Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies.

ABSTRACT: Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR.We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.

SUBMITTER: Zhou P

PROVIDER: S-EPMC2879018 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies.

Zhou Pei P Wagner Gerhard G

Journal of biomolecular NMR 20100101 1

Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques ...[more]

PMID: 19731047

Similar Datasets

NMR studies of dynamic biomolecular conformational ensembles.

Project description:Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA.

| S-EPMC4325279 | biostudies-literature

On the potential of hyperpolarized water in biomolecular NMR studies.

Project description:A main obstacle arising when using ex situ hyperpolarization to increase the sensitivity of biomolecular NMR is the fast relaxation that macromolecular spins undergo upon being transferred from the polarizer to the spectrometer, where their observation takes place. To cope with this limitation, the present study explores the use of hyperpolarized water as a means to enhance the sensitivity of nuclei in biomolecules. Methods to achieve proton polarizations in excess of 5% in water transferred into the NMR spectrometer were devised, as were methods enabling this polarization to last for up to 30 s. Upon dissolving amino acids and polypeptides sited at the spectrometer into such hyperpolarized water, a substantial enhancement of certain biomolecular amide and amine proton resonances was observed. This exchange-driven (1)H enhancement was further passed on to side-chain and to backbone nitrogens, owing to spontaneous one-bond Overhauser processes. (15)N signal enhancements >500 over 11.7 T thermal counterparts could thus be imparted in a kinetic process that enabled multiscan signal averaging. Besides potential bioanalytical uses, this approach opens interesting possibilities in the monitoring of dynamic biomolecular processes, including solvent accessibility and exchange process.

| S-EPMC5040483 | biostudies-literature

Design and applications of water irradiation devoid RF pulses for ultra-high field biomolecular NMR spectroscopy.

Project description:Water suppression is of paramount importance for many biological and analytical NMR spectroscopy applications. Here, we report the design of a new set of binomial-like radio frequency (RF) pulses that elude water irradiation while exciting or refocusing the remainder of the 1H spectrum. These pulses were generated using a combination of an evolutionary algorithm and artificial intelligence. They display higher sensitivity relative to classical water suppression schemes and tunable water selectivity to avoid suppressing 1H resonances near the water signal. The broad bandwidth excitation obtained with these RF pulses makes them suitable for several NMR applications at high and ultra-high-field magnetic fields.

| S-EPMC9578148 | biostudies-literature

Integrative NMR for biomolecular research.

Project description:NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html ).

| S-EPMC4861749 | biostudies-literature

Straightforward, effective calibration of SPINAL-64 decoupling results in the enhancement of sensitivity and resolution of biomolecular solid-state NMR.

Project description:We describe a simple yet highly effective optimization strategy for SPINAL-64 ¹H decoupling conditions for magic-angle spinning solid-state NMR. With adjustment of the phase angles in a coupled manner, the optimal conditions resulting from three parameter optimizations can be determined with adjustment of a single phase. Notably, echo T? relaxation times for ¹³C and ¹?N show significant enhancement (up to 64%), relative to the previous described SPINAL-64 conditions, under the moderate ¹H decoupling levels (60-100 kHz) and MAS rate (13.3 kHz) commonly employed for high-resolution SSNMR spectroscopy of proteins. Additionally, we also investigated the effect at higher spinning rate (33.3 kHz) and compared the results with other ¹H decoupling schemes (TPPM, XiX), as well as SPINAL-64 with the originally reported optimal values.

| S-EPMC3065959 | biostudies-literature

The solubility product extends the buffering concept to heterotypic biomolecular condensates.

Project description:Biomolecular condensates are formed by liquid-liquid phase separation (LLPS) of multivalent molecules. LLPS from a single ("homotypic") constituent is governed by buffering: above a threshold, free monomer concentration is clamped, with all added molecules entering the condensed phase. However, both experiment and theory demonstrate that buffering fails for the concentration dependence of multicomponent ("heterotypic") LLPS. Using network-free stochastic modeling, we demonstrate that LLPS can be described by the solubility product constant (Ksp): the product of free monomer concentrations, accounting for the ideal stoichiometries governed by the valencies, displays a threshold above which additional monomers are funneled into large clusters; this reduces to simple buffering for homotypic systems. The Ksp regulates the composition of the dilute phase for a wide range of valencies and stoichiometries. The role of Ksp is further supported by coarse-grained spatial particle simulations. Thus, the solubility product offers a general formulation for the concentration dependence of LLPS.

| S-EPMC8289413 | biostudies-literature

A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in ¹?F NMR studies of proteins.

Project description:The elucidation of distinct protein conformers or states by fluorine ((19)F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the (19)F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H2O = 4) to polar (MeOH:H2O = 0.25). (19)F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl]-2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.

| S-EPMC6675403 | biostudies-literature

Enhancement of pea protein solubility and thermal stability for acidic beverage applications via endogenous Maillard-induced glycation and chromatography purification.

Project description:A clean-label process to endogenously glycate and purify pea protein was investigated. The production of maltodextrin from pea starch with a specific dextrose equivalent (DE) was optimized. The produced maltodextrin (14.6 DE) was used to initiate a limited and controlled Maillard-induced glycation of pea protein. The partially glycated pea protein (PG-PP) was subjected to hydrophobic interaction chromatography to remove unreacted carbohydrate, followed by characterization of the purified product. The extent of Maillard-induced glycation was monitored by assessing changes in color, free amino groups, and protein/glycoprotein profiles. The purified PG-PP was evaluated for thermal denaturation, surface properties, protein secondary structure, protein solubility, thermal stability, and digestibility. Maillard-induced glycation was limited to initial stages and resulted in a moderate blockage of amine groups (∼30%). The purified PG-PP had a relatively low surface hydrophobicity, a markedly enhanced protein solubility (∼90%) at pH 3.4, and a nonimpacted protein in vitro digestibility (∼100%). This work provided the impetus needed for future scale-up and process optimization for the production of value-added pea protein ingredient intended for high protein beverage applications.

| S-EPMC9958256 | biostudies-literature

Overcoming the quantum limit of optical amplification in monolithic waveguides.

Project description:[Figure: see text].

| S-EPMC8443169 | biostudies-literature

Engineered solubility tag for solution NMR of proteins.

Project description:The low solubility of many proteins hinders large scale expression and purification as well as biophysical measurements. Here, we devised a general strategy to solubilize a protein by conjugating it at a solvent-exposed position to a 6 kDa protein that was re-engineered to be highly soluble. We applied this method to the CARD domain of Apoptosis-associated speck-like protein containing a CARD (ASC), which represents one member of a class of proteins that are notoriously prone to aggregation. Attachment of the tag to a cysteine residue, introduced by site-directed mutagenesis at its self-association interface, improved the solubility of the ASC CARD over 50-fold under physiological conditions. Although it is not possible to use nuclear magnetic resonance (NMR) to obtain a high quality 2D correlation spectrum of the wild type domain under physiological conditions, we demonstrate that NMR relaxation parameters of the solubilized variant are sufficiently improved to facilitate virtually any demanding measurement. The method shown here represents a straightforward approach for dramatically increasing protein solubility, enabled by ease of labeling as well as flexibility in tag placement with minimal perturbation to the target.

| S-EPMC3831679 | 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