Monitoring ssDNA Binding to the DnaB Helicase from Helicobacter pylori by Solid‐State NMR Spectroscopy

DnaB helicases are bacterial, ATP‐driven enzymes that unwind double‐stranded DNA during DNA replication. Herein, we study the sequential binding of the “non‐hydrolysable” ATP analogue AMP‐PNP and of single‐stranded (ss) DNA to the dodecameric DnaB helicase from Helicobacter pylori using solid‐state NMR. Phosphorus cross‐polarization experiments monitor the binding of AMP‐PNP and DNA to the helicase. ¹³C chemical‐shift perturbations (CSPs) are used to detect conformational changes in the protein upon binding. The helicase switches upon AMP‐PNP addition into a conformation apt for ssDNA binding, and AMP‐PNP is hydrolyzed and released upon binding of ssDNA. Our study sheds light on the conformational changes which are triggered by the interaction with AMP‐PNP and are needed for ssDNA binding of H. pylori DnaB in vitro. They also demonstrate the level of detail solid‐state NMR can provide for the characterization of protein–DNA interactions and the interplay with ATP or its analogues.     

Serial Polarization Transfer by Combination of Cross-Relaxation and Rotational Resonance for Sensitivity-Enhanced Solid-State NMR

Methods which induce site-specificity and sensitivity enhancement in solid-state magic-angle spinning NMR spectroscopy become more important for structural biology due to the increasing size of molecules under investigation. Recently, several strategies have been developed to increase site specificity and thus reduce signal overlap. Under dynamic nuclear polarization (DNP) for NMR signal enhancement, it is possible to use cross-relaxation transfer induced by select dynamic groups within the molecules which is exploited by SCREAM-DNP (Specific Cross Relaxation Enhancement by Active Motions under DNP). Here, we present an approach where we additionally reintroduce the homonuclear dipolar coupling with rotational resonance (R²) during SCREAM-DNP to further boost the selectivity of the experiment. Detailed analysis of the polarization buildup dynamics of ¹³C-methyl polarization source and ¹³C-carbonyl target in 2-¹³C-ethyl 1-¹³C-acetate provides information about the sought-after and spurious transfer pathways. We show that dipolar-recoupled transfer rates greatly exceed the DNP buildup dynamics in our model system, indicating that significantly larger distances can be selectively and efficiently hyperpolarized.     

A solid-state NMR study of cellulose degradation

A series of laboratory-aged transformer insulating papers were investigated using solid-state NMR spectroscopy. Carbon-13 CPMAS, and proton MAS experiments were carried out along with static proton relaxation (T₁, and T₁) and free induction decay (FID) measurements. Some proton CRAMPS and proton-carbon-13 correlation (WISE) experiments were also undertaken. A change in the proton T₁ and FID with ageing was detected. No detectable change was found in the proton T₁. Some amorphous cellulose was detected in the carbon-13 spectrum. There was, however, no evidence for a substantial change in the nature of the cellulose with ageing. The carbon-13 spectra from some aged samples showed signals not present in the spectrum from an unaged sample. This was taken to be evidence of chemical degradation. Proton MAS and the WISE exeriment gave some information about the nature of the water in the sample.     

Functional Dynamics of Deuterated β2‐Adrenergic Receptor in Lipid Bilayers Revealed by NMR Spectroscopy

G‐protein‐coupled receptors (GPCRs) exist in conformational equilibrium between active and inactive states, and the former population determines the efficacy of signaling. However, the conformational equilibrium of GPCRs in lipid bilayers is unknown owing to the low sensitivities of their NMR signals. To increase the signal intensities, a deuteration method was developed for GPCRs expressed in an insect cell/baculovirus expression system. The NMR sensitivities of the methionine methyl resonances from the β₂‐adrenergic receptor (β₂AR) in lipid bilayers of reconstituted high‐density lipoprotein (rHDL) increased by approximately 5‐fold upon deuteration. NMR analyses revealed that the exchange rates for the conformational equilibrium of β₂AR in rHDLs were remarkably different from those measured in detergents. The timescales of GPCR signaling, calculated from the exchange rates, are faster than those of receptor tyrosine kinases and thus enable rapid neurotransmission and sensory perception.     

脂双层膜表面结构与稳定性的原子力显微镜研究

用原子力显微镜研究了1,2－二油酸甘油－3－磷酸－1甘油（DOPG）脂双层膜 的表面结构与稳定性。实验结果表明,原子力显微镜的探针与脂双层膜的相互作用 导致脂双层膜表面产生一个永久的损伤。静电相互作用对脂双层膜结构和稳定性的 影响表明,在NaCl溶液中制成的脂质体,随着NaCl浓度的增加,它们的双层膜更稳 定。在低的NaCl浓度则经常被损伤,在1 mol/L NaCl溶液中制备的指双层变得更稳 定。在KCl溶液中结果恰好相反。在高的KCl浓度中经常被损伤,随着KCl浓度的降 低,它们的双层膜更稳定。葡萄糖和蔗糖对脂双层膜结构有稳定作用。     

NMR Spectroscopic Assignment of Backbone and Side‐Chain Protons in Fully Protonated Proteins: Microcrystals,Sedimented Assemblies,and Amyloid Fibrils

We demonstrate sensitive detection of alpha protons of fully protonated proteins by solid‐state NMR spectroscopy with 100–111 kHz magic‐angle spinning (MAS). The excellent resolution in the Cα‐Hα plane is demonstrated for 5 proteins, including microcrystals, a sedimented complex, a capsid and amyloid fibrils. A set of 3D spectra based on a Cα–Hα detection block was developed and applied for the sequence‐specific backbone and aliphatic side‐chain resonance assignment using only 500 μg of sample. These developments accelerate structural studies of biomolecular assemblies available in submilligram quantities without the need of protein deuteration.     

Interaction of Polystyrene Nanoparticles with Supported Lipid Bilayers: Impact of Nanoparticle Size and Protein Corona

Polystyrene is one of the most widely used plastics. This article reports on the interaction of 50 and 210 nm polystyrene nanoparticles (PSNPs) with human serum albumin (HSA) and transferrin (Tf), as well as their effect on supported lipid bilayers (SLBs), using experimental and theoretical approaches. Dynamic light scattering (DLS) and atomic force microscopy (AFM) measurements show that the increase in diameter for the PSNP-protein bioconjugates depends on nanoparticle size and type of proteins. The circular dichroism (CD) spectroscopy results demonstrate that the proteins preserve their structures when they interact with PSNPs at physiological temperatures. The quartz crystal microbalance (QCM) technique reveals that PSNPs and their bioconjugates show no strong interactions with SLBs. On the contrary, the molecular dynamics simulations (MDS) show that both proteins bind strongly to the lipid bilayer (SLBs) when compared to their binding to a polystyrene surface model. The interaction is strongly dependent on the protein and lipid bilayer composition. Both the PSNPs and their bioconjugates show no toxicity in human umbilical vein endothelial (HUVEC) cells; however, bare 210 nm PSNPs and 50 nm PSNP-Tf bioconjugates show an increase in reactive oxygen species production. This study may be relevant for assessing the impact of plastics on health.     

Weak and Transient Protein Interactions Determined by Solid‐State NMR

Despite their roles in controlling many cellular processes, weak and transient interactions between large structured macromolecules and disordered protein segments cannot currently be characterized at atomic resolution by X‐ray crystallography or solution NMR. Solid‐state NMR does not suffer from the molecular size limitations affecting solution NMR, and it can be applied to molecules in different aggregation states, including non‐crystalline precipitates and sediments. A solid‐state NMR approach based on high magnetic fields, fast magic‐angle sample spinning, and deuteration provides chemical‐shift and relaxation mapping that enabled the characterization of the structure and dynamics of the transient association between two regions in an 80 kDa protein assembly. This led to direct verification of a mechanism of regulation of E. coli DNA metabolism.     

PHRONESIS: A One-Shot Approach for Sequential Assignment of Protein Resonances by Ultrafast MAS Solid-State NMR Spectroscopy

Solid-state NMR (ssNMR) spectroscopy has emerged as the method of choice to analyze the structural dynamics of fibrillar, membrane-bound, and crystalline proteins that are recalcitrant to other structural techniques. Recently, ¹H detection under fast magic angle spinning and multiple acquisition ssNMR techniques have propelled the structural analysis of complex biomacromolecules. However, data acquisition and resonance-specific assignments remain a bottleneck for this technique. Here, we present a comprehensive multi-acquisition experiment (PHRONESIS) that simultaneously generates up to ten 3D ¹H-detected ssNMR spectra. PHRONESIS utilizes broadband transfer and selective pulses to drive multiple independent polarization pathways. High selectivity excitation and de-excitation of specific resonances were achieved by high-fidelity selective pulses that were designed using a combination of an evolutionary algorithm and artificial intelligence. We demonstrated the power of this approach with microcrystalline U-¹³C,¹⁵N GB1 protein, reaching 100 % of the resonance assignments using one data set of ten 3D experiments. The strategy outlined in this work opens up new avenues for implementing novel ¹H-detected multi-acquisition ssNMR experiments to speed up and expand the application to larger biomolecular systems.     

Magic-angle-spinning-induced local ordering in polymer electrolytes and its effects on solid-state diffusion and relaxation NMR measurements

Magic-angle-spinning (MAS) enhances sensitivity and resolution in solid-state nuclear magnetic resonance (NMR) measurements. MAS is obtained by aerodynamic levitation and drive of a rotor, which results in large centrifugal forces that may affect the physical state of soft materials, such as polymers, and subsequent solid-state NMR measurements. Here, we investigate the effects of MAS on the solid-state NMR measurements of a polymer electrolyte for lithium-ion battery applications, poly(ethylene oxide) (PEO) doped with the lithium salt LiTFSI. We show that MAS induces local chain ordering, which manifests itself as characteristic lineshapes with doublet-like splittings in subsequent solid-state ¹ H, ⁷ Li, and ¹⁹ F static NMR spectra characterizing the PEO chains and solvated ions. MAS results in distributions of stresses and hence local chain orientations within the rotor, yielding distributions in the local magnetic susceptibility tensor that give rise to the observed NMR anisotropy and lineshapes. The effects of MAS were investigated on solid-state ⁷ Li and ¹⁹ F pulsed-field-gradient (PFG) diffusion and ⁷Li longitudinal relaxation NMR measurements. Activation energies for ion diffusion were affected modestly by MAS. ⁷Li longitudinal relaxation rates, which are sensitive to lithium-ion dynamics in the nanosecond regime, were essentially unchanged by MAS. We recommend that NMR researchers studying soft polymeric materials use only the spin rates necessary to achieve the desired enhancements in sensitivity and resolution, as well as acquire static NMR spectra after MAS experiments to reveal any signs of stress-induced local ordering.     

The Effect of Cholesterol on Membrane Dynamics on Different Timescales in Lipid Bilayers from Fast Field‐Cycling NMR Relaxometry Studies of Unilamellar Vesicles

The general applicability of fast field‐cycling nuclear magnetic resonance relaxometry in the study of dynamics in lipid bilayers is demonstrated through analysis of binary unilamellar liposomes composed of 1,2‐dioleoyl‐sn‐glycero‐3‐posphocholine (DOPC) and cholesterol. We extend an evidence‐based method to simulating the NMR relaxation response, previously validated for single‐component membranes, to evaluate the effect of the sterol molecule on local ordering and dynamics over multiple timescales. The relaxometric results are found to be most consistent with the partitioning of the lipid molecules into affected and unaffected portions, rather than a single averaged phase. Our analysis suggests that up to 25 mol %, each cholesterol molecule orders three DOPC molecules, providing experimental backup to the findings of many molecular dynamics studies. A methodology is established for studying dynamics on multiple timescales in unilamellar membranes of more complex compositions.     

脱氧胆酸钠与支撑磷脂双层膜作用的电化学研究

以支撑磷脂双层膜(supported bilayer lipid membrane, s-BLM)作为生物膜模型, 采用循环伏安法和交流阻抗技术研究了脱氧胆酸钠(sodium deoxycholate, NaDC)与s-BLM的相互作用. 结果表明, NaDC能降低磷脂分子的有序性, 诱发s-BLM上形成孔洞或缺陷, 并且它们之间的这种相互作用对作用时间、NaDC溶液的浓度和pH值以及胆固醇的存在与否具有依赖性, 并且作用后的s-BLM在0.1 mol/L的KCl溶液中能够自我修复, 这表明NaDC与s-BLM的相互作用是可逆的.     

固体核磁共振在介孔分子筛研究中的应用

介绍了强功率质子去耦、交叉极化、魔角旋转等同体高分辨核磁共振技术的原理,综述了固体高分辨核磁共振技术在介孔分子筛结构与形态研究中的应用及近年来的发展情况.     

Specific Lipid Studies in Complex Membranes by Solid-State NMR Spectroscopy

Specific interactions with phospholipids are often critical for the function of proteins or drugs, but studying these interactions at high resolution remains difficult, especially in complex membranes that mimic biological conditions. In principle, molecular interactions with phospholipids could be directly probed by solid-state NMR (ssNMR). However, due to the challenge to detect specific lipids in mixed liposomes and limited spectral sensitivity, ssNMR studies of specific lipids in complex membranes are scarce. Here, by using purified biological ¹³C,¹⁵N-labeled phospholipids, we show that we can selectively detect traces of specific lipids in complex membranes. In combination with ¹H-detected ssNMR, we show that our approach provides unprecedented high-resolution insights into the mechanisms of drugs that target specific lipids. This broadly applicable approach opens new opportunities for the molecular characterization of specific lipid interactions with proteins or drugs in complex fluid membranes.     

双层类脂膜修饰玻碳电极研究去甲肾上腺素电化学行为及其分析应用

报道了去甲肾上腺素在双层类脂膜修饰玻碳电极上的电化学行为。在 0 .8～ - 0 .3V(vs.Ag/AgCl)电位范围内 ,于 pH 6 .5、0 .0 1mol/LKH2 PO4 Na2 HPO4底液中 ,去甲肾上腺素产生很灵敏的氧化峰电流。该电流与去甲肾上腺素浓度在 3.5× 10 -6～ 3.1× 10 -4mol/L范围内呈良好线性关系。该电极可作为检测去甲肾上腺素的新型的高灵敏度电化学生物传感器。     

Probing the Lipid Annular Belt by Gas‐Phase Dissociation of Membrane Proteins in Nanodiscs

Interactions between membrane proteins and lipids are often crucial for structure and function yet difficult to define because of their dynamic and heterogeneous nature. Here, we use mass spectrometry to demonstrate that membrane protein oligomers ejected from nanodiscs in the gas phase retain large numbers of lipid interactions. The complex mass spectra that result from gas‐phase dissociation were assigned using a Bayesian deconvolution algorithm together with mass defect analysis, allowing us to count individual lipid molecules bound to membrane proteins. Comparison of the lipid distributions measured by mass spectrometry with molecular dynamics simulations reveals that the distributions correspond to distinct lipid shells that vary according to the type of protein–lipid interactions. Our results demonstrate that nanodiscs offer the potential for native mass spectrometry to probe interactions between membrane proteins and the wider lipid environment.     

Dissociation of the Signaling Protein K-Ras4B from Lipid Membranes Induced by a Molecular Tweezer

Oncogenic Ras mutations occur in more than 30 % of human cancers. K-Ras4B is the most frequently mutated isoform of Ras proteins. Development of effective K-Ras4B inhibitors has been challenging, hence new approaches to inhibit this oncogenic protein are urgently required. The polybasic domain of K-Ras4B with its stretch of lysine residues is essential for its plasma membrane targeting and localization. Employing CD and fluorescence spectroscopy, confocal fluorescence, and atomic force microscopy we show that the molecular tweezer CLR01 is able to efficiently bind to the lysine stretch in the polybasic domain of K-Ras4B, resulting in dissociation of the K-Ras4B protein from the lipid membrane and disintegration of K-Ras4B nanoclusters in the lipid bilayer. These results suggest that targeting of the polybasic domain of K-Ras4B by properly designed tweezers might represent an effective strategy for inactivation of K-Ras4B signaling.