism spectroscopy to be largely alpha-helix. The C-terminal domain (114 aa) is homologous to FKBP12 and other FKBPs but has a potential nuclear targeting sequence and a unique insertion of seven amino acids in one of its loops. FKBP25 displays the rotamase activity characteristic of FKBPs; the activity is inhibited by the immunosuppressants rapamycin (Ki = 0.9 nM) and FK506 (Ki = 160 nM), but not cyclosporin A. The protein, its rapamycin selectivity, and the potential nuclear targeting sequence are discussed in terms of the structure of hFKBP12.
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Affiliation(s)
- A Galat
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138
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45
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Fretz H, Albers MW, Galat A, Standaert RF, Lane WS, Burakoff SJ, Bierer BE, Schreiber SL. Rapamycin and FK506 binding proteins (immunophilins). J Am Chem Soc 2002. [DOI: 10.1021/ja00004a051] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
The ability to orchestrate the transport of proteins between nucleus and cytoplasm provides cells with a powerful regulatory mechanism. Selective translocation between these compartments is often used to propagate cellular signals, and it is an intimate part of the processes that control cell division, viral replication, and other cellular events. Therefore, precise experimental control over protein localization, through the agency of light, would provide a powerful tool for the study and manipulation of these events. To this end, a prototype photoregulated nuclear localization signal (NLS) was derived from a native NLS. A library of 30 mutants of the bipartite NLS from Xenopus laevis nucleoplasmin containing a novel, photoisomerizable amino acid was prepared by parallel, solid-phase synthesis and screened in vitro for binding to the nuclear import receptor karyopherin alpha, which mediates the nuclear import of cellular proteins. A single peptide was identified in which the cis and trans photoisomers bind the receptor differentially. The strategy used to obtain this peptide is systematic and empirical; therefore, it is potentially applicable to any peptide-receptor system.
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Affiliation(s)
- S B Park
- Texas A&M University, Department of Chemistry, PO Box 30012, College Station, TX 77842-3012, USA
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Kopytek SJ, Standaert RF, Dyer JC, Hu JC. Chemically induced dimerization of dihydrofolate reductase by a homobifunctional dimer of methotrexate. Chem Biol 2000; 7:313-21. [PMID: 10801470 DOI: 10.1016/s1074-5521(00)00109-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Chemically induced dimerization (CID) can be used to manipulate cellular regulatory pathways from signal transduction to transcription, and to create model systems for study of the specific interactions between proteins and small-molecule chemical ligands. However, few CID systems are currently available. The properties of, and interactions between, Escherichia coli dihydrofolate reductase (DHFR) and the ligand methotrexate (MTX) meet many of the desired criteria for the development of a new CID system. RESULTS BisMTX, a homobifunctional version of MTX, was synthesized and tested for its ability to induce dimerization of DHFR. Gel-filtration analysis of purified DHFR confirmed that, in vitro, the protein was a monomer in the absence of dimerizer drug; in the presence of bisMTX, a complex of twice the monomeric molecular weight was observed. Furthermore, the off-rate was found to be 0.0002 s(-1), approximately 100 times slower than that reported for DHFR-MTX. Interestingly, the addition of excess bisMTX did not result in formation of the binary complex (1 protein:1 dimerizer) over the ternary complex (2 proteins:1 dimerizer), which suggests cooperative binding interactions (affinity modulation) between the two DHFR molecules in the bisMTX:DHFR(2) ternary complex. CONCLUSIONS The combination of DHFR and bisMTX provides a new CID system with properties that could be useful for applications in vivo. Formation of the bisMTX:DHFR(2) ternary complex in vitro is promoted over a wide range of dimerizer concentrations, consistent with the idea that formation of the ternary complex recruits energetically favorable interactions between the DHFR monomers in the complex.
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Affiliation(s)
- S J Kopytek
- Department of Biochemistry and Biophysics, Texas A&M University, TX 77843-2128, USA
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Connolly MD, Park SB, Reedy BM, Standaert RF. A simple, solid-phase binding assay for the nuclear import receptor karyopherin alpha. Part 1: direct binding. Bioorg Med Chem Lett 2000; 10:951-4. [PMID: 10853666 DOI: 10.1016/s0960-894x(00)00134-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The nuclear import receptor karyopherin alpha recognizes nuclear localization signals (NLSs), peptides that direct the transport of proteins into the nucleus. A simple, colorimetric assay has been developed to facilitate the identification and comparison of karyopherin ligands by direct and competitive binding using NLSs immobilized on the solid phase (TentaGel resin).
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Affiliation(s)
- M D Connolly
- Department of Chemistry, Texas A&M University, College Station 77842-3012, USA
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49
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Park SB, Reedy BM, Standaert RF. A simple, solid-phase binding assay for the nuclear import receptor karyopherin alpha. Part 2: competitive binding. Bioorg Med Chem Lett 2000; 10:955-6. [PMID: 10853667 DOI: 10.1016/s0960-894x(00)00135-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A qualitative assay for the evaluation of soluble ligands of the nuclear import receptor karyopherin alpha has been developed. The assay relies on competition with an immobilized ligand, the nuclear localization signal (NLS) from nucleoplasmin, for binding to the receptor, which is detected by an enzyme-linked colorimetric method.
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Affiliation(s)
- S B Park
- Department of Chemistry, Texas A&M University, College Station 77842-3012, USA
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50
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Abstract
[reaction: see text] Furanomycin is a Streptomyces metabolite that substitutes for isoleucine in protein translation. We report a concise and modular synthesis starting from the Garner aldehyde and proceeding in seven steps to furanomycin. The key steps include a stereoselective acetylide addition and the Ag+-mediated cyclization of an alpha-allenic alcohol to construct the trans-2,5-dihydrofuran. The efficiency (12% overall yield) and flexibility of the route will provide ample quantities of furanomycin and analogues for protein engineering.
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Affiliation(s)
- M P VanBrunt
- Texas A&M University, Department of Chemistry, College Station 77842-3012, USA
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