Magnetic Resonance Letters最新文献_第2页

Characterization of kerogen nanopores using 2D NMR relaxation and MD simulations 利用二维核磁共振弛豫和MD模拟表征干酪根纳米孔

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-11-01 Epub Date: 2025-05-30 DOI: 10.1016/j.mrl.2025.200220

Philip M. Singer , Yunke Liu , Xinglin Wang , George J. Hirasaki , Arjun Valiya Parambathu , Walter G. Chapman , Dilipkumar N. Asthagiri , Eva G. Vinegar , Harold J. Vinegar

{"title":"Characterization of kerogen nanopores using 2D NMR relaxation and MD simulations","authors":"Philip M. Singer , Yunke Liu , Xinglin Wang , George J. Hirasaki , Arjun Valiya Parambathu , Walter G. Chapman , Dilipkumar N. Asthagiri , Eva G. Vinegar , Harold J. Vinegar","doi":"10.1016/j.mrl.2025.200220","DOIUrl":"10.1016/j.mrl.2025.200220","url":null,"abstract":"<div><div>The characterization of kerogen nanopores is crucial for predicting the geostorage capacity and recoverability of natural gas in unconventional gas shale reservoirs. Towards this end, a powerful technique is presented which integrates 2D NMR <em>T</em><sub>1</sub>-<em>T</em><sub>2</sub> relaxation measurements with molecular dynamics (MD) simulations of hydrocarbons confined in the nanopores of kerogen. The integrated NMR-MD technique is demonstrated using <em>T</em><sub>1</sub>-<em>T</em><sub>2</sub> measurements of kerogen isolates and organic-rich chalks saturated with heptane, together with MD simulations of heptane completely dissolved in a realistic kerogen model. The NMR-MD results are used to extract the swelling ratio and nanopore size distribution of kerogen as a function of depth in the reservoir. The effects of organic nanoconfinement on the <em>T</em><sub>1</sub> relaxation dispersion and <em>T</em><sub>2</sub> residual dipolar coupling of heptane are investigated, as well as the effect of downhole effective stress on the kerogen nanopore size as a function of depth and compaction. Potential applications in partially depleted gas shale reservoirs are discussed, including CO<sub>2</sub> utilization/geostorage, geostorage of green H<sub>2</sub>, and integration of the NMR-MD technique with thermodynamic models for predicting the competitive sorption of gas mixtures in kerogen.</div></div>","PeriodicalId":93594,"journal":{"name":"Magnetic Resonance Letters","volume":"5 4","pages":"Article 200220"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145468738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NMR-guided rational exploration of co-factors in boosting the Pfu DNA polymerase 核磁共振引导下促进Pfu DNA聚合酶的辅助因子的合理探索

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-11-01 Epub Date: 2025-05-22 DOI: 10.1016/j.mrl.2025.200218

Yihao Chen , Mingjun Zhu , Ruishen Ding , Xiaoling Zhao , Zhiqing Tao , Xu Zhang , Maili Liu , Lichun He

{"title":"NMR-guided rational exploration of co-factors in boosting the Pfu DNA polymerase","authors":"Yihao Chen , Mingjun Zhu , Ruishen Ding , Xiaoling Zhao , Zhiqing Tao , Xu Zhang , Maili Liu , Lichun He","doi":"10.1016/j.mrl.2025.200218","DOIUrl":"10.1016/j.mrl.2025.200218","url":null,"abstract":"<div><div>With rapid developments of emerging technologies like synthetic biology, the demand for DNA polymerases with superior activities including higher thermostability and processivity has increased significantly. Thus, rational optimization of the performance of DNA polymerase is of great interest. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique used for studying protein structure and dynamics. It provides the atomic resolution information of enzymes under their functional solution environment to reveal the active sites (hot spots) of the enzyme, which could be further used for optimizing the performance of enzymes. In our previous work, we identified hot spot residues of <em>Pyrococcus furiosus</em> DNA polymerase (<em>Pfu</em> pol). We aim to employ these binding hot spots to screen for co-factors of <em>Pfu</em> pol, particularly targeting those molecules exhibiting weak intermolecular interactions. To validate this concept, we first demonstrated the feasibility of utilizing hot spot residues as screening probes for auxiliary factors by employing the well-characterized Tween-20 as a model system. Employing these hot spots as probes, two new co-factors, the heat shock protein TkHSP20 from <em>Thermococcus Kodakaraensis</em> and the chemical chaperone <span>l</span>-arginine, are identified to interact with <em>Pfu</em> pol to boost its performance in amplifying long DNA fragments by enhancing the thermal stability and the processivity of the <em>Pfu</em> pol. This NMR-based approach requires no prior assignment information of target enzymes, guiding the rational exploration of novel co-factors for <em>Pfu</em> pol. Moreover, our approach is not dependent on structural data or bioinformatics. Therefore, it has significant potential for application in various enzymes to expedite the progress in enzyme engineering.</div></div>","PeriodicalId":93594,"journal":{"name":"Magnetic Resonance Letters","volume":"5 4","pages":"Article 200218"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145468736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transmembrane association of DDR1 and DDR2 mediated by Leucine zipper motifs 亮氨酸拉链基序介导的DDR1和DDR2的跨膜结合

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-11-01 Epub Date: 2025-05-23 DOI: 10.1016/j.mrl.2025.200217

Feiyu Huang , Yuzhe Li , Peng Zhang , Jinqian Li , Can Xie , Junfeng Wang , Tiantian Cai

{"title":"Transmembrane association of DDR1 and DDR2 mediated by Leucine zipper motifs","authors":"Feiyu Huang , Yuzhe Li , Peng Zhang , Jinqian Li , Can Xie , Junfeng Wang , Tiantian Cai","doi":"10.1016/j.mrl.2025.200217","DOIUrl":"10.1016/j.mrl.2025.200217","url":null,"abstract":"<div><div>Discoidin domain receptors (DDRs) are single-pass transmembrane proteins belonging to receptor tyrosine kinases (RTKs) family, which are activated by collagen ligands with unusual slow, sustained kinetics, distinguishing them from canonical RTKs. While DDRs play critical roles in cell adhesion, differentiation, and cancer progression, their activation mechanisms remain partly understood. Here, we investigated the transmembrane domains (TMDs) of DDR1 and DDR2 to elucidate their interaction dynamics in membrane. Using bacterial adenylate cyclase two-hybrid (BACTH) assays, we demonstrated robust homotypic interactions and even stronger heterotypic associations between DDRTMDs. NMR spectroscopy of DDR1TMD and DDR2TMD reconstituted in lipid bilayer-mimetic bicelles showed obvious chemical shift alterations, further validating the stability of their heterocomplex formation. Systematic mutagenesis identified leucine zipper motifs rather than GXXXA motifs mediated both homo- and hetero-associations of DDR1TMD and DDR2TMD. These findings demonstrated the TMD as a critical mediator of DDRs oligomerization and revealed their interaction patterns within membrane. Our study advances the understanding of DDR signaling regulation and highlights transmembrane domain interactions as potential targets for modulating DDR-related pathologies.</div></div>","PeriodicalId":93594,"journal":{"name":"Magnetic Resonance Letters","volume":"5 4","pages":"Article 200217"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145468737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Revisiting classical diffusion magnetic resonance methods as a means to measure time-dependent diffusion 回顾经典扩散磁共振方法作为测量随时间扩散的手段

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-11-01 Epub Date: 2025-04-22 DOI: 10.1016/j.mrl.2025.200197

Teddy X. Cai , Nathan H. Williamson , Peter J. Basser

{"title":"Revisiting classical diffusion magnetic resonance methods as a means to measure time-dependent diffusion","authors":"Teddy X. Cai , Nathan H. Williamson , Peter J. Basser","doi":"10.1016/j.mrl.2025.200197","DOIUrl":"10.1016/j.mrl.2025.200197","url":null,"abstract":"<div><div>The field of diffusion microstructural magnetic resonance (MR) aims to probe time-dependent diffusion, i.e., an ensemble-averaged mean-squared displacement ⟨<em>r</em><sup>2</sup>(<em>t</em>)⟩ that is not linear in time. This time-dependence contains rich information about the surrounding microenvironment. MR methods to measure time-dependent diffusion quantitatively, however, require either non-standard pulse sequences, such as oscillating gradients, or make non-physical assumptions, such as infinitely narrow gradient pulses. Here, we argue that standard spin echo and stimulated echo MR sequences can be used to probe ⟨<em>r</em><sup>2</sup>(<em>t</em>)⟩ directly. In particular, we propose a framework in which the log-signal ratio obtained from a pair of measurements with different inter-pulse spacing <em>Δ</em> is proportional to the MSD between these two <em>Δ</em> values along the gradient direction <em>x</em>: <span><math><mrow><mo>⟨</mo><mrow><msubsup><mrow><mi>r</mi></mrow><mrow><mi>x</mi></mrow><mrow><mn>2</mn></mrow></msubsup><mrow><mo>(</mo><mrow><msub><mrow><mi>Δ</mi></mrow><mrow><mn>2</mn></mrow></msub></mrow><mo>)</mo></mrow></mrow><mo>⟩</mo></mrow><mo>−</mo><mrow><mo>⟨</mo><mrow><msubsup><mrow><mi>r</mi></mrow><mrow><mi>x</mi></mrow><mrow><mn>2</mn></mrow></msubsup><mrow><mo>(</mo><mrow><msub><mrow><mi>Δ</mi></mrow><mrow><mn>1</mn></mrow></msub></mrow><mo>)</mo></mrow></mrow><mo>⟩</mo></mrow></math></span>. The framework is quantitative for short, finite-duration gradient pulses and under the Gaussian phase approximation (GPA). To validate the framework, we consider one-dimensional diffusion between impermeable, parallel planes, as well as periodically-spaced, permeable planes. Excellent agreement is obtained between the estimation and the ground truth in the regime where the GPA is expected to hold. Importantly, the GPA can be made to hold for any underlying microstructure, making the proposed framework widely applicable.</div></div>","PeriodicalId":93594,"journal":{"name":"Magnetic Resonance Letters","volume":"5 4","pages":"Article 200197"},"PeriodicalIF":1.7,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145468734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

OFC: Outside Front Cover OFC：外封面

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-11-01 Epub Date: 2025-11-08 DOI: 10.1016/S2772-5162(25)00068-3

引用次数: 0

Extreme quadrupolar nuclei under control: Ultra-wideline solid-state NMR at 36 T 极端四极核控制：超宽线固态核磁共振在36t

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-11-01 Epub Date: 2025-07-25 DOI: 10.1016/j.mrl.2025.200238

Luming Peng

引用次数: 0

NMR methods for investigating functionally relevant biomolecular dynamics 研究功能相关生物分子动力学的核磁共振方法

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-11-01 Epub Date: 2025-03-19 DOI: 10.1016/j.mrl.2025.200195

Yangzhuoyue Jin , Yingxian Cui , Tairan Yuwen

引用次数: 0

Cryoporometry for short T2 samples: A T1 filter method applied to battery electrode characterization 短T2样品的低温孔隙法：一种用于电池电极表征的T1滤波方法

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-08-01 Epub Date: 2025-02-11 DOI: 10.1016/j.mrl.2025.200180

Marc Fleury , Thibaud Chevalier , Benjamin Nicot , Quentin Denoyelle , Julien Bernard

{"title":"Cryoporometry for short T2 samples: A T1 filter method applied to battery electrode characterization","authors":"Marc Fleury , Thibaud Chevalier , Benjamin Nicot , Quentin Denoyelle , Julien Bernard","doi":"10.1016/j.mrl.2025.200180","DOIUrl":"10.1016/j.mrl.2025.200180","url":null,"abstract":"<div><div>The pore size distribution is often an important parameter for transport processes in porous media. Cryoporometry experiments can provide such data in the meso and macropore size up to 1 μm providing the sample temperature is finely controlled. We use a Peltier based system inserted directly into the NMR probe to control the temperature within 0.05 °C and impose temperature ramps down to 0.002 °C/min, necessary to characterize the largest pore sizes. The pore size information in the macropore range cannot be obtained from gas adsorption techniques while mercury injection is questionable for the material considered here. For porous materials made of paramagnetic minerals such as lithium-iron phosphate (LiFePO<sub>4</sub>, LFP) or nickel-manganese-cobalt oxides (NMC) and saturated with octamethylcyclotetrasiloxane (OMCTS), the <em>T</em><sub>2</sub> relaxation times are very short such as protons from the liquid and frozen phases cannot be separated. Hence the usual cryoporometry experiment cannot be performed. Instead, we propose to use the <em>T</em><sub>1</sub> contrast to separate these phases. The method is studied in detail along with some temperature effects linked with the <em>T</em><sub>1</sub> variation of the bulk frozen OMCTS. We show an example on two cathode materials part of industrial battery product.</div></div>","PeriodicalId":93594,"journal":{"name":"Magnetic Resonance Letters","volume":"5 3","pages":"Article 200180"},"PeriodicalIF":1.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144934274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rigid and stable nitroxide spin label for high-resolution distance measurements on proteins by DEER experiments 刚性和稳定的氮氧化物自旋标签，用于高分辨率的距离测量蛋白质的DEER实验

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-08-01 Epub Date: 2025-02-28 DOI: 10.1016/j.mrl.2025.200194

Ya-Ting Chen , Xing Zhang , Jia-Liang Chen , Bin-Bin Pan , Daniella Goldfarb , Yin Yang , Xun-Cheng Su

{"title":"Rigid and stable nitroxide spin label for high-resolution distance measurements on proteins by DEER experiments","authors":"Ya-Ting Chen , Xing Zhang , Jia-Liang Chen , Bin-Bin Pan , Daniella Goldfarb , Yin Yang , Xun-Cheng Su","doi":"10.1016/j.mrl.2025.200194","DOIUrl":"10.1016/j.mrl.2025.200194","url":null,"abstract":"<div><div>The distance distributions between two site-specifically anchored spin labels in a protein, measured by pulsed electron-electron double resonance (PELDOR or DEER), provide rich sources of structural and conformational restraints on the proteins or their complexes. The rigid connection of the nitroxide spin label to the protein improves the accuracy and precision of distance measurement. We report a new spin labelling approach by formation of thioester bond between nitroxide (NO) spin label, NOAI (NO spin labels activated by acetylimidazole), and a protein thiol, and this spin labeling method has demonstrated high performance in DEER distance measurement on proteins. The results showed that NOAI has shorter connection to the protein ligation site than 2, 2, 5, 5-tetramethyl-pyrroline-1-oxyl methanethiosulfonate (MTSL) and 3-maleimido-proxyl (M-Prox) in the respective protein conjugate and produces narrower distance distributions for the tested proteins including ubiquitin (Ub), immunoglobulin-binding β1 domain of streptococcal protein G (GB1), and second mitochondria-derived activator of caspases (Smac). The NOAI protein conjugate connected by a thioester bond is resistant to reducing reagent and offers high-fidelity DEER distance measurements in cell lysates.</div></div>","PeriodicalId":93594,"journal":{"name":"Magnetic Resonance Letters","volume":"5 3","pages":"Article 200194"},"PeriodicalIF":1.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144934216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adaptive k-space learning and high-dimensional subsets embedding for parallel MRI reconstruction 自适应k空间学习和高维子集嵌入并行MRI重构

IF 1.7

Magnetic Resonance Letters Pub Date : 2025-08-01 Epub Date: 2024-12-29 DOI: 10.1016/j.mrl.2024.200175

Zhonghui Wu , Yuxia Huang , Yu Guan, Qiegen Liu

{"title":"Adaptive k-space learning and high-dimensional subsets embedding for parallel MRI reconstruction","authors":"Zhonghui Wu , Yuxia Huang , Yu Guan, Qiegen Liu","doi":"10.1016/j.mrl.2024.200175","DOIUrl":"10.1016/j.mrl.2024.200175","url":null,"abstract":"<div><div>Magnetic resonance imaging (MRI) inherently requires considerable time for data acquisition, but obtaining multi-contrast MRI data further prolongs this process, thereby increasing susceptibility to motion artifacts. It is worth noting that the multi-contrast MR images have both structural similarities and unique contrast information. Therefore, to take advantage of their similarities while preserving their distinctive characteristics, we proposed a new method called high-dimensional subsets embedding (HDSE). This novel approach is based on the frame of low-rank modeling of local <em>k</em>-space neighborhoods with parallel imaging (P-LORAKS). Specifically, our approach utilizes the structural similarity of multi-contrast MR images to process different <em>k</em>-space data through two independent channels. In one channel, we individually separate the complementary <em>T</em><sub>1</sub>-<em>T</em><sub>2</sub> <em>k</em>-space data and directly construct a new subset of local <em>k</em>-space, allowing the model to better capture structural correlations between multiple contrasts. In another channel, we provide global under-sampled <em>T</em><sub>2</sub>-weighted <em>k</em>-space data further constrain image acquisition in high-dimensional space to maintain image consistency and reduce noise amplification. These two different channels information is fused together to form high-dimensional feature objects. Besides, we embed the constructed objects into P-LORAKS in various ways to enhance the reconstruction performance. Experimental results demonstrated that the aided reconstruction of local subsets fusion and the high-dimensional reconstruction of adaptive global constraints can improve the accuracy of image reconstruction and enhance the robustness of the model.</div></div>","PeriodicalId":93594,"journal":{"name":"Magnetic Resonance Letters","volume":"5 3","pages":"Article 200175"},"PeriodicalIF":1.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144934213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0