{"title":"Understanding Huntingtin protein aggregation in cell mimicking environments","authors":"Apurva Mishra, Pramit K. Chowdhury","doi":"10.1016/j.bbapap.2025.141099","DOIUrl":"10.1016/j.bbapap.2025.141099","url":null,"abstract":"<div><div>Protein aggregation plays a crucial role in various neurodegenerative diseases, including Huntington's disease. Understanding the factors influencing aggregation kinetics is essential for deciphering disease mechanisms. This research paper investigates the aggregation of a mutant Huntingtin protein (HD39Q) under various conditions, focusing on the impact of macromolecular crowding agents. The study employs multiple techniques, including fluorescence spectroscopy, circular dichroism, and nanoparticle tracking analysis, to characterize the aggregation kinetics and morphology. The results demonstrate that crowding agents significantly accelerate aggregation, with different agents exhibiting varying effects depending on their physicochemical properties. Fluorescence correlation spectroscopy provides insights into early-stage oligomerization. Confocal and scanning electron microscopy help visualize the resulting aggregates and fibrils. These findings contribute to a better understanding of how intracellular-like environments influence protein aggregation and provide valuable insights into the biophysical properties of aggregation-prone proteins.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141099"},"PeriodicalIF":2.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fei Yuan , FeiMing Huang , Xiaoyu Cao , Yu-Hang Zhang , KaiYan Feng , YuSheng Bao , Tao Huang , Yu-Dong Cai
{"title":"Integrative multi-omics machine learning reveals novel driver genes associations in lung adenocarcinoma","authors":"Fei Yuan , FeiMing Huang , Xiaoyu Cao , Yu-Hang Zhang , KaiYan Feng , YuSheng Bao , Tao Huang , Yu-Dong Cai","doi":"10.1016/j.bbapap.2025.141113","DOIUrl":"10.1016/j.bbapap.2025.141113","url":null,"abstract":"<div><div>Lung adenocarcinoma remains a major challenge in cancer research due to its complex molecular underpinnings. In this study, we developed an integrated machine learning framework to identify novel driver genes associated with lung adenocarcinoma by leveraging multi-omics data. We curated gene candidates from methylation, RNAseq, mutation, and miRNA levels, and mapped them onto a protein–protein interaction network from STRING to generate informative feature vectors using a node2vec method. Furthermore, they were also represented by GO and KEGG enrichment features. All features were then refined through a multi-step process, beginning with the Boruta algorithm for filtering and followed by the minimum redundancy maximum relevance method for ranking. An incremental feature selection strategy was employed to determine the optimal feature subsets, which were used to build predictive models with random forest and support vector machine classifiers. To address class imbalance, synthetic sampling was applied, and ten-fold cross-validation ensured model robustness. Consequently, we predicted 428, 105, 1039, and 1748 potential lung adenocarcinoma driver genes for RNAseq, methylation, mutation, and miRNA levels, respectively. Integrated analysis of overlapping gene sets further highlighted key candidates, including PQLC3, FAM192A, FAM83D, SPRED1, SFTPB, and TM4SF5, with high composite probability scores. Some identified genes may be the driver genes of lung adenocarcinoma and have some druggable potential. These findings provide new insights into the molecular mechanisms of lung adenocarcinoma and suggest promising targets for future diagnostic and therapeutic strategies.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141113"},"PeriodicalIF":2.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145487707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Insights into key kinase regulatory network of LARP1 based on co-occurring phosphorylation events","authors":"Ashika Bangera, Nazah Naurah, Samseera Ummar, Poornima Ramesh, Rajesh Raju","doi":"10.1016/j.bbapap.2025.141103","DOIUrl":"10.1016/j.bbapap.2025.141103","url":null,"abstract":"<div><div>LARP1 (La-related protein 1) is an important mediator of translation regulation that stabilizes terminal oligopyrimidine motif-containing mRNAs. LARP1, being a direct target of mechanistic Target of Rapamycin Complex 1 (mTORC1), undergoes phosphorylation in the presence of growth factors. Phosphorylation-dependent conformational changes in LARP1 dictate its ability to stabilize or repress mRNAs with 5′ terminal oligopyrimidine (TOP), which code for key proteins in ribosome biogenesis and translation. Due to this important role, LARP1 is involved in cancer cell survival, facilitating selective translation of oncogenic proteins with a tradeoff in cap-dependent translation. As the function of LARP1 is governed by phosphorylation, this review provides phosphoproteomics-based regulatory network of LARP1, identifying major phosphorylation sites, upstream kinases, and interactors, with mutual co-differential regulation events. Extensive literature synthesis identified 11 major phosphorylation sites of LARP1, and an understanding of interaction dynamics that contribute to functional plasticity of LARP1. Specially, this article synthesizes the co-regulatory network of LARP1 with other proteins, and the interactions central to mTOR signaling, phosphorylation of LARP1, and its functional role in disease manifestation. This approach focusing on the LARP1-kinase regulatory network is crucial in untangling its miscellaneous role in cancer, which provides novel therapeutic paths for malignancies.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141103"},"PeriodicalIF":2.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Novel interactions between FOXP2 and PAX6: Implications for neural development and autism spectrum disorders","authors":"Jessica Brothwell , Olamide Jeje , Dineo Mashamaite , Sylvia Fanucchi","doi":"10.1016/j.bbapap.2025.141110","DOIUrl":"10.1016/j.bbapap.2025.141110","url":null,"abstract":"<div><div>FOXP2 and PAX6 are transcription factors essential for neural development, with mutations in both linked to autism spectrum disorders (ASDs). Their DNA-binding domains include a forkhead domain (FHD) for FOXP2 and a paired domain (PD) plus homeodomain (HD) for PAX6. We investigated whether the FOXP2 FHD interacts directly with PAX6 PD or HD, and how such interactions influence DNA binding. Fluorescence anisotropy showed that all three domains bind specifically to their respective DNA targets with similar affinities. The FOXP2 FHD also interacts directly with both PAX6 PD and HD, with low micromolar binding affinities. Despite its stronger intrinsic DNA affinity, the FHD was displaced from its target DNA by both PAX6 domains, suggesting that protein–protein interactions can override DNA affinity under competitive conditions. In contrast, FOXP2 could not displace PD or HD from their DNA targets. Molecular docking supported these findings: DNA–protein interfaces were largely unchanged by the second protein, but protein–protein interfaces were strongly influenced by DNA occupancy. The H3 helix of FHD was identified as a central point for assembly, contributing to both DNA and protein interfaces. When FHD was bound to DNA, H3 was occupied, forcing PD or HD to dock at alternative, less optimal sites. HD maintained stronger contacts in these rearranged states, consistent with its greater competitive strength. This asymmetric interplay indicates competitive dominance by PAX6 and suggests mechanisms that could underlie transcriptional regulation in neurodevelopment.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141110"},"PeriodicalIF":2.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145487705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jia Hang , Huiwen Sun , Chengzhen Gao, Yan Zhu, Lijuan Yang, Yan Li
{"title":"LncRNA CERS6 - AS1 mediates the IGF2BP1/LIN28B axis to promote proliferation, migration and invasion in ovarian cancer","authors":"Jia Hang , Huiwen Sun , Chengzhen Gao, Yan Zhu, Lijuan Yang, Yan Li","doi":"10.1016/j.bbapap.2025.141117","DOIUrl":"10.1016/j.bbapap.2025.141117","url":null,"abstract":"<div><div>Ovarian cancer remains a significant clinical challenge for women's health, making it imperative to elucidate its underlying molecular mechanisms. LncRNA CERS6-AS1 and LIN28B-binding proteins play a vital role in the development of ovarian cancer. The expression levels of CERS6-AS1 and LIN28B in ovarian cancer tissues and cell lines were evaluated using qPCR. Protein levels were analyzed through IHC. The survival rate was assessed using the Kaplan-Meier curve. LIN28B or CERS6-AS1 was silenced via RNA interference (shRNA), and the effects on proliferation, migration, and invasion were examined through cell cloning, scratch assays, and Transwell assays. RNA pull-down and RIP experiments confirmed the binding of CERS6-AS1 to IGF2BP1 and enhances on the stability of LIN28B mRNA. Finally, LIN28B overexpression was performed for functional recovery experiments. Elevated expression of CERS6-AS1 and LIN28B was observed in both clinical ovarian cancer specimens and derived cell lines. The knockdown of LIN28B suppressed ovarian cancer cell proliferation, migration and invasion. Molecular investigations revealed that CERS6-AS1 stabilized LIN28B through IGF2BP1 binding. Furthermore, CERS6-AS1 depletion similarly attenuated malignant phenotypes, effects that were rescued by LIN28B overexpression. Collectively, the CERS6-AS1-regulated IGF2BP1/LIN28B signaling axis promoted ovarian cancer progression by enhancing tumor cell proliferation, migration and invasion, highlighting this pathway as a promising therapeutic target.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141117"},"PeriodicalIF":2.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145601994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Taiz dos Reis Santos , Mariana Nascimento Romero Trujilho , João Pedro Martins Silva Costa , Laurade Azevedo Maffeis Dalzoto , Ane Caroline Moreira Duarte , Karolaine Stella Siqueirade Moraes Valdivia , Ana Júliade Oliveira Machado , Vitória Caroline Domingues Rios , Tatiane Faustino de Moraes , Wagner Alves de Souza Judice , Marcelo Ferreira Marcondes , Maurício Ferreira Marcondes Machado
{"title":"Role of N-terminal of metacaspase of Candida albicans in calcium binding.","authors":"Taiz dos Reis Santos , Mariana Nascimento Romero Trujilho , João Pedro Martins Silva Costa , Laurade Azevedo Maffeis Dalzoto , Ane Caroline Moreira Duarte , Karolaine Stella Siqueirade Moraes Valdivia , Ana Júliade Oliveira Machado , Vitória Caroline Domingues Rios , Tatiane Faustino de Moraes , Wagner Alves de Souza Judice , Marcelo Ferreira Marcondes , Maurício Ferreira Marcondes Machado","doi":"10.1016/j.bbapap.2025.141090","DOIUrl":"10.1016/j.bbapap.2025.141090","url":null,"abstract":"<div><div>Metacaspases are members of the CD clan and share structural similarities with mammalian caspases but possess unique features. This study delves into the <em>Candida albicans</em> metacaspase CaMCA-Ia, a type I metacaspase. CaMCA-Ia demonstrates Ca<sup>2+</sup>-dependent autoprocessing and presents a hydrophobic N-terminal, which differs from that of type II metacaspases. Truncated CaMCA-Ia (CaMCA-Ia-ΔN86), lacking 86 N-terminal amino acids, undergoes gradual self-processing and intermolecular processing. Calcium addition induces multistep processing, leading to maturation. Like mammalian caspases, CaMCA-Ia-ΔN86 can activate other molecules, indicate intermolecular activation and accelerating maturation. Distinct binding sites for the full-length and truncated forms of CaMCA-Ia in interaction with Ca<sup>2+</sup> underscore the N-terminal's role in altering calcium affinity. These findings enhance the understanding of metacaspases' intricate activation and maturation dynamics, offering insights into potential drug targets for pathogenic fungi. The CaMCA mutants D252A, D268A, D299A, and D268/269 A display varied responses to calcium, while the corresponding CaMCA-Ia-ΔN86 mutants exhibit different processing patterns. The D268/299 A mutant showed processing after 48 h of incubation with calcium. Alterations in CaMCA structure and function, such as the deletion of the N-terminus and changes in the aspartates at the calcium-binding site, provide important insights into how CaMCA enzymatic activity and autoprocessing are regulated.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 6","pages":"Article 141090"},"PeriodicalIF":2.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144738199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evolution in neuropsychiatric cis-regulatory enhancers through human-specific neuronal mutations within transcription factor binding sites","authors":"Rabail Zehra Raza , Saad Raza , Sumayyah Naveed , Shahid Ali","doi":"10.1016/j.bbapap.2025.141095","DOIUrl":"10.1016/j.bbapap.2025.141095","url":null,"abstract":"<div><div><em>cis</em>-Regulatory elements (CREs) in multicellular genomes play a significant role in precise regulation of the genes. Increasing evidence has shown that alterations in CREs have had a drastic effect on the human brain evolution, neuronal cell adaptation and physiology. The human-specific sequence acceleration in CREs has not only changed the overall cognitive function of the human brain, but also seems to have strongly increased the risk of developing psychiatric disorders. Mapping the human-specific neuronal mutations within CREs remains to be a challenge and can largely impact the way DNA binding domain of the transcription factors interact with the CREs. In this study, we have identified human-specific neuronal mutations within transcription factor binding sites in neuropsychiatric enhancers of three major psychiatric disorders i.e. autism spectrum disorder, schizophrenia and bipolar disorder and studied the impact of human-specific neuronal mutations on binding affinities with the respective transcription factors via molecular dynamic simulation. Moreover, we have also identified signals of positive selection in the same set of empirically confirmed neuropsychiatric enhancers and correlated it with the way transcription factors bind with the human-specific and their counterpart ancestral allele harboring transcription factor binding sites.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 6","pages":"Article 141095"},"PeriodicalIF":2.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leila Rezaei Somee , Mansi Upadhyay , Rahul Shobhawat , Ashutosh Kumar , Mohammad Bagher Shahsavani , Stephanie Simon , Atiyeh Ghasemi , Issa Zarei , Massoud Amanlou , Ali Akbar Saboury , Ali Akbar Moosavi-Movahedi , Reza Yousefi
{"title":"The role of the N-terminal p.R56Q mutation in modulating oligomerization and chaperone activity of human αB-crystallin in relation to cardiomyopathy","authors":"Leila Rezaei Somee , Mansi Upadhyay , Rahul Shobhawat , Ashutosh Kumar , Mohammad Bagher Shahsavani , Stephanie Simon , Atiyeh Ghasemi , Issa Zarei , Massoud Amanlou , Ali Akbar Saboury , Ali Akbar Moosavi-Movahedi , Reza Yousefi","doi":"10.1016/j.bbapap.2025.141094","DOIUrl":"10.1016/j.bbapap.2025.141094","url":null,"abstract":"<div><div>αB-crystallin (αB-Cry), a critical small heat shock protein, is crucial for cellular proteostasis, especially in the heart and lens. αB-Cry mutations can disrupt its chaperone activity, leading to pathological conditions such as myopathy, cardiomyopathy, and cataracts. The p.R56Q mutation in the N-terminal domain, a region that participates in oligomerization as well as interactions with key proteins such as desmin and αA-Cry, has been associated with cardiomyopathy. However, its specific pathogenic mechanism is not well understood. This study aimed to elucidate the structural and functional consequences of the p.R56Q mutation. Recombinant p.R56Q αB-Cry was purified by chromatographic methods. Moreover, spectroscopic, microscopic, and computational techniques were employed to assess the influence of the mutation on protein function, structure, and stability. Our findings indicated that the p.R56Q mutation leads to significant alterations in human αB-Cry secondary to quaternary structures. The mutant protein was less stable and more prone to forming amyloid-like aggregates. The p.R56Q αB-Cry also formed larger oligomers and exhibited enhanced chaperone activity compared to its wild-type (Wt) protein counterpart. Interestingly, it had a greater affinity for binding to desmin and αA-Cry. While increased chaperone function might be expected to have protective effects, it could interfere paradoxically with critical cellular processes, such as apoptosis, and thus enhance disease pathogenesis. This research provides new insights into the molecular mechanisms underlying αB-Cry-associated cardiomyopathy by highlighting how the p.R56Q mutation alters structural dynamics and chaperone activity.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 6","pages":"Article 141094"},"PeriodicalIF":2.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Min Seon Ha , Chang Woo Han , Mi Suk Jeong , Se Bok Jang
{"title":"Structural insights of the complex formed by KRAS G12V and a novel TIG3 peptide","authors":"Min Seon Ha , Chang Woo Han , Mi Suk Jeong , Se Bok Jang","doi":"10.1016/j.bbapap.2025.141091","DOIUrl":"10.1016/j.bbapap.2025.141091","url":null,"abstract":"<div><div>Pancreatic cancer remains a severe malignancy with a dismal 5-year survival rate, and most pancreatic cancer patients harbor KRAS mutations, which are critical targets for anti-cancer drug development. However, the structural characteristics of KRAS present challenges for therapeutic targeting. In this study, we developed a novel peptide derived from TIG3 protein, a type II tumor suppressor, and confirmed its moderate affinity binding to KRAS G12V. X-ray crystallography revealed that this peptide binds near the Switch II domain of KRAS G12V, causing conformational changes likely to affect its activity. Furthermore, the peptide reduced the viability of cancer cell lines harboring the KRAS G12V mutation, thus demonstrating its potential as a KRAS G12V inhibitor. Our results indicate that the developed novel TIG3 peptide is a promising candidate for KRAS-targeted therapy and provide structural insights useful for the development of pancreatic ductal adenocarcinoma therapeutics.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 6","pages":"Article 141091"},"PeriodicalIF":2.3,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}