Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Promising general solution to the problem of ligating peptides and glycopeptides.

ABSTRACT: Our global goal is that of synthesizing complex polypeptides and glycopeptides in homogeneous form. Chemistry-derived access to homogeneous biologics could well have useful consequences in the discovery of drugs and vaccines. The key finding in this study is that thio acids can become highly competent acyl donors following even trace levels of oxidative activation, thereby undergoing amide bond formation upon reaction with N-terminal peptides. Though our data set does not establish the specific mechanism of this reaction, a framework to account for the fact that minute levels of oxidation actuate amide bond formation with high turnover is offered. An apparently general coupling of thio acids (including complex peptide thio acids with N-termini of complex peptides) has thus been realized. These ligations are conducted with minimal ?-epimerization in the C-terminal group and allow for the coupling of N-terminal and C-terminal glycopeptides en route to homogeneous glycoproteins.

SUBMITTER: Wang P

PROVIDER: S-EPMC3020898 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Promising general solution to the problem of ligating peptides and glycopeptides.

Wang Ping P Danishefsky Samuel J SJ

Journal of the American Chemical Society 20101104 47

Our global goal is that of synthesizing complex polypeptides and glycopeptides in homogeneous form. Chemistry-derived access to homogeneous biologics could well have useful consequences in the discovery of drugs and vaccines. The key finding in this study is that thio acids can become highly competent acyl donors following even trace levels of oxidative activation, thereby undergoing amide bond formation upon reaction with N-terminal peptides. Though our data set does not establish the specific ...[more]

PMID: 21049949

Similar Datasets

General solution for rapid scan EPR deconvolution problem.

Project description:A general solution for the RS EPR deconvolution problem has been derived. This solution permits the use of arbitrary magnetic field scans. As a result, constraints on the current experimental designs can be lifted. For example, a trapezoidal waveform can be used to accelerate the scan rate without affecting the signal bandwidth. The assumptions made to develop the previous algorithms are mathematically validated.

| S-EPMC7575242 | biostudies-literature

A general solution for the 2-pyridyl problem.

Project description:Problem solved: an air-stable 2-pyridyl borane that can effectively couple to a wide range of aryl and heteroaryl halides and pseudohalides has evaded the synthesis community for decades. The discovery that Cu(DEA)(2) powerfully enables palladium-mediated cross-couplings with air-stable boronates 1 has finally provided a general solution to this problem. DEA=diethanolamine, DMF=N,N'-dimethylformamide, Tf=trifluoromethanesulfonyl.

| S-EPMC3433254 | biostudies-literature

microTaboo: a general and practical solution to the k-disjoint problem.

Project description:A common challenge in bioinformatics is to identify short sub-sequences that are unique in a set of genomes or reference sequences, which can efficiently be achieved by k-mer (k consecutive nucleotides) counting. However, there are several areas that would benefit from a more stringent definition of "unique", requiring that these sub-sequences of length W differ by more than k mismatches (i.e. a Hamming distance greater than k) from any other sub-sequence, which we term the k-disjoint problem. Examples include finding sequences unique to a pathogen for probe-based infection diagnostics; reducing off-target hits for re-sequencing or genome editing; detecting sequence (e.g. phage or viral) insertions; and multiple substitution mutations. Since both sensitivity and specificity are critical, an exhaustive, yet efficient solution is desirable.We present microTaboo, a method that allows for efficient and extensive sequence mining of unique (k-disjoint) sequences of up to 100 nucleotides in length. On a number of simulated and real data sets ranging from microbe- to mammalian-size genomes, we show that microTaboo is able to efficiently find all sub-sequences of a specified length W that do not occur within a threshold of k mismatches in any other sub-sequence. We exemplify that microTaboo has many practical applications, including point substitution detection, sequence insertion detection, padlock probe target search, and candidate CRISPR target mining.microTaboo implements a solution to the k-disjoint problem in an alignment- and assembly free manner. microTaboo is available for Windows, Mac OS X, and Linux, running Java 7 and higher, under the GNU GPLv3 license, at: https://MohammedAlJaff.github.io/microTaboo.

| S-EPMC5414201 | biostudies-other

Needle phobia among adult Jordanians: General awareness, prevalence; and exploring microneedles as a promising solution

Project description: Not available

| S-EPMC10511100 | biostudies-literature

Chemoselective Solution- and Solid-Phase Synthesis of Disulfide-Linked Glycopeptides.

Project description:Glycosylation of peptides and proteins is a widely employed strategy to mimic important post-translational modifications or to modulate the physicochemical properties of peptides to enhance their delivery. Furthermore, glycosylation via a sulfur atom imparts increased chemical and metabolic stability to the resulting glycoconjugates. Herein, we report a simple and chemoselective procedure to prepare disulfide-linked glycopeptides. Acetate-protected glycosylsulfenyl hydrazines are shown to be highly reactive with the thiol group of cysteine residues within peptides, both in solution and as part of conventional solid-phase peptide synthesis protocols. The efficiency of this glycosylation methodology with unprotected carbohydrates is also demonstrated, which avoids the need for deprotection steps and further extends its utility, with disulfide-linked glycopeptides produced in excellent yields. Given the importance of glycosylated peptides in structural glycobiology, pharmacology, and therapeutics, the methodology outlined provides easy access to disulfide-linked glycopeptides as molecules with multiple biological applications.

| S-EPMC9638999 | biostudies-literature

Preemption versus Entrenchment: Towards a Construction-General Solution to the Problem of the Retreat from Verb Argument Structure Overgeneralization.

Project description:Participants aged 5;2-6;8, 9;2-10;6 and 18;1-22;2 (72 at each age) rated verb argument structure overgeneralization errors (e.g., *Daddy giggled the baby) using a five-point scale. The study was designed to investigate the feasibility of two proposed construction-general solutions to the question of how children retreat from, or avoid, such errors. No support was found for the prediction of the preemption hypothesis that the greater the frequency of the verb in the single most nearly synonymous construction (for this example, the periphrastic causative; e.g., Daddy made the baby giggle), the lower the acceptability of the error. Support was found, however, for the prediction of the entrenchment hypothesis that the greater the overall frequency of the verb, regardless of construction, the lower the acceptability of the error, at least for the two older groups. Thus while entrenchment appears to be a robust solution to the problem of the retreat from error, and one that generalizes across different error types, we did not find evidence that this is the case for preemption. The implication is that the solution to the retreat from error lies not with specialized mechanisms, but rather in a probabilistic process of construction competition.

| S-EPMC4412412 | biostudies-literature

Antifreeze peptides and glycopeptides, and their derivatives: potential uses in biotechnology.

Project description:Antifreeze proteins (AFPs) and glycoproteins (AFGPs), collectively called AF(G)Ps, constitute a diverse class of proteins found in various Arctic and Antarctic fish, as well as in amphibians, plants, and insects. These compounds possess the ability to inhibit the formation of ice and are therefore essential to the survival of many marine teleost fishes that routinely encounter sub-zero temperatures. Owing to this property, AF(G)Ps have potential applications in many areas such as storage of cells or tissues at low temperature, ice slurries for refrigeration systems, and food storage. In contrast to AFGPs, which are composed of repeated tripeptide units (Ala-Ala-Thr)n with minor sequence variations, AFPs possess very different primary, secondary, and tertiary structures. The isolation and purification of AFGPs is laborious, costly, and often results in mixtures, making characterization difficult. Recent structural investigations into the mechanism by which linear and cyclic AFGPs inhibit ice crystallization have led to significant progress toward the synthesis and assessment of several synthetic mimics of AFGPs. This review article will summarize synthetic AFGP mimics as well as current challenges in designing compounds capable of mimicking AFGPs. It will also cover our recent efforts in exploring whether peptoid mimics can serve as structural and functional mimics of native AFGPs.

| S-EPMC3721219 | biostudies-literature

Genetic algorithm solution for double digest problem.

Project description:The strongly NP-Hard Double Digest Problem, for reconstructing the physical map of DNA sequence, in now using for efficient genotyping. Most of the existing methods are inefficient in tackling large instances due to the large search space for the problem which grows as a factorial function (a!)(b!) of the numbers a and b of the DNA fragments generated by the two restriction enzymes. Also, none of the existing methods are able to handle the erroneous data. In this paper, we develop a novel method based on genetic algorithm for solving this problem and it is adapted to handle the erroneous data. Our genetic algorithm is implemented and compared with the other well-known existing algorithms. The obtained results show the efficiency (speedup) of our algorithm with respect to the other methods, specially for erroneous data.

| S-EPMC3374354 | biostudies-literature

Solution of the Kirchhoff-Plateau Problem.

Project description:The Kirchhoff-Plateau problem concerns the equilibrium shapes of a system in which a flexible filament in the form of a closed loop is spanned by a liquid film, with the filament being modeled as a Kirchhoff rod and the action of the spanning surface being solely due to surface tension. We establish the existence of an equilibrium shape that minimizes the total energy of the system under the physical constraint of noninterpenetration of matter, but allowing for points on the surface of the bounding loop to come into contact. In our treatment, the bounding loop retains a finite cross-sectional thickness and a nonvanishing volume, while the liquid film is represented by a set with finite two-dimensional Hausdorff measure. Moreover, the region where the liquid film touches the surface of the bounding loop is not prescribed a priori. Our mathematical results substantiate the physical relevance of the chosen model. Indeed, no matter how strong is the competition between surface tension and the elastic response of the filament, the system is always able to adjust to achieve a configuration that complies with the physical constraints encountered in experiments.

| S-EPMC5479363 | biostudies-other

A cellular solution to an information-processing problem.

Project description:Signaling receptors on the cell surface are mobile and have evolved to efficiently sense and process mechanical or chemical information. We pose the problem of identifying the optimal strategy for placing a collection of distributed and mobile sensors to faithfully estimate a signal that varies in space and time. The optimal strategy has to balance two opposing objectives: the need to locally assemble sensors to reduce estimation noise and the need to spread them to reduce spatial error. This results in a phase transition in the space of strategies as a function of sensor density and efficiency. We show that these optimal strategies have been arrived at multiple times in diverse cell biology contexts, including the stationary lattice architecture of receptors on the bacterial cell surface and the active clustering of cell-surface signaling receptors in metazoan cells.

| S-EPMC4151762 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data