Protein Science最新文献

Function within disorder: Small heat shock proteins use different functional regions to chaperone tau aggregation. 功能紊乱：小的热休克蛋白使用不同的功能区域来陪伴tau聚集。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-10-01 DOI: 10.1002/pro.70780

Mia Cervantes, Maria K Janowska, Lisa M Tuttle, Miklos Guttman, Abhinav Nath, Rachel E Klevit

{"title":"Function within disorder: Small heat shock proteins use different functional regions to chaperone tau aggregation.","authors":"Mia Cervantes, Maria K Janowska, Lisa M Tuttle, Miklos Guttman, Abhinav Nath, Rachel E Klevit","doi":"10.1002/pro.70780","DOIUrl":"10.1002/pro.70780","url":null,"abstract":"In numerous neurodegenerative diseases known collectively as tauopathies, the microtubule-associated protein tau forms fibrillar aggregates that are hallmarks of disease pathology. Tauopathies represent a substantial fraction of diseases associated with protein misfolding. Cellular chaperones known as small heat shock proteins (sHSPs) play a critical role in maintaining protein homeostasis by delaying the onset of protein aggregation. Two sHSPs, HSPB1 (Hsp27) and HSPB5 (αB-crystallin), are constitutively expressed in the brain and neurons. Here, we show that HSPB1 and HSPB5 delay tau aggregation in vitro through distinct mechanisms dictated by their disordered N-terminal regions (NTRs). HSPB1 inhibits tau aggregation under normal cellular conditions, whereas HSPB5 displays activity toward tau when activated by stress conditions such as pH acidosis. Using chimeric HSPB1/HSPB5 constructs in which small NTR subregions are swapped, we identify functional regions within the NTRs that modulate chaperone function for tau. The functional regions contain known sites of phosphorylation, suggesting that they are also control points that respond to cellular stress conditions. Our findings support an emerging model in which specific functional motifs within disordered regions of sHSPs govern activity and client engagement under normal and stress conditions.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 10","pages":"e70780"},"PeriodicalIF":5.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977751","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

Symmetry analysis and ancestral sequence reconstruction reveal a symmetrical translocation pathway and activity determinants of ZIP metal transporters. 对称性分析和祖先序列重建揭示了ZIP金属转运蛋白的对称易位途径和活性决定因素。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-10-01 DOI: 10.1002/pro.70802

Yao Zhang, Tianqi Wang, Hongyan Zhao, Jian Hu

{"title":"Symmetry analysis and ancestral sequence reconstruction reveal a symmetrical translocation pathway and activity determinants of ZIP metal transporters.","authors":"Yao Zhang, Tianqi Wang, Hongyan Zhao, Jian Hu","doi":"10.1002/pro.70802","DOIUrl":"10.1002/pro.70802","url":null,"abstract":"Membrane transporters frequently exhibit internal structural symmetry, reflecting evolutionary origins through gene duplication and fusion events, and this feature has been widely used to infer transport mechanisms. Yet its application to the Zrt-/Irt-like protein (ZIP) family of divalent metal transporters, which are crucial for trace metal homeostasis, has not been fully explored. Here, we apply combined symmetry analysis and ancestral sequence reconstruction (ASR) to study the ZIP family. We show that internal symmetry is broadly present across prokaryotic ZIPs and is more prominent in reconstructed ancestral sequences, supporting an evolutionary pathway in which the modern 8-transmembrane (TM) ZIP fold arose from duplication, circular permutation, and fusion of an ancestral 4-TM protein. Leveraging this symmetry framework, we identify a continuous and symmetric metal translocation pathway composed of symmetric entry, transport, and exit sites in the ZIP fold and define gates that ensure alternating access. Application of this structural model to human ZIP4 enables identification of the gate-forming residues, and functional studies reveal that two residues (T529 and V533) in the external gate play a crucial role in controlling metal transport. In addition, comparison with ancestral sequences uncovers a set of LIV-1 subfamily-specific metal-chelating residues (D504, E541, and D544) that break the symmetry in the ancestral sequences. Functional studies showed that these residues play distinct roles in transport. Together, our study demonstrates that combining internal symmetry analysis and ASR for the ZIP family facilitates elucidation of the metal translocation mechanism and identification of subfamily-specific features that regulate transport function.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 10","pages":"e70802"},"PeriodicalIF":5.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977780","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

RheoScale 2.0: Revealing the hidden roles of protein positions via substitution patterns. RheoScale 2.0：通过取代模式揭示蛋白质位置的隐藏作用。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-10-01 DOI: 10.1002/pro.70804

David H Liu, Shwetha Sreenivasan, Carter J Gray, Hannah C Cleveland, Liskin Swint-Kruse

{"title":"RheoScale 2.0: Revealing the hidden roles of protein positions via substitution patterns.","authors":"David H Liu, Shwetha Sreenivasan, Carter J Gray, Hannah C Cleveland, Liskin Swint-Kruse","doi":"10.1002/pro.70804","DOIUrl":"10.1002/pro.70804","url":null,"abstract":"A central challenge in molecular biology is understanding how amino acid substitutions modulate various features of protein function and stability. To illuminate the complexities of this relationship, high-throughput (HTP) assays are increasingly used to assess site-saturating mutagenesis libraries. A common downstream analysis is to average the set of 20 outcomes at each amino acid position for comparison with structural and evolutionary features. Average values clearly identify positions that tolerate most substitutions (neutral positions) and positions where most substitutions abolish activity (toggle positions). However, average values conceal the existence of rheostat positions, where different amino acid substitutions sample a wide range of outcomes. To quantitatively identify rheostat positions, we previously developed a histogram-based analysis that we here expand by: (i) incorporating new position classes observed in experimental studies of rheostat positions; (ii) formalizing a hierarchy of class assignments; (iii) refining error-based identification of neutral positions; and (iv) statistically assessing the robustness of class assignments to changes in experimental and computational parameters. RheoScale 2.0 is implemented in Excel and newly implemented in Python for facile integration with existing HTP pipelines; all parameters are customizable. Example analyses are shown for three HTP datasets of the SARS-CoV-2 papain-like protease. Results illustrate two aspects that influence interpretation of HTP data: First, position assignments (and substitution outcomes) depend highly on the measured feature. Second, many protein positions play multiple roles in the sequence-structure-function relationship. The recognition of varied position roles will advance understanding of pathogen evolution, protein engineering, and variant interpretation for personalized medicine.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 10","pages":"e70804"},"PeriodicalIF":5.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13592226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012829","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

Topologically complex knotted proteins are processed differentially by ATP-dependent proteases ClpXP and ClpAP. 拓扑结构复杂的结蛋白被atp依赖性蛋白酶ClpXP和ClpAP处理的方式不同。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-10-01 DOI: 10.1002/pro.70789

Soham Mukherjee, Hema Chandra Kotamarthi

{"title":"Topologically complex knotted proteins are processed differentially by ATP-dependent proteases ClpXP and ClpAP.","authors":"Soham Mukherjee, Hema Chandra Kotamarthi","doi":"10.1002/pro.70789","DOIUrl":"10.1002/pro.70789","url":null,"abstract":"Knotted proteins can present a distinct topological and mechanical challenge to the AAA+ cellular degradation machineries, determined by the relative size of the knot and the pore dimensions of these enzymes. In this study, we investigated the degradation mechanism of knotted proteins of different topological complexities by two E. coli. AAA+ proteases ClpXP and ClpAP. While ClpXP efficiently degraded all knotted substrates, regardless of their topology, ClpAP exhibited a striking functional divergence. Despite its robust double-ring ATPase architecture, ClpAP failed to degrade the 41-knotted miRFP and degraded the 31-knotted CAIX and more complex 52-knotted UCHL1 slower than ClpXP. We have demonstrated that this disparity is not dictated merely by absolute knot complexity, but is critically governed by the length of the knot tail, which determines whether a knot can spontaneously unthread or is forced to tighten during the translocation. Furthermore, based on the slower processing of a sterically constrained covalent dimeric substrate Arc-ssrA, we propose that ClpAP's hindered processing of knotted substrates stems from its smaller axial pore. Overall, we propose a unified physical model in which the successful degradation of a knotted protein relies on a delicate interplay among knot compaction, tail-mediated unthreading, and the architectural permissiveness of the unfoldase pore.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 10","pages":"e70789"},"PeriodicalIF":5.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977757","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

Conformational ensembles of the disordered 4E-BP2:eIF4E complex restrained by smFRET experiments. smFRET实验抑制无序4E-BP2:eIF4E复合物的构象集成。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-10-01 DOI: 10.1002/pro.70777

Spencer Smyth, Zi Hao Liu, Thomas E Tsangaris, Teresa Head-Gordon, Julie D Forman-Kay, Claudiu C Gradinaru

{"title":"Conformational ensembles of the disordered 4E-BP2:eIF4E complex restrained by smFRET experiments.","authors":"Spencer Smyth, Zi Hao Liu, Thomas E Tsangaris, Teresa Head-Gordon, Julie D Forman-Kay, Claudiu C Gradinaru","doi":"10.1002/pro.70777","DOIUrl":"10.1002/pro.70777","url":null,"abstract":"Eukaryotic cap-dependent translation initiation is regulated by binding of the predominantly folded eukaryotic initiation factor 4E (eIF4E) to the intrinsically disordered eIF4E binding proteins (4E-BPs). Here, we report full-length atomistic conformational ensembles generated by IDPConformerGenerator and optimized by X-EISDv2 workflow for both apo 4E-BP2, the neuronal 4E-BP, and 4E-BP2 in complex with eIF4E, using data from single-molecule fluorescence and nuclear magnetic resonance (NMR), together with select coordinates from a 4E-BP1:eIF4E crystal structure. Structural sampling within dynamic complexes is often underappreciated, with NMR and crystal structure data for 4E-BP:eIF4E suggesting different degrees of structural heterogeneity. Our ensemble models validated by solution spectroscopy data enable comparison of free 4E-BP2 and its complex with eIF4E. This shows a delocalization of contacts around canonical regions, which supports previous findings of unidirectional conditional occupancy of the binding sites. Two new contact regions emerged: one between the disordered N-termini of eIF4E and 4E-BP2, which may play an allosteric role in tuning the binding affinity, and the other between the C-terminus of 4E-BP2 and an extended region of eIF4E, which is consistent with the extended, dynamic binding interface that we reported previously. These results support a model of translation regulation in which the dynamic 4E-BP2:eIF4E complex facilitates accessibility of regulatory sites of 4E-BP2 when bound.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 10","pages":"e70777"},"PeriodicalIF":5.6,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13575984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970893","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

Quaternary structures of Streptococcus pneumoniae nucleoside diphosphate kinase: From hexamers to supramolecular assemblies. 肺炎链球菌核苷二磷酸激酶的四级结构：从六聚体到超分子组装体。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70735

Julie Kerboeuf, Paul Nouri, Frédéric Galisson, Laetitia Daury, Marie-France Giraud, Olivier Lambert, Cédric Orelle, Lionel Ballut, Elise Kaplan, Jean-Michel Jault, Cécile Gonzalez

{"title":"Quaternary structures of Streptococcus pneumoniae nucleoside diphosphate kinase: From hexamers to supramolecular assemblies.","authors":"Julie Kerboeuf, Paul Nouri, Frédéric Galisson, Laetitia Daury, Marie-France Giraud, Olivier Lambert, Cédric Orelle, Lionel Ballut, Elise Kaplan, Jean-Michel Jault, Cécile Gonzalez","doi":"10.1002/pro.70735","DOIUrl":"10.1002/pro.70735","url":null,"abstract":"The nucleoside diphosphate kinase (NDK) is a key enzyme that controls the balance of nucleotide pools in all living organisms. Beyond this fundamental role, NDKs exert pleiotropic effects in many cellular processes, including cell development, signal transduction, differentiation, tumor metastasis, and gene expression. The quaternary structure of NDK is typically hexameric-organized as a trimer of dimers in eukaryotic cells and in many prokaryotes-though in some species it can also be tetrameric. Here, we report the crystal structure of Streptococcus pneumoniae NDK (SpNDK) in its apo state (1.2 Å) and in an adenosine diPhosphate (ADP)-vanadate-bound state (3.4 Å). In both structures, SpNDK adopts a hexameric assembly and the fold of each monomer is highly conserved compared to NDKs from other organisms. A notable feature is the extended Kpn-loop, which plays a key role in stabilizing the hexamer. The protein exhibited remarkably high thermal stability (Tm ~ 76°C). However, mutation of R28 (R28A), which interacts with the Kpn-loop, destabilized the hexamer, lowering the Tm by >20°C. Unexpectedly, size-exclusion chromatography and mass photometry revealed that wild-type SpNDK exists as an equilibrium mixture of hexamers, dodecamers, and higher-order supramolecular assemblies. Using cryo-electron microscopy, we solved the three Dimensional (3D) structure of the hexameric state at 2.47 Å resolution, and resolved dodecameric assemblies of the protein. Since the oligomeric state of the NDK influences its cellular function, further investigations will be needed to address the in vivo relevance of these findings, in line with the broad and multifaceted roles of this enzyme family.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70735"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13451967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148689912","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

Structural and biophysical characterization of Mycobacterium tuberculosis DciA reveals functional convergence in DnaB helicase recognition. 结核分枝杆菌DciA的结构和生物物理特性揭示了DnaB解旋酶识别的功能趋同。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70771

Daniele Mazzoletti, Andrea Garavaglia, Hayden Fisher, Nicholas Gao, Castrese Morrone, Paul Dominic B Olinares, Brian T Chait, David Jeruzalmi, Riccardo Miggiano

{"title":"Structural and biophysical characterization of Mycobacterium tuberculosis DciA reveals functional convergence in DnaB helicase recognition.","authors":"Daniele Mazzoletti, Andrea Garavaglia, Hayden Fisher, Nicholas Gao, Castrese Morrone, Paul Dominic B Olinares, Brian T Chait, David Jeruzalmi, Riccardo Miggiano","doi":"10.1002/pro.70771","DOIUrl":"10.1002/pro.70771","url":null,"abstract":"In bacteria, DnaB replicative helicases are essential for unwinding genomic DNA to provide the single-stranded templates required for replication. The recruitment of the hexameric DnaB helicase to the origin of replication is mediated by distinct mechanisms that rely on specialized factors known as helicase loaders. The DciA family of helicase loaders exhibits distinct architectures that differ in the arrangement of the KH and DnaB-binding lasso domains. In this study, we probe the predicted structural architecture of the Mycobacterium tuberculosis (Mt) DciA helicase loader and its interplay with the cognate helicase MtDnaB. Native mass spectrometry and small-angle X-ray scattering (SAXS) analyses reveal that MtDciA adopts a monomeric and compact architecture in solution. We demonstrate that MtDnaB binds MtDciA with nanomolar affinity, likely forming a 2:1 complex at the Docking Helix-Linker Helix (DH-LH) interface of the replicative helicase. We predict that the intein-containing immature MtDnaBi will fail to form the active hexamer. As such, we suggest that MtDciA will show little to no affinity for intein-containing MtDnaBi.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70771"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13501899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148809082","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

Multimerization of a rationally designed nanobody for enhanced avidity toward Aβ42 oligomers. 一个合理设计的纳米体的多聚，以增强对a β42低聚物的亲和性。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70754

Magdalena Nowinska, Elijah Suh, Casey Mogilevsky, Michele Vendruscolo

{"title":"Multimerization of a rationally designed nanobody for enhanced avidity toward Aβ42 oligomers.","authors":"Magdalena Nowinska, Elijah Suh, Casey Mogilevsky, Michele Vendruscolo","doi":"10.1002/pro.70754","DOIUrl":"10.1002/pro.70754","url":null,"abstract":"Alzheimer's disease affects tens of millions of people worldwide and is associated with the self-assembly of the Aβ42 peptide into amyloid aggregates. Among the species formed during this process, soluble oligomeric intermediates are the most closely linked to neurotoxicity and are therefore an attractive target for both therapeutic and diagnostic strategies. Their conformational heterogeneity and transient nature, however, have so far hindered the development of reagents that recognize them selectively, and no fully quantitative biomarker of Aβ42 oligomers is widely available. To address this problem, we use a rationally designed conformation-specific single-domain antibody, DesAbO, which binds selectively to Aβ42 oligomers. By using enzyme-linked immunosorbent assay, we show that encoding self-assembling multimerization domains in the DesAbO plasmid yields multimeric variants with increased avidity toward Aβ42 oligomers. In aggregation assays, the multimeric variants inhibited Aβ42 aggregation at concentrations at which the monomeric form was no longer effective, with the SB175 trimer performing best. These results show how multimerization can be used to enhance the recognition of Aβ42 oligomers and offer a route toward diagnostic and therapeutic agents for Alzheimer's disease and other protein misfolding disorders.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70754"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13488367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148797427","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

Donor-induced conformational gating and substrate-assisted catalysis in α-1,3-galactosyltransferase. α-1,3-半乳糖转移酶的供体诱导构象门控和底物辅助催化。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70770

Javier A Linares-Pastén, Antoni Planas

{"title":"Donor-induced conformational gating and substrate-assisted catalysis in α-1,3-galactosyltransferase.","authors":"Javier A Linares-Pastén, Antoni Planas","doi":"10.1002/pro.70770","DOIUrl":"10.1002/pro.70770","url":null,"abstract":"Retaining glycosyltransferases catalyze the formation of stereochemically conserved glycosidic bonds through mechanisms that remain debated. Using bovine α1,3-galactosyltransferase (α3GalT) as a model, we combine mutagenesis, equilibrium unfolding, kinetics, and molecular dynamics simulations to understand how donor-induced loop ordering promotes catalysis. Alanine-scanning mutagenesis of the C-terminal loop (Thr358-Val368) identified Lys359, Tyr361, and Arg365 as critical for donor binding, catalysis, and ligand-dependent stabilization. In addition, D225A and E317A were inactive and showed minimal ligand-induced stabilization, consistent with impaired metal binding and substrate stabilization, respectively. Donor binding induces an ordered conformation in the C-terminus, reducing its local flexibility by 30% and pre-organizing the active site for catalysis. MD-derived energy profiles differed markedly for the donor (UDP-Gal) and acceptor (lactose) in the ternary complex. In this context, experimental apparent Kₘ values indicate higher donor affinity than acceptor affinity. Our results show that donor binding stabilizes the C-terminal loop, assembling a competent complex for catalysis. These findings support a general coupling between conformational gating, donor stabilization, and the catalytic mechanism in retaining GT-A-fold enzymes.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70770"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13476921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148761005","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

4-Ethyl phenyl sulfate binding to human serum albumin. 4-苯基硫酸乙酯与人血清白蛋白的结合。

IF 5.6 3区生物学

Protein Science Pub Date : 2026-09-01 DOI: 10.1002/pro.70755

Vida Dehghan Niestanak, Jacopo Zattoni, Ryan T McKay, Marcello Tonelli, Maral Aminpour, Larry D Unsworth

{"title":"4-Ethyl phenyl sulfate binding to human serum albumin.","authors":"Vida Dehghan Niestanak, Jacopo Zattoni, Ryan T McKay, Marcello Tonelli, Maral Aminpour, Larry D Unsworth","doi":"10.1002/pro.70755","DOIUrl":"10.1002/pro.70755","url":null,"abstract":"Protein-bound uremic toxins (PBUTs) such as 4-ethylphenyl sulfate (4-EPS) challenge kidney failure management due to strong binding to human serum albumin (HSA), thus limiting dialysis clearance. This study examined 4-EPS-HSA interactions using saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR), isothermal titration calorimetry (ITC), in silico analysis via molecular docking, molecular dynamics (MD), and molecular mechanics Generalized Born surface area (MM/GBSA) simulations. STD-NMR qualitatively showed competitive binding with the site-specific ligands, warfarin and ibuprofen, indicating interaction with both Sudlow Sites I and II; competitive ITC results also showed competition between these molecules. ITC analysis using a two-component model indicated two distinct binding interactions with association constants Ka1 = 6.62 × 105 M-1 (entropically unfavorable) and Ka2 = 2.71 × 104 M-1 (enthalpically favorable), respectively. Docking models were used to analyze representative binding poses at Sudlow Sites I and II, while MD revealed hydrophobic stabilization at Site I and polar interactions at Site II. MM/GBSA per-residue decomposition identified key stabilizing residues. Circular dichroism measurements showed that the observed binding effects are not accompanied by gross protein unfolding. Comparisons with other PBUTs, including indoxyl sulfate and p-cresyl sulfate, indicated the role of electrostatic and hydrophobic forces involved in binding. These findings advance understanding of PBUT-HSA interactions and inform strategies for improved toxin removal in kidney failure treatments.","PeriodicalId":20761,"journal":{"name":"Protein Science","volume":"35 9","pages":"e70755"},"PeriodicalIF":5.6,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13463429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148713404","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