Protein Science最新文献_第10页

DJ-1 in human lenses: Potential role in preventing advanced glycation endproduct formation. 人晶状体中的DJ-1：预防晚期糖基化终产物形成的潜在作用。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70375

Sandip K Nandi, Rooban B Nahomi, Shivani Rathee, Neeti Gupta, Sanjeev Kumar Mittal, Ram H Nagaraj

{"title":"DJ-1 in human lenses: Potential role in preventing advanced glycation endproduct formation.","authors":"Sandip K Nandi, Rooban B Nahomi, Shivani Rathee, Neeti Gupta, Sanjeev Kumar Mittal, Ram H Nagaraj","doi":"10.1002/pro.70375","DOIUrl":"10.1002/pro.70375","url":null,"abstract":"The amino groups of lysine and arginine residues in proteins react with reducing sugars and carbonyl compounds to form advanced glycation endproducts (AGEs). Several AGEs have been detected in human lenses, and their levels have been shown to increase with age and cataract formation. AGEs can lead to structural changes, yellow pigmentation, and cross-linking of lens proteins. Studies have shown a positive correlation between AGEs levels and lens age, stiffness, and cataracts. Recent research suggests that DJ-1 can inhibit the accumulation of AGEs in cellular proteins by reversing the early glycation steps. Our study found that DJ-1 is present in epithelial cells and the outer cortex of the human lens. DJ-1 is catalytically active in human lenses, and its ability to metabolize methylglyoxal (MGO) into D-lactate diminishes as the lens ages. The formation of MGH-1 from MGO was promoted in lens proteins treated with the DJ-1 inhibitor. Recombinant DJ-1 prevents α-dicarbonyl-mediated cross-linking and AGE accumulation in human αB-crystallin. DJ-1 prevents glyoxal-mediated cell death and AGE accumulation in human lens epithelial cells. Taken together, our results suggest that DJ-1 in the human lens hinders AGE accumulation. Enhancing its activity using pharmacological agents can potentially delay or prevent the onset of presbyopia and cataracts.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 12","pages":"e70375"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12612599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145506628","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

The product of Ellman's reaction inhibits cholinesterases. 埃尔曼反应的产物抑制胆碱酯酶。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70371

Jure Stojan, Xavier Brazzolotto

{"title":"The product of Ellman's reaction inhibits cholinesterases.","authors":"Jure Stojan, Xavier Brazzolotto","doi":"10.1002/pro.70371","DOIUrl":"10.1002/pro.70371","url":null,"abstract":"Kinetic and crystallographic studies reveal that the binding of the thiocholine-thionitrobenzoic acid product, released during the measurement of thioester-analog substrates hydrolysis according to Ellman's method, inhibits cholinesterases by a pure competitive mechanism. This can only be recorded as the progressive accumulation of the product upon subsequent additions of substrate aliquots. A wide affinity variation was observed among several tested enzymes, with the highest values found in human butyrylcholinesterase and Torpedo acetylcholinesterase. Nearly two orders of magnitude lower affinities were determined with human, mouse, and electrophorus acetylcholinesterases, and human atypical butyrylcholinesterase. These findings can be explained by the unexpected accommodation of the thiocholine-thionitrobenzoic acid in the active site of human butyrylcholinesterase, with the positively charged trimethylammonium choline pointing to the enzyme's peripheral site. At the same time, the carboxyl group of the nitrobenzoic moiety interacts with the enzyme's oxyanion hole. This explains the virtual absence of product inhibition in atypical human butyrylcholinesterase (D70G), purified or in plasma.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 12","pages":"e70371"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12611867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145506080","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

Structures of two LarA-like nickel-pincer nucleotide cofactor-utilizing enzymes with a single catalytic histidine residue. 两种具有单一催化组氨酸残基的类lara钳形镍核苷酸辅助因子利用酶的结构。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70362

Santhosh Gatreddi, Sundharraman Subramanian, Dexin Sui, Tianqi Wang, Julian Urdiain-Arraiza, Benoît Desguin, Robert P Hausinger, Kristin N Parent, Jian Hu

{"title":"Structures of two LarA-like nickel-pincer nucleotide cofactor-utilizing enzymes with a single catalytic histidine residue.","authors":"Santhosh Gatreddi, Sundharraman Subramanian, Dexin Sui, Tianqi Wang, Julian Urdiain-Arraiza, Benoît Desguin, Robert P Hausinger, Kristin N Parent, Jian Hu","doi":"10.1002/pro.70362","DOIUrl":"10.1002/pro.70362","url":null,"abstract":"The nickel-pincer nucleotide (NPN) cofactor catalyzes the racemization/epimerization of α-hydroxy acids in enzymes of the LarA family. The established proton-coupled hydride transfer mechanism requires two catalytic histidine residues that alternately act as general acids and general bases. Notably, however, a fraction of LarA homologs (LarAHs) lack one of the active site histidine residues, replacing it with an asparaginyl side chain that cannot participate in acid/base catalysis. Here, we investigated two such LarAHs and solved their cryo-electron microscopic structures with and without loaded NPN cofactor, respectively. The structures revealed a consistent octameric assembly that is unprecedented in the LarA family and unveiled a new set of active site residues that likely recognize and process substrates differently from those of the well-studied LarAHs. Genomic context analysis suggested their potential involvement in carbohydrate metabolism. Together, these findings lay the groundwork for expanding the breadth of reactions and the range of mechanisms of LarA enzymes.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 12","pages":"e70362"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12611868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145506168","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

Membrane-forming phospholipids allosterically modulate native-state prolyl isomerization in a CNG channel. 成膜磷脂在CNG通道中变构调节原生丙烯异构化。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70383

Ashley J Newton, Robert D Latvala, Adefoluke E Kuforiji, Philipp A M Schmidpeter

{"title":"Membrane-forming phospholipids allosterically modulate native-state prolyl isomerization in a CNG channel.","authors":"Ashley J Newton, Robert D Latvala, Adefoluke E Kuforiji, Philipp A M Schmidpeter","doi":"10.1002/pro.70383","DOIUrl":"10.1002/pro.70383","url":null,"abstract":"Ion channel activity is intricately linked to the surrounding lipid environment, yet the molecular effects of lipid-mediated regulation remain largely understudied. Here, we show that membrane-forming phospholipids, which are known to modulate the activity of the cyclic nucleotide-gated channel SthK from Spirochaeta thermophila, exhibit effects that extend well beyond the membrane boundary. Using stopped-flow flux assays, we demonstrate that anionic lipids, which are known to promote channel opening, also affect the fast-to-slow activation ratio and the cAMP potency in SthK. Enzymatic catalysis studies confirm that this occurs by altering the cis/trans equilibrium at Pro300 in the apo state. Additionally, cryogenic electron microscopy structures of SthK reveal lipid-dependent conformational changes that propagate from the bundle crossing into the cytosolic domains. All observed effects correlate with the electronegativity of the lipid headgroup, indicating a common underlying mechanism. Our results highlight membrane-forming phospholipids as allosteric regulators of SthK, controlling multiple functional characteristics of the channel.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 12","pages":"e70383"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12631857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145565106","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

PLNet: Persistent Laplacian neural network for protein-protein binding free energy prediction. 用于蛋白质结合自由能预测的持续拉普拉斯神经网络。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70377

Xingjian Xu, Chunmei Wang, Guo-Wei Wei, Jiahui Chen

{"title":"PLNet: Persistent Laplacian neural network for protein-protein binding free energy prediction.","authors":"Xingjian Xu, Chunmei Wang, Guo-Wei Wei, Jiahui Chen","doi":"10.1002/pro.70377","DOIUrl":"10.1002/pro.70377","url":null,"abstract":"Recent advances in topology-based modeling have greatly improved molecular prediction tasks, particularly in protein-ligand binding affinity. However, when the focus shifts to predicting protein-protein interactions (PPIs) binding free energy, the question becomes significantly more challenging due to the ineffective use of topological features and the lack of reliable datasets. In this work, we propose a persistent-Laplacian machine learning framework centered on the Persistent-Laplacian Neural Network (PLNet), which encodes each protein chain at the binding interface using both persistent Laplacian-based features and protein language model embeddings. It can achieve a promising Pearson correlation of 0.80 under leave-out-protein-out cross-validation on our newly assembled benchmark dataset, P2P, which includes 6886 protein complexes drawn from existing sources. For comparison, we also implement a gradient-boosting decision tree model under the same settings. This baseline method highlights the advantage of PLNet in capturing complex topology-aware descriptors in PPI prediction.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 12","pages":"e70377"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12631946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145565120","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

Nuclear Magnetic Resonance-based fragment screen of the E3 ligase Fem-1 homolog B. E3连接酶Fem-1同源物B的核磁共振片段筛选。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70365

Jade M Katinas, Kangsa Amporndanai, Ashley J Taylor, Kristie L Rose, Peter C Gareiss, Roberto A Crespo, Jason Phan, Alex G Waterson, Stephen W Fesik

引用次数: 0

PDB-CAT: A user-friendly tool to classify and analyze PDB protein-ligand complexes. PDB- cat：一个用户友好的工具分类和分析PDB蛋白配体复合物。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70379

Ariadna Llop-Peiró, Said Trujillo-De León, Gerard Pujadas, Santiago Garcia-Vallvé, Aleix Gimeno

{"title":"PDB-CAT: A user-friendly tool to classify and analyze PDB protein-ligand complexes.","authors":"Ariadna Llop-Peiró, Said Trujillo-De León, Gerard Pujadas, Santiago Garcia-Vallvé, Aleix Gimeno","doi":"10.1002/pro.70379","DOIUrl":"10.1002/pro.70379","url":null,"abstract":"The Protein Data Bank (PDB) contains more than 235,000 three-dimensional biostructures and is growing at a rate of nearly 10% per year. The PDB is essential to gain knowledge on how proteins and ligands interact and how these interactions are correlated with the quantitative activity of each ligand/target pair. Unfortunately, the lack of a tool that can classify structures as apo or holo, that is by no means straightforward, and differentiate between covalent and non-covalent ligand-protein complexes makes it difficult to obtain the structures that belong to each set. To address this issue, we present PDB-CAT, a user-friendly tool that facilitates the categorization and extraction of key information from PDBx/mmCIF files through an efficient parallelized implementation. PDB-CAT uses a blacklist-based approach to automatically identify the ligand in a complex. It then classifies the PDB files based on ligand presence: structures without a ligand are classified as apo, whereas those with a ligand are classified as covalently or non-covalently bound, depending on the type of binding. As well as making this classification, the program can verify if there are any mutations in the protein sequence by comparing it to a reference sequence. An example is included to illustrate two different uses: the classification of SARS-CoV-2 Main Protease complexes depending on their variant, and the complete screening of the PDBbindv2020, achieved in <10 min. PDB-CAT is now available on GitHub (https://github.com/URV-cheminformatics/PDB-CAT) and the corresponding tutorial on GitBook (https://ariadnallopps-organization.gitbook.io/pdb-cat).","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 12","pages":"e70379"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12612595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145506586","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

Structure-guided engineering of protein stability through core hydrophobicity. 通过核心疏水性进行蛋白质稳定性的结构引导工程。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-12-01 DOI: 10.1002/pro.70360

Aravind Ravichandran, Anindita Puri, Suhas H Bhate, Batul Ismail Habibullah, Gajendra Singh, Ranabir Das

{"title":"Structure-guided engineering of protein stability through core hydrophobicity.","authors":"Aravind Ravichandran, Anindita Puri, Suhas H Bhate, Batul Ismail Habibullah, Gajendra Singh, Ranabir Das","doi":"10.1002/pro.70360","DOIUrl":"10.1002/pro.70360","url":null,"abstract":"Engineering thermostable proteins is advantageous for industrial and biomedical applications, where improved thermal stability can enhance conformational integrity, prolong functional half-life, and increase catalytic efficiency at elevated temperatures. We explored modifying the length of buried hydrocarbon chains to improve protein thermal stability. By optimizing the hydrophobic core through targeted amino acid substitutions, we aimed to minimize internal voids and improve core packing. To achieve this, we developed an algorithm that replaces buried hydrophobic residues with longer or bulkier hydrophobic side chains. The algorithm calculates the free energy of unfolding (ΔG) for each substitution, selecting only significantly stabilizing configurations. Functionally important residues and contact networks were excluded from mutation to preserve protein function. We applied the method to several proteins from the beta-grasp fold family. For experimental validation, we chose NEDD8, a beta-grasp protein with poor solubility and low thermal stability. Two subtle substitutions predicted by our algorithm increased NEDD8's thermal stability by 1.7 kcal/mol and raised its melting point by 17°C. MD simulations and NMR spectroscopy revealed reduced conformational fluctuations and increased stabilizing interactions, such as hydrogen bonding and electrostatic contacts. Functional assays confirmed that the substitutions did not perturb NEDD8's global fold or interactions with cofactors and enzymes. These results highlight the effectiveness of tuning buried hydrophobic residues to enhance protein stability without compromising function. This strategy could serve as a general framework for designing robust therapeutic proteins and enzymes for industrial or biomedical applications.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 12","pages":"e70360"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12613165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145506119","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

Structural mechanisms for cold-adapted activity of phosphoenolpyruvate carboxykinase. 磷酸烯醇丙酮酸羧激酶冷适应活性的结构机制。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-11-01 DOI: 10.1002/pro.70326

Matthew J McLeod, Shauhin Yazdani, Sarah A E Barwell, Todd Holyoak

{"title":"Structural mechanisms for cold-adapted activity of phosphoenolpyruvate carboxykinase.","authors":"Matthew J McLeod, Shauhin Yazdani, Sarah A E Barwell, Todd Holyoak","doi":"10.1002/pro.70326","DOIUrl":"10.1002/pro.70326","url":null,"abstract":"Temperature is a critical factor in enzyme function, as most enzymes are thermally activated. Across Earth's diverse environments (-20 to 120°C), enzymes have evolved to function optimally at their organism's growth temperature. Thermophilic enzymes must resist denaturation, while psychrophilic enzymes must maintain activity with limited thermal energy. Although principles underlying thermostability are well established, the mechanisms governing kinetic adaptation to temperature remain less understood. To investigate this, we characterized the kinetics and determined a comprehensive series of X-ray crystal structures of a psychrophilic, GTP-dependent phosphoenolpyruvate carboxykinase (PEPCK) bound to substrates and non-reactive mimics of the reaction coordinate. These structures were compared to those of a mesophilic PEPCK. PEPCK is a dynamic enzyme requiring substantial conformational changes during catalysis, particularly ordering of the active site Ω-loop lid. The psychrophilic enzyme exhibited a reduced catalytic efficiency (kcat/KM) and lower optimal temperature (Topt) relative to its mesophilic counterpart. Structural comparisons revealed substitutions in the Ω-loop that likely increase the entropic cost of loop ordering and reduce enthalpic stabilization, hindering efficient active site closure. These results provide a mechanistic basis for cold adaptation in enzyme catalysis, linking specific structural features to altered kinetic behavior. Understanding such adaptations not only advances our knowledge of enzyme evolution but also informs protein engineering efforts aimed at designing efficient biocatalysts for industrial applications operating at non-physiological temperatures.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 11","pages":"e70326"},"PeriodicalIF":5.2,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12529880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145302780","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

Special issue title: The Protein Society 39^th Annual Symposium, June 26 - 29, 2025, San Francisco, California. 特刊标题：蛋白质学会第39届年会，2025年6月26日至29日，加州旧金山。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-11-01 DOI: 10.1002/pro.70288

引用次数: 0