Pub Date : 2026-01-29DOI: 10.1016/j.bpj.2026.01.046
Ashley B. Hiett, Grant S. Hisao, Anne E. Robinson, Emma A. Morrison, Katherine A. Henzler-Wildman
{"title":"Multidrug Resistance Transporter EmrE is Only Moderately Sensitive to Lipid Composition","authors":"Ashley B. Hiett, Grant S. Hisao, Anne E. Robinson, Emma A. Morrison, Katherine A. Henzler-Wildman","doi":"10.1016/j.bpj.2026.01.046","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.046","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"14 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071651","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 : 2026-01-29DOI: 10.1016/j.bpj.2026.01.044
Shane LeCompte, Prosenjit Bagchi
{"title":"Influence of leukocyte adhesion on partitioning of healthy and diabetic red blood cells at vascular bifurcations","authors":"Shane LeCompte, Prosenjit Bagchi","doi":"10.1016/j.bpj.2026.01.044","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.044","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"77 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146072079","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 : 2026-01-27DOI: 10.1016/j.bpj.2026.01.043
Qinfang Sun, Sriram Aiyer, Avik Biswas, Allan Haldane, Sompriya Chatterjee, Nobuyuki Matubayasi, Dmitry Lyumkis, Ronald M. Levy
Predicting the positions of water molecules at the protein interface remains a formidable challenge in structural biology, fueling active research in this field. Here, we present a novel approach based on molecular dynamics (MD) simulations that utilize statistical thermodynamic signatures of water at protein interfaces that can be used to improve the accuracy of water placement in maps derived by cryogenic electron microscopy (cryo-EM). We employ an analysis based on the excess chemical potential, or the Work to Transfer (WT) a water molecule from the bulk to the interface. WT is a measure of the thermodynamic balance between the interaction energy of an interfacial water molecule with the protein and its free energy of interaction with all the other solvent molecules. WT is proportional to the log ratio of the local density of water molecules at the protein interface to the bulk density. Using apoferritin as a benchmark system, we found that 85% of the top 100 water locations with the most favorable excess chemical potential values are observed in one or more structures whose locations were determined from high resolution cryo-EM maps deposited in the PDB. 70% of the top 200 water locations indexed by excess chemical potential were also observed in PDB structures derived from the cryo-EM maps. The MD simulations are performed without experimental density restraints, and yet the water positions with favorable WT values correlate strongly to their corresponding position within experimentally defined maps. This work paves the way for the development of a cryo-EM water placement and refinement tool that integrates molecular dynamics simulations of the excess chemical potential with cryo-EM data for accurate modeling of water networks.
{"title":"Predicting Water at the Protein Interface in Cryo-EM Structures from MD-Excess Chemical Potential","authors":"Qinfang Sun, Sriram Aiyer, Avik Biswas, Allan Haldane, Sompriya Chatterjee, Nobuyuki Matubayasi, Dmitry Lyumkis, Ronald M. Levy","doi":"10.1016/j.bpj.2026.01.043","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.043","url":null,"abstract":"Predicting the positions of water molecules at the protein interface remains a formidable challenge in structural biology, fueling active research in this field. Here, we present a novel approach based on molecular dynamics (MD) simulations that utilize statistical thermodynamic signatures of water at protein interfaces that can be used to improve the accuracy of water placement in maps derived by cryogenic electron microscopy (cryo-EM). We employ an analysis based on the excess chemical potential, or the Work to Transfer (WT) a water molecule from the bulk to the interface. WT is a measure of the thermodynamic balance between the interaction energy of an interfacial water molecule with the protein and its free energy of interaction with all the other solvent molecules. WT is proportional to the log ratio of the local density of water molecules at the protein interface to the bulk density. Using apoferritin as a benchmark system, we found that 85% of the top 100 water locations with the most favorable excess chemical potential values are observed in one or more structures whose locations were determined from high resolution cryo-EM maps deposited in the PDB. 70% of the top 200 water locations indexed by excess chemical potential were also observed in PDB structures derived from the cryo-EM maps. The MD simulations are performed without experimental density restraints, and yet the water positions with favorable WT values correlate strongly to their corresponding position within experimentally defined maps. This work paves the way for the development of a cryo-EM water placement and refinement tool that integrates molecular dynamics simulations of the excess chemical potential with cryo-EM data for accurate modeling of water networks.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"130 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056258","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 : 2026-01-27DOI: 10.1016/j.bpj.2026.01.037
Niranjan Sarpangala, Ajay Gopinathan
Intracellular transport by teams of molecular motors is an essential cell-biological process that ensures the proper distribution of organelles, and other materials within cells. These teams of motors cooperate and compete in complex ways to achieve desired transport velocity and runlength. In-vitro experiments have observed that coupling motors through a lipid membrane that mimics in vivo membrane-bound cargoes leads to a higher cargo velocity. However, the mechanisms behind this increase in lipid cargo velocity are unclear. Here we seek to understand these mechanisms using Brownian dynamics simulations. We show that an underlying heterogeneity in single motor velocity is essential for the increased velocity of lipid cargoes. Our simulations also show that while the runlengths of both rigid and lipid cargoes increase, and the velocities decrease, with an increase in the fraction of slower motors, lipid cargoes can travel faster and substantially further with the same degree of heterogeneity, suggesting functional advantages of motor velocity heterogeneity. Together, our work explains mechanisms behind previous experimental observations and generates new experimentally testable predictions on velocities and runlengths relevant for in vivo transport.
{"title":"Membrane-bound cargo carried by teams of motors with heterogeneous velocities go faster and further","authors":"Niranjan Sarpangala, Ajay Gopinathan","doi":"10.1016/j.bpj.2026.01.037","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.037","url":null,"abstract":"Intracellular transport by teams of molecular motors is an essential cell-biological process that ensures the proper distribution of organelles, and other materials within cells. These teams of motors cooperate and compete in complex ways to achieve desired transport velocity and runlength. <ce:italic>In-vitro</ce:italic> experiments have observed that coupling motors through a lipid membrane that mimics <ce:italic>in vivo</ce:italic> membrane-bound cargoes leads to a higher cargo velocity. However, the mechanisms behind this increase in lipid cargo velocity are unclear. Here we seek to understand these mechanisms using Brownian dynamics simulations. We show that an underlying heterogeneity in single motor velocity is essential for the increased velocity of lipid cargoes. Our simulations also show that while the runlengths of both rigid and lipid cargoes increase, and the velocities decrease, with an increase in the fraction of slower motors, lipid cargoes can travel faster and substantially further with the same degree of heterogeneity, suggesting functional advantages of motor velocity heterogeneity. Together, our work explains mechanisms behind previous experimental observations and generates new experimentally testable predictions on velocities and runlengths relevant for <ce:italic>in vivo</ce:italic> transport.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"293 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056259","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 : 2026-01-24DOI: 10.1016/j.bpj.2026.01.031
Sarah Warrelmann, Gerrit H.U. Lamm, Kirill Kovalev, Josef Wachtveitl
{"title":"Diverging pH dependence and photocycle dynamics across members of the CryoRhodopsin clade","authors":"Sarah Warrelmann, Gerrit H.U. Lamm, Kirill Kovalev, Josef Wachtveitl","doi":"10.1016/j.bpj.2026.01.031","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.031","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"258 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146033194","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 : 2026-01-24DOI: 10.1016/j.bpj.2026.01.028
Mauricio Garcia-Benitez, Matthew Scott, Ross Carlson, Radhakrishnan Mahadevan
{"title":"Membrane and Proteome Allocation Constraints in Escherichia coli Models during Overflow Metabolism","authors":"Mauricio Garcia-Benitez, Matthew Scott, Ross Carlson, Radhakrishnan Mahadevan","doi":"10.1016/j.bpj.2026.01.028","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.01.028","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"7 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146033193","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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