Characterization of Specific Protein Association by 15N CPMG Relaxation Dispersion NMR: The GB1A34F Monomer−Dimer Equilibrium

Biophysical Investigation of the Interplay between the Conformational Species of Domain-Swapped GB1 Amyloid Mutant through Real-Time Monitoring of Amyloid Fibrillation

Mutant polypeptide GB1HS#124^F26A, which is known to aggregate into amyloid-like fibrils, has been utilized as a model in this study for gaining insights into the mechanism of domain-swapped aggregation through real-time monitoring. Size exclusion with UV monitoring at 280 nm and dynamic light scattering (DLS) profiles through different time points of fibrillation reveal that the dimer transitions into monomeric intermediates during the aggregation, which could further facilitate domain swapping to form amyloid fibrils. The 1D ¹H and 2D ¹H-¹³C HSQC nuclear magnetic resonance (NMR) spectra profiling through different time points of fibrillation reveal that there may be some other species present along with the dimer during aggregation which contribute to different trends for the intensity of protons in the spectral peaks. Diffusion NMR reveals changes in the mobility of the dimeric species during the process of aggregation, indicating that the dimer gives rise to other lower molecular weight species midway during aggregation, which further add up to form the oligomers and amyloid fibrils successively. The present work is a preliminary study which explores the possibility of utilizing biophysical methods to gain atomistic level insights into the different stages of aggregation.

Quantification of natural abundance NMR data differentiates the solution behavior of monoclonal antibodies and their fragments

Biotherapeutics are an important class of molecules for the treatment of a wide range of diseases. They include low molecular weight peptides, highly engineered protein scaffolds and monoclonal antibodies. During their discovery and development, assessments of the biophysical attributes is critical to understanding the solution behavior of therapeutic proteins and for de-risking liabilities. Thus, methods that can quantify, characterize, and provide a basis to inform risks and drive the selection of more optimal antibody and alternative scaffolds are needed. Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides a means to probe antibody and antibody-like molecules in solution, at atomic resolution, under any formulated conditions. Here, all samples were profiled at natural abundance requiring no isotope enrichment. We present a numerical approach that quantitates two-dimensional methyl spectra. The approach was tested with a reference dataset that contained different types of antibody and antibody-like molecules. This dataset was processed through a procedure we call a Random Sampling of NMR Peaks for Covariance Analysis. This analysis revealed that the first two components were well correlated with the hydrodynamic radius of the molecules included in the reference set. Higher-order principal components were also linked to dynamic features between different tethered antibody-like molecules and contributed to decisions around candidate selection. The reference set provides a basis to characterize molecules with unknown solution behavior and is sensitive to the behavior of a molecule formulated under different conditions. The approach is independent of protein design, scaffold, formulation and provides a facile method to quantify solution behavior.

Origin of conformational dynamics in a globular protein

Protein structures are dynamic, undergoing motions that can play a vital role in function. However, the link between primary sequence and conformational dynamics remains poorly understood. Here, we studied how conformational dynamics can arise in a globular protein by evaluating the impact of individual core-residue substitutions in DANCER-3, a streptococcal protein G domain β1 variant that we previously designed to undergo a specific mode of conformational exchange that has never been observed in the wild-type protein. Using a combination of solution NMR experiments and molecular dynamics simulations, we demonstrate that only two mutations are necessary to create this conformational exchange, and that these mutations work synergistically, with one destabilizing the native structure and the other allowing two new conformational states to be accessed on the energy landscape. Overall, our results show how dynamics can appear in a stable globular fold, a critical step in the molecular evolution of dynamics-linked functions.

Chemical Exchange

The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety of spin relaxation parameters have been developed that provide quantitative information on interconversion kinetics, thermodynamic properties, and structural features of molecular states populated to a fraction of a percent at equilibrium and otherwise unobservable by other NMR approaches. The ongoing development of more sophisticated experimental techniques and the necessity to apply these methods to larger and more complex molecular systems engenders a corresponding need for theoretical advances describing such techniques and facilitating data analysis in applications. This review surveys current aspects of the theory of chemical exchange, as utilized in ZZ-exchange; Hahn and Carr-Purcell-Meiboom-Gill (CPMG) spin-echo; and R_1ρ, chemical exchange saturation transfer (CEST), and dark state saturation transfer (DEST) spin-locking experiments. The review emphasizes theoretical results for kinetic topologies with more than two interconverting states, both to obtain compact analytical forms suitable for data analysis and to establish conditions for distinguishability between alternative kinetic schemes.

Protein shape modulates crowding effects

Protein-protein interactions are usually studied in dilute buffered solutions with macromolecule concentrations of <10 g/L. In cells, however, the macromolecule concentration can exceed 300 g/L, resulting in nonspecific interactions between macromolecules. These interactions can be divided into hard-core steric repulsions and "soft" chemical interactions. Here, we test a hypothesis from scaled particle theory; the influence of hard-core repulsions on a protein dimer depends on its shape. We tested the idea using a side-by-side dumbbell-shaped dimer and a domain-swapped ellipsoidal dimer. Both dimers are variants of the B1 domain of protein G and differ by only three residues. The results from the relatively inert synthetic polymer crowding molecules, Ficoll and PEG, support the hypothesis, indicating that the domain-swapped dimer is stabilized by hard-core repulsions while the side-by-side dimer shows little to no stabilization. We also show that protein cosolutes, which interact primarily through nonspecific chemical interactions, have the same small effect on both dimers. Our results suggest that the shape of the protein dimer determines the influence of hard-core repulsions, providing cells with a mechanism for regulating protein-protein interactions.

Surface Charge Modulates Protein-Protein Interactions in Physiologically Relevant Environments

Protein-protein interactions are fundamental to biology yet are rarely studied under physiologically relevant conditions where the concentration of macromolecules can exceed 300 g/L. These high concentrations cause cosolute-complex contacts that are absent in dilute buffer. Understanding such interactions is important because they organize the cellular interior. We used 19F nuclear magnetic resonance, the dimer-forming A34F variant of the model protein GB1, and the cosolutes bovine serum albumin (BSA) and lysozyme to assess the effects of repulsive and attractive charge-charge dimer-cosolute interactions on dimer stability. The interactions were also manipulated via charge-change variants and by changing the pH. Charge-charge repulsions between BSA and GB1 stabilize the dimer, and the effects of lysozyme indicate a role for attractive interactions. The data show that chemical interactions can regulate the strength of protein-protein interactions under physiologically relevant crowded conditions and suggest a mechanism for tuning the equilibrium thermodynamics of protein-protein interactions in cells.

Self-Assembly of Human Profilin-1 Detected by Carr-Purcell-Meiboom-Gill Nuclear Magnetic Resonance (CPMG NMR) Spectroscopy

Protein oligomerization in the cell has important implications for both health and disease, and an understanding of the mechanisms by which proteins can self-associate is, therefore, of critical interest. Initial stages of the oligomerization process can be hard to detect, as they often involve the formation of sparsely populated and transient states that are difficult to characterize by standard biophysical approaches. Using relaxation dispersion nuclear magnetic resonance spectroscopy, we study the oligomerization of human profilin-1, a protein that regulates the polymerization of actin. We show that in solution and at millimolar concentrations profilin-1 is predominantly monomeric. However, fits of concentration-dependent relaxation data are consistent with the formation of a higher-order oligomer that is generated via a multistep process. Together with crystallographic data for profilin-2, a homologue of the protein studied here, our results suggest that profilin-1 forms a sparsely populated tetrameric conformer in solution.

Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease

Under the selective pressure of therapy, HIV-1 protease mutants resistant to inhibitors evolve to confer drug resistance. Such mutations can impact both the dynamics and structures of the bound and unbound forms of the enzyme. Flap+ is a multidrug-resistant variant of HIV-1 protease with a combination of primary and secondary resistance mutations (L10I, G48V, I54V, V82A) and a strikingly altered thermodynamic profile for darunavir (DRV) binding relative to the wild-type protease. We elucidated the impact of these mutations on protein dynamics in the DRV-bound state using molecular dynamics simulations and NMR relaxation experiments. Both methods concur in that the conformational ensemble and dynamics of protease are impacted by the drug resistance mutations in Flap+ variant. Surprisingly this change in ensemble dynamics is different from that observed in the unliganded form of the same variant (Cai, Y. et al. J. Chem. Theory Comput.2012, 8, 3452–3462). Our comparative analysis of both inhibitor-free and bound states presents a comprehensive picture of the altered dynamics in drug-resistant mutant HIV-1 protease and underlies the importance of incorporating dynamic analysis of the whole system, including the unliganded state, into revealing drug resistance mechanisms.

GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data

Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial μs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. Hence, we present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data ( http://code.google.com/p/guardd/). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements χ (2)-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community.

Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination

A strength of NMR spectroscopy is its ability to monitor, on an atomic level, molecular changes and interactions. In this review, which is intended for non-spectroscopist, we describe major uses of NMR in protein science beyond solution structure determination. After first touching on how NMR can be used to quickly determine whether a mutation induces structural perturbations in a protein, we describe the unparalleled ability of NMR to monitor binding interactions over a wide range of affinities, molecular masses and solution conditions. We discuss the use of NMR to measure the dynamics of proteins at the atomic level and over a wide range of timescales. Finally, we outline new and expanding areas such as macromolecular structure determination in multicomponent systems, as well as in the solid state and in vivo.

Dimerization of protein G B1 domain at low pH: a conformational switch caused by loss of a single hydrogen bond

A number of signals in the NMR spectrum of the B1 domain of staphylococcal protein G (GB1) show a chemical shift dependence on the concentration of the protein at pH 3 but not at neutral pH, implying the existence of self-association at low pH. NMR backbone relaxation experiments show that GB1 undergoes a slow conformational exchange at pH 3, which is not seen at higher pH. Analysis of relaxation dispersion experiments yields a self-association constant of 50 mM, and shows that (15)N chemical shift changes in the dimer interface are up to 3 ppm. The shift changes measured from concentration-dependent HSQC spectra and from relaxation dispersion show good consistency. Measurements of chemical shifts as a function of pH show that a hydrogen bond between the sidechains of Asp44 and Gln40 is broken when Asp44 is protonated, and that loss of this hydrogen bond leads to the breaking of the (i, i + 4) backbone helical hydrogen bond from Asp44 HN to Gln40 O, and therefore to a loss of two residues from the C-terminal end of the helix. This weakens the helix structure and facilitates the loss of further helical structure thus permitting dimerization, which is suggested to occur in the same way as observed for the A42F mutant of GB1 (Jee et al., Proteins 2007;71:1420-1431), by formation of an antiparallel beta-sheet between the edge strands 2 in two monomers. The monomer/dimer ratio is thus a finely balanced equilibrium even in the wild type protein.

Characterizing dynamic protein-protein interactions using differentially scaled paramagnetic relaxation enhancement

Paramagnetic relaxation enhancement (PRE) is a powerful NMR technique that allows direct visualization of minor species. The PRE is obtained by conjugating a paramagnetic probe, such as EDTA-Mn(2+), at a specific cysteine residue. For a fast exchange between major and minor species, the observed PRE rate approaches population-weighted average of PRE values for both states. We have employed a tripeptide of Cu(2+)-binding paramagnetic probe that yields a much weaker PRE effect than EDTA-Mn(2+) does. We show that by using two probes of different paramagnetic strengths attached at the same site, the relative population and exchange time scale can be extracted, providing that the dynamic event occurs in the second to millisecond regime. Hence, this improved PRE scheme, differentially scaled paramagnetic relaxation enhancement (DiSPRE), permits both temporal and spatial characterization of a dynamic system. When applying the DiSPRE scheme to reassess the weak interactions between the N-terminal domain of enzyme I and phosphocarrier protein (HPr) from the bacterial phosphotransferase system, we have identified a minor species of excited-state complex with a approximately 4% population and exchanging with the stereospecific complex at approximately 1100 s(-1). Such species is distinct from other encounter complexes previously characterized and is likely a result of promiscuity of the HPr binding interface.

Structural characterization of the EphA4-Ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity

EphA and EphB receptors preferentially bind ephrin-A and ephrin-B ligands, respectively, but EphA4 is exceptional for its ability to bind all ephrins. Here, we report the crystal structure of the EphA4 ligand-binding domain in complex with ephrin-B2, which represents the first structure of an EphA-ephrin-B interclass complex. A loose fit of the ephrin-B2 G-H loop in the EphA4 ligand-binding channel is consistent with a relatively weak binding affinity. Additional surface contacts also exist between EphA4 residues Gln(12) and Glu(14) and ephrin-B2. Mutation of Gln(12) and Glu(14) does not cause significant structural changes in EphA4 or changes in its affinity for ephrin-A ligands. However, the EphA4 mutant has approximately 10-fold reduced affinity for ephrin-B ligands, indicating that the surface contacts are critical for interclass but not intraclass ephrin binding. Thus, EphA4 uses different strategies to bind ephrin-A or ephrin-B ligands and achieve binding promiscuity. NMR characterization also suggests that the contacts of Gln(12) and Glu(14) with ephrin-B2 induce dynamic changes throughout the whole EphA4 ligand-binding domain. Our findings shed light on the distinctive features that enable the remarkable ligand binding promiscuity of EphA4 and suggest that diverse strategies are needed to effectively disrupt different Eph-ephrin complexes.

Dimerisation of the UBA domain of p62 inhibits ubiquitin binding and regulates NF-kappaB signalling

The ubiquitin (Ub)-binding p62 scaffold protein (encoded by the SQSTM1 gene) regulates a diverse range of signalling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors and is an important regulator of macroautophagy. Mutations within the gene encoding p62 are commonly found in patients with Paget's disease of bone and largely cluster within the C-terminal ubiquitin-associated (UBA) domain, impairing its ability to bind Ub, resulting in dysregulated NF-kappaB signalling. However, precisely how Ub-binding is regulated at the molecular level is unclear. NMR relaxation dispersion experiments, coupled with concentration-dependent NMR, CD, isothermal titration calorimetry and fluorescence kinetic measurements, reveal that the p62 UBA domain forms a highly stable dimer (K(dim) approximately 4-12 microM at 298 K). NMR analysis shows that the dimer interface partially occludes the Ub-binding surface, particularly at the C-terminus of helix 3, making UBA dimerisation and Ub-binding mutually exclusive processes. Somewhat unusually, the monomeric UBA appears to be the biologically active form and the dimer appears to be the inactive one. Engineered point mutations in loop 1 (E409K and G410K) are shown to destabilise the dimer interface, lead to a higher proportion of the bound monomer and, in NF-kappaB luciferase reporter assays, are associated with reduced NF-kappaB activity compared with wt-p62.

Dynamics of the RING domain from human TRAF6 by 15N NMR spectroscopy: implications for biological function

Activation of transcription factor NF-kappaB requires Lys63-linked polyubiquitination of the E3 ubiquitin ligase TRAF6 via protein-protein interactions mediated by a RING domain. In this study, intra- and intermolecular chemical exchange processes of the TRAF6 RING domain were analyzed by (15)N NMR spectroscopy. Micro- to millisecond time scale motions were assessed through R 1, R 2, NOE, and cross-correlated relaxation measurements, and the kinetics of these motions were quantified with relaxation dispersion. The relaxation experiments indicate that the protein core is rigid, consistent with the functional requirement that RING domains form a binding scaffold for E2 ubiquitin conjugation enzymes. Chemical exchange is observed at the C-terminal end of the main alpha-helix of the RING domain. The C-terminal end of the main alpha-helix from the RING domain is involved in E2-E3 interactions, and modulation of slow motions for this region of the helix may be a general mechanism by which these interactions achieve ubiquitin transfer. Chemical shift mapping indicates that the TRAF6 RING domain does not self-associate in solution. Numerous RING domains are homo- or heterodimeric, and this is thought to be a functional necessity for recruitment of substrates for ubiquitination, or recruitment of multiple E2 enzymes for efficient substrate ubiquitination. However, lack of self-association for the RING domain from TRAF6, and the observation that the intact protein is a trimer, suggests that close association of RING domains within a homodimeric scaffold may not be a fundamental requirement for biological function.