Applications of NMR spectroscopy to systems biochemistry

Abstract

The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other ‘omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.

Exploring cancer metabolism using stable isotope-resolved metabolomics (SIRM)

“…Advances in 1D and 2D NMR have enabled isotopomer analysis in complex biological samples without fractionation (8). Coupling NMR and UHR-FTMS with an atom-resolved metabolic database and tracing tools can provide robust and unprecedented reconstruction of interconnected pathways and networks (8,10,16,17).…”

Recent Advances in NMR-Based Metabolomics

“…A recent review of this area describes various direct and isotope-edited 1D and 2D NMR methods to profile metabolites and their isotopomer distributions. 14 The article also illustrates in detail various in vitro, ex vivo , and in vivo studies that have been made, focusing on gaining systematic and novel metabolic insights in different biological systems, including humans. A number of critical steps involving sample preparation, including rapid cryoquenching, extraction, and chemoselective derivatization are required to achieve robustness in the analysis.…”

Ultra-High Field NMR and MRI—The Role of Magnet Technology to Increase Sensitivity and Specificity

“…Moving from organic chemistry to structural biology allows studies of the structure, dynamics and function of larger and more complex biological macromolecules [35]. Data and references for all data points are given in the Supplementary Materials.…”

“…Technically, the 1.2 GHz and higher systems depend on further progress in HTS conductor developments and HTS-based NMR magnet technology, including superconducting joints, switches and cables. Application wise, such systems will open up a broad range of interdisciplinary research applications in structural biology, catalysis, sustainable energy development as well as biomedical applications, to name just a few [35,37].…”