Protein Science最新文献_第8页

Inhibition of tau aggregation by the CCT3 and CCT7 apical domains. CCT3和CCT7顶端结构域对tau聚集的抑制作用。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70162

Miki Ben-Maimon, Nadav Elad, Segev Naveh-Tassa, Yaakov Levy, Amnon Horovitz

引用次数: 0

The WRC domain of GRF transcription factors: Structure and DNA recognition. GRF转录因子的WRC结构域：结构和DNA识别。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70172

Franco A Biglione, Nahuel D González Schain, Javier F Palatnik, Rodolfo M Rasia

{"title":"The WRC domain of GRF transcription factors: Structure and DNA recognition.","authors":"Franco A Biglione, Nahuel D González Schain, Javier F Palatnik, Rodolfo M Rasia","doi":"10.1002/pro.70172","DOIUrl":"10.1002/pro.70172","url":null,"abstract":"Growth-regulating factors (GRFs) belong to a family of transcription factors found in plants which display important roles in growth and development. GRF transcriptional activity is finely tuned by regulatory processes involving post-transcriptional repression exerted by microRNA miR396, and protein-protein interactions involving a family of co-transcriptional regulators known as GRF-interacting factors (GIFs). In this way, the activity of GRF target genes is modulated by a highly complex interplay between GRF/GIF isoform diversity and expression patterns along with miR396 and GIF gradients throughout plant tissues. At the protein level, GRFs are composed of two highly evolutionarily conserved domains known as QLQ and WRC and a less conserved C-terminal trans-activation domain. Whereas QLQ mediates GRF-GIF interaction by forming a complex with a conserved domain called SNH (by SYT N-terminal homology) found in GIFs' N-terminal region, the WRC has been proposed as a putative zinc finger domain responsible for target DNA recognition and nuclear import. However, the structural aspects governing GRF transcriptional activity and target recognition remain unknown. In this work, we applied bioinformatic and biophysical analysis to comprehensively characterize the structural features that modulate the biological function of this protein family with a focus on the WRC domain. We provide insights into the structure of the WRC domain in GRFs and explore the WRC features driving GRFs:DNA complex formation. These findings offer new insights into how WRC domains modulate the biological functions of GRFs, laying the groundwork for future studies on their structure-function relationship in gene regulation and development of plants.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70172"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120257/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174691","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

Enhanced protein extraction and quantification protocol for microsamples: An ultra-sensitive workflow for low-volume, low-concentration total protein lysates. 增强蛋白质提取和定量方案的微样品：一个超敏感的工作流程，低体积，低浓度的总蛋白裂解物。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-06-01 DOI: 10.1002/pro.70161

Taylor Wilcox, Michael E Widlansky, Justin Westhoff, Jingli Wang, Rong Ying, Abigail Thorgerson, Michelle L Roberts

{"title":"Enhanced protein extraction and quantification protocol for microsamples: An ultra-sensitive workflow for low-volume, low-concentration total protein lysates.","authors":"Taylor Wilcox, Michael E Widlansky, Justin Westhoff, Jingli Wang, Rong Ying, Abigail Thorgerson, Michelle L Roberts","doi":"10.1002/pro.70161","DOIUrl":"10.1002/pro.70161","url":null,"abstract":"Accurate protein quantification at low concentrations and small volumes is critical for advancing small-scale research, such as microvasculature studies. However, existing microscale protocols often require ≥5 μL of sample or highly concentrated lysates, limiting their applicability in contexts with scarce material. To overcome these limitations, we developed the Nano-Extraction BCA-Optimized Workflow (NEBOW), a novel method requiring only 2 μL of sample and capable of detecting protein concentrations as low as 0.01 mg/mL. Optimized for the NanoDrop™ One UV-Vis Spectrophotometer, this workflow demonstrated significantly enhanced sensitivity and reproducibility compared to the standard BCA assay. Paired t tests (p < 0.01) and TOST equivalence testing (15% margin) confirmed key differences, with the NEBOW method producing steeper standard curves and more consistent results at low concentrations. Bland-Altman analysis showed that standard BCA tends to overestimate protein levels, while the NEBOW method maintained accuracy across a range of low-input samples. Western blot validation supported the improved performance of the new workflow. This approach offers a reliable, cost-effective solution for protein quantification when sample availability is limited, without sacrificing accuracy or sample integrity.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 6","pages":"e70161"},"PeriodicalIF":4.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079893","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

N-terminomics and proteomics analysis of Calpain-2 reveal key proteolytic processing of metabolic and cell adhesion proteins. Calpain-2的n端组学和蛋白质组学分析揭示了代谢蛋白和细胞粘附蛋白的关键蛋白水解过程。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-05-01 DOI: 10.1002/pro.70144

Anjali Kapilan, Mitchell Bulluss, Alexander R Ziegler, Mohamed Dabaja, Afshin Derakhshani, Anthonia Anowai, Victoria Armstrong, Rhiannon Campden, Daniel Young, Young Joo Sun, Nichollas E Scott, Laura E Edgington-Mitchell, Vinit B Mahajan, Antoine Dufour

{"title":"N-terminomics and proteomics analysis of Calpain-2 reveal key proteolytic processing of metabolic and cell adhesion proteins.","authors":"Anjali Kapilan, Mitchell Bulluss, Alexander R Ziegler, Mohamed Dabaja, Afshin Derakhshani, Anthonia Anowai, Victoria Armstrong, Rhiannon Campden, Daniel Young, Young Joo Sun, Nichollas E Scott, Laura E Edgington-Mitchell, Vinit B Mahajan, Antoine Dufour","doi":"10.1002/pro.70144","DOIUrl":"https://doi.org/10.1002/pro.70144","url":null,"abstract":"Aberrant levels of the cysteine protease Calpain-2 have been linked to neurodegeneration, inflammation, and cancer, yet our understanding of this protease and its substrates remains limited. Systematic studies to identify Calpain-2 substrates have been largely confined to peptide libraries or in vitro studies, which fail to represent physiological cellular conditions and physiologically relevant substrates. To identify existing and novel Calpain-2 substrates, we used a genetic approach to knockout Calpain-2 in the THP-1 human monocyte-like cells, followed by proteomic and N-terminomic/TAILS mass spectrometry approaches to identify Calpain-2 substrates. We identified 51 substrates that may be cleaved directly by Calpain-2 or indirectly by downstream proteases. The direct cleavage of selected substrates by Calpain-2 was confirmed using in vitro assays. Finally, metabolomics analysis identified a role for Calpain-2 in the regulation of pyrimidine and glutathione metabolism. Our unbiased and quantitative mass spectrometry analytical pipeline provides new evidence on the physiological functions of Calpain-2 and its newly identified substrates in THP-1 cells.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 5","pages":"e70144"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12023407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018444","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

Mass balance approximation of unfolding boosts potential-based protein stability predictions. 展开的质量平衡近似提高了基于电位的蛋白质稳定性预测。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-05-01 DOI: 10.1002/pro.70134

Ivan Rossi, Guido Barducci, Tiziana Sanavia, Paola Turina, Emidio Capriotti, Piero Fariselli

引用次数: 0

Improving split-HaloTag through computational protein engineering. 利用计算蛋白工程改进split-HaloTag。

IF 5.2 3区生物学

Protein Science Pub Date : 2025-05-01 DOI: 10.1002/pro.70123

Jonas Wilhelm, Lennart Nickel, Yin-Hsi Lin, Julien Hiblot, Kai Johnsson

引用次数: 0

Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials. 纤维蛋白生物材料中异二聚体荧光生物传感器的固定化和增强。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-05-01 DOI: 10.1002/pro.70119

Rebecca M Booth, Amanda Jons, Xue Gong, Shounak Banerjee, Britt Faulk, Hays Rye, Christopher Bystroff, Sarah E Bondos

{"title":"Immobilization and enhancement of a heterodimeric fluorescence biosensor in fibrous protein biomaterials.","authors":"Rebecca M Booth, Amanda Jons, Xue Gong, Shounak Banerjee, Britt Faulk, Hays Rye, Christopher Bystroff, Sarah E Bondos","doi":"10.1002/pro.70119","DOIUrl":"https://doi.org/10.1002/pro.70119","url":null,"abstract":"Leave-one-out green fluorescent proteins (LOO_GFPs) have a reduced quantum yield relative to the parent protein and form fluorescent oligomers in the unbound state. Immobilizing LOO_GFPs in materials composed of the Drosophila protein Ultrabithorax (Ubx) via gene fusion increased the fluorescent signal, significantly stabilized the biosensor, and prevented oligomerization into fluorescent aggregates, which has the potential to elevate the sensor's noise well above the signal. Interactions between LOO_GFP and Ubx hampered analyte rebinding. By optimizing the concentrations of LOO_GFP, salt, and detergent in the assay, the signal to noise ratio for the biosensor increased fourfold. These modified fibers represent the first incorporation of a protein complementation assay into protein-based materials, as well as the first incorporation, via gene fusion, of a heterodimeric functional protein into materials composed of a different self-assembling protein. This study highlights the advantages and identifies potential pitfalls associated with protein immobilization in materials.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 5","pages":"e70119"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12012991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028844","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

Crowding-induced stabilization and destabilization in a single protein. 单个蛋白质的拥挤诱导稳定性和不稳定性。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-05-01 DOI: 10.1002/pro.70126

Jordyn M Markle, Tarynn D Neal, Hania S Kantzer, Gary J Pielak

{"title":"Crowding-induced stabilization and destabilization in a single protein.","authors":"Jordyn M Markle, Tarynn D Neal, Hania S Kantzer, Gary J Pielak","doi":"10.1002/pro.70126","DOIUrl":"10.1002/pro.70126","url":null,"abstract":"The protein concentration in cells can reach 300 g/L. These crowded conditions affect protein stability. Classic crowding theories predict entropically driven stabilization, which occurs via steric repulsion, but growing evidence shows a role for non-covalent chemical interactions. To aid our understanding of physiologically relevant crowding, we used NMR-detected 1H-2H exchange to examine a simple, semi-reductionist system: protein self-crowding at the residue level using the widely studied model globular protein, GB1 (the B1 domain streptococcal protein G) at concentrations up to its solubility limit, 100 g/L. The surprising result is that self-crowding stabilizes some residues but destabilizes others, contradicting predictions. Two other observations are also contradictory. First, temperature-dependence data show that stabilization can arise enthalpically, not just entropically. Second, concentration-dependence data show destabilization often increases with increasing concentration. These results show a key role for chemical interactions. More specifically, self-crowding increases the free energy required to expose those residues that are only exposed upon complete unfolding, and stabilization of these globally unfolding residues increases with GB1 concentration, a result we attribute to repulsive chemical interactions between GB1 molecules. On the other hand, residues exposed upon local unfolding tend to be destabilized, with destabilization increasing with concentration, a result we attribute to attractive chemical interactions between GB1 molecules.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 5","pages":"e70126"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12012844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144041962","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

Molecular mechanisms of RaTG13 and SARS-CoV-2 RBD bound to Rhinolophus affinis bat ACE2. RaTG13和SARS-CoV-2 RBD结合亲和鼻蝗ACE2的分子机制

IF 4.5 3区生物学

Protein Science Pub Date : 2025-05-01 DOI: 10.1002/pro.70117

Chenghai Wang, Min Li, Xiaoyan Nan, Yang Deng, Shilong Fan, Jun Lan

{"title":"Molecular mechanisms of RaTG13 and SARS-CoV-2 RBD bound to Rhinolophus affinis bat ACE2.","authors":"Chenghai Wang, Min Li, Xiaoyan Nan, Yang Deng, Shilong Fan, Jun Lan","doi":"10.1002/pro.70117","DOIUrl":"10.1002/pro.70117","url":null,"abstract":"The discovery of the RaTG13 coronavirus in Rhinolophus affinis bats in 2013, sharing 96.3% genome homology with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), suggested bats as the origin of SARS-CoV-2. Although both human angiotensin-converting enzyme 2 (hACE2) and Rhinolophus affinis bat ACE2 (bACE2-Ra, seven polymorphic variants named 01-07) are known to serve as entry receptors for these coronaviruses, the binding mechanism of RaTG13 receptor binding domain (RBD) bound to bACE2-Ra remains poorly understood. Here, we found that RaTG13 RBD bound to bACE2-Ra-07 with a weaker affinity (2.42 μM) compared with SARS-CoV-2 RBD (372 nM). Additional glycosylation at residue N370 of RaTG13 had little influence on bACE2-Ra-07 binding by RaTG13 RBD. Crystal structures of the SARS-CoV-2 and RaTG13 N370Q RBD bound to bACE2-Ra-07 were solved. Interface analysis and surface plasmon resonance (SPR) assay indicated that residue substitutions at 493, 498, 501, and 505 may play a more important role in the cross-species recognition of bACE2-Ra-07 by the SARS-CoV-2 RBD. Besides, the N370Q mutation enhanced the binding affinity between the RBD of pangolin coronavirus isolated from Guangxi (PCoV-GX) and the bACE2-Ra-07 receptor by over 10-fold. Furthermore, the recently prevalent SARS-CoV-2 variant RBDs extensively retained the interaction with the bACE2-Ra-07 receptor. Our findings give new lights on the cross-species evolution of SARS-CoV-2 and prompt the urgency to monitor the circulation of coronaviruses in bats to better prevent future spillover.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 5","pages":"e70117"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12012733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144046044","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

PackPPI: An integrated framework for protein-protein complex side-chain packing and ΔΔG prediction based on diffusion model. PackPPI：基于扩散模型的蛋白质复合物侧链包装和ΔΔG预测的集成框架。

IF 4.5 3区生物学

Protein Science Pub Date : 2025-05-01 DOI: 10.1002/pro.70110

Jingkai Zhang, Yuanyan Xiong

{"title":"PackPPI: An integrated framework for protein-protein complex side-chain packing and ΔΔG prediction based on diffusion model.","authors":"Jingkai Zhang, Yuanyan Xiong","doi":"10.1002/pro.70110","DOIUrl":"10.1002/pro.70110","url":null,"abstract":"Deep learning methods have played an increasingly pivotal role in advancing side-chain packing and mutation effect prediction (ΔΔG) for protein complexes. Although these two tasks are inherently closely related, they are typically treated separately in practice. Furthermore, the lack of effective post-processing in most approaches results in sub-optimal refinement of generated conformations, limiting the plausibility of the predicted conformations. In this study, we introduce an integrated framework, PackPPI, which employs a diffusion model and a proximal optimization algorithm to improve side-chain prediction for protein complexes while using learned representations to predict ΔΔG. The results demonstrate that PackPPI achieved the lowest atom RMSD (0.9822) on the CASP15 dataset. The proximal optimization algorithm effectively reduces spatial clashes between side-chain atoms while maintaining a low-energy landscape. Furthermore, PackPPI achieves state-of-the-art performance in predicting binding affinity changes induced by multi-point mutations on the SKEMPI v2.0 dataset. These findings underscore the potential of PackPPI as a robust and versatile computational tool for protein design and engineering. The implementation of PackPPI is available at https://github.com/Jackz915/PackPPI.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"34 5","pages":"e70110"},"PeriodicalIF":4.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12012842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144064180","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