氢氘交换质谱技术在蛋白质和蛋白复合物结构研究中的应用进展

蛋白质是生命功能的执行者,其功能的发挥受自身结构动态变化、与其他生物分子的相互作用及修饰等因素的调节。因此,对蛋白质及蛋白复合物结构的研究有助于揭示重要生命过程中的分子机理与机制。氢氘交换质谱(Hydrogen deuterium exchange mass spectrometry,HDX-MS)是研究蛋白质结构、动态变化和相互作用的强有力工具,也是传统生物物理手段的重要补充。该文综述了HDX-MS的基本原理、机制、实验方法和研究最新进展,并从蛋白质自身动态变化、蛋白质-小分子相互作用、蛋白质-蛋白质相互作用3个方面介绍了近年来HDX-MS在蛋白及蛋白复合物研究中的应用进展。     

Symmetrization of Cationic Hydrogen Bridges of Protonated Sponges Induced by Solvent and Counteranion Interactions as Revealed by NMR Spectroscopy

The properties of the intramolecular hydrogen bonds of doubly ¹⁵N‐labeled protonated sponges of the 1,8‐bis(dimethylamino)naphthalene (DMANH⁺) type have been studied as a function of the solvent, counteranion, and temperature using low‐temperature NMR spectroscopy. Information about the hydrogen‐bond symmetries was obtained by the analysis of the chemical shifts δ_H and δ_N and the scalar coupling constants J(N,N), J(N,H), J(H,N) of the ¹⁵NH¹⁵N hydrogen bonds. Whereas the individual couplings J(N,H) and J(H,N) were averaged by a fast intramolecular proton tautomerism between two forms, it is shown that the sum |J(N,H)+J(H,N)| generally represents a measure of the hydrogen‐bond strength in a similar way to δ_H and J(N,N). The NMR spectroscopic parameters of DMANH⁺ and of 4‐nitro‐DMANH⁺ are independent of the anion in the case of CD₃CN, which indicates ion‐pair dissociation in this solvent. By contrast, studies using CD₂Cl₂, [D₈]toluene as well as the freon mixture CDF₃/CDF₂Cl, which is liquid down to 100 K, revealed an influence of temperature and of the counteranions. Whereas a small counteranion such as trifluoroacetate perturbed the hydrogen bond, the large noncoordinating anion tetrakis[3,5‐bis(trifluoromethyl)phenyl]borate B[{C₆H₃(CF₃)₂}₄]^? (BARF^?), which exhibits a delocalized charge, made the hydrogen bond more symmetric. Lowering the temperature led to a similar symmetrization, an effect that is discussed in terms of solvent ordering at low temperature and differential solvent order/disorder at high temperatures. By contrast, toluene molecules that are ordered around the cation led to typical high‐field shifts of the hydrogen‐bonded proton as well as of those bound to carbon, an effect that is absent in the case of neutral NHN chelates.     

杂环化合物氢交换的核磁共振研究

芳香族化合物在酸的作用下可发生可逆的氢交换。该过程是质子对芳香环作亲电进攻,生成过渡态的芳烃离子,后者再失去氢离子完成了氢的化学交换,因而本质是亲电取代反应。例如某些简单的芳香族化合物用重水     

Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside–RNA recognition, glucose‐nucleobase pairs have been examined. Deoxyoligonucleotides with a 6‐deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6‐Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6‐deoxyglucose‐guanine pair closely resembles a purine‐pyrimidine geometry. Quantum chemical calculations indicate that glucose‐purine pairs are as stable as a natural T‐A pair.     

Ultrasensitive Anion Detection by NMR Spectroscopy: A Supramolecular Strategy Based on Modulation of Chemical Exchange Rate

NMR spectroscopy is a powerful tool for monitoring molecular interactions and is widely used to characterize supramolecular systems at the atomic level. NMR is limited for sensing purposes, however, due to low sensitivity. Dynamic processes such as conformational changes or binding events can induce drastic effects on NMR spectra in response to variations in chemical exchange (CE) rate, which can lead to new strategies in the design of supramolecular sensors through the control and monitoring of CE rate. Here, we present an indirect NMR anion sensing technique in which increased CE rate, due to anion‐induced conformational flexibility of a relatively rigid structure of a novel sensor, allows ultrasensitive anion detection as low as 120 nM .     

Unambiguous Determination of Protein Arginine Ionization States in Solution by NMR Spectroscopy

Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge‐neutral are rare and potentially controversial. Herein, we present a ¹³C‐detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the ¹⁵N^η and ¹⁵N^ϵ chemical shifts of an arginine head group are correlated with that of the directly attached ¹³C^ζ. In the resulting spectrum, the number of protons in the arginine head group can be obtained directly from the ¹⁵N–¹H scalar coupling splitting pattern. We applied this method to unambiguously determine the ionization state of the R52 side chain in the photoactive yellow protein from Halorhodospira halophila . Although only three H^η atoms were previously identified by neutron crystallography, we show that R52 is predominantly protonated in solution.     

Measurement of Very Fast Exchange Rates of Individual Amide Protons in Proteins by NMR Spectroscopy

NMR spectroscopy is a pivotal technique to measure hydrogen exchange rates in proteins. However, currently available NMR methods to measure backbone exchange are limited to rates of up to a few per second. To raise this limit, we have developed an approach that is capable of measuring proton exchange rates up to approximately 10⁴ s⁻¹. Our method relies on the detection of signal loss due to the decorrelation of antiphase operators 2N_xH_z by exchange events that occur during a series of pi pulses on the ¹⁵N channel. In practice, signal attenuation was monitored in a series of 2D H(CACO)N spectra, recorded with varying pi-pulse spacing, and the exchange rate was obtained by numerical fitting to the evolution of the density matrix. The method was applied to the small calcium-binding protein Calbindin D_9k, where exchange rates up to 600 s⁻¹ were measured for amides, where no signal was detectable in ¹⁵N−¹H HSQC spectra. A temperature variation study allowed us to determine apparent activation energies in the range 47–69 kJ mol⁻¹ for these fast exchanging amide protons, consistent with hydroxide-catalyzed exchange.     

Insights into Intramolecular Trp and His Side‐Chain Orientation and Stereospecific π Interactions Surrounding Metal Centers: An Investigation Using Protein Metal‐Site Mimicry in Solution

Metal‐binding scaffolds incorporating a Trp/His‐paired epitope are instrumental in giving novel insights into the physicochemical basis of functional and mechanistic versatility conferred by the Trp–His interplay at a metal site. Herein, by coupling biometal site mimicry and ¹H and ¹³C NMR spectroscopy experiments, modular constructs EDTA‐(L ‐Trp, L ‐His) (EWH; EDTA=ethylenediamino tetraacetic acid) and DTPA‐(L ‐Trp, L ‐His) (DWH; DTPA=diethylenetriamino pentaacetic acid) were employed to dissect the static and transient physicochemical properties of hydrophobic/hydrophilic aromatic interactive modes surrounding biometal centers. The binding feature and identities of the stoichiometric metal‐bound complexes in solution were investigated by using ¹H and ¹³C NMR spectroscopy, which facilitated a cross‐validation of the carboxylate, amide oxygen, and tertiary amino groups as the primary ligands and indole as the secondary ligand, with the imidazole (Im) N3 nitrogen being weakly bound to metals such as Ca²⁺ owing to a multivalency effect. Surrounding the metal centers, the stereospecific orientation of aromatic rings in the diastereoisomerism is interpreted with the Ca²⁺–EWH complex. With respect to perturbed Trp side‐chain rotamer heterogeneity, drastically restricted Trp side‐chain flexibility and thus a dynamically constrained rotamer interconversion due to π interactions is evident from the site‐selective ¹³C NMR spectroscopic signal broadening of the Trp indolyl C3 atom. Furthermore, effects of Trp side‐chain fluctuation on indole/Im orientation were the subject of a 2D NMR spectroscopy study by using the Ca²⁺‐bound state; a C? H2(indolyl)/C? H5(Im⁺) connectivity observed in the NOESY spectra captured direct evidence that the N? H1 of the Ca²⁺–Im⁺ unit interacted with the pyrrole ring of the indole unit in Ca²⁺‐bound EWH but not in DWH, which is assignable to a moderately static, anomalous, T‐shaped, interplanar π⁺–π stacking alignment. Nevertheless, a comparative ¹³C NMR spectroscopy study of the two homologous scaffolds revealed that the overall response of the indole unit arises predominantly from global attractions between the indole ring and the entire positively charged first coordination sphere. The study thus demonstrates the coordination‐sphere/geometry dependence of the Trp/His side‐chain interplay, and established that π interactions allow ¹³C NMR spectroscopy to offer a new window for investigating Trp rotamer heterogeneity near metal‐binding centers.     

Designing Foldamer–Foldamer Interactions in Solution: The Roles of Helix Length and Terminus Functionality in Promoting the Self‐Association of Aminoisobutyric Acid Oligomers

The biological activity of antibiotic peptaibols has been linked to their ability to aggregate, but the structure–activity relationship for aggregation is not well understood. Herein, we report a systematic study of a class of synthetic helical oligomer (foldamer) composed of aminoisobutyric acid (Aib) residues, which mimic the folding behavior of peptaibols. NMR spectroscopic analysis was used to quantify the dimerization constants in solution, which showed hydrogen‐bond donors at the N terminus promoted aggregation more effectively than similar modifications at the C terminus. Elongation of the peptide chain also favored aggregation. The geometry of aggregation in solution was investigated by means of titrations with [D₆]DMSO and 2D NOE NMR spectroscopy, which allowed the NH protons most involved in intermolecular hydrogen bonds in solution to be identified. X‐ray crystallography studies of two oligomers allowed a comparison of the inter‐ and intramolecular hydrogen‐bonding interactions in the solid state and in solution and gave further insight into the geometry of foldamer–foldamer interactions. These solution‐based and solid‐state studies indicated that the preferred geometry for aggregation is through head‐to‐tail interactions between the N and C termini of adjacent Aib oligomers.     

Non‐Ideal Behaviour and Solution Interactions in Binary DMSO Solutions

The structure and dynamics of hydrogen‐bonded structures are of significant importance in understanding many binary mixtures. Since self‐diffusion is very sensitive to changes in the molecular weight and shape of the diffusing species, hydrogen‐bonded associated structures in dimethylsulfoxide–methanol (DMSO–MeOH) and DMSO–ethanol (DMSO–EtOH) mixtures are investigated using nuclear magnetic resonance (NMR) diffusion experiments and molecular dynamics (MD) simulations over the entire composition range at 298 K. The self‐diffusion coefficients of DMSO–MeOH and DMSO–EtOH mixtures decrease by up to 15% and 10%, respectively, with DMSO concentration, indicating weaker association as compared to DMSO–water mixtures. The calculated heat of mixing and radial distribution functions reveal that the intermolecular structures of DMSO–MeOH and DMSO–EtOH mixtures do not change on mixing. DMSO–alcohol hydrogen‐bonded dimers are the dominant species in mixtures. Direct comparison of the simulated and experimental data afford greater insights into the structural properties of binary mixtures.     

Hydrogen Isotope Exchange Reactions in an Electrical Discharge

Hydrogen isotope exchange reactions occurring in (H₂O, D₂)or (D₂O, H₂) reacting system under a DC electricaldischarge were investigated using spectroscopic methods such asFourier-transform infrared (FTIR) and plasma emission spectroscopy(PES). The progress of the reactions was determined by real-time measurementof the IR absorbance of HDO molecule, a major product of the reaction. Theprogress of the reaction was studied as a function of the temperature, thecurrent density, and the composition of the reactants, while the pressure ofthe system was maintained at approximately 67 mbar. The results revealedthat the discharge method was far more effective in facilating the exchangereaction than was the conventional catalytic method. The (H₂O, D₂)system also generated a significant amount of D₂O besides HDO andHD as the ratio of D₂ to H₂O was increased. Thetransient species of the system, such as H or D atoms, were monitored duringthe discharge using emission spectroscopy. The analysis of the final products by mass spectroscopy confirmed that neither H₂ nor O₂was among the major products of the system in the discharge.     

Dynamic Interactions in Synthetic Receptors: A Guest Exchange Saturation Transfer Study

The accumulated knowledge regarding molecular architectures is based on established, reliable, and accessible analytical tools that provide robust structural and functional information on assemblies. However, both the dynamicity and low population of noncovalently interacting moieties within studied molecular systems limit the efficiency and accuracy of traditional methods. Herein, the use of a saturation transfer-based NMR approach to study the dynamic binding characteristics of an anion to a series of synthetic receptors derived from bambusuril macrocycles is demonstrated. The exchange rates of BF₄⁻ are mediated by the side chains on the receptor (100 s⁻¹<k_ex<5000 s⁻¹), which play a critical role in receptor-anion binding dynamics. The signal amplification obtained with this approach allows for the identification of different types of intermolecular interactions between the receptor and the anion, something that could not have been detected by techniques hitherto used to study molecular assemblies. These findings, which are supported by a computational molecular dynamic study, demonstrate the uniqueness and added value of this NMR method.     

Search for a Strong,Virtually “No‐Shift” Hydrogen Bond: A Cage Molecule with an Exceptional OH⋅⋅⋅F Interaction

Reported herein is the synthesis of a molecule containing an unusually strong hydrogen bond between an OH donor and a covalent F acceptor, a heretofore somewhat ill‐defined if not controversial interaction. This unique hydrogen bond is to a large extent a product of the tight framework of the rigid caged system. Remarkably, the interaction shows little to no perceptible shift in the OH stretch of the IR spectrum relative to appropriate nonhydrogen‐bound standards in fairly non‐interactive solvents. This fascinating example of what has been termed a virtual “no‐shift” hydrogen bond is investigated through NMR (coupling constants, isotopic chemical shift perturbations, proton exchange rates) and IR studies which all tell a consistent story.     

13C Spin-Lattice Relaxation Times and the Mobility of Organic Molecules in Solution

While the chemical shifts and coupling constants of ¹³C NMR belong to the most powerful tools available to the organic chemist for the solution of structural problems, increasing interest is being shown in ¹³C spin-lattice relaxation times T₁ as structural parameters. Together with the nuclear Overhauser effects arising by proton decoupling of ¹³C NMR spectra, the T₁ values of ¹³C nuclei in a molecule permit conclusions to be drawn with regard to relaxation mechanisms. They reflect the inter- and intramolecular mobility of a molecule, and thus complement the results of temperature-dependent NMR spectroscopy. The T₁ differences within a molecule show, for instance, whether the molecular motion is anisotropic in solution, whether the internal motion of groups is subject to steric hindrance, the extent to which strong intermolecular or interionic interactions affect the flexibility of the molecule, and which parts of the molecule are rigid and which are flexible. Finally, differences between the T₁ values measured for the ¹³C nuclei of a molecule frequently provide a reliable aid in the assignment of ¹³C NMR spectra, particularly in cases of signal crowding and multiplet overlapping.     

Fast Proton Exchange in Histidine: Measurement of Rate Constants through Indirect Detection by NMR Spectroscopy

Owing to its imidazole side chain, histidine participates in various processes such as enzyme catalysis, pH regulation, metal binding, and phosphorylation. The determination of exchange rates of labile protons for such a system is important for understanding its functions. However, these rates are too fast to be measured directly in an aqueous solution by using NMR spectroscopy. We have obtained the exchange rates of the NH₃⁺ amino protons and the labile NH^ε2 and NH^δ1 protons of the imidazole ring by indirect detection through nitrogen‐15 as a function of temperature (272 K<T<293 K) and pH (1.3<pH<4.9) of uniformly nitrogen‐15‐ and carbon‐13‐labeled L ‐histidine ? HCl ? H₂O. Exchange rates up to 8.5×10⁴ s^?1 could be determined (i.e., lifetimes as short as 12 μs). The three chemical shifts δ_Hi of the invisible exchanging protons H_i and the three one‐bond scalar coupling constants ¹J(N,H_i) could also be determined accurately.