Trp-cage is a synthetic 20-residue miniprotein that uses tertiary contacts to stabilize its native conformation. NMR, circular dichroism (CD), and UV-resonance Raman spectroscopy were used to probe its energy landscape. In this quadrupole/time-of-flight study, electrospray ionization charge state distribution (CSD) and solution-phase H/D exchange are used to probe Trp-cage's tertiary structure. The CSDs of Trp-cage and its mutant provide spectra showing a pH-dependent conformation change. Solution-phase H/D exchange in 30% deuterated trifluoroethanol solution of the wild type shows increased protection of one labile hydrogen in the native state. Together, CSDs and solution-phase H/D exchange are demonstrated to constitute a simple but effective means to follow conformation changes in a small tertiary protein.
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http://dx.doi.org/10.1016/j.jasms.2006.09.001 | DOI Listing |
Anal Chem
September 2024
Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States.
Solution-phase hydrogen/deuterium exchange (HDX) coupled to native ion mobility spectrometry mass spectrometry (IMS-MS) can provide complementary structural information about the conformational dynamics of biological molecules. In the present work, the solution-stable isotope labeling (SIL) combined with trapped ion mobility spectrometry (TIMS) in tandem with top-down electron capture dissociation (ECD) is illustrated for the structural characterization of the solution native states of ubiquitin. Four different ubiquitin electrospray solution conditions: (i) single-tip nondeuterated, (ii) theta tip for online SIL HDX, (iii) single-tip SIL-deuterated, and (iv) theta tip for online SIL H/D back exchange (HDbX), were investigated to assess the H/D exchange reactivities of native ubiquitin.
View Article and Find Full Text PDFAcc Chem Res
March 2024
Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, U.K.
Infrared (IR) spectroscopy probes molecular structure at the level of the chemical bond or functional group. In the case of proteins, the most informative band in the IR spectrum is the amide I band, which arises predominantly from the C═O stretching vibration of the peptide link. The folding of proteins into secondary and tertiary structures leads to vibrational coupling between peptide units, generating specific amide I spectral signatures that provide a fingerprint of the macromolecular conformation.
View Article and Find Full Text PDFChem Sci
April 2022
Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
Amyloid proteins that undergo self-assembly to form insoluble fibrillar aggregates have attracted much attention due to their role in biological and pathological significance in amyloidosis. This study aims to understand the amyloid aggregation dynamics of insulin (INS) in HO using two-dimensional infrared (2D-IR) spectroscopy. Conventional IR studies have been performed in DO to avoid spectral congestion despite distinct H-D isotope effects.
View Article and Find Full Text PDFAnal Chem
June 2020
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark.
Hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) enables the study of protein dynamics by measuring the time-resolved deuterium incorporation into a protein incubated in DO. Using electron-based fragmentation in the gas phase it is possible to measure deuterium uptake at single-residue resolution. However, a prerequisite for this approach is that the solution-phase labeling is conserved in the gas phase prior to precursor fragmentation.
View Article and Find Full Text PDFAnalyst
April 2020
Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX 76798, USA.
Hydrogen/deuterium exchange coupled to mass spectrometry (HDX-MS) is a well-established technique for structural analysis of proteins. In HDX experiments it is common to label for multiple, different lengths of time to characterize protein structures and dynamics. However, applications of HDX to carbohydrates have been limited due to the rapid exchange rates of hydroxyls, which have also prevented the development and application of methods that sample HDX at multiple timepoints.
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