Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle Assisted NMR Spin Relaxation

Intracellular environment can change protein conformational dynamics in cells through weak interactions

Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.

Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics

The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides quantitative information on the amplitudes and time scales of motional processes. Unfortunately, with a few exceptions, the NMR data do not provide direct insights into the atomic details of dynamic trajectories. Residual dipolar couplings, measured by solution NMR, are very precise parameters reporting on the time-averaged bond-vector orientations and may offer the opportunity to derive correctly weighted dynamic ensembles of structures for cases where multiple high-resolution x-ray structures are available. Applications to the SARS-CoV-2 main protease, M^pro, and ubiquitin highlight this complementarity of NMR and crystallography for quantitative assessment of internal motions.

How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from ¹⁵N relaxation and side-chain dynamics from ¹³C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.

Quantitative Multistate Binding Model of Silica Nanoparticle-Protein Interactions Obtained from Multinuclear Spin Relaxation

Nanoparticle-assisted NMR spin relaxation (NASR), which makes internal protein dynamics in solution directly observable on nanosecond to microsecond time scales, has been applied to different nuclei and relaxation processes of the same protein system. A model is presented describing the transient interaction between ubiquitin and anionic silica nanoparticles for the unified interpretation of a wealth of experimental data including ²H, ¹³C, and ¹⁵N relaxation of methyl side chain and backbone moieties. The best model, implemented using a stochastic Liouville equation, describes the exchange process via an intermediary encounter state between free and fully nanoparticle-bound protein. The implication of the three-state binding model on the interpretation of NASR data is discussed.

Binding Between Antibiotics and Polystyrene Nanoparticles Examined by NMR

Elucidating the interactions between plastic nanoparticles and small molecules is important to understanding these interactions as they occur in polluted waterways. For example, plastic that breaks down into micro- and nanoscale particles will interact with small molecule pollutants that are also present in contaminated waters. Other components of natural water, such as dissolved organic matter, will also influence these interactions. Here we use a collection of complementary NMR techniques to examine the binding between polystyrene nanoparticles and three common antibiotics, belonging to a class of molecules that are expected to be common in polluted water. Through examination of proton NMR signal intensity, relaxation times, saturation-transfer difference (STD) NMR, and competition STD-NMR, we find that the antibiotics have binding strengths in the order amoxicillin < metronidazole ≪ levofloxacin. Levofloxacin is able to compete for binding sites, preventing the other two antibiotics from binding. The presence of tannic acid disrupts the binding between levofloxacin and the polystyrene nanoparticles, but does not influence the binding between metronidazole and these nanoparticles.

NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions

A survey, primarily based on work in the authors' laboratory during the last 10 years, is provided of recent developments in NMR studies of exchange processes involving protein-ligand and protein-protein interactions. We start with a brief overview of the theoretical background of Dark state Exchange Saturation Transfer (DEST) and lifetime line-broadening (ΔR₂) NMR methodology. Some limitations of the DEST/ΔR₂ methodology in applications to molecular systems with intermediate molecular weights are discussed, along with the means of overcoming these limitations with the help of closely related exchange NMR techniques, such as the measurements of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, exchange-induced chemical shifts or rapidly-relaxing components of relaxation decays. Some theoretical underpinnings of the quantitative description of global dynamics of proteins on the surface of very high molecular weight particles (nanoparticles) are discussed. Subsequently, several applications of DEST/ΔR₂ methodology are described from a methodological perspective with an emphasis on providing examples of how kinetic and relaxation parameters for exchanging systems can be reliably extracted from NMR data for each particular model of exchange. Among exchanging systems that are not associated with high molecular weight species, we describe several exchange NMR-based studies that focus on kinetic modelling of transient pre-nucleation oligomerization of huntingtin peptides that precedes aggregation and fibril formation.

Quantitative Measurement of Multiprotein Nanoparticle Interactions Using NMR Spectroscopy

An effective intensity-based reference is a cornerstone for quantitative nuclear magnetic resonance (NMR) studies, as the molecular concentration is encoded in its signal. In theory, NMR is well suited for the measurement of competitive protein adsorption onto nanoparticle (NP) surfaces, but current referencing systems are not optimized for multidimensional experiments. Presented herein is a simple and novel referencing system using ¹⁵N tryptophan (Trp) as an external reference for ¹H-¹⁵N 2D NMR experiments. The referencing system is validated by the determination of the binding capacity of a single protein onto gold NPs. Then, the Trp reference is applied to protein mixtures, and signals from each protein are accurately quantified. All results are consistent with previous studies, but with substantially higher precision, indicating that the Trp reference can accurately calibrate the residue peak intensities and reduce systematic errors. Finally, the proposed Trp reference is used to kinetically monitor in situ and in real time the competitive adsorption of different proteins. As a challenging test case, we successfully apply our approach to a mixture of protein variants differing by only a single residue. Our results show that the binding of one protein will affect the binding of the other, leading to an altered NP corona composition. This work therefore highlights the importance of studying protein-NP interactions in protein mixtures in situ, and the referencing system developed here enables the quantification of binding kinetics and thermodynamics of multiple proteins using various ¹H-¹⁵N 2D NMR techniques.

Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation

Amino-acid side-chain properties in proteins are key determinants of protein function. NMR spin relaxation of side chains is an important source of information about local protein dynamics and flexibility. However, traditional solution NMR relaxation methods are most sensitive to sub-nanosecond dynamics lacking information on slower ns-μs time-scale motions. Nanoparticle-assisted NMR spin relaxation (NASR) of methyl-side chains is introduced here as a window into these ns-μs dynamics. NASR utilizes the transient and nonspecific interactions between folded proteins and slowly tumbling spherical nanoparticles (NPs), whereby the increase of the relaxation rates reflects motions on time scales from ps all the way to the overall tumbling correlation time of the NPs ranging from hundreds of ns to μs. The observed motional amplitude of each methyl group can then be expressed by a model-free NASR S² order parameter. The method is demonstrated for ²H-relaxation of CH₂D methyl moieties and cross-correlated relaxation of CH₃ groups for proteins Im7 and ubiquitin in the presence of anionic silica-nanoparticles. Both types of relaxation experiments, dominated by either quadrupolar or dipolar interactions, yield highly consistent results. Im7 shows additional dynamics on the intermediate time scales taking place in a functionally important loop, whereas ubiquitin visits the majority of its conformational substates on the sub-ns time scale. These experimental observations are in good agreement with 4-10 μs all-atom molecular dynamics trajectories. NASR probes side-chain dynamics on a much wider range of motional time scales than previously possible, thereby providing new insights into the interplay between protein structure, dynamics, and molecular interactions that govern protein function.

NMR Spin Relaxation Theory of Biomolecules Undergoing Highly Asymmetric Exchange with Large Interaction Partners

The transient interactions of proteins and other molecules with much larger structures, such as synthetic or biological nanoparticles, lead to certain types of enhanced nuclear magnetic resonance (NMR) spin relaxation effects, which can be accurately measured by multidimensional solution NMR techniques. These relaxation effects provide new information about the nanostructures and the protein, their interactions, internal dynamics, and associated kinetic and thermodynamic parameters, such as exchange rates and populations. Although theoretical treatments exist that cover either the fast or slow exchange limits, a theoretical treatment that applies to all practically relevant exchange processes is still missing. A unified theoretical framework is presented for this purpose based on a stochastic Liouville equation (SLE). It covers nuclear spin dynamics, overall rotational diffusion of both the protein and the nanostructure, the exchange process between a free state and a bound state, and internal protein dynamics. Although the numerical implementation of the SLE typically involves large matrices, it is shown here that it is computationally still tractable for situations relevant in practice. Application of the theory demonstrates how transverse relaxation is substantially impacted by the kinetics of binding on a wide range of exchange timescales. It is further shown that when exchange occurs on the appropriate timescale, transverse relaxation is able to report on internal dynamics far slower than observable by traditional transverse relaxation experiments. The SLE will allow the realistic and quantitative interpretation of experimental NMR data reporting about transient protein-nanoparticle interactions, thereby providing a powerful tool for the characterization of protein dynamics modes on a vast range of timescales including motions that may be functionally relevant.

Degree of N-Methylation of Nucleosides and Metabolites Controls Binding Affinity to Pristine Silica Surfaces

Biological molecules interact with silica (SiO₂) surfaces with binding affinities that greatly vary depending on their physical-chemical properties. However, the quantitative characterization of biological compounds adsorbed on silica surfaces, especially of compounds involved in fast, reversible interactions, has been challenging, and the driving forces are not well understood. Here, we show how carbon-13 NMR spin relaxation provides quantitative atomic-detail information about the transient molecular binding to pristine silica surfaces, represented by colloidally dispersed silica nanoparticles (SNPs). Based on the quantitative analysis of almost two dozen biological molecules, we find that the addition of N-methyl motifs systematically increases molecular binding affinities to silica in a nearly quantitatively predictable manner. Among the studied compounds are methylated nucleosides, which are common in epigenetic signaling in nucleic acids. The quantitative understanding of N-methylation may open up new ways to detect and separate methylated nucleic acids or even regulate their cellular functions.