Biochemistry Biochemistry最新文献

Alternative Role of B/b Knob-Hole Interactions in the Fibrin Assembly. B/b 节孔相互作用在纤维蛋白组装中的替代作用

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-27 DOI: 10.1021/acs.biochem.4c00695

Tatyana Platonova, Oleksii Hrabovskyi, Volodymyr Chernyshenko, Yevhenii Stohnii, Yevhenii Kucheriavyi, Kateryna Baidakova, Daria Korolova, Anna Urbanowicz, Serhiy Komisarenko

{"title":"Alternative Role of B/b Knob-Hole Interactions in the Fibrin Assembly.","authors":"Tatyana Platonova, Oleksii Hrabovskyi, Volodymyr Chernyshenko, Yevhenii Stohnii, Yevhenii Kucheriavyi, Kateryna Baidakova, Daria Korolova, Anna Urbanowicz, Serhiy Komisarenko","doi":"10.1021/acs.biochem.4c00695","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00695","url":null,"abstract":"The self-assembly of fibrin is a vital process in blood clotting, primarily facilitated by the interactions between knobs \"A\" and \"B\" in the central E region of one molecule and the corresponding holes \"a\" and \"b\" in the peripheral D regions of two other fibrin molecules. However, the precise function of the interactions between knob \"B\" and hole \"b\" during fibrin polymerization remains a subject of ongoing debate. The present study focuses on investigating intermolecular interactions between knob \"B\" and hole \"b\". We investigated the D-E-D interactions within the fibrin protofibril to accomplish this objective. Our investigation involved studying the formation of supramolecular complexes involving desAB fibrin with fibrin(ogen) fragments, specifically the D-dimer and D fragment. The research utilized analytical size-exclusion chromatography, SDS-PAGE and densitometry of SDS-PAGE images, dynamic light scattering measurements, turbidity studies, electron microscopy, and computer modeling. Our findings indicate that the interference of the D fragment into classical D-E-D interaction occurs through knob \"B\" of the fibrin molecule. Molecular dynamics simulations elucidate the binding of only one D region, attributed to the shift of the D-dimer toward the fibrin desAB molecule. The formation of such a complex can be considered evidence supporting the potential mechanism of the branching of protofibrils. According to this theoretical mechanism, the inclusion of the D region from an external fibrin molecule into D-E-D interactions is facilitated through \"B/b\" contacts.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044909","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 Noncatalytic Cysteine Residue Modulates Cobalamin Reactivity in the Human B₁₂ Processing Enzyme CblC.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-25 DOI: 10.1021/acs.biochem.4c00613

Anna J Esser, Santiago Sastre, Thien-Ly Julia Dinh, Viola Tanner, Victoria Wingert, Katharina Klotz, Donald W Jacobsen, Ute Spiekerkoetter, Oliver Schilling, Ari Zeida, Rafael Radi, Luciana Hannibal

{"title":"A Noncatalytic Cysteine Residue Modulates Cobalamin Reactivity in the Human B12 Processing Enzyme CblC.","authors":"Anna J Esser, Santiago Sastre, Thien-Ly Julia Dinh, Viola Tanner, Victoria Wingert, Katharina Klotz, Donald W Jacobsen, Ute Spiekerkoetter, Oliver Schilling, Ari Zeida, Rafael Radi, Luciana Hannibal","doi":"10.1021/acs.biochem.4c00613","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00613","url":null,"abstract":"Human CblC catalyzes the indispensable processing of dietary vitamin B12 by the removal of its β-axial ligand and an either one- or two-electron reduction of its cobalt center to yield cob(II)alamin and cob(I)alamin, respectively. Human CblC possesses five cysteine residues of an unknown function. We hypothesized that Cys149, conserved in mammals, tunes the CblC reactivity. To test this, we recreated an evolutionary early variant of CblC, namely, Cys149Ser, as well as Cys149Ala. Surprisingly, substitution of Cys149 for serine or alanine led to faster observed rates of glutathione-driven dealkylation of MeCbl compared to wild-type CblC. The reaction yielded aquacobalamin and stoichiometric formation of S-methylglutathione as the demethylation products. Determination of end-point oxidized glutathione revealed significantly uncoupled electron transfer in both mutants compared with the wild type. Long incubation times revealed the conversion of aquacobalamin to cob(II)alamin in the presence of oxygen in mutants Cys149Ser and Cys149Ala but not in wild-type CblC, all without an effect on dealkylation rates. This finding is reminiscent of the catalytic behavior of CblC from Caenorhabditis elegans, wherein Cys149 is naturally substituted by Ser, and the reaction mechanism differs from that of human CblC precisely by the unusual stabilization of cob(II)alamin in the presence of oxygen. Thus, Cys149 tunes the catalytic activity of human CblC by minimizing uncoupled electron transfer that forms GSSG. This occurs at the expense of a slower observed rate constant for the demethylation of MeCbl. This adjustment is compatible with diminished needs for intracellular turnover of cobalamins and with life under increased oxygen concentration.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143035351","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

Functional Characterization of Two Polymerizing Glycosyltransferases for the Addition of N-Acetyl-d-galactosamine to the Capsular Polysaccharide of Campylobacter jejuni.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-24 DOI: 10.1021/acs.biochem.4c00704

Dao Feng Xiang, Tamari Narindoshvili, Frank M Raushel

{"title":"Functional Characterization of Two Polymerizing Glycosyltransferases for the Addition of N-Acetyl-d-galactosamine to the Capsular Polysaccharide of Campylobacter jejuni.","authors":"Dao Feng Xiang, Tamari Narindoshvili, Frank M Raushel","doi":"10.1021/acs.biochem.4c00704","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00704","url":null,"abstract":"The exterior surface of the human pathogen Campylobacter jejuni 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, N-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 N-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 C. jejuni.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-24 DOI: 10.1021/acs.biochem.4c00688

Kristina V Boyko, Rebecca A Bernstein, Minji Kim, Jamie H D Cate

{"title":"Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection.","authors":"Kristina V Boyko, Rebecca A Bernstein, Minji Kim, Jamie H D Cate","doi":"10.1021/acs.biochem.4c00688","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00688","url":null,"abstract":"In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create \"orthogonal\" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling the mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here, we engineered the Escherichia coli ribosome to prevent binding of bS1 to the 30S subunit and separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomes in vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have an improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of binding of bS1 to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031515","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

Identification of the Polymerizing Glycosyltransferase Required for the Addition of d-Glucuronic Acid to the Capsular Polysaccharide of Campylobacter jejuni.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-24 DOI: 10.1021/acs.biochem.4c00703

Dao Feng Xiang, Alexander S Riegert, Tamari Narindoshvili, Frank M Raushel

{"title":"Identification of the Polymerizing Glycosyltransferase Required for the Addition of d-Glucuronic Acid to the Capsular Polysaccharide of Campylobacter jejuni.","authors":"Dao Feng Xiang, Alexander S Riegert, Tamari Narindoshvili, Frank M Raushel","doi":"10.1021/acs.biochem.4c00703","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00703","url":null,"abstract":"Campylobacter jejuni is the leading cause of food poisoning in Europe and North America. The exterior surface of this bacterium is encased by a capsular polysaccharide that is attached to a diacyl glycerol phosphate anchor via a poly-Kdo (3-deoxy-d-manno-oct-2-ulosinic acid) linker. In the HS:2 serotype of C. jejuni NCTC 11168, the repeating trisaccharide consists of d-ribose, N-acetyl-d-glucosamine, and d-glucuronate. Here, we show that the N-terminal domain of Cj1432 (residues 1-356) is responsible for the reaction of the C2 hydroxyl group from the terminal d-ribose moiety of the growing polysaccharide chain with UDP-d-glucuronate as the donor substrate. This discovery represents the first biochemical identification and functional characterization of a glycosyltransferase responsible for the polymerization of the capsular polysaccharide of C. jejuni. The product of the reaction catalyzed by the N-terminal domain of Cj1432 is the substrate for the reaction catalyzed by the C-terminal domain of Cj1438 (residues 453-776). This enzyme catalyzes amide bond formation using the C6 carboxylate of the terminal d-glucuronate moiety and (S)-serinol phosphate as substrates. It is also shown that Cj1435 catalyzes the hydrolysis of phosphate from the product catalyzed by the C-terminal domain of Cj1438. These results demonstrate that amide decoration of the d-glucuronate moiety occurs after the incorporation of this sugar into the growing polysaccharide chain.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031500","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

Chemical Logic of Peptide Branching by Iterative Nonlinear Nonribosomal Peptide Synthetases.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-23 DOI: 10.1021/acs.biochem.4c00749

Jinping Yang, Adam Balutowski, Megan Trivedi, Timothy A Wencewicz

{"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":"https://doi.org/10.1021/acs.biochem.4c00749","url":null,"abstract":"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 Acinetobacter baumannii. We untangled the unusual branching mechanism of fimsbactin A biosynthesis through a combination of bioinformatics, site-directed mutagenesis, in vitro 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-N-to-O-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.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-23","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}

引用次数: 0

Yeast Eukaryotic Initiation Factor 4B Remodels the MRNA Entry Site on the Small Ribosomal Subunit.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-23 DOI: 10.1021/acs.biochem.4c00489

Ayushi Datey, Prafful Sharma, Faisal Tarique Khaja, Huma Rahil, Tanweer Hussain

{"title":"Yeast Eukaryotic Initiation Factor 4B Remodels the MRNA Entry Site on the Small Ribosomal Subunit.","authors":"Ayushi Datey, Prafful Sharma, Faisal Tarique Khaja, Huma Rahil, Tanweer Hussain","doi":"10.1021/acs.biochem.4c00489","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00489","url":null,"abstract":"Eukaryotic Initiation Factor 4 (eIF4) is a group of factors that activates mRNA for translation and recruit 43S preinitiation complex (PIC) to the mRNA 5' end, forming the 48S PIC. The eIF4 factors include mRNA 5' cap-binding protein eIF4E, ATP-dependent RNA helicase eIF4A, and scaffold protein eIF4G, which anchors eIF4A and eIF4E. Another eIF4 factor, eIF4B, stimulates the RNA helicase activity of eIF4A and facilitates mRNA recruitment. However, the mechanisms by which eIF4B binds the 40S ribosomal subunit and promotes mRNA recruitment remain poorly understood. Using cryo-Eletron Microscopy (cryo-EM), we obtained a map of the yeast 40S ribosomal subunit in a complex with eIF4B (40S-eIF4B complex). An extra density, tentatively assigned to yeast eIF4B, was observed near the mRNA entry channel of the 40S, contacting ribosomal proteins uS10, uS3, and eS10 as well as rRNA helix h16. Predictive modeling of the 40S-eIF4B complex suggests that the N-terminal domain of eIF4B binds near the mRNA entry channel, overlapping with the extra density observed in the 40S-eIF4B map. The partially open conformation of 40S in the 40S-eIF4B map is incompatible with eIF3j binding observed in the 48S PIC. Additionally, the extra density at the mRNA entry channel poses steric hindrance for eIF3g binding in the 48S PIC. Thus, structural insights suggest that eIF4B facilitates the release of eIF3j and the relocation of the eIF3b-g-i module during mRNA recruitment, thereby advancing our understanding of eIF4B's role in translation initiation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021297","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

Glutamine Synthetase: Diverse Regulation and Functions of an Ancient Enzyme.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-22 DOI: 10.1021/acs.biochem.4c00763

Markus C B Tecson, Cyrina Geluz, Yuly Cruz, Eric R Greene

{"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":"https://doi.org/10.1021/acs.biochem.4c00763","url":null,"abstract":"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 Escherichia coli 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.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Collagen Alpha 1(XI) Amino-Terminal Domain Modulates Type I Collagen Fibril Assembly. 胶原α 1（XI）氨基末端结构域调节I型胶原原纤维组装。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-22 DOI: 10.1021/acs.biochem.4c00434

Abu Sayeed Chowdhury, Julia Thom Oxford

{"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":"https://doi.org/10.1021/acs.biochem.4c00434","url":null,"abstract":"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.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Understanding Folding of bFGF and Potential Cellular Protective Mechanisms of Neural Cells. 了解bFGF折叠与神经细胞潜在的细胞保护机制。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-01-21 Epub Date: 2025-01-03 DOI: 10.1021/acs.biochem.4c00297

Robert J Allsopp, Jeffery B Klauda

{"title":"Understanding Folding of bFGF and Potential Cellular Protective Mechanisms of Neural Cells.","authors":"Robert J Allsopp, Jeffery B Klauda","doi":"10.1021/acs.biochem.4c00297","DOIUrl":"10.1021/acs.biochem.4c00297","url":null,"abstract":"Traumatic brain injury (TBI) is a serious health condition that affects an increasing number of people, especially veterans and athletes. TBI causes serious consequences because of its long-lasting impact on the brain and its alarming frequency of occurrence. Although the brain has some natural protective mechanisms, the processes that trigger them are poorly understood. Fibroblast growth factor (FGF) proteins interact with receptor proteins to protect cells. Gaps in the literature include how basic-FGF (bFGF) is activated by heparin, can heparin-like molecules induce neural protection, and the effect of allosteric binding on bFGF activity. To fill the gap in our understanding, we applied temperature replica exchange to study the influence of heparin binding to bFGF and how mutations in bFGF influence stability. A new favorable binding site was identified by comparing free energies computed from the potential of mean force (PMF). Although the varied sugars studied resulted in different interactions with bFGF compared to heparin, they each produced structural effects similar to those of bFGF that likely facilitate receptor binding and signaling. Our results also demonstrate how point mutations can trigger the same conformational change that is believed to promote favorable interactions with the receptor. A deeper atomic-level understanding of how chemicals are released during TBI is needed to improve the development of new treatments for TBI and could contribute to a better understanding of other diseases.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"509-524"},"PeriodicalIF":2.9,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142918816","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