Pub Date : 2026-01-31DOI: 10.1016/j.bpj.2026.01.048
Gavin Shuyang Ni, Hetian Su, Yingqi Zhu, Anshika Dhiman, Huan-Xiang Zhou, Wei Lin, Nan Hao
{"title":"Tardigrade Dsup: Interactions with DNA and protection of cells from oxidative stress","authors":"Gavin Shuyang Ni, Hetian Su, Yingqi Zhu, Anshika Dhiman, Huan-Xiang Zhou, Wei Lin, Nan Hao","doi":"10.1016/j.bpj.2026.01.048","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.048","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"30 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146089421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-31DOI: 10.1016/j.bpj.2026.01.052
Ruth Nussinov, Hyunbum Jang
{"title":"Condensates and Cell States: A New Paradigm for Understanding Tumor Biology","authors":"Ruth Nussinov, Hyunbum Jang","doi":"10.1016/j.bpj.2026.01.052","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.052","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"28 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146095772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-31DOI: 10.1016/j.bpj.2026.01.035
Kristin P. Kim, Abigail Brooks, Christopher A. Lemmon
{"title":"Investigating TGF-β1-induced Renal Fibrosis in a Parallel Computational-Experimental Spheroid System","authors":"Kristin P. Kim, Abigail Brooks, Christopher A. Lemmon","doi":"10.1016/j.bpj.2026.01.035","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.035","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"29 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146089422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-30DOI: 10.1016/j.bpj.2026.01.038
Katie Lynn Whitcomb, Kurt Warncke
{"title":"Protein Structure and Coupled Solvent Dynamics in α-Synuclein Fibrils under Controlled Confinement","authors":"Katie Lynn Whitcomb, Kurt Warncke","doi":"10.1016/j.bpj.2026.01.038","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.038","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"44 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146072076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-30DOI: 10.1016/j.bpj.2026.01.055
Yilun Han,Yu Xia
Protein phosphorylation is crucial in many cellular functions. Although the existence of functionally dispensable phosphosites is well recognized, previous estimation of dispensable content in the phosphoproteome has not quantitatively assessed how functional dispensability of a phosphosite is related to the degree of its perturbation specificity, i.e., the number of environmental perturbations where the phosphosite is phosphorylated. Here, we address this question by integrating a high-quality, perturbation-specific yeast phosphoproteome with site-specific evolutionary rate relative to adjacent residues of the site in the protein sequence (denoted "relative evolutionary rate"), a proxy for functional dispensability. We observe extreme heterogeneity in perturbation specificity among phosphosites, where the majority of phosphosites are phosphorylated either under only a few perturbations (denoted "conditional phosphosites") or across nearly all perturbations (denoted "near-universal phosphosites"), yielding a bimodal distribution of perturbation specificity. Our evolutionary analyses reveal that, in disordered regions, perturbation specificity is a key correlate of functional dispensability of phosphosites. Conditional and near-universal phosphosites exhibit significantly higher and lower average relative evolutionary rate than all other experimental and literature-curated phosphoproteome datasets considered, respectively. These trends remain robust even when residue burial is controlled, suggesting that conditional and near-universal phosphosites contain the highest and the lowest levels of dispensable content in disordered regions respectively among all phosphoproteome datasets considered. Using the near-universal phosphosites and serine/threonine sites not known to be phosphorylated to set the lower and upper bounds of the dispensable content spectrum, we estimate that ∼30%-40% of phosphosites in disordered regions of the yeast phosphoproteome are functionally dispensable.
{"title":"Relationship between perturbation specificity and functional dispensability in yeast phosphoproteome.","authors":"Yilun Han,Yu Xia","doi":"10.1016/j.bpj.2026.01.055","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.055","url":null,"abstract":"Protein phosphorylation is crucial in many cellular functions. Although the existence of functionally dispensable phosphosites is well recognized, previous estimation of dispensable content in the phosphoproteome has not quantitatively assessed how functional dispensability of a phosphosite is related to the degree of its perturbation specificity, i.e., the number of environmental perturbations where the phosphosite is phosphorylated. Here, we address this question by integrating a high-quality, perturbation-specific yeast phosphoproteome with site-specific evolutionary rate relative to adjacent residues of the site in the protein sequence (denoted \"relative evolutionary rate\"), a proxy for functional dispensability. We observe extreme heterogeneity in perturbation specificity among phosphosites, where the majority of phosphosites are phosphorylated either under only a few perturbations (denoted \"conditional phosphosites\") or across nearly all perturbations (denoted \"near-universal phosphosites\"), yielding a bimodal distribution of perturbation specificity. Our evolutionary analyses reveal that, in disordered regions, perturbation specificity is a key correlate of functional dispensability of phosphosites. Conditional and near-universal phosphosites exhibit significantly higher and lower average relative evolutionary rate than all other experimental and literature-curated phosphoproteome datasets considered, respectively. These trends remain robust even when residue burial is controlled, suggesting that conditional and near-universal phosphosites contain the highest and the lowest levels of dispensable content in disordered regions respectively among all phosphoproteome datasets considered. Using the near-universal phosphosites and serine/threonine sites not known to be phosphorylated to set the lower and upper bounds of the dispensable content spectrum, we estimate that ∼30%-40% of phosphosites in disordered regions of the yeast phosphoproteome are functionally dispensable.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"40 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146095504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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