18 Works

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Effects of sequence context on the binding of tryptophan-containing peptides by the cucurbit[8]uril–methyl viologen complex

Omar A. Ali, Eric M. Olson & Adam R. Urbach
(2013). Effects of sequence context on the binding of tryptophan-containing peptides by the cucurbit[8]uril–methyl viologen complex. Supramolecular Chemistry: Vol. 25, No. 12, pp. 863-868.

Multivalent Recognition of Peptides by Modular Self-Assembled Receptors

Joseph J. Reczek, Aimee A. Kennedy, Brian T. Halbert & Adam R. Urbach
Developing nontraditional approaches to the synthesis and characterization of multivalent compounds is critical to our efforts to study and interface with biological systems and to build new noncovalent materials. This paper demonstrates a biomimetic approach to the construction of discrete, modular, multivalent receptors via molecular self-assembly in aqueous solution. Scaffolds presenting 1−3 viologen groups recruit a respective 1−3 copies of the synthetic host, cucurbit[8]uril, in a noncooperative manner and with a consistent equilibrium association constant...

Cucurbit[8]uril Rotaxanes

Vijayakumar Ramalingam & Adam R. Urbach
The synthesis of [2]rotaxanes, each comprising a viologen core threaded through a cucurbit[8]uril (Q8, Figure 1) macrocycle and stoppered by tetraphenylmethane groups, and their binding to second guests as inclusion complexes in organic and aqueous media are described. Stoppering was observed to have little effect on binding. Chemical modification of the threaded guest was used to control solubility and binding characteristics, thus demonstrating a novel approach to making artificial receptors with readily modifiable properties.

Data from: Early and Middle Triassic trends in diversity, evenness, and size of foraminifers on a carbonate platform in south China: Implications for tempo and mode of biotic recovery from the end-Permian mass extinction

Jonathan L. Payne, Mindi Summers, Brianna L. Rego, Demir Altiner, Jiayong Wei, Meiyi Yu & Daniel J. Lehrmann
Delayed biotic recovery from the end-Permian mass extinction has long been interpreted to result from environmental inhibition. Recently, evidence of more rapid recovery has begun to emerge, suggesting the role of environmental inhibition was previously overestimated. However, there have been few high-resolution taxonomic and ecological studies spanning the full Early and Middle Triassic recovery interval, leaving the precise pattern of recovery and underlying mechanisms poorly constrained. In this study, we document Early and Middle Triassic...

Life history and environment predict variation in testosterone across vertebrates

Jerry Husak, Matthew Fuxjager, Michele A. Johnson, Maren Vitousek, Jeremy Donald, Clinton David Francis, Wolfgang Goymann, Michaela Hau, Bonnie Kircher, Rosemary Knapp, Lynn B. Martin, Eliot Miller, Laura Schoenle & Tony Williams
Endocrine systems act as key intermediaries between organisms and their environments. This interaction leads to high variability in hormone levels, but we know little about the ecological factors that influence this variation within and across major vertebrate groups. We study this topic by assessing how various social and environmental dynamics influence testosterone levels across the entire vertebrate tree of life. Our analyses show that breeding season length and mating system are the strongest predictors of...

Data from: Early Triassic benthic invertebrates from the Great Bank of Guizhou, South China: systematic palaeontology and palaeobiology

William J. Foster, Daniel J. Lehrmann, Jaime A. Hirtz, Mackenzie White, Meiyi Yu, Li Ji & Rowan C. Martindale
To further our understanding on the evolution, selectivity, and ecological composition of marine communities following the latest Permian mass extinction, new collections from underrepresented regions in the immediate extinction aftermath are required. Here, we provide new systematic data and the first palaeobiological account of the benthic invertebrate community from the Great Bank of Guizhou, South China. We systematically describe 3 brachiopod species, 26 bivalve species, 11 gastropod species, 1 microconchid, and 1 crinoid species. The...

Charge-Mediated Recognition of N-Terminal Tryptophan in Aqueous Solution by a Synthetic Host

Meghan E. Bush, Nicole D. Bouley & Adam R. Urbach
The molecular recognition of peptides and proteins in aqueous solution by designed molecules remains an elusive goal with broad implications for basic biochemical research and for sensors and separations technologies. This paper describes the recognition of N-terminal tryptophan in aqueous solution by the synthetic host cucurbit[8]uril (Q8). Q8 is known to form 1:1:1 heteroternary complexes with methyl viologen (MV) and a second aromatic guest. Here, the complexes of Q8·MV with (i) the four natural aromatic...

Molecular Recognition of Methionine-Terminated Peptides by Cucurbit[8]uril

Zoheb Hirani, Hailey F. Taylor, Emily F. Babcock, Andrew T. Bockus, C. Daniel Varnado, Christopher W. Bielawski & Adam Urbach
This Article describes the molecular recognition of peptides containing an N-terminal methionine (Met) by the synthetic receptor cucurbit[8]uril (Q8) in aqueous solution and with submicromolar affinity. Prior work established that Q8 binds with high affinity to peptides containing aromatic amino acids, either by simultaneous binding of two aromatic residues, one from each of two different peptides, or by simultaneous binding of an aromatic residue and its immediate neighbor on the same peptide. The additional binding...

Cucurbit[7]uril–Tetramethylrhodamine Conjugate for Direct Sensing and Cellular Imaging

Andrew T. Bockus, Lauren Smith, Amy G. Grice, Omar A. Ali, Carolyn C. Young, William Mobley, Ashley Leek, James L. Roberts, Brittany Vinciguerra, Lyle Isaacs & Adam Urbach
This paper describes the design and synthesis of a conjugate (Q7R) comprising the synthetic host cucurbit[7]uril (Q7) linked to the fluorescent dye tetramethylrhodamine (TMR), and the characterization of its optical and guest-binding properties as well as its cellular uptake. Q7R was synthesized in two steps from monofunctionalized azidobutyl-Q7 and NHS-activated TMR. The fluorescence of Q7R is quenched upon guest binding, and this observable was used to determine equilibrium dissociation constant (Kd) values. Unexpectedly, the Kd...

Nanomolar Binding of Peptides Containing Noncanonical Amino Acids by a Synthetic Receptor

Leigh A. Logsdon, Christopher L. Schardon, Vijayakumar Ramalingam, Sharon K. Kwee & Adam R. Urbach
This paper describes the molecular recognition of phenylalanine derivatives and their peptides by the synthetic receptor cucurbit[7]uril (Q7). The 4-tert-butyl and 4-aminomethyl derivatives of phenylalanine (tBuPhe and AMPhe) were identified from a screen to have 20–30-fold higher affinity than phenylalanine for Q7. Placement of these residues at the N-terminus of model tripeptides (X-Gly-Gly), resulted in no change in affinity for tBuPhe-Gly-Gly, but a remarkable 500-fold increase in affinity for AMPhe-Gly-Gly, which bound to Q7 with...

Sequence-Specific Recognition and Cooperative Dimerization of N-Terminal Aromatic Peptides in Aqueous Solution by a Synthetic Host

Lisa M. Heitmann, Alexander B. Taylor, P. John Hart & Adam R. Urbach
This article describes the selective recognition and noncovalent dimerization of N-terminal aromatic peptides in aqueous solution by the synthetic host compound, cucurbit[8]uril (Q8). Q8 is known to bind two aromatic guests simultaneously and, in the presence of methyl viologen, to recognize N-terminal tryptophan over internal and C-terminal sequence isomers. Here, the binding of Q8 to aromatic peptides in the absence of methyl viologen was studied by isothermal titration calorimetry (ITC), 1H NMR spectroscopy, and X-ray...

Benzobis(imidazolium)-Cucurbit[8]uril Complexes for Binding and Sensing Aromatic Compounds in Aqueous Solution

Frank Biedermann, Urs Rauwald, Monika Cziferszky, Kyle A. Williams, Lauren D. Gann, Bi Y. Guo, Adam R. Urbach, Christopher W. Bielawski & Oren A. Scherman
Abstract The utilities of benzobis(imidazolium) salts (BBIs) as stable and fluorescent components of supramolecular assemblies involving the macrocyclic host, cucurbit[8]uril (CB[8]), are described...

Sequence-Specific Inhibition of a Nonspecific Protease

Leigh A. Logsdon & Adam R. Urbach
A nonspecific exopeptidase, aminopeptidase N (APN), is inhibited sequence-specifically by a synthetic host, cucurbit[7]uril (Q7), which binds with high affinity and specificity to N-terminal phenylalanine (Phe) and 4-(aminomethyl)phenylalanine (AMPhe) and prevents their removal from the peptide. Liquid chromatography experiments demonstrated that in the presence of excess Q7, APN quantitatively converts the pentapeptides Thr-Gly-Ala-X-Met into the dipeptides X-Met (X = Phe, AMPhe). The resulting Q7-bound products are completely stable to proteolytic digestion for at least 24...

Determining Protease Substrate Selectivity and Inhibition by Label-Free Supramolecular Tandem Enzyme Assays

Werner M. Nau, Adam R. Urbach, Vijayakumar Ramalingam & Garima Ghale
An analytical method has been developed for the continuous monitoring of protease activity on unlabeled peptides in real time by fluorescence spectroscopy. The assay is enabled by a reporter pair comprising the macrocycle cucurbit[7]uril (CB7) and the fluorescent dye acridine orange (AO). CB7 functions by selectively recognizing N-terminal phenylalanine residues as they are produced during the enzymatic cleavage of enkephalin-type peptides by the metalloendopeptidase thermolysin. The substrate peptides (e.g., Thr-Gly-Ala-Phe-Met-NH2) bind to CB7 with moderately...

Sequence-Specific, Nanomolar Peptide Binding via Cucurbit[8]uril-Induced Folding and Inclusion of Neighboring Side Chains

Lauren C. Smith, David G. Leach, Brittney E. Blaylock, Omar A. Ali & Adam R. Urbach
This paper describes the molecular recognition of the tripeptide Tyr-Leu-Ala by the synthetic receptor cucurbit[8]uril (Q8) in aqueous buffer with nanomolar affinity and exceptional specificity. This combination of characteristics, which also applies to antibodies, is desirable for applications in biochemistry and biotechnology but has eluded supramolecular chemists for decades. Building on prior knowledge that Q8 binds to peptides with N-terminal aromatic residues, a library screen of 105 peptides was designed to test the effects of...

Molecular Recognition of Insulin by a Synthetic Receptor

Jordan M. Chinai, Alexander B. Taylor, Lisa M. Ryno, Nicholas D. Hargreaves, Christopher A. Morris, P. John Hart & Adam R. Urbach
The discovery of molecules that bind tightly and selectively to desired proteins continues to drive innovation at the interface of chemistry and biology. This paper describes the binding of human insulin by the synthetic receptor cucurbit[7]uril (Q7) in vitro. Isothermal titration calorimetry and fluorescence spectroscopy experiments show that Q7 binds to insulin with an equilibrium association constant of 1.5 × 106 M−1 and with 50−100-fold selectivity versus proteins that are much larger but lack an...

Effects of the number and placement of positive charges on viologen–cucurbit[n]uril interactions

Adam R. Urbach & Gretchen A. Vincil
(2008). Effects of the number and placement of positive charges on viologen–cucurbit[n]uril interactions. Supramolecular Chemistry: Vol. 20, No. 8, pp. 681-687.

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