生物分子液-液相分离的物理化学机制

近年来,有关生物分子通过液-液相分离机制进行组织定位、功能调控的研究发展迅速。相分离产生的聚集体在众多细胞活动事件中发挥了关键作用。这些聚集体的生物功能是以相分离的物理化学性质为基础的。本文将从相分离聚集体的基本性质、相图、微观结构,相分离的统计热力学、实验和分子模拟研究等方面阐释相分离物理化学机制研究相关进展。对于生物分子相分离的重要功能体系进行了列举和归纳,收集了相分离研究的模式体系,探讨了生物分子相分离的生物功能同物理化学机制之间的关系,总结了生物分子相分离的调控机制和调控分子的设计方法,并对生物分子相分离物理化学机制研究的未来发展方向进行了展望。     

Towards a Precise NMR Quantification of Acute Phase Inflammation Proteins from Human Serum

Nuclear Magnetic Resonance (NMR) spectra of human serum and plasma show, besides metabolites and lipoproteins, two characteristic signals termed GlycA and B arising from the acetyl groups of glycoprotein glycans from acute phase proteins, which constitute good markers for inflammatory processes. Here, we report a comprehensive assignment of glycoprotein glycan NMR signals observed in human serum, showing that GlycA and GlycB signals originate from Neu5Ac and GlcNAc moieties from N-glycans, respectively. Diffusion-edited NMR experiments demonstrate that signal components can be associated with specific acute phase proteins. Conventionally determined concentrations of acute phase glycoproteins correlate well with distinct features in NMR spectra (R² up to 0.9422, p-value <0.001), allowing the simultaneous quantification of several acute phase inflammation proteins. Overall, a proteo-metabolomics NMR signature of significant diagnostic potential is obtained within 10–20 min acquisition time. This is exemplified in serum samples from COVID-19 and cardiogenic shock patients showing significant changes in several acute phase proteins compared to healthy controls.     

On-Site Measurement of Fat and Protein Contents in Milk Using Mobile NMR Technology

Robust and easy-to-use NMR sensor technology is proposed for accurate, on-site determination of fat and protein contents in milk. The two parameters are determined using fast consecutive ¹H and ³⁵Cl low-field NMR experiments on milk samples upon the 1:1 addition of a low-cost contrast solution. Reliable and accurate measurements are obtained without tedious calibrations and the need for extensive database information and may readily be conducted by non-experts in production site environments. This enables on-site application at farms or dairies, or use in laboratories harvesting significant reductions in costs and time per analysis as compared to wet-chemistry analysis. The performance is demonstrated for calibration samples, various supermarket milk products, and raw milk samples, of which some were analyzed directly in the milking room. To illustrate the wide application range, the supermarket milk products included both conventionally/organically produced, lactose-free milk, cow’s, sheep’s and goat’s milk, homogenized and unhomogenized milk, and a broad nutrient range (0.1–9% fat, 1–6% protein). Excellent agreement between NMR measurements and reference values, without corrections or changes in calibration for various products and during extensive periods of experiment conduction (4 months) demonstrates the robustness of the procedure and instrumentation. For the raw milk samples, correlations between NMR and IR, NMR and wet-chemistry, as well as IR and wet-chemistry results, show that NMR, in terms of accuracy, compares favorably with the other methods.     

Quantification of taxanes in a leaf and twig extract from Taxus baccata L. using 13C NMR spectroscopy

In the course of our ongoing work on the chemical characterization of Taxus baccata L. growing wild in Corsica, we have developed and validated a method for direct quantification of taxane derivatives by ¹³C NMR using 10‐deacetylbaccatin III as reference compound and 1,6‐hexanediol as internal standard. We have observed good accuracy (relative errors between 0.3% and 3.5%), linearity (R² = 0.999) and precision (reproducibility 8.5 mg ± 1.1%) of the measurements. The experimental procedure was applied to the quantification of six identified taxanes in a fraction of chromatography of a methanol extract of T. baccata leaves. This method can be applied to other compounds bearing the taxane skeleton. Copyright © 2013 John Wiley & Sons, Ltd.     

NMR assignments of unusual flavonoids from the kino of Eucalyptus citriodora

Two unusual flavonoids, 3,5,4',5'-tetrahydroxy-7-methoxy-6-[1-(p-hydroxy-phenyl)ethyl]flavanone (1) and 3,5,7,4',5'-pentahydroxy-6-[1-(p-hydroxy-phenyl)ethyl] flavanone (2), were isolated from the kino of Eucalyptus citriodora. Structural elucidation of the new compounds were established on the basis of spectral data, particularly by the use of 1D NMR and several 2D shift-correlated NMR pulse sequences ((1)H, (1)H-COSY, HMQC, HMBC).     

Efficient modeling of symmetric protein aggregates from NMR data

An efficient approach to determine the structures of symmetric protein aggregates from liquid and solid-state NMR data is presented. Any symmetry can be used (cyclic or dihedral point symmetries, helical symmetries, crystallographic symmetries). Because the starting point is the random structure of the monomer, the knowledge of the 3D structure of the monomer is not required.     

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.     

类蜘蛛丝聚合物结构及分子运动的固体核磁共振研究

运用固体核磁共振(NMR)技术研究了聚丙氨酸多肽片段(Ala)5与高分子齐聚物聚苯乙烯(PS, 分子量2000)及聚异戊二烯(PI, 分子量2210)共聚而成的类蜘蛛丝蛋白聚合物——聚苯乙烯-co-聚丙氨酸聚合物(PS-co-PAL)和聚异戊二烯-co-聚丙氨酸聚合物(PI-co-PAL)的结构及分子运动. 聚合物13C CP/MAS NMR(交叉极化/魔角旋转核磁共振)谱及其旋转坐标系中自旋-晶格弛豫时间(T1ρ(13C))的结果表明, 此两种聚合物中多肽片段(Ala)5具有相同的化学位移, 即相似的化学环境和二级结构, 并具有相近的T1ρ(13C), 即类似的聚集态结构. 聚合物的宏观力学性质明显不同: 常温下, PS-co-PAL呈硬颗粒状, PI-co-PAL呈橡胶状且易拉伸. 结果说明聚合物力学性质与高分子链段的性质密切相关. PI-co-PAL聚合物的PI链段, 其骨架—CH2CH—的T1ρ为(5.3±0.4) ms, 而PS-co-PAL聚合物的PS链段, 其骨架—CH2CH—的T1ρ为(47.0±5.5) ms, 说明二聚合物中PI链段较PS链段更为柔软. 另外, 基于密度泛函理论(DFT)的化学位移计算证明, 聚合物PS-co-PAL和PI-co-PAL中多肽片段(Ala)5的二面角均为(-131°, 142°), 说明它们以β-折叠构象存在.     

用NMR分析可生物降解的两亲性嵌段共聚物的相对分子质量和组成

凝胶渗透色谱(GPC)法是根据聚合物分子链流体力学体积大小的比较来测定聚合物相对分子质量(以下简称分子量)的,测得的聚合物分子量与聚合物分子链在溶剂中的构象有关[1]。两亲性嵌段共聚物分子链中亲水链段和亲油链段的极性差异很大,几乎在任何溶剂中它们的构象都不相同,因此可     

Study of chemically inequivalent N(CH3)4 ions in [N(CH3)4]2ZnBr4 near the phase transition temperature using 1H MAS NMR, 13C CP/MAS NMR,and 14N NMR

The temperature dependences of the chemical shifts and intensities of ¹H, ¹³C, and ¹⁴N nuclei in tetramethylammonium tetrabromozincate, [N(CH₃)₄]₂ZnBr₄, were investigated using single-crystal nuclear magnetic resonance (NMR) and magic angle spinning (MAS) NMR spectroscopy to elucidate the structural geometry near the phase transition temperature. Based on the analysis of the ¹³C cross-polarization (CP)/MAS NMR and ¹⁴N NMR spectra, the two chemically inequivalent N(1) (CH₃)₄ and N(2) (CH₃)₄ ions were distinguished. Furthermore, the ¹⁴N NMR spectrum at the phase transition temperature indicated the existence of the ferroelastic characteristics of the N(CH₃)₄ ions.     

Thermal,dielectric and barocaloric properties of NH4HSO4 crystallized from an aqueous solution and the melt

A study of heat capacity, thermal dilatation, permittivity, dielectric loops and susceptibility to hydrostatic pressure was carried out on quasi-ceramic samples of NH₄HSO₄ obtained from an aqueous solution as well as the melt. The main parameters of the successive P2₁/c (T₁) ↔ Pc (T₂) ↔ P1 phase transitions did not depend on the method of preparation of the samples, and were close to those determined in previous studies of single crystal and powder, except for the sign and magnitude of the baric coefficient for T₂. Direct measurements of the pressure effect on the permittivity and thermal properties showed dT₂/dp = −123 K·GPa⁻¹, which is consistent in terms of magnitude and sign with the baric coefficient evaluated using dilatometric and calorimetric data in the framework of the Clausius-Clapeyron equation. Thus, the temperature region of the ferroelectric Pc phase existence is extended under pressure. A strong decrease in the entropy jump at the Pc ↔ P1 transformation with an increase in pressure, and the linear dependence of T₂ on pressure, indicate that an increase in pressure shifts this phase transition towards the tricritical point on the T–p phase diagram. A significant barocaloric effect was found in the region of the Pc ↔ P1 phase transition.     

Structure elucidation and NMR spectral assignment of five new xanthones from the bark of Garcinia xanthochymus

Five new xanthones, namely Garcinexanthones A-E (1-5), were isolated from the barks of Garcinia xanthochymus. Their structures were elucidated by spectral analysis, primarily NMR, MS, and UV. The complete assignments of the (1)H NMR and (13)C NMR chemical shifts for the compounds were achieved by using 1D and 2D NMR techniques, including DEPT, HSQC, and HMBC NMR experiments.     

NMR elucidation of some ligands derived from the pentacycloundecane skeleton

The complete NMR elucidation of three novel pentacycloundecane (PCU)-derived ligands is reported. 2D NMR techniques are used to overcome the problem of major overlapping of methine signals on the cage skeleton. The compounds were synthesized as potential ligands to be used in asymmetric catalysis. They represent the first instance where aromatic moieties have been attached directly to the cage skeleton using lithiation techniques. The X-ray crystal structure of one of the ligands was obtained. The X-ray structure was helpful in determining the potential NOESY interactions within the set of molecules. For the other ligands a high level Density Functional Theory (DFT) optimization was performed [B3LYP/6-31+g(d)] to visualize possible NOE interactions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structural elucidation and NMR spectral assignment of three new furostanol saponins from the roots of Tupistra chinensis

Three new furostanol saponins (1–3) were isolated from the roots of Tupistra chinensis (T. chinensis). And their structures were elucidated on the basis of NMR and mass spectrometry (MS) spectral analysis. Copyright © 2009 John Wiley & Sons, Ltd.     

Mechanisms of Chaperones as Active Assistant/Protector for Proteins: Insights from NMR Studies

Molecular chaperones are diverse families of proteins that play key roles in protein homeostasis. They assist the folding of client proteins or prevent them from irreversible aggregation under stress conditions. Diverse chaperone families contribute to different aspects of protein homeostasis by interacting with a wide range of client proteins. Despite the vital roles of chaperones in cell survival, the molecular mechanisms underlying chaperone functions remain elusive, due to the non‐specificity of chaperone‐client interactions and the intrinsic flexibility of the clients. Our understanding of the chaperone functional mechanisms, especially regarding chaperone‐client interactions, has greatly expanded in recent years, thanks to the significant contribution from various NMR studies. Solution NMR methods have unique advantages in characterizing disordered protein structures, detecting weak and non‐specific interactions, and probing conformational dynamics of proteins and protein complexes, etc., and therefore are especially powerful in the studies of chaperone structure‐function relationships. In this review, we summarize some of the current knowledge of molecular chaperones, with emphasis on common features of chaperone‐client interactions and examples on a number of specific systems in which solution NMR methods were used to provide essential insights into their functional mechanisms.      

NMR analysis of the O‐antigen polysaccharide from Escherichia coli strain F171

The structure of the O‐antigen polysaccharide from Escherichia coli strain F171 has been determined. NMR analysis of the polysaccharide showed that it was composed of pentasaccharide repeating units. The ¹H and ¹³C signals were assigned by 2D NMR techniques which revealed severe spectral overlap for key resonances at substitution positions. The structure of the repeating unit was deduced from ¹H,¹³C HMBC and, in particular, by ¹H,¹H NOESY experiments as follows: The structure is identical with that of the O‐antigen from Escherichia coli O25 previously determined by chemical degradation methods and the strain F171 should therefore belong to this serogroup. Copyright © 2003 John Wiley & Sons, Ltd.     

Folding of the Tau Protein on Microtubules

Microtubules are regulated by microtubule‐associated proteins. However, little is known about the structure of microtubule‐associated proteins in complex with microtubules. Herein we show that the microtubule‐associated protein Tau, which is intrinsically disordered in solution, locally folds into a stable structure upon binding to microtubules. While Tau is highly flexible in solution and adopts a β‐sheet structure in amyloid fibrils, in complex with microtubules the conserved hexapeptides at the beginning of the Tau repeats two and three convert into a hairpin conformation. Thus, binding to microtubules stabilizes a unique conformation in Tau.