Biochemistry Biochemistry最新文献

{"title":"A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements","authors":"Samuel Lee,&nbsp;Shuting Yan,&nbsp;Abhishek Dey,&nbsp;Alain Laederach and Tamar Schlick*,&nbsp;","doi":"10.1021/acs.biochem.4c0064110.1021/acs.biochem.4c00641","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00641https://doi.org/10.1021/acs.biochem.4c00641","url":null,"abstract":"<p >Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against COVID-19. In this process, a −1 shift in the ribosomal reading frame encodes alternative viral proteins. Any interference with this process profoundly affects viral replication and propagation. For SARS-CoV-2, two RNA sites associated with ribosomal frameshifting are positioned on the 5′ and 3′ of the frameshifting residues. Although much attention has been focused on the 3′ frameshift element (FSE), the 5′ stem-loop (attenuator hairpin, AH) can play a role. Yet the relationship between the two regions is unknown. In addition, multiple folds of the FSE and FSE-containing RNA regions have been discovered. To gain more insight into these RNA folds in the larger sequence context that includes AH, we apply our graph-theory-based modeling tools to represent RNA secondary structures, “RAG” (RNA-As-Graphs), to generate conformational landscapes that suggest length-dependent conformational distributions. We show that the AH region can coexist as a stem-loop with main and alternative 3-stem pseudoknots of the FSE (dual graphs 3_6 and 3_3 in our notation) but that an alternative stem 1 (AS1) can disrupt the FSE pseudoknots and trigger other folds. A critical length for AS1 of 10-bp regulates key folding transitions. Together with designed mutants and available experimental data, we present a sequential view of length-dependent folds during frameshifting and suggest their mechanistic roles. These structural and mutational insights into both ends of the FSE advance our understanding of the SARS-CoV-2 frameshifting mechanism by suggesting how alternative folds play a role in frameshifting and defining potential therapeutic intervention techniques that target specific folds.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 4","pages":"953–966 953–966"},"PeriodicalIF":2.9,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.biochem.4c00641","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143428322","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}

{"title":"Frataxin Traps Low Abundance Quaternary Structure to Stimulate Human Fe–S Cluster Biosynthesis","authors":"Seth A. Cory,&nbsp;Cheng-Wei Lin,&nbsp;Shachin Patra,&nbsp;Steven M. Havens,&nbsp;Christopher D. Putnam,&nbsp;Mehdi Shirzadeh,&nbsp;David H. Russell and David P. Barondeau*,&nbsp;","doi":"10.1021/acs.biochem.4c0073310.1021/acs.biochem.4c00733","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00733https://doi.org/10.1021/acs.biochem.4c00733","url":null,"abstract":"<p >Iron–sulfur clusters are essential protein cofactors synthesized in human mitochondria by an NFS1-ISD11-ACP-ISCU2-FXN assembly complex. Surprisingly, researchers have discovered three distinct quaternary structures for cysteine desulfurase subcomplexes, which display similar interactions between NFS1-ISD11-ACP protomeric units but dramatically different dimeric interfaces between the protomers. Although the role of these different architectures is unclear, possible functions include regulating activity and promoting the biosynthesis of distinct sulfur-containing biomolecules. Here, crystallography, native ion-mobility mass spectrometry, and chromatography methods reveal the Fe–S assembly subcomplex exists as an equilibrium mixture of these different quaternary structures. Isotope labeling and native mass spectrometry experiments show that the NFS1-ISD11-ACP complexes disassemble into protomers, which can then undergo exchange reactions and dimerize to reform native complexes. Single crystals isolated in distinct architectures have the same activity profile and activation by the Friedreich’s ataxia (FRDA) protein frataxin (FXN) when rinsed and dissolved in assay buffer. These results suggest FXN functions as a “molecular lock” and shifts the equilibrium toward one of the architectures to stimulate the cysteine desulfurase activity and promote iron–sulfur cluster biosynthesis. An NFS1-designed variant similarly shifts the equilibrium and partially replaces FXN in activating the complex. We propose that eukaryotic cysteine desulfurases are unusual members of the morpheein class of enzymes that control their activity through their oligomeric state. Overall, the findings support architectural switching as a regulatory mechanism linked to FXN activation of the human Fe–S cluster biosynthetic complex and provide new opportunities for therapeutic interventions of the fatal neurodegenerative disease FRDA.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 4","pages":"903–916 903–916"},"PeriodicalIF":2.9,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.biochem.4c00733","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143428467","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}

{"title":"Impact of Fluctuations in the Peridinin-Chlorophyll a-Protein on the Energy Transfer: Insights from Classical and QM/MM Molecular Dynamics Simulations","authors":"Monja Sokolov,&nbsp; and ,&nbsp;Qiang Cui*,&nbsp;","doi":"10.1021/acs.biochem.4c0056810.1021/acs.biochem.4c00568","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00568https://doi.org/10.1021/acs.biochem.4c00568","url":null,"abstract":"<p >The peridinin-chlorophyll a-protein is a light-harvesting complex found in dinoflagellates, which has an unusually high fraction of carotenoids. The carotenoids are directly involved in the energy transfer to chlorophyll with high efficiency. The detailed mechanism of energy transfer and the roles of the protein in the process remain debated in the literature, in part because most calculations have focused on a limited number of chromophore structures. Here we investigate the magnitude of the fluctuations of the site energies of individual and coupled chromophores, as the results are essential to the understanding of experimental spectra and the energy transfer mechanism. To this end, we sampled conformations of the PCP complex by means of classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. Subsequently we performed (supermolecular) excitation energy calculations on a statistically significant number of snapshots using TD-LC-DFT/CAM-B3LYP and the semiempirical time-dependent long-range corrected density functional tight binding (TD-LC-DFTB2) as the QM method. We observed that the magnitude of the site energy fluctuations is large compared to the differences of the site energies between the chromophores, and this also holds for the coupled chromophores. We also investigated the composition of the coupled states, the effect of coupling on the absorption spectra, as well as transition dipole moment orientations and the possibility of delocalized states with Chl a. Our study thus complements previous computational studies relying on a single structure and establishes the most prominent features of the coupled chromophores that are essential to the robustness of the energy transfer process.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 4","pages":"879–894 879–894"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143428495","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}

{"title":"Discovery of Peptidic Siderophore Degradation by Screening Natural Product Profiles in Marine-Derived Bacterial Mono- and Cocultures.","authors":"Mónica Monge-Loría, Weimao Zhong, Nadine H Abrahamse, Stephen Hartter, Neha Garg","doi":"10.1021/acs.biochem.4c00706","DOIUrl":"10.1021/acs.biochem.4c00706","url":null,"abstract":"<p><p>Coral reefs are hotspots of marine biodiversity, which results in the synthesis of a wide variety of compounds with unique molecular scaffolds, and bioactivities, rendering reefs an ecosystem of interest. The chemodiversity stems from the intricate relationships between inhabitants of the reef, as the chemistry produced partakes in intra- and interspecies communication, settlement, nutrient acquisition, and defense. However, the coral reefs are declining at an unprecedented rate due to climate change, pollution, and increased incidence of pathogenic diseases. Among pathogens, <i>Vibrio</i> spp. bacteria are key players resulting in high mortality. Thus, alternative strategies such as application of beneficial bacteria isolated from disease-resilient species are being explored to lower the burden of pathogenic species. Here, we apply coculturing of a coral-derived pathogenic species of <i>Vibrio</i> and beneficial bacteria and leverage recent advancements in untargeted metabolomics to discover engineerable beneficial traits. By chasing chemical change in coculture, we report <i>Microbulbifer</i> spp.-mediated degradation of amphibactins, produced by <i>Vibrio</i> spp. bacteria to sequester iron. Additional biochemical experiments revealed that the degradation occurs in the peptide backbone and requires the enzyme fraction of <i>Microbulbifer</i>. A reduction in iron affinity is expected due to the loss of one Fe(III) binding moiety. Therefore, we hypothesize that this degradation shapes community behaviors as it pertains to iron acquisition, a limiting nutrient in the marine environment, and survival. Furthermore, <i>Vibrio</i> sp. bacteria suppressed natural product synthesis by beneficial bacteria. Understanding biochemical mechanisms behind these interactions will enable engineering probiotic bacteria capable of lowering pathogenic burdens during heat waves and incidence of disease.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"634-654"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142976827","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}

{"title":"Chemical Logic of Peptide Branching by Iterative Nonlinear Nonribosomal Peptide Synthetases.","authors":"Jinping Yang, Adam Balutowski, Megan Trivedi, Timothy A Wencewicz","doi":"10.1021/acs.biochem.4c00749","DOIUrl":"10.1021/acs.biochem.4c00749","url":null,"abstract":"<p><p>Branch-point syntheses in nonribosomal peptide assembly are rare but useful strategies to generate tripodal peptides with advantageous hexadentate iron-chelating capabilities, as seen in siderophores. However, the chemical logic underlying the peptide branching by nonribosomal peptide synthetase (NRPS) often remains complex and elusive. Here, we review the common strategies for the biosynthesis of branched nonribosomal peptides (NRPs) and present our biochemical investigation on the NRPS-catalyzed assembly of fimsbactin A, a branched mixed-ligand siderophore produced by the human pathogenic strain <i>Acinetobacter baumannii</i>. We untangled the unusual branching mechanism of fimsbactin A biosynthesis through a combination of bioinformatics, site-directed mutagenesis, <i>in vitro</i> reconstitution, molecular modeling, and molecular dynamics simulation. Our findings clarify the roles of the fimsbactin NRPS enzymes, uncovering catalytically redundant domains and identifying the multifunctional nature of the FbsF cyclization (Cy) domain. We demonstrate the dynamic interplay between l-serine and 2,3-dihydroxybenzoic acid derived dipeptides, partitioning between amide and ester forms via a 1,2-<i>N</i>-to-<i>O</i>-acyl shift orchestrated by the noncanonical, multichannel FbsF Cy domain. The branching event occurs in a secondary condensation event facilitated by this Cy domain with two dipeptidyl intermediates, which generates a branched tetrapeptide thioester. Finally, the terminal condensation domain of FbsG recruits a soluble nucleophile to release the final product. This study advances our understanding of the intricate biosynthetic pathways and chemical logic employed by NRPSs, shedding light on the mechanisms underlying the synthesis of complex branched peptides.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"719-734"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027434","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}

{"title":"Functional Characterization of Two Polymerizing Glycosyltransferases for the Addition of <i>N</i>-Acetyl-d-galactosamine to the Capsular Polysaccharide of <i>Campylobacter jejuni</i>.","authors":"Dao Feng Xiang, Tamari Narindoshvili, Frank M Raushel","doi":"10.1021/acs.biochem.4c00704","DOIUrl":"10.1021/acs.biochem.4c00704","url":null,"abstract":"<p><p>The exterior surface of the human pathogen <i>Campylobacter jejuni</i> is coated with a capsular polysaccharide (CPS) that consists of a repeating sequence of 2-5 different sugars that can be modified with various molecular decorations. In the HS:2 serotype from strain NCTC 11168, the repeating unit within the CPS is composed of d-ribose, <i>N</i>-acetyl-d-galactosamine, and a d-glucuronic acid that is further amidated with either serinol or ethanolamine. The d-glucuronic acid moiety is also decorated with d-glycero-l-gluco-heptose. Here, we show that two different GT2 glycosyltransferases catalyze the transfer of <i>N</i>-acetyl-d-galactosamine from UDP-NAc-d-galactosamine furanoside to the C4-hydroxyl group of the d-glucuronamide moiety at the growing end of the capsular polysaccharide chain. Catalytic activity was not observed with glycosides of d-glucuronic acid, and thus, the C6-carboxylate of the d-glucuronic acid moiety must be amidated prior to chain elongation. One of these enzymes comprises the N-terminal domain of Cj1438 (residues 1-325) and the other is from the N-terminal domain of Cj1434 (residues 1-327). These two glycosyltransferases are ∼87% identical in sequence, but it is not clear why there are two glycosyltransferases from the same gene cluster that apparently catalyze the same reaction. This discovery represents the second polymerizing glycosyltransferase that has been isolated and functionally characterized for the biosynthesis of the capsular polysaccharide in the HS:2 serotype of <i>C. jejuni</i>.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"591-599"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031498","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}

{"title":"Discovery of the Cytocapsular Membrane as Hallmark of Malignant Tumors.","authors":"Tingfang Yi, Gerhard Wagner","doi":"10.1021/acs.biochem.4c00576","DOIUrl":"10.1021/acs.biochem.4c00576","url":null,"abstract":"<p><p>While optimizing cancer cell growth conditions, we discovered that cancer stem cells can generate second membranes outside the plasma membranes forming compartments separated from the extracellular matrix. The encapsulating membranes can extend and generate long cytocapsular tubes, wherein multiple cells can migrate. SILAC proteomics of the second cytocapsular membranes identified 400 membrane proteins, and a small subset of them are highly upregulated in cytocapsular cancers compared to normal tissues. The ATP-dependent calcium pump PMCA2 is one of the highest upregulated factors of the cytocapsular membrane, and antibodies serve as biomarkers for malignant tumors, as checked for 293 subtypes of cancers. Cytocapsular tumors have not been described before, possibly because the CC membranes do not exhibit epitopes targeted by conventional methods, and no efforts have been made to search for new cancer specific organelles. Antibodies against PMCA2 can now be used to map cancer evolution pathways in human bodies by comparisons of more than 12 000 annotated specimens from tissue banks worldwide. The current research reveals that the native malignant cancer cell is enclosed in a cytocapsular membrane. With the PMCA2 cancer biomarker available, the development of human cancers can be studied from cancer tissue banks and clinical cancer biopsies with a previously unknown diversity. The emerging knowledge on cancer-driving biomarkers opens doors for new routes in cancer diagnosis, surgery, therapy, and treatments.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"555-562"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142826605","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}

{"title":"Glutamine Synthetase: Diverse Regulation and Functions of an Ancient Enzyme.","authors":"Markus C B Tecson, Cyrina Geluz, Yuly Cruz, Eric R Greene","doi":"10.1021/acs.biochem.4c00763","DOIUrl":"10.1021/acs.biochem.4c00763","url":null,"abstract":"<p><p>Glutamine synthetase (GS) is a ubiquitous enzyme central to nitrogen metabolism, catalyzing the ATP-dependent formation of glutamine from glutamate and ammonia. Positioned at the intersection of nitrogen metabolism with carbon metabolism, the activity of GS is subject to sophisticated regulation. While the intricate regulatory pathways that govern <i>Escherichia coli</i> GS were established long ago, recent work has demonstrated that homologues are controlled by multiple distinct regulatory patterns, such as the metabolite induced oligomeric state formation in archaeal GS by 2-oxoglutarate. Such work was enabled in large part by advances in cryo-electron microscopy (cryoEM) that allowed greater structural access to this large enzyme complex, such as assessment of the large heterogeneous oligomeric states of GS and protein-interactor-GS complexes. This perspective highlights recent advances in understanding GS regulation, focusing on the dynamic interplay between its oligomeric state, metabolite binding, and protein interactors. These interactions modulate GS activity, influencing cellular processes such as nitrogen assimilation, carbon metabolism, and stress responses. Furthermore, we explore the emerging concept of GS \"moonlighting\" functions, revealing its roles in palmitoylation, cell cycle regulation, and ion channel modulation. These diverse functions highlight a newfound versatility of GS beyond its primary catalytic role and suggest complex roles in health and disease that warrant further study.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"547-554"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021295","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}

{"title":"Journey of PROTAC: From Bench to Clinical Trial and Beyond.","authors":"Kyli Berkley, Julian Zalejski, Nidhi Sharma, Ashutosh Sharma","doi":"10.1021/acs.biochem.4c00577","DOIUrl":"10.1021/acs.biochem.4c00577","url":null,"abstract":"<p><p>Proteolysis-targeting chimeras (PROTACs) represent a transformative advancement in drug discovery, offering a method to degrade specific intracellular proteins. Unlike traditional inhibitors, PROTACs are bifunctional molecules that target proteins for elimination, enabling the potential treatment of previously \"undruggable\" proteins. This concept, pioneered by Crews and his team, introduced the use of small molecules to link a target protein to an E3 ubiquitin ligase, inducing ubiquitination and subsequent degradation of the target protein. By promoting protein degradation rather than merely inhibiting function, PROTACs present a novel therapeutic strategy with enhanced specificity and effectiveness, especially in areas such as cancer and neurodegenerative diseases. Since their initial discovery, the field of PROTAC research has rapidly expanded with numerous PROTACs now designed to target a wide range of disease-relevant proteins. The substantial research, investment, and collaboration across academia and the pharmaceutical industry reflect the growing interest in PROTACs. This Review discusses the journey of PROTACs from initial discovery to clinical trials, highlighting advancements and challenges. Additionally, recent developments in fluorescent and photogenic PROTACs, used for real-time tracking of protein degradation, are presented, showcasing the evolving potential of PROTACs in targeted therapy.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"563-580"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941438","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}

{"title":"Collagen Alpha 1(XI) Amino-Terminal Domain Modulates Type I Collagen Fibril Assembly.","authors":"Abu Sayeed Chowdhury, Julia Thom Oxford","doi":"10.1021/acs.biochem.4c00434","DOIUrl":"10.1021/acs.biochem.4c00434","url":null,"abstract":"<p><p>The amino-terminal domain of collagen α1(XI) plays a key role in controlling fibrillogenesis. However, the specific mechanisms through which various isoforms of collagen α1(XI) regulate this process are not fully understood. We measured the kinetics of collagen type I self-assembly in the presence of specific collagen α1(XI) isoforms. Molecular dynamics simulations, protein-protein docking studies, and molecular mechanics Poisson-Boltzmann surface area were utilized to understand the molecular mechanisms. In vitro, in silico, and thermodynamic studies demonstrated an isoform-specific effect on self-assembly kinetics. Our results indicate isoform-specific differences in the rate constants, activation energy, and free energy of binding. These differences may result from isoform-specific interaction dynamics and modulation of steric hindrance due to the chemically distinct variable regions. We show that isoform A interacts with collagen type I due in part to the acidic variable region, increasing the activation energy of fibril growth while decreasing the rate constant during the growth phase. In contrast, the basic variable region of isoform B may result in less steric hindrance than isoform A. Isoform 0 demonstrated the highest activation energy and the lowest rate constant during the growth phase. Although the presence of isoforms reduced the rate constants for fibril growth, an increase in total turbidity during the plateau phase was observed compared to controls. Overall, these results are consistent with collagen α1(XI) NTD isoforms facilitating fibrillogenesis by increasing the final yield by reducing the rate of the lag and/or growth phases, while extending the duration of the growth phase.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"735-747"},"PeriodicalIF":2.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996266","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}