Biophysical chemistry最新文献_第10页

Investigating the role of axonal ion channel cooperativity in action potential dynamics: Studies on Hodgkin-Huxley's model 研究轴突离子通道合作性在动作电位动力学中的作用：霍奇金-赫胥黎模型研究

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-05-08 DOI: 10.1016/j.bpc.2024.107257

Jitender Kumar , Patrick Das Gupta , Subhendu Ghosh

引用次数: 0

Improved analysis of NMR chemical shift perturbations through an error estimation method 通过误差估算方法改进核磁共振化学位移扰动分析

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-05-06 DOI: 10.1016/j.bpc.2024.107255

Kyoko Furuita , Chojiro Kojima

引用次数: 0

Exploring the physicochemical properties of the integration of Tristearoyl uridine in Langmuir monolayers: An approach to cell membrane modeling for prodrugs 探索三苯甲酰基尿苷在朗缪尔单层中整合的物理化学特性：原药细胞膜建模方法

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-05-06 DOI: 10.1016/j.bpc.2024.107256

Felipe Almeida Moreira , Jhon Fernando Berrío Escobar , Cristiano Giordani , Luciano Caseli

{"title":"Exploring the physicochemical properties of the integration of Tristearoyl uridine in Langmuir monolayers: An approach to cell membrane modeling for prodrugs","authors":"Felipe Almeida Moreira , Jhon Fernando Berrío Escobar , Cristiano Giordani , Luciano Caseli","doi":"10.1016/j.bpc.2024.107256","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107256","url":null,"abstract":"<div><p>Understanding the mechanisms by which drugs interact with cell membranes is crucial for unraveling the underlying biochemical and biophysical processes that occur on the surface of these membranes. Our research focused on studying the interaction between an ester-type derivative of tristearoyl uridine and model cell membranes composed of lipid monolayers at the air-water interface. For that, we selected a specific lipid to simulate nontumorigenic cell membranes, namely 1,2-dihexadecanoyl-<em>sn</em>-glycero-3-phospho-<span>l</span>-serine. We noted significant changes in the surface pressure-area isotherms, with a noticeable shift towards larger areas, which was lower than expected for ideal mixtures, indicating monolayer condensation. Furthermore, the viscoelastic properties of the interfacial film demonstrated an increase in both the elastic and viscous parameters for the mixed film. We also observed structural alterations using vibrational spectroscopy, which revealed an increase in the all-trans to gauche conformers ratio. This confirmed the stiffening effect of the prodrug on the lipid monolayer. In summary, this study indicates that this lipophilic prodrug significantly impacts the lipid monolayer's thermodynamic, rheological, electrical, and molecular characteristics. This information is crucial for understanding how the drug interacts with specific sites on the cellular membrane. It also has implications for drug delivery, as the drug's passage into the cytosol may involve traversing the lipid bilayer.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"310 ","pages":"Article 107256"},"PeriodicalIF":3.8,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140893860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-resolution heteronuclear correlations between spin-1/2 and half-integer quadrupolar nuclei under fast MAS solid-state NMR 快速 MAS 固态 NMR 下自旋-1/2 和半整数四极核之间的高分辨率异核相关性

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-05-03 DOI: 10.1016/j.bpc.2024.107254

Manoj Kumar Pandey , Yusuke Nishiyama

{"title":"High-resolution heteronuclear correlations between spin-1/2 and half-integer quadrupolar nuclei under fast MAS solid-state NMR","authors":"Manoj Kumar Pandey , Yusuke Nishiyama","doi":"10.1016/j.bpc.2024.107254","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107254","url":null,"abstract":"<div><p>High isotropic resolution is essential for the structural elucidation of samples with multiple sites. In this study, utilizing the benefits of TRAPDOR-based heteronuclear multiple quantum coherence (T-HMQC) and a pair of one rotor period long cosine amplitude modulated low-power (cos-lp) pulse-based symmetric-split-<em>t</em><sub>1</sub> multiple-quantum magic angle spinning (MQMAS) methods, we have developed a proton-detected 2D <sup>35</sup>Cl/<sup>1</sup>H T-HMQC-MQMAS pulse sequence under fast MAS (70 kHz) to achieve high-resolution in the indirect dimension of the spin-3/2 (<sup>35</sup>Cl) nuclei connected via protons. As T-HMQC polarizes not only single-quantum central transition (SQ<sub>CT</sub>) but also triple-quantum (TQ) coherences, the proposed 2D pulse sequence is implemented via selection of two coherence pathways (SQ<sub>CT</sub> <span><math><mo>→</mo></math></span>TQ <span><math><mo>→</mo></math></span>SQ<sub>CT</sub> and TQ <span><math><mo>→</mo></math></span> SQ<sub>CT</sub> <span><math><mo>→</mo></math></span>TQ) resulting in the <sup>35</sup>Cl isotropic dimension and is superior to the existing double-quantum satellite-transition (DQ<sub>ST</sub>) T-HMQC in terms of resolution.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"310 ","pages":"Article 107254"},"PeriodicalIF":3.8,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity 基于结构的抗体-抗原结合亲和力在线工具评估基准

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-04-30 DOI: 10.1016/j.bpc.2024.107253

Jiayi Xu , Jianting Gong , Xiaochen Bo , Yigang Tong , Zilin Ren , Ming Ni

{"title":"A benchmark for evaluation of structure-based online tools for antibody-antigen binding affinity","authors":"Jiayi Xu , Jianting Gong , Xiaochen Bo , Yigang Tong , Zilin Ren , Ming Ni","doi":"10.1016/j.bpc.2024.107253","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107253","url":null,"abstract":"<div><p>The prediction of binding affinity changes caused by missense mutations can elucidate antigen-antibody interactions. A few accessible structure-based online computational tools have been proposed. However, selecting suitable software for particular research is challenging, especially research on the SARS-CoV-2 spike protein with antibodies. Therefore, benchmarking of the mutation-diverse SARS-CoV-2 datasets is critical. Here, we collected the datasets including 1216 variants about the changes in binding affinity of antigens from 22 complexes for SARS-CoV-2 S proteins and 22 monoclonal antibodies as well as applied them to evaluate the performance of seven binding affinity prediction tools. The tested tools' Pearson correlations between predicted and measured changes in binding affinity were between −0.158 and 0.657, while accuracy in classification tasks on predicting increasing or decreasing affinity ranged from 0.444 to 0.834. These tools performed relatively better on predicting single mutations, especially at epitope sites, whereas poor performance on extremely decreasing affinity. The tested tools were relatively insensitive to the experimental techniques used to obtain structures of complexes. In summary, we constructed a list of datasets and evaluated a range of structure-based online prediction tools that will explicate relevant processes of antigen-antibody interactions and enhance the computational design of therapeutic monoclonal antibodies.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"311 ","pages":"Article 107253"},"PeriodicalIF":3.8,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141068645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Self-assembly of spin-labeled antimicrobial peptides magainin 2 and PGLa in lipid bilayers 自旋标记的抗菌肽 magainin 2 和 PGLa 在脂质双层膜中的自组装

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-04-22 DOI: 10.1016/j.bpc.2024.107251

Victoria N. Syryamina , Christopher Aisenbrey , Maria Kardash , Sergei A. Dzuba , Burkhard Bechinger

{"title":"Self-assembly of spin-labeled antimicrobial peptides magainin 2 and PGLa in lipid bilayers","authors":"Victoria N. Syryamina , Christopher Aisenbrey , Maria Kardash , Sergei A. Dzuba , Burkhard Bechinger","doi":"10.1016/j.bpc.2024.107251","DOIUrl":"10.1016/j.bpc.2024.107251","url":null,"abstract":"<div><p>The cationic antimicrobial peptides PGLa and magainin 2 (Mag2) are known for their antimicrobial activity and synergistic enhancement in antimicrobial and membrane leakage assays. Further use of peptides in combinatory therapy requires knowledge of the mechanisms of action of both individual peptides and their mixtures. Here, electron paramagnetic resonance (EPR), double electron-electron resonance (DEER, also known as PELDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies were applied to study self-assembly and localization of spin-labeled PGLa and Mag2 in POPE/POPG membranes with a wide range of peptide/lipid ratios (P/L) from ∼1/1500 to 1/50. EPR and DEER data showed that both peptides tend to organize in clusters, which occurs already at the lowest peptide/lipid molar ratio of 1/1500 (0.067 mol%). For individual peptides, these clusters are quite dense with intermolecular distances of the order of ∼2 nm. In the presence of a synergistic peptide partner, these homo-clusters are transformed into lipid-diluted hetero-clusters. These clusters are characterized by a local surface density that is several times higher than expected from a random distribution. ESEEM data indicate a slightly different insertion depth of peptides in hetero-clusters when compared to homo-clusters.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"310 ","pages":"Article 107251"},"PeriodicalIF":3.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0301462224000802/pdfft?md5=978c2d3eff98400fc4cd7684e01656f1&pid=1-s2.0-S0301462224000802-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140795515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neuroinflammation induced by amyloid-forming pancreatic amylin: Rationale for a mechanistic hypothesis 淀粉样蛋白形成的胰淀粉样蛋白诱发的神经炎症：机理假说的依据

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-04-22 DOI: 10.1016/j.bpc.2024.107252

Noah S. Leibold, Florin Despa

引用次数: 0

Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway R2D2 dsRBD1 和 dsRBD2 中的关键精氨酸残基在黑腹果蝇 RNAi 通路中引领 siRNA 识别

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-04-18 DOI: 10.1016/j.bpc.2024.107247

Ramdas Aute , Nilam Waghela , Mandar V. Deshmukh

{"title":"Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway","authors":"Ramdas Aute , Nilam Waghela , Mandar V. Deshmukh","doi":"10.1016/j.bpc.2024.107247","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107247","url":null,"abstract":"<div><p>In <em>Drosophila melanogaster</em>, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5′-phosphate (5<em>'</em><em>-</em>P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, we have performed structural, biophysical, and biochemical characterization of R2D2 dsRBDs. We found that the solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, we show that R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5′-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5<em>'</em>-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. Our study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5′-phosphate as an authentic mark on functional siRNA.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"310 ","pages":"Article 107247"},"PeriodicalIF":3.8,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140643587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Thermodynamics of oligomerization and Helix-to-sheet structural transition of amyloid β-protein on anionic phospholipid vesicles 淀粉样β蛋白在阴离子磷脂囊泡上的寡聚化和螺旋到片状结构转变的热力学研究

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-04-18 DOI: 10.1016/j.bpc.2024.107248

Keisuke Ikeda, Yuuki Sugiura, Hiroyuki Nakao, Minoru Nakano

{"title":"Thermodynamics of oligomerization and Helix-to-sheet structural transition of amyloid β-protein on anionic phospholipid vesicles","authors":"Keisuke Ikeda, Yuuki Sugiura, Hiroyuki Nakao, Minoru Nakano","doi":"10.1016/j.bpc.2024.107248","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107248","url":null,"abstract":"<div><p>Understanding oligomerization and aggregation of the amyloid-β protein is important to elucidate the pathological mechanisms of Alzheimer's disease, and lipid membranes play critical roles in this process. In addition to studies reported by other groups, our group has also reported that the negatively-charged lipid bilayers with a high positive curvature induced α-helix-to-β-sheet conformational transitions of amyloid-β-(1–40) upon increase in protein density on the membrane surface and promoted amyloid fibril formation of the protein. Herein, we investigated detailed mechanisms of the conformational transition and oligomer formation of the amyloid-β protein on the membrane surface. Changes in the fractions of the three protein conformers (free monomer, membrane-bound α-helix-rich conformation, and β-sheet-rich conformation) were determined from the fluorescent spectral changes of the tryptophan probe in the protein. The helix-to-sheet structural transition on the surface was described by a thermodynamic model of octamer formation driven by entropic forces including hydrophobic interactions. These findings provide useful information for understanding the self-assembly of amyloidogenic proteins on lipid membrane surfaces.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"310 ","pages":"Article 107248"},"PeriodicalIF":3.8,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140638239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural packing of the non-amyloid component core domain in α-synuclein plays a role in the stability of the fibrils α-突触核蛋白中非淀粉样成分核心结构域的结构包装对纤维的稳定性起作用

IF 3.8 3区生物学

Biophysical chemistry Pub Date : 2024-04-16 DOI: 10.1016/j.bpc.2024.107239

Karina Abramov-Harpaz , Sapir Lan-Mark , Yifat Miller

{"title":"Structural packing of the non-amyloid component core domain in α-synuclein plays a role in the stability of the fibrils","authors":"Karina Abramov-Harpaz , Sapir Lan-Mark , Yifat Miller","doi":"10.1016/j.bpc.2024.107239","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107239","url":null,"abstract":"<div><p>Parkinson's disease (PD) is one of many neurodegenerative diseases. The protein associated with PD is α-synuclein (AS). Aggregation of AS protein into oligomers, protofilaments, and finally to fibrils yields to the development of PD. The aggregation process of AS leads to the formation of polymorphic AS fibrils. Herein, we compared four polymorphic full-length AS<sub>1</sub><sub>–</sub><sub>140</sub> fibrils, using extensive computational tools. The main conclusion of this study emphasizes the role of the structurally packed non-amyloid component (NAC) core domain in AS fibrils. Polymorphic AS fibrils that presented a packed NAC core domain, exhibited more β-sheets and fewer fluctuations in the NAC domain. Hence, these AS fibrils are more stable and populated than the AS fibrils, by which the NAC domains are more exposed, more fluctuate and less packed in the fibrillary structure. Therefore, this study emphasizes the importance of the NAC domain packing in the morphology of AS fibrils. The results obtained in this study will initiate future studies to develop compounds to prevent and inhibit AS aggregation.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"310 ","pages":"Article 107239"},"PeriodicalIF":3.8,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140643588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0