Biochimica et biophysica acta. Proteins and proteomics最新文献

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Identification of dystrophin Dp71dΔ71-associated proteins in PC12 cells by quantitative proteomics 通过定量蛋白质组学鉴定 PC12 细胞中的肌营养不良蛋白 Dp71dΔ71 相关蛋白。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2025-01-01 Epub Date: 2024-09-28 DOI: 10.1016/j.bbapap.2024.141049
Coztli Azotla-Vilchis , Candelaria Merino-Jiménez , Emmanuel Ríos-Castro , Jorge Aragón , Víctor Ceja , Cecilia Montanez
{"title":"Identification of dystrophin Dp71dΔ71-associated proteins in PC12 cells by quantitative proteomics","authors":"Coztli Azotla-Vilchis ,&nbsp;Candelaria Merino-Jiménez ,&nbsp;Emmanuel Ríos-Castro ,&nbsp;Jorge Aragón ,&nbsp;Víctor Ceja ,&nbsp;Cecilia Montanez","doi":"10.1016/j.bbapap.2024.141049","DOIUrl":"10.1016/j.bbapap.2024.141049","url":null,"abstract":"<div><div>Dystrophin Dp71 is essential for the development of the nervous system. Its alteration is associated with intellectual disability. Different Dp71 isoforms are generated by alternative splicing; however, their functions have not been fully described. Here, we identified Dp71d<sub>Δ71</sub>-associated proteins to understand the complex functions. PC12 cells, stably transfected with pTRE2pur-Myc/Dp71d<sub>Δ71</sub> or pTRE2pur-Myc empty vector (EV), were analyzed by immunoprecipitation followed with quantitative proteomics with data-independent acquisition and ion mobility separation. We used the Top3 method to quantify absolutely every protein detected. A total of 106 proteins were quantified with Progenesis QI software and the database UP000002494. Seven new proteins associated with Dp71d<sub>Δ71</sub> were selected with at least 2-fold quantity between immunoprecipitated proteins of PC12-Myc/Dp71d<sub>Δ71</sub> versus PC12-EV cells. These results revealed new proteins that interact with Dp71d<sub>Δ71</sub>, including β-Tubulin, S-adenosylmethionine synthase isoform type-2, adapter molecule crk, helicase with zinc finger 2, WD repeat domain 93, cyclin-L2 and myosin-10, which are related to cell migration and/or cell growth. The results lay the foundation for future research on the relationship between these proteins and Dp71 isoforms.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141049"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Investigation of adipocyte differentiation based on proteomics and intact N-glycopeptide modificationomics 基于蛋白质组学和完整 N-糖肽修饰组学的脂肪细胞分化研究。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2025-01-01 Epub Date: 2024-10-09 DOI: 10.1016/j.bbapap.2024.141052
Xin-Yu Li , Nuerbiye Nuermaimaiti , Xuanyu Meng , Xiaozheng Zhang , Aikedaimu Abudukeremu , Yihuai He , Wenting Ma , Xuelei Chen , Shangkun Li , Jiaxin Sun , Yaqun Guan
{"title":"Investigation of adipocyte differentiation based on proteomics and intact N-glycopeptide modificationomics","authors":"Xin-Yu Li ,&nbsp;Nuerbiye Nuermaimaiti ,&nbsp;Xuanyu Meng ,&nbsp;Xiaozheng Zhang ,&nbsp;Aikedaimu Abudukeremu ,&nbsp;Yihuai He ,&nbsp;Wenting Ma ,&nbsp;Xuelei Chen ,&nbsp;Shangkun Li ,&nbsp;Jiaxin Sun ,&nbsp;Yaqun Guan","doi":"10.1016/j.bbapap.2024.141052","DOIUrl":"10.1016/j.bbapap.2024.141052","url":null,"abstract":"<div><h3>Objective</h3><div>To investigate the role of N-glycosylation modification of proteins in adipocyte differentiation during the adipogenic process.</div></div><div><h3>Methods</h3><div>SVF cells and adipocytes were analyzed for proteomics and intact N-glycopeptide modificationomics.Differential expression of proteins, glycoforms, and sites between the two groups was screened and subjected to Gene Ontology (GO) functional enrichment analysis, KEGG pathway enrichment analysis, and protein-protein interaction (PPI) network analysis. The top 20 most significantly differentially expressed adipogenic differentiation-related proteins were identified, and the most pronouncedly altered proteins were analyzed for glycoforms, glycan chains, and sites.</div></div><div><h3>Results</h3><div>Proteomics analysis identified 39,392 peptides and 5208 proteins, while intact N-glycopeptide modification profiling identified 3293 intact glycopeptides, 426 proteins, and 161 glycan chains. Proteomics identified 2510 differentially expressed proteins, with CD36 (Cluster of Differentiation 36, CD36) significantly upregulated. In adipocytes, CD36 had 4 N-glycosylation sites: N79, N220, N320, N417, with N320 being a newly identified site. GO enrichment results indicated that CD36 is associated with fatty acid oxidation, lipid oxidation, and fatty acid uptake into cells.</div></div><div><h3>Conclusion</h3><div>Multiple proteins undergo N-glycosylation modification during adipocyte differentiation, with CD36, a fatty acid translocase, being significantly expressed in adipocytes. This suggests that N-glycosylation modification of CD36 may play a crucial role in adipocyte differentiation, providing a foundation for further investigation into the function of CD36 N-glycosylation in adipocyte differentiation.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141052"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Structural insights into the mechanism underlying the dual cofactor specificity of glyoxylate reductase from Acetobacter aceti in the β-hydroxyacid dehydrogenase family 从结构上揭示β-羟基酸脱氢酶家族中乙酸醋酸杆菌乙醛酸还原酶的双辅助因子特异性机制。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2025-01-01 Epub Date: 2024-10-03 DOI: 10.1016/j.bbapap.2024.141051
Toma Rani Majumder , Takuya Yoshizawa , Masao Inoue , Riku Aono , Hiroyoshi Matsumura , Hisaaki Mihara
{"title":"Structural insights into the mechanism underlying the dual cofactor specificity of glyoxylate reductase from Acetobacter aceti in the β-hydroxyacid dehydrogenase family","authors":"Toma Rani Majumder ,&nbsp;Takuya Yoshizawa ,&nbsp;Masao Inoue ,&nbsp;Riku Aono ,&nbsp;Hiroyoshi Matsumura ,&nbsp;Hisaaki Mihara","doi":"10.1016/j.bbapap.2024.141051","DOIUrl":"10.1016/j.bbapap.2024.141051","url":null,"abstract":"<div><div>The β-hydroxyacid dehydrogenase family exhibits diverse cofactor preferences: some enzymes favor NAD, others favor NADP, and a subset can utilize both NAD and NADPH. Glyoxylate reductase from <em>Acetobacter aceti</em> JCM 20276 (AacGR) exhibits a dual cofactor specificity for NADPH and NADH in its catalytic reduction of glyoxylate to glycolate. In contrast to conventional cofactor-discriminating motifs, NRX and DXX, found in NADP- and NAD-specific enzymes, respectively, AacGR has a TPS motif in the equivalent position. Here we report X-ray crystallographic analysis of AacGR in its ligand-free form, and in complexes with NADPH and NADH, revealing critical interactions: Ser41 of the TPS motif interacted with the 2′-phosphate group of NADPH, while no analogous interaction occurred with the ribose hydroxy groups of NADH. Moreover, the TPS motif resided within a characteristic β-turn-like structure adjacent to a long flexible loop. Site-directed mutagenesis and kinetic analyses suggest that Ser41 facilitates NADPH binding, while the lack of a direct interaction of the TPS motif with NADH may allow for NADH utilization. The conformational dynamics of the TPS-containing β-turn-like structure along with the flexible loop likely govern the dual cofactor specificity and catalytic turnover of AacGR.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141051"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Assembly of Hydrophobin class I from Agaricus bisporus produced different amyloid-like fibrils 组装双孢蘑菇中的 I 类亲水蛋白可产生不同的淀粉样纤维。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2025-01-01 Epub Date: 2024-09-26 DOI: 10.1016/j.bbapap.2024.141048
Jesús Rojas-Osnaya, Hugo Nájera
{"title":"Assembly of Hydrophobin class I from Agaricus bisporus produced different amyloid-like fibrils","authors":"Jesús Rojas-Osnaya,&nbsp;Hugo Nájera","doi":"10.1016/j.bbapap.2024.141048","DOIUrl":"10.1016/j.bbapap.2024.141048","url":null,"abstract":"<div><div>This work studied the extraction, purification, characterization, and assembly of hydrophobin class I from <em>Agaricus bisporus</em> (ABH4)<em>.</em> The highest soluble protein concentration was obtained from the pinhead, the extraction and purification were efficient for hydrophobin class I, obtaining a band of 12 kDa. The identified sequence of hydrophobin presented the eight cysteine residues; for the prediction of the structure, hydrophobin presented more alpha helix structures than beta sheets. It was observed that the hydrophobin managed to decrease and increase the contact angle in Teflon and glass, respectively, finding a micellar critical concentration of 221 μg mL<sup>−1</sup>. ThT experiments demonstrated that the production of fibrils decreased at basic pH, while acidic and neutral pH favoured the formation of fibrils. Likewise, the addition of colloidal Teflon affects the formation of fibrils. Circular dichroism spectra proved that hydrophobin class I undergo changes in its secondary structure, increasing its alpha helix and beta sheet content after vortexing. It was observed that the analysis by scanning electron microscopy and atomic force microscopy of the hydrophobin produced different amyloid-like structures in glass and mica.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141048"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142340301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Unlocking the wound-healing potential: An integrative in silico proteomics and in vivo analysis of Tacorin, a bioactive protein fraction from Ananas comosus (L.) Merr. Stem 打开伤口愈合的潜力:一个集成的硅蛋白质组学和体内分析Tacorin,一个生物活性蛋白组分,从Ananas comosus (L.)稳定。茎
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2025-01-01 Epub Date: 2024-11-26 DOI: 10.1016/j.bbapap.2024.141060
Puji Rahayu , Doni Dermawan , Florensia Nailufar , Erna Sulistyaningrum , Raymond R. Tjandrawinata
{"title":"Unlocking the wound-healing potential: An integrative in silico proteomics and in vivo analysis of Tacorin, a bioactive protein fraction from Ananas comosus (L.) Merr. Stem","authors":"Puji Rahayu ,&nbsp;Doni Dermawan ,&nbsp;Florensia Nailufar ,&nbsp;Erna Sulistyaningrum ,&nbsp;Raymond R. Tjandrawinata","doi":"10.1016/j.bbapap.2024.141060","DOIUrl":"10.1016/j.bbapap.2024.141060","url":null,"abstract":"<div><div>Tacorin, a bioactive protein fraction derived from pineapple stem (<em>Ananas comosus</em>), has emerged as a promising therapeutic agent for wound healing. This study employs an integrated approach, combining <em>in silico</em> proteomics and <em>in vivo</em> investigations, to unravel the molecular mechanisms underlying Tacorin's wound healing properties. In the domain of <em>in silico</em> proteomics, the composition of Tacorin is elucidated through LC/MS-MS protein sequencing, revealing ananain (23.77 kDa) and Jacalin-like lectin (14.99 kDa) as its predominant constituents. Molecular protein-protein docking simulations unveil favorable interactions between Tacorin's components and key regulators of wound healing, including TGF-β, TNF-α, and MMP-2. The calculated free binding energies indicate strong binding affinities between Tacorin proteins and their target receptors. Specifically, ananain demonstrates a binding affinity of −12.2 kcal/mol with TGF-β, suggesting its potential as a potent activator of TGF-β-mediated signaling, while Jacalin-like lectin exhibits the most favorable binding affinity of −8.7 kcal/mol with TNF-α. Subsequent 100 ns molecular dynamics (MD) simulations provide insights into the dynamic behavior and stability of Tacorin-receptor complexes, shedding light on the molecular determinants of Tacorin's therapeutic effects. Complementing the <em>in silico</em> analyses, <em>in vivo</em> studies evaluate Tacorin's efficacy in wound healing using skin and uterine incision models. Tacorin treatment accelerates wound closure and promotes tissue repair in both models, as evidenced by macroscopic observations and histological assessments. Overall, this study provides compelling evidence of Tacorin's therapeutic potential in wound healing and underscores the importance of elucidating its molecular mechanisms for further development and clinical translation.</div></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1873 1","pages":"Article 141060"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142748237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 potential pharmacological chaperones that selectively stabilize mutated Aspartoacylases in Canavan disease 鉴定可选择性稳定卡纳万病中突变的天冬酰化酶的潜在药理伴侣。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-11-01 Epub Date: 2024-08-09 DOI: 10.1016/j.bbapap.2024.141043
Nitesh Kumar Poddar , Yasanandana S. Wijayasinghe , Ronald E. Viola
{"title":"Identification of potential pharmacological chaperones that selectively stabilize mutated Aspartoacylases in Canavan disease","authors":"Nitesh Kumar Poddar ,&nbsp;Yasanandana S. Wijayasinghe ,&nbsp;Ronald E. Viola","doi":"10.1016/j.bbapap.2024.141043","DOIUrl":"10.1016/j.bbapap.2024.141043","url":null,"abstract":"<div><p>Canavan disease is caused by mutations in the <em>ASPA</em> gene, leading to diminished catalytic activity of aspartoacylase in the brain. Clinical missense mutations are found throughout the enzyme structure, with many of these mutated enzymes having not only decreased activity but also compromised stability. High-throughput screening of a small molecule library has identified several compounds that significantly increase the thermal stability of the E285A mutant enzyme, the most predominant clinical mutation in Canavan disease, while having a negligible effect on the native enzyme. Based on the initial successes, some structural analogs of these initial hits were selected for further examination. Glutathione, NAAG and patulin were each confirmed to be competitive inhibitors, indicating the binding of these compounds at the dimer interface or near the active site of the E285A enzyme. The experimental results were theoretically examined with the help of the docking analysis method. The structure activity-guided optimization of these compounds can potentially lead to potential pharmacological chaperones that could alleviate the detrimental effect of <em>ASPA</em> mutations in Canavan patients.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 6","pages":"Article 141043"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Assigning roles in Chlamydomonas ribosome biogenesis: The conserved factor NIP7 确定衣藻核糖体生物发生过程中的角色:保守因子 NIP7
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-11-01 Epub Date: 2024-08-30 DOI: 10.1016/j.bbapap.2024.141045
Raissa Ferreira Gutierrez , Heloisa Ciol , Angélica L. Carrillo Barra , Diego Antonio Leonardo , Juliana S. Avaca-Crusca , Otavio H. Thiemann , Nilson Ivo Tonin Zanchin , Ana P. Ulian Araujo
{"title":"Assigning roles in Chlamydomonas ribosome biogenesis: The conserved factor NIP7","authors":"Raissa Ferreira Gutierrez ,&nbsp;Heloisa Ciol ,&nbsp;Angélica L. Carrillo Barra ,&nbsp;Diego Antonio Leonardo ,&nbsp;Juliana S. Avaca-Crusca ,&nbsp;Otavio H. Thiemann ,&nbsp;Nilson Ivo Tonin Zanchin ,&nbsp;Ana P. Ulian Araujo","doi":"10.1016/j.bbapap.2024.141045","DOIUrl":"10.1016/j.bbapap.2024.141045","url":null,"abstract":"<div><p>Ribosome biogenesis (RB) is a highly conserved process across eukaryotes that results in the assembly of functional ribosomal subunits. Studies in <em>Saccharomyces cerevisiae</em> and <em>Homo sapiens</em> have identified numerous RB factors (RBFs), including the NIP7 protein, which is involved in late-stage pre-60S ribosomal maturation. NIP7 expression has also been observed in <em>Chlamydomonas reinhardtii</em>, highlighting its evolutionary significance. This study aimed to characterize the function of the NIP7 protein from <em>C. reinhardtii</em> (<em>Cr</em>Nip7) through protein complementation assays and a paromomycin resistance test, assessing its ability to complement the role of NIP7 in yeast. Protein interaction studies were conducted via yeast two-hybrid assay to identify potential protein partners of <em>Cr</em>Nip7. Additionally, rRNA modeling analysis was performed using the predicted structure of <em>Cr</em>Nip7 to investigate its interaction with rRNA. The study revealed that <em>Cr</em>Nip7 can complement the role of NIP7 in yeast, implicating <em>Cr</em>Nip7 in the biogenesis of the 60S ribosomal subunit. Furthermore, two possible partner proteins of CrNip7, UNC-p and G-patch, were identified through yeast two-hybrid assay. The potential of these proteins to interact with CrNip7 was explored through in silico analyses. Furthermore, nucleic acid interaction was also evaluated, indicating the involvement of the N- and C-terminal domains of CrNIP7 in interacting with rRNA. Collectively, our findings provide valuable insights into the RBFs CrNip7, offering novel information for comparative studies on RB among eukaryotic model organisms, shedding light on its evolutionary conservation and functional role across species.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 6","pages":"Article 141045"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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 interfacial regions in misfolded transthyretin oligomers 识别折叠错误的转甲状腺素寡聚体中的界面区
IF 3.2 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-09-01 Epub Date: 2024-05-23 DOI: 10.1016/j.bbapap.2024.141027
Anvesh K.R. Dasari , Matthew F. Coats , Abdullah B. Ali , Kwang Hun Lim
{"title":"Identification of the interfacial regions in misfolded transthyretin oligomers","authors":"Anvesh K.R. Dasari ,&nbsp;Matthew F. Coats ,&nbsp;Abdullah B. Ali ,&nbsp;Kwang Hun Lim","doi":"10.1016/j.bbapap.2024.141027","DOIUrl":"https://doi.org/10.1016/j.bbapap.2024.141027","url":null,"abstract":"<div><p>Misfolding and aggregation of transthyretin (TTR) is associated with numerous ATTR amyloidosis. TTR aggregates extracted from ATTR patients consist of not only full-length TTR, but also N-terminally truncated TTR fragments that can be produced by proteolytic cleavage, suggesting the presence of multiple misfolding pathways. Here, we report mechanistic studies of an early stage of TTR aggregation to probe the oligomerization process for the full-length as well as N-terminally truncated TTR. Our kinetic analyses using size exclusion chromatography revealed that amyloidogenic monomers dissociated from wild-type (WT) as well as pathogenic variants (V30M and L55P) form misfolded dimers, which self-assemble into oligomers, precursors of fibril formation. Dimeric interfaces in the full-length misfolded oligomers were investigated by examining the effect of single-point mutations on the two β-strands (F and H). The single-point mutations on the two β-strands (E92P on strand F and T119W on strand H) inhibited the dimerization of misfolded monomers, while the TTR variants can still form native dimers through the same F and H strands. These results suggest that the two strands are involved in intermolecular associations for both native and misfolded dimers, but detailed intermolecular interactions are different in the two forms of dimers. In the presence of a proteolytic enzyme, TTR aggregation is greatly accelerated. The two mutations on the two β-strands, however, inhibited TTR aggregation even in the presence of a proteolytic enzyme, trypsin. These results suggest that the two β-strands (F and H) play a critical role in aggregation of the N-terminally truncated TTR as well.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141027"},"PeriodicalIF":3.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141097790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Kinetic characterization of the C-terminal domain of Malonyl-CoA reductase 丙二酰-CoA 还原酶 C 端结构域的动力学特征。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-09-01 Epub Date: 2024-07-15 DOI: 10.1016/j.bbapap.2024.141033
Mirela Tkalcic Cavuzic (Tkalčić Čavužić) , Amanda Silva de Sousa , Jeremy R. Lohman , Grover L. Waldrop
{"title":"Kinetic characterization of the C-terminal domain of Malonyl-CoA reductase","authors":"Mirela Tkalcic Cavuzic (Tkalčić Čavužić) ,&nbsp;Amanda Silva de Sousa ,&nbsp;Jeremy R. Lohman ,&nbsp;Grover L. Waldrop","doi":"10.1016/j.bbapap.2024.141033","DOIUrl":"10.1016/j.bbapap.2024.141033","url":null,"abstract":"<div><p>Malonyl-CoA reductase utilizes two equivalents of NADPH to catalyze the reduction of malonyl-CoA to 3-hydroxypropionic acid (3HP). This reaction is part of the carbon fixation pathway in the phototrophic bacterium <em>Chloroflexus aurantiacus</em>. The enzyme is composed of two domains. The C-terminal domain catalyzes the reduction of malonyl-CoA to malonic semialdehyde, while the N-terminal domain catalyzes the reduction of the aldehyde to 3HP. The two domains can be produced independently and retain their enzymatic activity. This report focuses on the kinetic characterization of the C-terminal domain. Initial velocity patterns and inhibition studies showed the kinetic mechanism is ordered with NADPH binding first followed by malonyl-CoA. Malonic semialdehyde is released first, while CoA and NADP<sup>+</sup> are released randomly. Analogs of malonyl-CoA showed that the thioester carbon is reduced, while the carboxyl group is needed for proper positioning. The enzyme transfers the pro-<em>S</em> hydrogen of NADPH to malonyl-CoA and pH rate profiles revealed that a residue with a pK<sub>a</sub> value of about 8.8 must be protonated for activity. Kinetic isotope effects indicated that NADPH is not sticky (that is, NADPH dissociates from the enzyme faster than the rate of product formation) and product release is partially rate-limiting. Moreover, the mechanism is stepwise with the pH dependent step occurring before or after hydride transfer. The findings from this study will aid in the development of an eco-friendly biosynthesis of 3HP which is an industrial chemical used in the production of plastics and adhesives.</p></div>","PeriodicalId":8760,"journal":{"name":"Biochimica et biophysica acta. Proteins and proteomics","volume":"1872 5","pages":"Article 141033"},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141632515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Exploring liquid-liquid phase separation in the organisation of Golgi matrix proteins 探索高尔基体基质蛋白组织中的液-液相分离。
IF 2.5 4区 生物学
Biochimica et biophysica acta. Proteins and proteomics Pub Date : 2024-09-01 Epub Date: 2024-06-23 DOI: 10.1016/j.bbapap.2024.141029
Luis Felipe S. Mendes , Carolina G. Oliveira , Kevin F. Simões , Emanuel Kava , Antonio J. Costa-Filho
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