9 research outputs found
Nitrodibenzofuran: A One- and Two-Photon Sensitive Protecting Group That Is Superior to Brominated Hydroxycoumarin for Thiol Caging in Peptides
Photoremovable
protecting groups are important for a wide range
of applications in peptide chemistry. Using Fmoc-Cys(Bhc-MOM)-OH,
peptides containing a Bhc-protected cysteine residue can be easily
prepared. However, such protected thiols can undergo isomerization
to a dead-end product (a 4-methylcoumarin-3-yl thioether) upon photolysis.
To circumvent that photoisomerization problem, we explored the use
of nitrodibenzofuran (NDBF) for thiol protection by preparing cysteine-containing
peptides where the thiol is masked with an NDBF group. This was accomplished
by synthesizing Fmoc-Cys(NDBF)-OH and incorporating that residue into
peptides by standard solid-phase peptide synthesis procedures. Irradiation
with 365 nm light or two-photon excitation with 800 nm light resulted
in efficient deprotection. To probe biological utility, thiol group
uncaging was carried out using a peptide derived from the protein
K-Ras4B to yield a sequence that is a known substrate for protein
farnesyltransferase; irradiation of the NDBF-caged peptide in the
presence of the enzyme resulted in the formation of the farnesylated
product. Additionally, incubation of human ovarian carcinoma (SKOV3)
cells with an NDBF-caged version of a farnesylated peptide followed
by UV irradiation resulted in migration of the peptide from the cytosol/Golgi
to the plasma membrane due to enzymatic palmitoylation. Overall, the
high cleavage efficiency devoid of side reactions and significant
two-photon cross-section of NDBF render it superior to Bhc for thiol
group caging. This protecting group should be useful for a plethora
of applications ranging from the development of light-activatable
cysteine-containing peptides to the development of light-sensitive
biomaterials
Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods
Identification of small molecules by liquid chromatography-mass spectrometry (LC-MS) can be greatly improved if the chromatographic retention information is used along with mass spectral information to narrow down the lists of candidates. Linear retention indexing remains the standard for sharing retention data across labs, but it is unreliable because it cannot properly account for differences in the experimental conditions used by various labs, even when the differences are relatively small and unintentional. On the other hand, an approach called "retention projection" properly accounts for many intentional differences in experimental conditions, and when combined with a "back-calculation" methodology described recently, it also accounts for unintentional differences. In this study, the accuracy of this methodology is compared with linear retention indexing across eight different labs. When each lab ran a test mixture under a range of multi-segment gradients and flow rates they selected independently, retention projections averaged 22-fold more accurate for uncharged compounds because they properly accounted for these intentional differences, which were more pronounced in steep gradients. When each lab ran the test mixture under nominally the same conditions, which is the ideal situation to reproduce linear retention indices, retention projections still averaged 2-fold more accurate because they properly accounted for many unintentional differences between the LC systems. To the best of our knowledge, this is the most successful study to date aiming to calculate (or even just to reproduce) LC gradient retention across labs, and it is the only study in which retention was reliably calculated under various multi-segment gradients and flow rates chosen independently by labs
Retention projection enables accurate calculation of liquid chromatographic retention times across labs and methods
Identification of small molecules by liquid chromatography-mass spectrometry (LC-MS) can be greatly improved if the chromatographic retention information is used along with mass spectral information to narrow down the lists of candidates. Linear retention indexing remains the standard for sharing retention data across labs, but it is unreliable because it cannot properly account for differences in the experimental conditions used by various labs, even when the differences are relatively small and unintentional. On the other hand, an approach called “retention projection” properly accounts for many intentional differences in experimental conditions, and when combined with a “back-calculation” methodology described recently, it also accounts for unintentional differences. In this study, the accuracy of this methodology is compared with linear retention indexing across eight different labs. When each lab ran a test mixture under a range of multi-segment gradients and flow rates they selected independently, retention projections averaged 22-fold more accurate for uncharged compounds because they properly accounted for these intentional differences, which were more pronounced in steep gradients. When each lab ran the test mixture under nominally the same conditions, which is the ideal situation to reproduce linear retention indices, retention projections still averaged 2-fold more accurate because they properly accounted for many unintentional differences between the LC systems. To the best of our knowledge, this is the most successful study to date aiming to calculate (or even just to reproduce) LC gradient retention across labs, and it is the only study in which retention was reliably calculated under various multi-segment gradients and flow rates chosen independently by labs