Elucidating the mechanisms underlying protein conformational switching using NMR spectroscopy

1H-NMR Lipidomics, Comparing Fatty Acids and Lipids in Cow, Goat, Almond, Cashew, Soy, and Coconut Milk Using NMR and Mass Spectrometry

Background/Objectives: Lipids are an important component of human nutrition. Conventional milk is obtained from animals, and dairy milk is consumed by many people worldwide. Recently, milk consumers have been increasingly shifting towards plant-based milk options. The aim of the study was the qualitative identification of lipid metabolites in animal- and plant-based milk, the identification and comparison of the fatty acids (FAs) of milk, and the qualitative identification of the lipid groups among the milk varieties. Methods: Milk samples were obtained from local grocery stores. Lipids were extracted using a modified Folch method and analyzed using nuclear magnetic resonance (NMR) metabolomics. Gas and liquid chromatography mass spectrometry methods (GC-MS and LC-MS) were used to identify the FAs and lipid groups. Lipid weights were compared and the NMR profiles of the lipids analyzed by multivariate statistical analysis. Principal component analysis was performed for the milk lipids obtained from the animal, and plant milk varieties. Results: Clustering of NMR data showed two main clusters: cow/almond/cashew and goat/soy/coconut. GC-MS analysis of the methylated fatty acids (FAs) showed the presence of 12:0, 14:0, 16:0, 16:1, 17:0, 18:0, 18:1, 18:2, 20:1, and 20:2 in all milk types, while FAs 19:0 and 20:4 were observed only in the dairy milk. LC-MS data showed common masses that may indicate the presence of mono- and diacyl glycerols and several lysophospholipids among the different types of milk. Conclusions: This study shows the advantage of using NMR, GC-MS, and LC-MS to differentiate the lipids among different milk types and compare them on one platform.

Transient excited states of the metamorphic protein Mad2 and their implications for function

The spindle checkpoint complex is a key surveillance mechanism in cell division that prevents premature separation of sister chromatids. Mad2 is an integral component of this spindle checkpoint complex that recognizes cognate substrates such as Mad1 and Cdc20 in its closed (C-Mad2) conformation by fastening a "seatbelt" around short peptide regions that bind to the substrate recognition site. Mad2 is also a metamorphic protein that adopts not only the fold found in C-Mad2, but also a structurally distinct open conformation (O-Mad2) which is incapable of binding substrates. Here, we show using chemical exchange saturation transfer (CEST) and relaxation dispersion (CPMG) NMR experiments that Mad2 transiently populates three other higher free energy states with millisecond lifetimes, two in equilibrium with C-Mad2 (E1 and E2) and one with O-Mad2 (E3). E1 is a mimic of substrate-bound C-Mad2 in which the N-terminus of one C-Mad2 molecule inserts into the seatbelt region of a second molecule of C-Mad2, providing a potential pathway for autoinhibition of C-Mad2. E2 is the "unbuckled" conformation of C-Mad2 that facilitates the triage of molecules along competing fold-switching and substrate binding pathways. The E3 conformation that coexists with O-Mad2 shows fluctuations at a hydrophobic lock that is required for stabilizing the O-Mad2 fold and we hypothesize that E3 represents an early intermediate on-pathway towards conversion to C-Mad2. Collectively, the NMR data highlight the rugged free energy landscape of Mad2 with multiple low-lying intermediates that interlink substrate-binding and fold-switching, and also emphasize the role of molecular dynamics in its function.

Competition in drug binding and … the race to equilibrium

Binding kinetics has become a popular topic in pharmacology due to its potential contribution to the selectivity and duration of drug action. Yet, the overall kinetic aspects of complex binding mechanisms are still merely described in terms of elaborate algebraic equations. Interestingly, it has been recommended some 10 years ago to examine such mechanisms in terms of binding fluxes instead of the conventional rate constants. Alike the velocity of product formation in enzymology, those fluxes refer to the velocity by which one target species converts into another one. Novel binding flux-based approaches are utilized to get a better visual insight into the "competition" between two drugs/ligands for a single target as well as between induced fit- and conformational selection pathways for a single ligand within a thermodynamic cycle. The present data were obtained by differential equation-based simulations. Early on, the ligand-binding steps "race" to equilibrium (i.e., when their forward and reverse fluxes are equal) at their individual pace. The overall/global equilibrium is only reached later on. For the competition association assays, this parting might produce a transient "overshoot" of one of the bound target species. A similar overshoot may also show up within a thermodynamic cycle and, at first glance, suggest that the induced fit pathway dominates. Yet, present findings show that under certain circumstances, it could rather be the other way round. Novel binding flux-based approaches offer visually attractive insights into crucial aspects of "complex" binding mechanisms under non-equilibrium conditions.