Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data

Functional motions of ¹⁵N‐labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R_1ρ and CPMG‐type experiments. CEST also simultaneously reports on site‐specific R₁ and R₂ parameters. It is shown here how CEST‐derived R₁ and R₂ relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a “lean” version of the model‐free approach S² order parameters can be determined that match those from the standard model‐free approach applied to ¹⁵N R₁, R₂, and {¹H}‐¹⁵N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond‐to‐millisecond timescales.     

The Hunt for the Closed Conformation of the Fruit-Ripening Enzyme 1-Aminocyclopropane-1-carboxylic Oxidase: A Combined Electron Paramagnetic Resonance and Molecular Dynamics Study

1-Aminocyclopropane-1-carboxylic oxidase (ACCO) is a non-heme iron(II)-containing enzyme involved in the biosynthesis of the phytohormone ethylene, which regulates fruit ripening and flowering in plants. The active conformation of ACCO, and in particular that of the C-terminal part, remains unclear and open and closed conformations have been proposed. In this work, a combined experimental and computational study to understand the conformation and dynamics of the C-terminal part is reported. Site-directed spin-labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy was used. Mutagenesis experiments were performed to generate active enzymes bearing two paramagnetic labels (nitroxide radicals) anchored on cysteine residues, one in the main core and one in the C-terminal part. Inter-spin distance distributions were measured by pulsed EPR spectroscopy and compared with the results of molecular dynamics simulations. The results reveal the existence of a flexibility of the C-terminal part. This flexibility generates several conformations of the C-terminal part of ACCO that correspond neither to the existing crystal structures nor to the modelled structures. This highly dynamic region of ACCO raises questions on its exact function during enzymatic activity.     

Probing Transient Conformational States of Proteins by Solid‐State R1ρ Relaxation‐Dispersion NMR Spectroscopy

The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R_1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states.     

Intermolecular Interactions and Protein Dynamics by Solid‐State NMR Spectroscopy

Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1–antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site‐specific ¹⁵N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond–nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small‐amplitude overall anisotropic motion sampling the interaction interface in the complex.     

Deuterium MAS NMR Studies of Dynamics on Multiple Timescales: Histidine and Oxalic Acid

Deuterium (²H) magic‐angle spinning (MAS) nuclear magnetic resonance is applied to monitor the dynamics of the exchanging labile deuterons of polycrystalline L ‐histidine hydrochloride monohydrate‐d₇ and α‐oxalic acid dihydrate‐d₆. Direct experimental evidence of fast dynamics is obtained from T_1Z and T_1Q measurements. Further motional information is extracted from two‐dimensional single‐quantum (SQ) and double‐quantum (DQ) MAS spectra. Differences between the SQ and DQ linewidths clearly indicate the presence of motions on intermediate timescales for the carboxylic moiety and the D₂O in α‐oxalic acid dihydrate, and for the amine group and the D₂O in L ‐histidine hydrochloride monohydrate. Comparison of the relaxation rate constants of Zeeman and quadrupolar order with the relaxation rate constants of the DQ coherences suggests the co‐existence of fast and slow motional processes.     

Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR

Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using ¹⁵N rotating frame (R_1ρ) relaxation dispersion solid-state nuclear magnetic resonance spectroscopy over a wide range of spin-lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two-state exchange process with a common exchange rate of 1000 s⁻¹, corresponding to protein backbone motion on the timescale of 1 ms, and an excited-state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited-state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.     

Molecular Dynamics Simulation of the Binding Interaction between Hormone Glucagon Protein and Self-Assembled Monolayer Molecules

Restrained molecular dynamics simulations were performed to study the binding affinity of the peptide with alkanethiols of different tail-groups, S（CH2）7CH3, S（CH2）7OH and S（CH2）7COOH, which self-assembled on Au（111） surface in the presence of water molecules. The curves of binding affinity were calculated by fixing the center of mass of the peptide at various distances from the assembling surface. Simulation results show that the binding affin- ity is in the order as COOH-SAMs〉OH-SAMs〉CH3-SAMs, while 100% COOH-SAMs〉5% COOH-SAMS in concentration. The effects on binding affinity by different tail-groups were also studied. Results show that the binding affinity between COOH-SAMs and the peptide is bigger than those of the others and increasing the acidity of COOH-SAMs will result in stronger attractive power.     

Trianglimine-Mediated Selective Sieving of Cis Isomer from the Mixture of Dihaloethenes: A Combined Molecular Dynamics and DFT Investigation

The manufacture of alkenyl halides on a larger scale often results in the formation of a mixture of isomers, each having individual significant applications while their separation from each other is a strenuous task. Since most of the conventional distillation techniques are known to be intricate, energy consuming and expensive, the quest for an alternative separation strategies is still continuing. In this context, the recently reported trianglimine macrocycle - a new class of intrinsically porous material, is promising in discerning cis isomer from a mixture of cis and trans dichloroethene. Herein, an attempt has been made to apprehend the host-guest inclusion phenomenon accountable for the selectivity of cis over the trans isomers of 1,2-dihaloethene (F, Cl and Br) using molecular dynamics simulation and density functional calculations at ω-B97xd/6-311G+(d,p) level of theory. The average binding energy of selected snapshots has been calculated at different loadings, temperatures and pressures from molecular dynamics simulation. Our results show that trianglimine can stabilise the cis isomers of the dihaloethenes inside its cavity forming complexes with high interaction energies and the rationale behind the recyclability of the host molecule has been clarified. The outcomes of the calculations bring out the potential utility of this new host architecture to produce highly pure value added chemicals in industries.     

Comparative Analysis of Hydration Layer Reorientation Dynamics of Antifreeze Protein and Protein Cytochrome P450

Antifreeze proteins (AFPs) inhibit ice recrystallization by a mechanism remaining largely elusive. Dynamics of AFPs' hydration water and its involvement in the antifreeze activity have not been identified conclusively. We herein, by simulation and theory, examined the water reorientation dynamics in the first hydration layer of an AFP from the spruce budworm, Choristoneura fumiferana, compared with a protein cytochrome P450 (CYP). The increase of potential acceptor water molecules around donor water molecules leads to the acceleration of hydrogen bond exchange between water molecules. Therefore, the jump reorientation of water molecules around the AFP active region is accelerated. Due to the mutual coupling and excitation of hydrogen bond exchange, with the acceleration of hydrogen bond exchange, the rearrangement of the hydrogen bond network and the frame reorientation of water are accelerated. Therefore, the water reorientation dynamics of AFP is faster than that of CYP. The results of this study provide a new physical image of antifreeze protein and a new understanding of the antifreeze mechanism of antifreeze proteins.     

Approaching Dissolved Species in Ammonoacidic GaN Crystal Growth: A Combined Solution NMR and Computational Study

Solutions of gallium trihalides GaX₃ (X=F, Cl, Br, I) and their ammoniates in liquid ammonia were studied at ambient temperature under autogenous pressure by multinuclear (⁷¹Ga, ³⁵Cl, ⁸¹Br) NMR spectroscopy. To unravel the role of pH, the analyses were done both in absence and in presence of ammonium halides, which are employed as mineralizers during ammonoacidic gallium nitride crystal growth. While gallium trifluoride and its ammoniate were found to be too sparingly soluble to give rise to a NMR signal, the spectra of solutions of the heavier halides reveal the presence of a single gallium-containing species in all cases. DFT calculations and molecular dynamics simulations suggest the identification of this species as consisting of a [Ga(NH₃)₆]³⁺ cation and up to six surrounding halide anions, resulting in an overall trend towards negative complex charge. Quantitative ⁷¹Ga NMR studies on saturated solutions of GaCl₃ containing various amounts of additional NH₄Cl revealed a near linear increase of GaCl₃ solubility with mineralizer concentration of about 0.023 mol GaCl₃ per mol NH₄Cl at room temperature. These findings reflect the importance of Coulombic shielding for the inhibition of oligomerization and precipitation processes and help to rationalize both the low solubility of gallium halides in neutral ammonia solution and, in turn, the proliferating effect of the mineralizer during ammonoacidic gallium nitride formation.     

HMGB1–Carbenoxolone Interactions: Dynamics Insights from Combined Nuclear Magnetic Resonance and Molecular Dynamics

The interplay of protein dynamics and molecular recognition is of fundamental importance in biological processes. Atomic‐resolution insights into these phenomena may provide new opportunities for drug discovery. Herein, we have combined NMR relaxation experiments and residual dipolar coupling (RDC) measurements with molecular dynamics (MD) simulations to study the effects of the anti‐inflammatory drug carbenoxolone (CBNX) on the conformational properties and on the internal dynamics of a subdomain (box A) of high‐mobility group B protein (HMGB1). ¹⁵N relaxation data show that CBNX binding enhances the fast pico‐ to nanosecond motions of a loop and partially removes the internal motional anisotropy of the first two helices of box A. Dipolar wave analysis of amide RDC data shows that ligand binding induces helical distortions. In parallel, increased mobility of the loop upon ligand binding is highlighted by the essential dynamics analysis (EDA) of MD simulations. Moreover, simulations detect two possible orientations for CBNX, which induces two possible conformations of helix H3, one being similar to the free form and the second one causing a partial helical distortion. Finally, we introduce a new approach for the analysis of the internal coordination of protein residues that is consistent with experimental data and allows us to pinpoint which substructures of box A are dynamically affected by CBNX. The observations reported here may be useful for understanding the role of protein dynamics in binding at atomic resolution.     

Ferromagnetic 2p-2p and 4f-2p Couplings in a Macrocycle from Two Biradicals and Two Gadolinium(III) Ions

A new ground triplet biradical 2′,4′,6′-triisopropylbiphenyl-3,5-diyl bis(tert-butyl nitroxide) (iPr₃BPBN) was prepared and characterized by means of room-temperature ESR spectroscopy displaying a zero-field splitting pattern together with a half-field signal. Complex formation with gadolinium(III) 1,1,1,5,5,5-hexafluoropentane-2,4-dionate (hfac) afforded a macrocycle [{Gd(hfac)₃(μ-iPr₃BPBN)}₂]. As the X-ray crystallographic analysis clarified, the biradical serves as a bridging ligand, giving a 16-membered ring, where each nitroxide radical oxygen atom is directly bonded to a Gd³⁺ ion. The magnetic study revealed that the iPr₃BPBN bridge behaved as a practically triplet biradical and that the Gd³⁺-radical magnetic coupling was weakly ferromagnetic. The exchange parameters were estimated as 2j_rad-rad/k_B > 300 K and 2J_Gd-rad/k_B = 1.2 K in the H = −2J S₁•S₂ convention. The DFT calculation based on the atomic coordinates clarified the ground triplet nature in metal-free iPr₃BPBN and the enhanced triplet character upon coordination. The calculation also suggests that ferromagnetic coupling would be favorable when the Gd-O-N-C(sp²) torsion comes around 100°. The present results are compatible with the proposed magneto-structure relationship on the nitroxide-Gd compounds.     

Analysis of the Structure-Function-Dynamics Relationships of GALT Enzyme and of Its Pathogenic Mutant p.Q188R: A Molecular Dynamics Simulation Study in Different Experimental Conditions

The third step of the catabolism of galactose in mammals is catalyzed by the enzyme galactose-1-phosphate uridylyltransferase (GALT), a homodimeric enzyme with two active sites located in the proximity of the intersubunit interface. Mutations of this enzyme are associated to the rare inborn error of metabolism known as classic galactosemia; in particular, the most common mutation, associated with the most severe phenotype, is the one that replaces Gln188 in the active site of the enzyme with Arg (p.Gln188Arg). In the past, and more recently, the structural effects of this mutation were deduced on the static structure of the wild-type human enzyme; however, we feel that a dynamic view of the proteins is necessary to deeply understand their behavior and obtain tips for possible therapeutic interventions. Thus, we performed molecular dynamics simulations of both wild-type and p.Gln188Arg GALT proteins in the absence or in the presence of the substrates in different conditions of temperature. Our results suggest the importance of the intersubunit interactions for a correct activity of this enzyme and can be used as a starting point for the search of drugs able to rescue the activity of this enzyme in galactosemic patients.     

The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics

Despite the recent advances in the prediction of protein structures by deep neutral networks, the elucidation of protein-folding mechanisms remains challenging. A promising theory for describing protein folding is a coarse-grained statistical mechanical model called the Wako-Saitô-Muñoz-Eaton (WSME) model. The model can calculate the free-energy landscapes of proteins based on a three-dimensional structure with low computational complexity, thereby providing a comprehensive understanding of the folding pathways and the structure and stability of the intermediates and transition states involved in the folding reaction. In this review, we summarize previous and recent studies on protein folding and dynamics performed using the WSME model and discuss future challenges and prospects. The WSME model successfully predicted the folding mechanisms of small single-domain proteins and the effects of amino-acid substitutions on protein stability and folding in a manner that was consistent with experimental results. Furthermore, extended versions of the WSME model were applied to predict the folding mechanisms of multi-domain proteins and the conformational changes associated with protein function. Thus, the WSME model may contribute significantly to solving the protein-folding problem and is expected to be useful for predicting protein folding, stability, and dynamics in basic research and in industrial and medical applications.