Pub Date : 2025-10-13DOI: 10.1016/j.bbapap.2025.141101
Yurou Li, Kaiyong Zheng, Chunsheng Chen, Yi Wu, Shuai Li, Weihong Zhou, Xinqi Liu
NLRP3 is one of the central players in innate immune signaling. Upon stimulation, NLRP3 could oligomerize and recruit ASC, NEK7, and caspase 1 (CASP1), then assemble into inflammasome, triggering downstream inflammation and pyroptosis. Recently, it was reported that both potassium efflux dependent and independent signaling, could lead to the formation of dispersed TGN (dTGN), where NLRP3 was initially recruited. Interestingly, the phosphatidylinositol-4-phosphate (PI4P) enriched on dTGN is indispensable for NLRP3 recruitment. In this study, we found that Phafin2, which can bind PI4P and PI3P via its PH and FYVE domains respectively, could modulate the NLRP3 aggregation on dTGN, thus regulating the cell pyroptosis. Phafin2 affects NLRP3 aggregation indirectly by influencing the constitution of dTGN. Our study unravels Phafin2 might act as a critical regulator of NLRP3-mediated pyroptosis, thus providing a new therapeutic target for human diseases associated with NLRP3-involved inflammation.
{"title":"Phafin2 modulates the aggregation of NLRP3 on dispersed trans-Golgi network","authors":"Yurou Li, Kaiyong Zheng, Chunsheng Chen, Yi Wu, Shuai Li, Weihong Zhou, Xinqi Liu","doi":"10.1016/j.bbapap.2025.141101","DOIUrl":"10.1016/j.bbapap.2025.141101","url":null,"abstract":"<div><div>NLRP3 is one of the central players in innate immune signaling. Upon stimulation, NLRP3 could oligomerize and recruit ASC, NEK7, and caspase 1 (CASP1), then assemble into inflammasome, triggering downstream inflammation and pyroptosis. Recently, it was reported that both potassium efflux dependent and independent signaling, could lead to the formation of dispersed TGN (dTGN), where NLRP3 was initially recruited. Interestingly, the phosphatidylinositol-4-phosphate (PI4P) enriched on dTGN is indispensable for NLRP3 recruitment. In this study, we found that Phafin2, which can bind PI4P and PI3P via its PH and FYVE domains respectively, could modulate the NLRP3 aggregation on dTGN, thus regulating the cell pyroptosis. Phafin2 affects NLRP3 aggregation indirectly by influencing the constitution of dTGN. Our study unravels Phafin2 might act as a critical regulator of NLRP3-mediated pyroptosis, thus providing a new therapeutic target for human diseases associated with NLRP3-involved inflammation.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141101"},"PeriodicalIF":2.3,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145298143","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}
Pub Date : 2025-09-15DOI: 10.1016/j.bbapap.2025.141100
Lin Qi , Mark Isalan
De novo proteins represent a challenging frontier at the intersection of evolutionary biology and synthetic biology. Broadly, the term encompasses two distinct categories: naturally evolved de novo proteins, which arise from previously non-coding DNA, and synthetically designed de novo proteins, which are created from scratch through computational and experimental methods. This review provides an overview of the definitions, history, functional significance, and investigation methods for both categories. By examining potential challenges in current de novo protein research, this review highlights the growing convergence between natural evolutionary processes and rational protein engineering, reflecting their importance in biological discovery and human innovations.
{"title":"Structure prediction and engineering of de novo proteins","authors":"Lin Qi , Mark Isalan","doi":"10.1016/j.bbapap.2025.141100","DOIUrl":"10.1016/j.bbapap.2025.141100","url":null,"abstract":"<div><div><em>De novo</em> proteins represent a challenging frontier at the intersection of evolutionary biology and synthetic biology. Broadly, the term encompasses two distinct categories: naturally evolved <em>de novo</em> proteins, which arise from previously non-coding DNA, and synthetically designed <em>de novo</em> proteins, which are created from scratch through computational and experimental methods. This review provides an overview of the definitions, history, functional significance, and investigation methods for both categories. By examining potential challenges in current <em>de novo</em> protein research, this review highlights the growing convergence between natural evolutionary processes and rational protein engineering, reflecting their importance in biological discovery and human innovations.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141100"},"PeriodicalIF":2.3,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079608","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}
Pub Date : 2025-09-15DOI: 10.1016/j.bbapap.2025.141099
Apurva Mishra, Pramit K. Chowdhury
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.
{"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":"2025-09-15","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}
Scenedesmus quadricauda, a freshwater microalga, has gained attention for its high lipid accumulation potential. However, information on fatty acid (FA) biosynthesis pathways in Scenedesmus species remains limited. Biomass (1.010 gL−1) and lipid content (404 mgL−1) in S. quadricauda were found to be higher compared to other microalgal isolates under autotrophic nutrition. All biodiesel indices were found within the defined range of biodiesel (EN14214) and petro-diesel (EN590:2013) standards. The predominant fatty acid was palmitic acid (16:0), accounting for 33.201 % of the total. Further, homology study and 3D models of all subunits of S. quadricauda enzymes acetyl-CoA carboxylase (ACC) – the key enzyme of the FA biosynthetic pathway - identified distinct structural features. The biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), β-carboxyltransferases (β-CT) subunits of the heteromeric ACC of S. quadricauda showed homology with its eukaryotic counterparts, whereas the α -carboxyltransferases (α-CT) subunit showed homology with prokaryotic carboxyltransferase. In contrast, homologous enzymes in other Scenedesmus species were found to resemble prokaryotic forms exclusively. Conserved motifs such as the glycine-rich loop, ERYV motif, and AAAP motif were identified in the BC and BCCP enzymes. Malonyl-CoA:ACP transacylase (MAT) enzyme of S. quadricauda was of prokaryotic origin but showed structural divergence from its homologs in other Scenedesmus species. Fatty-acyl thioesterases (FAT) enzyme contained a duplication of two 4-hydroxybenzoyl-CoA thioesterase-like domains (4HBT). These unique sequences and binding sites in the fatty acid biosynthesis enzymes of S. quadricauda may contribute to the distinct regulation of carbon flux and lipid assembly compared to other species.
{"title":"Characterization of fatty acid biosynthesis in microalga Scenedesmus - from the perspective of biofuel production","authors":"Harshit Kumar Sharma , Ma. Belén Velázquez , Noelia Marchetti , Ma. Victoria Busi , Ajay Kumar , Julieta Barchiesi , Chitralekha Nag Dasgupta","doi":"10.1016/j.bbapap.2025.141097","DOIUrl":"10.1016/j.bbapap.2025.141097","url":null,"abstract":"<div><div><em>Scenedesmus quadricauda</em>, a freshwater microalga, has gained attention for its high lipid accumulation potential. However, information on fatty acid (FA) biosynthesis pathways in <em>Scenedesmus</em> species remains limited. Biomass (1.010 gL<sup>−1</sup>) and lipid content (404 mgL<sup>−1</sup>) in <em>S. quadricauda</em> were found to be higher compared to other microalgal isolates under autotrophic nutrition. All biodiesel indices were found within the defined range of biodiesel (EN14214) and petro-diesel (EN590:2013) standards. The predominant fatty acid was palmitic acid (16:0), accounting for 33.201 % of the total. Further, homology study and 3D models of all subunits of <em>S. quadricauda</em> enzymes acetyl-CoA carboxylase (ACC) – the key enzyme of the FA biosynthetic pathway - identified distinct structural features. The biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), β-carboxyltransferases (β-CT) subunits of the heteromeric ACC of <em>S. quadricauda</em> showed homology with its eukaryotic counterparts, whereas the α -carboxyltransferases (α-CT) subunit showed homology with prokaryotic carboxyltransferase. In contrast, homologous enzymes in other <em>Scenedesmus</em> species were found to resemble prokaryotic forms exclusively. Conserved motifs such as the glycine-rich loop, ERYV motif, and AAAP motif were identified in the BC and BCCP enzymes. Malonyl-CoA:ACP transacylase (MAT) enzyme of <em>S. quadricauda</em> was of prokaryotic origin but showed structural divergence from its homologs in other <em>Scenedesmus</em> species. Fatty-acyl thioesterases (FAT) enzyme contained a duplication of two 4-hydroxybenzoyl-CoA thioesterase-like domains (4HBT). These unique sequences and binding sites in the fatty acid biosynthesis enzymes of <em>S. quadricauda</em> may contribute to the distinct regulation of carbon flux and lipid assembly compared to other species.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1874 1","pages":"Article 141097"},"PeriodicalIF":2.3,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013758","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}
Pub Date : 2025-08-18DOI: 10.1016/j.bbapap.2025.141096
Morten Hulbæk Fog , Violaine Hubert , Corinne Sanglar , Marie Martin , Ines Hristovska , Szilvia Karpati , Frédéric Lerouge , Stéphane Parola , Olivier Pascual , Marlène Wiart , Jean-Marc Lancelin , Thomas Vorup-Jensen , Florence Guillière
Simvastatin is a primary cholesterol-lowering medication, but it has also been reported to possess anti-inflammatory properties. Notably, the CD18 integrins are targets for simvastatin antagonism of ligand binding, which may affect leukocyte adhesion and diapedesis. Lymphocyte-associated antigen (LFA)-1 is inhibited through an allosteric mechanism by binding the lactone form of simvastatin (simvastatin-lac) to a hydrophobic pocket in the major ligand binding domain, the alpha chain I domain. By contrast, crystallographic evidence showed that complement receptor 3 (CR3) is inhibited by simvastatin in its carboxylate form (simvastatin-carbox) chelated by an Mg2+ ion in the αMI metal ion-dependent adhesion site (MIDAS). We now report that the affinity (KD) of simvastatin-carbox for the αMI is ∼650 μM, which is significantly weaker than the 50 %-inhibitory concentration of simvastatin-lac at 50 μM. The simvastatin-carbox was incapable of inhibiting CR3 binding to iC3b, nor did it exert any neuroprotective or anti-inflammatory effects in the middle cerebral artery occlusion animal model of stroke, unlike what has been reported for simvastatin-lac. From available structural data on the CR3 ligand binding domain in complex with C3d, we suggest that simvastatin-lac makes a critical ternary complex with the ligand binding domain and its ligand before engaging, in its carboxylate form, the MIDAS. In this way, both the LFA-1 and CR3 are antagonized by simvastatin-lac but through fundamentally different mechanisms.
{"title":"Solution-based studies on the contact between the complement receptor 3 ligand-binding domain and simvastatin","authors":"Morten Hulbæk Fog , Violaine Hubert , Corinne Sanglar , Marie Martin , Ines Hristovska , Szilvia Karpati , Frédéric Lerouge , Stéphane Parola , Olivier Pascual , Marlène Wiart , Jean-Marc Lancelin , Thomas Vorup-Jensen , Florence Guillière","doi":"10.1016/j.bbapap.2025.141096","DOIUrl":"10.1016/j.bbapap.2025.141096","url":null,"abstract":"<div><div>Simvastatin is a primary cholesterol-lowering medication, but it has also been reported to possess anti-inflammatory properties. Notably, the CD18 integrins are targets for simvastatin antagonism of ligand binding, which may affect leukocyte adhesion and diapedesis. Lymphocyte-associated antigen (LFA)-1 is inhibited through an allosteric mechanism by binding the lactone form of simvastatin (simvastatin-lac) to a hydrophobic pocket in the major ligand binding domain, the alpha chain I domain. By contrast, crystallographic evidence showed that complement receptor 3 (CR3) is inhibited by simvastatin in its carboxylate form (simvastatin-carbox) chelated by an Mg<sup>2+</sup> ion in the α<sub>M</sub>I metal ion-dependent adhesion site (MIDAS). We now report that the affinity (<em>K</em><sub>D</sub>) of simvastatin-carbox for the α<sub>M</sub>I is ∼650 μM, which is significantly weaker than the 50 %-inhibitory concentration of simvastatin-lac at 50 μM. The simvastatin-carbox was incapable of inhibiting CR3 binding to iC3b, nor did it exert any neuroprotective or anti-inflammatory effects in the middle cerebral artery occlusion animal model of stroke, unlike what has been reported for simvastatin-lac. From available structural data on the CR3 ligand binding domain in complex with C3d, we suggest that simvastatin-lac makes a critical ternary complex with the ligand binding domain and its ligand before engaging, in its carboxylate form, the MIDAS. In this way, both the LFA-1 and CR3 are antagonized by simvastatin-lac but through fundamentally different mechanisms.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 6","pages":"Article 141096"},"PeriodicalIF":2.3,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144879930","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}
cis-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.
{"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":"2025-08-13","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}
Pub Date : 2025-08-13DOI: 10.1016/j.bbapap.2025.141094
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
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.
α b -晶体蛋白（αB-Cry）是一种重要的小热休克蛋白，对细胞的蛋白质平衡至关重要，特别是在心脏和晶状体中。αB-Cry突变可破坏其伴侣活性，导致肌病、心肌病和白内障等病理状况。n端结构域的p.R56Q突变与心肌病有关，该区域参与寡聚化以及与desmin和αA-Cry等关键蛋白的相互作用。然而，其具体的致病机制尚不清楚。本研究旨在阐明p.R56Q突变的结构和功能后果。重组p.R56Q αB-Cry经层析纯化。此外，利用光谱、显微镜和计算技术来评估突变对蛋白质功能、结构和稳定性的影响。我们的研究结果表明，p.R56Q突变导致人类αB-Cry二级至四级结构的显著改变。突变蛋白不太稳定，更容易形成淀粉样聚集体。与野生型（Wt）蛋白相比，p.R56Q αB-Cry也形成了更大的低聚物，并表现出更强的伴侣活性。有趣的是，它对desmin和αA-Cry的结合有更大的亲和力。虽然伴侣蛋白功能的增加可能具有保护作用，但它可能矛盾地干扰关键的细胞过程，如细胞凋亡，从而增强疾病的发病机制。这项研究通过强调p.R56Q突变如何改变结构动力学和伴侣活性，为α b - cry相关心肌病的分子机制提供了新的见解。
{"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":"2025-08-13","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}
Pub Date : 2025-07-31DOI: 10.1016/j.bbapap.2025.141091
Min Seon Ha , Chang Woo Han , Mi Suk Jeong , Se Bok Jang
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.
{"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":"2025-07-31","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}
Pub Date : 2025-07-28DOI: 10.1016/j.bbapap.2025.141090
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
Metacaspases are members of the CD clan and share structural similarities with mammalian caspases but possess unique features. This study delves into the Candida albicans metacaspase CaMCA-Ia, a type I metacaspase. CaMCA-Ia demonstrates Ca2+-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 Ca2+ 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.
metacaspase是CD家族的成员，与哺乳动物caspase具有结构相似性，但具有独特的特征。本研究深入研究了白色念珠菌metacaspase CaMCA-Ia，一种I型metacaspase。CaMCA-Ia表现出Ca2+依赖性的自动加工，并呈现一个疏水的n端，这与II型metacaspase不同。截断的CaMCA-Ia （CaMCA-Ia-ΔN86）缺少86个n端氨基酸，经过逐渐的自我加工和分子间加工。添加钙诱导多步骤加工，导致成熟。像哺乳动物的半胱天冬酶一样，CaMCA-Ia-ΔN86可以激活其他分子，表明分子间的激活和加速成熟。与Ca2+相互作用的CaMCA-Ia全长和截短形式的不同结合位点强调了n端在改变钙亲和力中的作用。这些发现增强了对metacaspase复杂的激活和成熟动力学的理解，为致病真菌的潜在药物靶点提供了见解。CaMCA突变体D252A、D268A、D299A和D268/269 A对钙表现出不同的反应，而相应的CaMCA- ia -ΔN86突变体表现出不同的加工模式。D268/299 A突变体与钙孵育48小时后出现加工。CaMCA结构和功能的改变，如n端缺失和钙结合位点天冬氨酸的变化，为CaMCA酶活性和自动加工是如何被调节提供了重要的见解。
{"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":"2025-07-28","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号