Two-dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments

Using NMR Titration Experiments to Study E. coli FAS-II- and AcpP-Mediated Protein-Protein Interactions

Acyl carrier proteins (ACPs) are central to many primary and secondary metabolic pathways. In E. coli fatty acid biosynthesis (FAB), the central ACP, AcpP, transports intermediates to a suite of partner proteins (PP) for iterative modification and elongation. The regulatory protein-protein interactions that occur between AcpP and the PP in FAB are poorly understood due to the dynamic and transient nature of these interactions. Solution-state NMR spectroscopy can reveal information at the atomic level through experiments such as the 2D heteronuclear single quantum coherence (HSQC). The following protocol describes NMR HSQC titration experiments that can elucidate biomolecular recognition events.

NMR lineshape analysis using analytical solutions of multi-state chemical exchange with applications to kinetics of host-guest systems

Nuclear magnetic resonance (NMR) lineshape analysis is a powerful tool for the study of chemical kinetics. Here we provide techniques for analysis of the relationship between experimentally observed spin kinetics (transitions between different environments [Formula: see text]) and corresponding chemical kinetics (transitions between distinct chemical species; e.g., free host and complexed host molecule). The advantages of using analytical solutions for two-, three- or generally N-state exchange lineshapes (without J-coupling) over the widely used numerical calculation for NMR spectral fitting are presented. Several aspects of exchange kinetics including the generalization of coalescence conditions in two-state exchange, the possibility of multiple processes between two states, and differences between equilibrium and steady-state modes are discussed. 'Reduced equivalent schemes' are introduced for spin kinetics containing fast-exchanging states, effectively reducing the number of exchanging states. The theoretical results have been used to analyze a host-guest system containing an oxoporphyrinogen complexed with camphorsulfonic acid and several other literature examples, including isomerization, protein kinetics, or enzymatic reactions. The theoretical treatment and experimental examples present an expansion of the systematic approach to rigorous analyses of systems with rich chemical kinetics through NMR lineshape analysis.

Distinct dissociation rates of murine and human norovirus P-domain dimers suggest a role of dimer stability in virus-host interactions

Norovirus capsids are icosahedral particles composed of 90 dimers of the major capsid protein VP1. The C-terminus of the VP1 proteins forms a protruding (P)-domain, mediating receptor attachment, and providing a target for neutralizing antibodies. NMR and native mass spectrometry directly detect P-domain monomers in solution for murine (MNV) but not for human norovirus (HuNoV). We report that the binding of glycochenodeoxycholic acid (GCDCA) stabilizes MNV-1 P-domain dimers (P-dimers) and induces long-range NMR chemical shift perturbations (CSPs) within loops involved in antibody and receptor binding, likely reflecting corresponding conformational changes. Global line shape analysis of monomer and dimer cross-peaks in concentration-dependent methyl TROSY NMR spectra yields a dissociation rate constant k_off of about 1 s⁻¹ for MNV-1 P-dimers. For structurally closely related HuNoV GII.4 Saga P-dimers a value of about 10⁻⁶s⁻¹ is obtained from ion-exchange chromatography, suggesting essential differences in the role of GCDCA as a cofactor for MNV and HuNoV infection.

NMR and native mass spectrometry reveal that the major capsid VP1 protein from murine and human norovirus exhibit distinct behaviors and are differentially regulated by the binding of glycochenodeoxycholic acid.

Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs

Many double-stranded RNA-binding domains (dsRBDs) interact with topologically distinct dsRNAs in biological pathways pivotal to viral replication, cancer causation, neurodegeneration, and so on. We hypothesized that the adaptability of dsRBDs is essential to target different dsRNA substrates. A model dsRBD and a few dsRNAs, slightly different in shape from each other, were used to test the systematic shape dependence of RNA on the dsRBD-binding using nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. NMR-based titrations showed a distinct binding pattern for the dsRBD with the topologically distinct dsRNAs. The line broadening upon RNA binding was observed to cluster in the residues lying in close proximity, thereby suggesting an RNA-induced conformational exchange in the dsRBD. Further, while the intrinsic microsecond dynamics observed in the apo-dsRBD were found to quench upon binding with the dsRNA, the microsecond dynamics got induced at residues spatially proximal to quench sites upon binding with the dsRNA. This apparent relay of conformational exchange suggests the significance of intrinsic dynamics to help adapt the dsRBD to target various dsRNA-shapes. The conformational pool visualized in MD simulations for the apo-dsRBD reported here has also been observed to sample the conformations seen previously for various dsRBDs in apo- and in dsRNA-bound state structures, further suggesting the conformational adaptability of the dsRBDs. These investigations provide a dynamic basis for the substrate promiscuity for dsRBD proteins.

Analysis of conformational exchange processes using methyl-TROSY-based Hahn echo measurements of quadruple-quantum relaxation

Transverse nuclear spin relaxation is a sensitive probe of chemical exchange on timescales on the order of microseconds to milliseconds. Here we present an experiment for the simultaneous measurement of the relaxation rates of two quadruple-quantum transitions in 13 CH3 -labelled methyl groups. These coherences are protected against relaxation by intra-methyl dipolar interactions and so have unexpectedly long lifetimes within perdeuterated biomacromolecules. However, these coherences also have an order of magnitude higher sensitivity to chemical exchange broadening than lower order coherences and therefore provide ideal probes of dynamic processes. We show that analysis of the static magnetic field dependence of zero-, double- and quadruple-quantum Hahn echo relaxation rates provides a robust indication of chemical exchange and can determine the signed relative magnitudes of proton and carbon chemical shift differences between ground and excited states. We also demonstrate that this analysis can be combined with established Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements, providing improved precision in parameter estimates, particularly in the determination of 1 H chemical shift differences.

A weakened interface in the P182L variant of HSP27 associated with severe Charcot-Marie-Tooth neuropathy causes aberrant binding to interacting proteins

HSP27 is a human molecular chaperone that forms large, dynamic oligomers and functions in many aspects of cellular homeostasis. Mutations in HSP27 cause Charcot-Marie-Tooth (CMT) disease, the most common inherited disorder of the peripheral nervous system. A particularly severe form of CMT disease is triggered by the P182L mutation in the highly conserved IxI/V motif of the disordered C-terminal region, which interacts weakly with the structured core domain of HSP27. Here, we observed that the P182L mutation disrupts the chaperone activity and significantly increases the size of HSP27 oligomers formed in vivo, including in motor neurons differentiated from CMT patient-derived stem cells. Using NMR spectroscopy, we determined that the P182L mutation decreases the affinity of the HSP27 IxI/V motif for its own core domain, leaving this binding site more accessible for other IxI/V-containing proteins. We identified multiple IxI/V-bearing proteins that bind with higher affinity to the P182L variant due to the increased availability of the IxI/V-binding site. Our results provide a mechanistic basis for the impact of the P182L mutation on HSP27 and suggest that the IxI/V motif plays an important, regulatory role in modulating protein-protein interactions.

High-resolution ex vivo NMR spectroscopy of human Z α1-antitrypsin

Genetic mutations predispose the serine protease inhibitor α1-antitrypsin to misfolding and polymerisation within hepatocytes, causing liver disease and chronic obstructive pulmonary disease. This misfolding occurs via a transiently populated intermediate state, but our structural understanding of this process is limited by the instability of recombinant α1-antitrypsin variants in solution. Here we apply NMR spectroscopy to patient-derived samples of α1-antitrypsin at natural isotopic abundance to investigate the consequences of disease-causing mutations, and observe widespread chemical shift perturbations for methyl groups in Z AAT (E342K). By comparison with perturbations induced by binding of a small-molecule inhibitor of misfolding we conclude that they arise from rapid exchange between the native conformation and a well-populated intermediate state. The observation that this intermediate is stabilised by inhibitor binding suggests a paradoxical approach to the targeted treatment of protein misfolding disorders, wherein the stabilisation of disease-associated states provides selectivity while inhibiting further transitions along misfolding pathways.