Biochemistry Biochemistry最新文献_第10页

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-08-05

Tyler B. Alt, AJ K. Croney and Graham R. Moran*,

引用次数: 0

Defining Factors that Influence the Stability of Tetrameric EgtB from Chloracidobacterium thermophilum: From pH Modulation to Affinity Tag Retention 影响嗜热氯酸杆菌四聚体EgtB稳定性的决定性因素：从pH调节到亲和标签保留。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-08-04 DOI: 10.1021/acs.biochem.5c00123

Kassidy W. Rodriguez, and , Katlyn K. Meier*,

{"title":"Defining Factors that Influence the Stability of Tetrameric EgtB from Chloracidobacterium thermophilum: From pH Modulation to Affinity Tag Retention","authors":"Kassidy W. Rodriguez,  and , Katlyn K. Meier*, ","doi":"10.1021/acs.biochem.5c00123","DOIUrl":"10.1021/acs.biochem.5c00123","url":null,"abstract":"Ergothioneine (EGT) is a vital antioxidant synthesized exclusively by microorganisms and is associated with various oxidative stress-related diseases in humans. EGT biosynthesis is catalyzed by a gene cluster containing the enzyme EgtB, a nonheme iron-dependent sulfoxide synthase. While multiple EgtB enzymes have been characterized, EgtB from Chloracidobacterium thermophilum (Cth) uniquely forms a homotetrameric structure, in contrast to the monomeric forms of its homologues. In this study, we applied biophysical and biochemical techniques to examine the secondary and quaternary structures of metal-free (apo) CthEgtB, focusing on how pH modulation and thermodynamic factors influence its stability and oligomerization. Herein, we show that key factors such as pH, temperature, and the presence of a 6xHistidine tag impact the enzyme’s structural integrity and thermal stability. This work underscores the importance of considering structural and environmental factors of sulfoxide synthases to alter or improve their catalytic efficiency.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 16","pages":"3526–3534"},"PeriodicalIF":3.0,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774312","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}

引用次数: 0

Bipartite Recognition of Tail-Anchored Proteins by Sgt2 Involves both the Cytosolic and Transmembrane Domains Sgt2对尾部锚定蛋白的两部分识别涉及细胞质和跨膜结构域。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-08-02 DOI: 10.1021/acs.biochem.5c00345

Man Wu, Tuo Ji, Chanjuan Wan, Simin Wang* and Chengdong Huang*,

{"title":"Bipartite Recognition of Tail-Anchored Proteins by Sgt2 Involves both the Cytosolic and Transmembrane Domains","authors":"Man Wu, Tuo Ji, Chanjuan Wan, Simin Wang* and Chengdong Huang*, ","doi":"10.1021/acs.biochem.5c00345","DOIUrl":"10.1021/acs.biochem.5c00345","url":null,"abstract":"Tail-anchored (TA) membrane proteins, defined by a single C-terminal transmembrane helix, are predominantly targeted to the endoplasmic reticulum (ER) via the post-translational GET pathway. While previous studies have characterized how chaperones shield the hydrophobic TA transmembrane domain (TMD), it remains unclear whether the cytosolic domain (TACD) contributes to recognition. Here, we show that Sgt2, the entry chaperone of the GET pathway, engages TA proteins through a bipartite mechanism: its C-terminal domain captures the TMD, while its N-terminal domain (Sgt2N) recognizes basic, α-helix-prone segments within TAsCD. NMR and mutational analyses reveal that binding is primarily driven by electrostatic complementarity at a conserved dimeric interface on Sgt2N. A structural model of the Sgt2N–TACD complex supports this binding mode, and competition experiments demonstrate that Get5UBL can effectively displace TAsCD from Sgt2N via the same surface. These findings define a dual-recognition mechanism in which both the TACD and TMD contribute to Sgt2 engagement, thereby reinforcing client safeguarding and suggesting a broader role for Sgt2 in TA protein targeting.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 16","pages":"3549–3558"},"PeriodicalIF":3.0,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768148","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}

引用次数: 0

Thermodynamics and Binding Mechanism of Insulin-like Growth Factor Binding Protein 1 (IGF2BP1) and Y3 RNA Interaction 胰岛素样生长因子结合蛋白1 （IGF2BP1）与Y3 RNA相互作用的热力学和结合机制

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-07-30 DOI: 10.1021/acs.biochem.5c00134

Shalini Mishra, Ajit Kumar, Priyanka Kumari, Kaiser Rasool, Souvik Maiti and Niyati jain*,

{"title":"Thermodynamics and Binding Mechanism of Insulin-like Growth Factor Binding Protein 1 (IGF2BP1) and Y3 RNA Interaction","authors":"Shalini Mishra, Ajit Kumar, Priyanka Kumari, Kaiser Rasool, Souvik Maiti and Niyati jain*, ","doi":"10.1021/acs.biochem.5c00134","DOIUrl":"10.1021/acs.biochem.5c00134","url":null,"abstract":"Y3 RNA is a conserved noncoding RNA involved in RNA-protein interactions, stress responses, and post-transcriptional regulation. It interacts with various RNA-binding proteins, including Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), which regulates mRNA stability, localization, and translation. However, the molecular basis of Y3 RNA recognition by IGF2BP1 remains unclear. In this study, we analyzed the structural conservation of Y3 RNA and characterized its interaction with IGF2BP1. Phylogenetic analysis showed that Y3 RNA is highly conserved across mammals, with over 90% sequence similarity and a preserved secondary structure featuring an apical stem-loop, lower stem, and pyrimidine-rich internal loop. UV melting experiments confirmed the predicted structural elements, revealing two distinct melting transitions corresponding to the upper and lower stems. Electrophoretic mobility shift assays (EMSA) and isothermal titration calorimetry (ITC) demonstrated that the IGF2BP1 binding to Y3 RNA is multimeric. It occurs via a biphasic mechanism as demonstrated by thermodynamic studies, primarily mediated by the KH3–4 di-domain. Mutational analysis identified the pyrimidine-rich internal loop as the key binding site, with minimal contributions from the apical stem-loop and lower stem. Thermodynamic studies revealed that one binding event is entropically driven, followed by the binding interactions which are enthalpically favorable. Our findings provide new insights into the conserved structural features of Y3 RNA and its recognition by IGF2BP1. Identifying key RNA elements involved in binding enhances our understanding of Y3 RNA’s functional roles and its potential impact on RNA-protein networks.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 16","pages":"3535–3548"},"PeriodicalIF":3.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740623","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}

引用次数: 0

An Orchestrated Interaction Network at the Binding Site of Human SERT Enables the Serotonin Occlusion and Import 人类SERT结合位点的协调相互作用网络使血清素闭塞和进口成为可能。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-07-28 DOI: 10.1021/acs.biochem.5c00240

Zhiyu Zhao, Po-Chao Wen and Emad Tajkhorshid*,

{"title":"An Orchestrated Interaction Network at the Binding Site of Human SERT Enables the Serotonin Occlusion and Import","authors":"Zhiyu Zhao, Po-Chao Wen and Emad Tajkhorshid*, ","doi":"10.1021/acs.biochem.5c00240","DOIUrl":"10.1021/acs.biochem.5c00240","url":null,"abstract":"Serotonin transporter (SERT) regulates serotonergic signals by reuptaking serotonin from the synaptic clefts back into the presynaptic neurons. The recent resolution of the serotonin–SERT complex in multiple conformational states outlined the complete serotonin import cycle. However, a detailed functional appreciation of SERT also involves deciphering the coupling between global structural changes in the transport cycle to the bound chemicals to be transported. By employing molecular dynamics (MD) simulations and free energy calculations in different ligand binding states, here, we reveal how serotonin binding to SERT initiates the global conformational changes essential for serotonin import. Only when serotonin is bound to the central binding site, wedged between transmembrane helices (TMs) 3 and 8, can the system form an interaction network that bridges the two helical domains of the protein, thereby promoting the closure of an extracellular hydrophobic gate and sealing the bound serotonin. To test the role of this hydrophobic gate closure, we designed a series of nonequilibrium MD simulations to steer the outward-facing ↔ occluded transition with different gating configurations. The difference in nonequilibrium work required to fuel the transition indicates that the transition is more likely to happen when the extracellular gate is closed. The transition is not promoted when the gate is open or when 5-HT moves away from TM3 and TM8 toward an alternate pose. Such a local–global coupling is likely shared by other monoamine transporters considering the conservation of all involved structural elements.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 16","pages":"3652–3662"},"PeriodicalIF":3.0,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144725927","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}

引用次数: 0

Oxidative Activation of the Heme Nitric Oxide/Oxygen-Binding Protein (H-NOX) from Caulobacter crescentus 新月茎杆菌血红素一氧化氮/氧结合蛋白（H-NOX）的氧化活化。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-07-27 DOI: 10.1021/acs.biochem.5c00262

Aishat Alatishe, Therese Albert, Cameron Christopher Lee-Lopez, Rashedul Hasan, Pierre Moënne-Loccoz, Kelly N. Chacón and Erik T. Yukl*,

{"title":"Oxidative Activation of the Heme Nitric Oxide/Oxygen-Binding Protein (H-NOX) from Caulobacter crescentus","authors":"Aishat Alatishe, Therese Albert, Cameron Christopher Lee-Lopez, Rashedul Hasan, Pierre Moënne-Loccoz, Kelly N. Chacón and Erik T. Yukl*, ","doi":"10.1021/acs.biochem.5c00262","DOIUrl":"10.1021/acs.biochem.5c00262","url":null,"abstract":"The heme nitric oxide/oxygen-binding proteins (H-NOX) are bacterial homologues of the sensor domain of mammalian soluble guanylate cyclase (sGC), a multidomain enzyme that catalyzes the production of cyclic guanosine monophosphate (cGMP) in response to NO. In facultative anaerobes, H-NOX proteins sense nitric oxide (NO) and regulate various communal behaviors including biofilm formation, motility, virulence, and quorum sensing. Rupture of the proximal heme iron-histidine bond during the formation of a five-coordinate low-spin ferrous nitrosyl (5cLS Fe(II)-NO) heme is thought to be required for H-NOX activation, allowing them to interact with downstream signaling partners such as diguanylate cyclases (DGC), phosphodiesterases (PDE), or histidine kinases (HK). Some H-NOX homologues also contain a conserved Cys-ligated zinc-binding site, which can respond to oxidative stress, at least in vitro. Although classified as an obligate aerobe, Caulobacter crescentus encodes an apparent NO-sensing hnox gene adjacent to that of the HK gene hnok. Spectroscopic analysis of the Cc H-NOX protein reveals characteristics similar to those of other NO-sensing H-NOX homologues, including the formation of a 5cLS Fe(II)-NO heme. Surprisingly, this form is completely noninhibitory to HnoK autophosphorylation, in contrast to what has been observed for every other related system to date. Rather, oxidation of the zinc ligand Cys residues activates Cc H-NOX. X-ray absorption fine structure (EXAFS) data reveal a change in zinc coordination upon oxidation but no loss of zinc. This work illustrates the breadth of H-NOX-signaling mechanisms and expands our understanding of signaling pathways in which this widespread protein participates.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 15","pages":"3345–3357"},"PeriodicalIF":3.0,"publicationDate":"2025-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144725928","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

Influence of Glycosaminoglycan Binding/Non-Binding Interactions on Bone Morphogenetic Protein-2 Unfolding Dynamics and Activity: Mechanistic Insights and Implications 糖胺聚糖结合/非结合相互作用对骨形态发生蛋白-2展开动力学和活性的影响：机制见解和意义。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-07-26 DOI: 10.1021/acs.biochem.5c00295

Devi Prasanna Behera, Suchismita Subadini and Harekrushna Sahoo*,

{"title":"Influence of Glycosaminoglycan Binding/Non-Binding Interactions on Bone Morphogenetic Protein-2 Unfolding Dynamics and Activity: Mechanistic Insights and Implications","authors":"Devi Prasanna Behera, Suchismita Subadini and Harekrushna Sahoo*, ","doi":"10.1021/acs.biochem.5c00295","DOIUrl":"10.1021/acs.biochem.5c00295","url":null,"abstract":"Glycosaminoglycans (GAGs), a class of carbohydrates integral to the extracellular matrix in biological systems, such as the connective tissue, cornea, and synovial fluid, significantly influence protein dynamics. This study investigates the unfolding kinetics and dynamics of Bone Morphogenetic Protein-2 (BMP-2) in the presence of glycosaminoglycans, specifically, hyaluronic acid (HA) and sulfated hyaluronic acid (SHA). The findings reveal that BMP-2 undergoes faster unfolding in the presence of SHA compared with HA in chemical denaturation. This accelerated unfolding can be attributed to a complex interplay between viscosity and the binding or nonbinding interactions between the glycosaminoglycans and the protein. Despite HA exhibiting a higher viscosity than SHA, the anisotropy of the intrinsic fluorophore of the protein demonstrates a significantly higher fluorescence anisotropy and anisotropy decay time in the SHA environment. Fluorescence lifetime measurements and rotational correlation times further substantiate this observation, with anisotropy kinetics indicating a binding interaction of BMP-2 with SHA. Additionally, the protein’s unfolding mechanism in the presence of HA and SHA follows a mixed pathway, involving both direct and indirect processes. Energetically, the unfolding of BMP-2 in the SHA environment is considerably more stable than that in HA, suggesting a more robust interaction between the protein and sulfated glycosaminoglycans.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 18","pages":"3901–3918"},"PeriodicalIF":3.0,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144853949","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}

引用次数: 0

Ancestral Sequence Reconstruction of the Ethylene-Forming Enzyme 乙烯生成酶的祖先序列重建。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-07-25 DOI: 10.1021/acs.biochem.5c00334

Shramana Chatterjee, Joel A. Rankin, Mark A. Farrugia, Bryce J. Delaney, Nathaniel S. Pascual, James VanAntwerp, Daniel R. Woldring*, Jian Hu* and Robert P. Hausinger*,

{"title":"Ancestral Sequence Reconstruction of the Ethylene-Forming Enzyme","authors":"Shramana Chatterjee, Joel A. Rankin, Mark A. Farrugia, Bryce J. Delaney, Nathaniel S. Pascual, James VanAntwerp, Daniel R. Woldring*, Jian Hu* and Robert P. Hausinger*, ","doi":"10.1021/acs.biochem.5c00334","DOIUrl":"10.1021/acs.biochem.5c00334","url":null,"abstract":"The ethylene-forming enzyme (EFE) catalyzes two main reactions: the conversion of 2-oxoglutarate (2OG) to ethylene plus CO2 and the oxidative decarboxylation of 2OG coupled to the C5 hydroxylation of l-arginine (l-Arg). EFE also facilitates two minor reactions: the uncoupled oxidative decarboxylation of 2OG and the generation of 3-hydroxypropionate (3HP) from 2OG. To better understand the evolution of this enzyme’s diverse activities, we demonstrated that two distantly related extant enzymes produce trace levels of ethylene and 3HP, and we examined the reactivities of 11 reconstructed ancestors. The structure of one ancestral protein was resolved by X-ray crystallography, while the others were modeled with AlphaFold2. These studies highlight the importance of residues located at the 2OG and l-Arg binding pockets for the varied activities. For example, effective formation of ethylene requires that the 2OG binding pocket be hydrophobic except for interactions with the substrate carboxylates. Newly identified changes near the l-Arg binding site exhibit significant effects on the reactivities of the enzyme's reactions. Analysis of the reconstructed ancestors suggests that the primordial enzyme exhibited both ethylene-forming and l-Arg hydroxylation activities with partition ratios like the extant examples; i.e., an enzyme capable of catalyzing predominantly one of these reactions did not subsequently develop the ability to affect the secondary reaction.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 15","pages":"3432–3445"},"PeriodicalIF":3.0,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12329707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144782998","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

A De Novo Designed Protein with Versatile Metal Binding and Tunable Hydrolytic Activity 一种全新设计的具有多功能金属结合和可调水解活性的蛋白质。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-07-23 DOI: 10.1021/acs.biochem.5c00259

Alexander M. Hoffnagle, Suppachai Srisantitham, Maximilian Neeley, Chia-Ying Tsai and F. Akif Tezcan*,

{"title":"A De Novo Designed Protein with Versatile Metal Binding and Tunable Hydrolytic Activity","authors":"Alexander M. Hoffnagle, Suppachai Srisantitham, Maximilian Neeley, Chia-Ying Tsai and F. Akif Tezcan*, ","doi":"10.1021/acs.biochem.5c00259","DOIUrl":"10.1021/acs.biochem.5c00259","url":null,"abstract":"Metalloenzyme superfamilies achieve diverse functions within a shared structural framework, and similar functional variety may be achievable in designed proteins. We have previously reported a computational approach that enables the de novo design of symmetric protein assemblies around metal centers with predefined coordination geometries. Here, we demonstrate that an artificial protein trimer, termed Tet4, whose structure was designed around an idealized tetrahedral His3/H2O–ZnII coordination motif, enables the high-affinity binding of several other divalent first-row transition metal ions in the same geometry as for ZnII. We then follow the proposed evolutionary path of a natural metalloenzyme superfamily by engineering a pseudosymmetric, single-chain variant of Tet4, scTet425. scTet425 allows us to introduce asymmetric point mutations that influence the catalytic properties of the metal center. We also demonstrate that we can further tune the enzymatic activity of Tet4 by designing a substrate pocket that improves Zn-Tet4’s affinity for a hydrolysis substrate, 4-methylumbelliferyl acetate.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 15","pages":"3261–3271"},"PeriodicalIF":3.0,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697087","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}

引用次数: 0

A Cooperative Model for Symmetric Ligand Binding to Protein Fibrils 对称配体与蛋白原纤维结合的合作模型。

IF 3 3区生物学

Biochemistry Biochemistry Pub Date : 2025-07-23 DOI: 10.1021/acs.biochem.5c00068

Matthew S. Smith*, William F. DeGrado, Michael Grabe and Brian K. Shoichet,

{"title":"A Cooperative Model for Symmetric Ligand Binding to Protein Fibrils","authors":"Matthew S. Smith*, William F. DeGrado, Michael Grabe and Brian K. Shoichet, ","doi":"10.1021/acs.biochem.5c00068","DOIUrl":"10.1021/acs.biochem.5c00068","url":null,"abstract":"A hallmark of neurodegenerative diseases like Alzheimer’s Disease (AD) and chronic traumatic encephalopathy (CTE) is the presence of toxic protein aggregates in neurons. In AD and CTE specifically, the protein tau forms insoluble fibrils that are hundreds of nanometers in length. Intriguingly, recent experimental structures suggest that tau ligands like the disaggregator EGCG and positron emission tomography (PET) tracers like GTP-1 and MK-6240 bind to tau fibrils in long stacks reflecting the symmetry of the protein across many binding sites. In these stacks, each ligand makes more contact with its symmetry mates than it does with the protein. To interpret the binding of these molecules and new ligands, we must understand the effects of the cooperativity between sites and the entropy coming from the number of sites. Here, we investigate a nearest-neighbors model of cooperativity and use statistical mechanics to derive binding isotherms for saturation and competition experiments. This model allows us to relate measured EC50 and IC50 values to the intrinsic binding affinity to a single site and to cooperativity across sites in ways resembling the Cheng–Prusoff Equation. Depending on the degree of cooperativity between molecular species, this model permits solutions that lack the steep binding curves expected from cooperative systems and even solutions resembling 2-site systems. We finally consider conditions for a fibril’s detection in a PET scan and practical matters of fitting this model’s parameters to data.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 15","pages":"3382–3392"},"PeriodicalIF":3.0,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697088","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}

引用次数: 0