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- Cucurbit[8]uril (5)
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- Binding affinity (2)
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Articles 1 - 21 of 21
Full-Text Articles in Physical Sciences and Mathematics
Visualising Dna: Footprinting And 1-2d Gels, Adam Urbach, Michael Waring
Visualising Dna: Footprinting And 1-2d Gels, Adam Urbach, Michael Waring
Adam R Urbach
The study of molecular recognition of DNA by natural and synthetic ligands has made enormous progress due in large part to the discovery and development of methods for separating DNA fragments by gel electrophoresis in one and two dimensions, and for characterizing DNA–ligand complexes by footprinting techniques.
Scope Of Amino Acid Recognition By Cucurbit[8]Uril, Preetika Rajgariah, Adam Urbach
Scope Of Amino Acid Recognition By Cucurbit[8]Uril, Preetika Rajgariah, Adam Urbach
Adam R Urbach
This paper describes the molecular recognition of amino acids by cucurbit[8]uril (Q8) and by the 1:1 complex between Q8 and methyl viologen (MV) in purely aqueous solution. These hosts are known to bind aromatic peptides with high affinity and sequence specificity, but prior work has focused on only a small subset of amino acids. In an effort to elucidate the scope and limitations of amino acid recognition by Q8 and Q8•MV, a comprehensive examination of the 20 genetically encoded amino acids was carried out by 1H NMR spectroscopy and isothermal titration calorimetry. We find that both Q8 and Q8•MV …
Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh Logsdon, Christopher Schardon, Vijayakumar Ramalingam, Sharon Kwee, Adam Urbach
Nanomolar Binding Of Peptides Containing Noncanonical Amino Acids By A Synthetic Receptor, Leigh Logsdon, Christopher Schardon, Vijayakumar Ramalingam, Sharon Kwee, Adam Urbach
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 an equilibrium dissociation constant (Kd) value of 0.95 nM in neutral phosphate buffer. Structure–activity studies revealed that three functional groups work in a positively cooperative …
Determining Protease Substrate Selectivity And Inhibition By Label-Free Supramolecular Tandem Enzyme Assays, Garima Ghale, Vijayakumar Ramalingam, Adam R. Urbach, Werner M. Nau
Determining Protease Substrate Selectivity And Inhibition By Label-Free Supramolecular Tandem Enzyme Assays, Garima Ghale, Vijayakumar Ramalingam, Adam R. Urbach, Werner M. Nau
Adam R Urbach
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 high affinity (K ≈ 104 M–1), while their cleavage products (e.g., Phe-Met-NH2) bind very tightly (K …
Dna Complexes: Durable Binders, Adam Urbach
Dna Complexes: Durable Binders, Adam Urbach
Adam R Urbach
The ability to program molecules to bind to specific sequences of DNA with high fidelity and stability is an important goal of chemical biology. Such molecules can compete with transcription-factor proteins and thus modulate the transcription of genes. They are therefore promising for both elucidating the complex regulation of mammalian gene expression, and developing pharmaceuticals and medical diagnostics targeted to genetic abberations. Writing in Nature Chemistry, Brent Iverson and co-workers have now described the excellent sequence specificity and unusual binding kinetics of a stable DNA–ligand complex, which exhibits a half-life of 16 days.
Charge-Mediated Recognition Of N-Terminal Tryptophan In Aqueous Solution By A Synthetic Host, Meghan Bush, Nicole Bouley, Adam Urbach
Charge-Mediated Recognition Of N-Terminal Tryptophan In Aqueous Solution By A Synthetic Host, Meghan Bush, Nicole Bouley, Adam Urbach
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 α-amino acids, (ii) four singly charged tryptophan derivatives, and (iii) four tryptophan-containing tripeptides were characterized by isothermal titration calorimetry, mass spectrometry, and UV−visible, fluorescence, and …
Molecular Recognition Of Insulin By A Synthetic Receptor, Jordan Chinai, Alexander Taylor, Lisa Ryno, Nicholas Hargreaves, Christopher Morris, P Hart, Adam Urbach
Molecular Recognition Of Insulin By A Synthetic Receptor, Jordan Chinai, Alexander Taylor, Lisa Ryno, Nicholas Hargreaves, Christopher Morris, P Hart, Adam Urbach
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 N-terminal aromatic residue, and with >1000-fold selectivity versus an insulin variant lacking the N-terminal phenylalanine (Phe) residue. The crystal structure of the Q7·insulin complex shows …
A Cucurbit[8]Uril Sponge, Vijayakumar Ramalingam, Sharon Kwee, Lisa Ryno, Adam Urbach
A Cucurbit[8]Uril Sponge, Vijayakumar Ramalingam, Sharon Kwee, Lisa Ryno, Adam Urbach
Adam R Urbach
This paper describes a convenient approach to quantitative removal of the synthetic host cucurbit[8]uril (Q8) from aqueous mixtures using a sepharose resin coated in memantine groups to selectively sequester Q8 in the presence of competing hosts and guests. The “Q8 sponge” can separate Q8 from Q6 and reverse the Q8-mediated dimerization of peptides.
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
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
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 residues adjacent to N-terminal Trp, Phe, or Tyr. The screen used tetramethylbenzobis(imidazolium) (MBBI) as a fluorescent indicator and resulted in the unexpected discovery that MBBI …
Blind Prediction Of Host-Guest Binding Affinities: A New Sampl3 Challenge, Hari S. Muddana, C Daniel Varnado, Christopher W. Bielawski, Adam R. Urbach, Lyle Isaacs, Matthew T. Geballe, Michael K. Gilson
Blind Prediction Of Host-Guest Binding Affinities: A New Sampl3 Challenge, Hari S. Muddana, C Daniel Varnado, Christopher W. Bielawski, Adam R. Urbach, Lyle Isaacs, Matthew T. Geballe, Michael K. Gilson
Adam R Urbach
The computational prediction of protein–ligand binding affinities is of central interest in early-stage drug-discovery, and there is a widely recognized need for improved methods. Low molecular weight receptors and their ligands—i.e., host–guest systems—represent valuable test-beds for such affinity prediction methods, because their small size makes for fast calculations and relatively facile numerical convergence. The SAMPL3 community exercise included the first ever blind prediction challenge for host–guest binding affinities, through the incorporation of 11 new host–guest complexes. Ten participating research groups addressed this challenge with a variety of approaches. Statistical assessment indicates that, although most methods performed well at predicting some …
Multivalent Recognition Of Peptides By Modular Self-Assembled Receptors, Joseph Reczek, Aimee Kennedy, Brian Halbert, Adam Urbach
Multivalent Recognition Of Peptides By Modular Self-Assembled Receptors, Joseph Reczek, Aimee Kennedy, Brian Halbert, Adam Urbach
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 (Ka) value of 2 × 106 M−1 per binding site. The assembled mono-, di-, and trivalent receptors bind to their cognate target peptides containing 1−3 …
Solid-Phase Synthesis Of Peptide−Viologen Conjugates, Joseph Reczek, Elisa Rebolini, Adam Urbach
Solid-Phase Synthesis Of Peptide−Viologen Conjugates, Joseph Reczek, Elisa Rebolini, Adam Urbach
Adam R Urbach
This paper presents a robust method for the conjugation of viologens to peptides using an amide coupling strategy that is compatible with standard Fmoc solid-phase peptide synthesis. Methodology is presented for monitoring the milligram scale process quantitatively by UV spectroscopy. This chemistry enables the synthesis of a broad range of asymmetric viologens in high yield at room temperature and is compatible with a wide range of functional groups, including amine, guanidinyl, thiol, carboxylic acid, phenol, and indole.
Molecular Recognition Of Amino Acids, Peptides, And Proteins By Cucurbit[N]Uril Receptors, Adam R. Urbach, Vijayakumar Ramalingam
Molecular Recognition Of Amino Acids, Peptides, And Proteins By Cucurbit[N]Uril Receptors, Adam R. Urbach, Vijayakumar Ramalingam
Adam R Urbach
At the forefront of the endeavor to understand and manipulate living systems is the design and study of receptors that bind with high affinity and selectivity to specific amino acids, peptides, and proteins. Cucurbit[n]urils are among the most promising class of synthetic receptors for these targets due to their high affinities and selectivities in aqueous media and to the unique combination of electrostatic and hydrophobic interactions that govern binding. The fundamental supramolecular chemistry in this area has been explored in depth, and novel, useful applications are beginning to emerge.
Sequence-Specific Inhibition Of A Nonspecific Protease, Leigh Logsdon, Adam Urbach
Sequence-Specific Inhibition Of A Nonspecific Protease, Leigh Logsdon, Adam Urbach
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 h. Structure–activity studies revealed a direct correlation between the extent of protection of an N-terminal amino acid and its affinity for Q7. Therefore, Q7 provides …
Effects Of The Number And Placement Of Positive Charges On Viologen–Cucurbit[N]Uril Interactions, Gretchen Vincil, Adam Urbach
Effects Of The Number And Placement Of Positive Charges On Viologen–Cucurbit[N]Uril Interactions, Gretchen Vincil, Adam Urbach
Adam R Urbach
Recent developments in the synthesis and applications of the cucurbit[n]uril family of synthetic hosts has led to an increasing interest in the detailed studies of their interactions with a wide variety of guests. This paper describes a quantitative study of the effects of the number and placement of positive charges on the binding of viologen guests to cucurbit[7]uril and cucurbit[8]uril. A series of viologen derivatives with one to four charges was characterised by isothermal titration calorimetry, 1H NMR spectroscopy and mass spectrometry to determine the stoichiometry, affinity and mode of binding. These data show that stoichiometry can be controlled by …
Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar Ali, Eric Olson, Adam Urbach
Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar Ali, Eric Olson, Adam Urbach
Adam R Urbach
This paper describes a novel assay for measuring the relative extent of peptide binding in a large parallel format and the use of this assay to explore the effects of sequence context on the binding of tryptophan (Trp)-containing peptides by the synthetic receptor comprising the noncovalent complex between cucurbit[8]uril and methyl viologen (i.e. Q8√MV). The extent of quenching of Trp fluorescence upon binding to Q8√MV was used to measure the relative extent of binding and thus the relative affinities of 104 Trp-containing peptides, in parallel, using a fluorescence plate reader. This study resulted in the remarkable observation that the identity …
Supramolecular Chemistry: A Capstone Course, Adam Urbach, Christopher Pursell, John Spence
Supramolecular Chemistry: A Capstone Course, Adam Urbach, Christopher Pursell, John Spence
Adam R Urbach
A fourth-year capstone course offers students an opportunity to integrate topics covered in the core disciplinary courses, to learn an advanced interdisciplinary topic, and to approach unfamiliar problems and literature. This article describes a fourth-year capstone course designed to incorporate components of faculty lectures, student seminars, and original, hands-on research projects in order to cover the topic of supramolecular chemistry in one semester with unusual depth. This approach should be applicable to other advanced topics in chemistry.
Benzobis(Imidazolium)–Cucurbit[8]Uril Complexes For Binding And Sensing Aromatic Compounds In Aqueous Solution, Frank Biedermann, Urs Rauwald, Monika Cziferszky, Kyle Williams, Lauren Gann, Bi Guo, Adam Urbach, Christopher Bielawski, Oren Scherman
Benzobis(Imidazolium)–Cucurbit[8]Uril Complexes For Binding And Sensing Aromatic Compounds In Aqueous Solution, Frank Biedermann, Urs Rauwald, Monika Cziferszky, Kyle Williams, Lauren Gann, Bi Guo, Adam Urbach, Christopher Bielawski, Oren Scherman
Adam R Urbach
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. CB[8] has the unusual ability to bind tightly and selectively to two different guests in aqueous media, typically methyl viologen (MV) as the first guest, followed by an indole, naphthalene, or catechol-containing second guest. Based on similar size, shape, and charge, tetramethyl benzobis(imidazolium) (MBBI) was identified as a potential alternative to MV that would increase the repertoire of guests for cucurbit[8]uril. Isothermal titration calorimetry (ITC) studies showed that MBBI binds to CB[8] in a 1:1 ratio with an …
Cucurbit[8]Uril Rotaxanes, Vijayakumar Ramalingam, Adam Urbach
Cucurbit[8]Uril Rotaxanes, Vijayakumar Ramalingam, Adam Urbach
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.
Sequence-Specific Recognition And Cooperative Dimerization Of N-Terminal Aromatic Peptides In Aqueous Solution By A Synthetic Host, Lisa Heitmann, Alexander Taylor, P Hart, Adam Urbach
Sequence-Specific Recognition And Cooperative Dimerization Of N-Terminal Aromatic Peptides In Aqueous Solution By A Synthetic Host, Lisa Heitmann, Alexander Taylor, P Hart, Adam Urbach
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 crystallography. The peptides studied were of sequence X-Gly-Gly, Gly-X-Gly, and Gly-Gly-X (X = Trp, Phe, Tyr, and His). Q8 selectively binds and dimerizes Trp-Gly-Gly …
Circular Dichroism Spectroscopy In The Undergraduate Curriculum, Adam Urbach
Circular Dichroism Spectroscopy In The Undergraduate Curriculum, Adam Urbach
Adam R Urbach
Circular dichroism spectropolarimetry (CD) is a method of optical spectroscopy that seems in most practical ways like UV−visible spectroscopy. The main difference between the two methods is that CD, instead of measuring the absorbance of light as a function of wavelength, measures the difference in absorbance of left versus right circularly polarized light as a function of wavelength. A CD spectrum is an observation of the structure of a chiral compound; it often serves as a “fingerprint” of the structure of biological molecules such as proteins and nucleic acids. For this reason, CD has been broadly applied in biochemistry and …